Genetic affinities of the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa

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Afro-Asiatic, ancient DNA, Cushitic, Ethiosemitic, North Omotic

The ancestral origin of the Afro-Asiatic-speaking groups inhabiting the Horn of Africa has long been a subject of debate among scholars. In the 2000s, with the advent of genomics, a number of scientists proposed that these communities were formed through contact between ancient West Eurasian and Sub-Saharan African individuals. They principally based this on admixture analyses, which compared the genomes of persons from various reference populations with those of Afro-Asiatic speakers from the Horn region. The earliest of these genomic studies typically used modern Europeans and modern West Africans as their proxy groups. However, as more global populations were analysed, it became clear to researchers that virtually every living individual is mixed to some degree, thereby making contemporary groups inadequate reference populations for genomic analysis. This realization prompted scientists to increasingly turn to ancient specimens, which they assumed — usually correctly — would be less admixed than modern individuals and therefore more reliable proxies.

Llorente et al. published one such paleogenetics study in 2015, analysing for the first time an indigenous hunter-gatherer from the Horn (see Ancient DNA from Ethiopia). At the time of publication, this forager individual, called Mota, was believed to be “purely” African and thus free of non-African admixture. Subsequent examination found that there, in fact, had been a software-related error; the specimen apparently did harbor some Eurasian ancestry, albeit a trivial amount (cf. Erratum). Consequently, researchers on the genetic affinities of the Horn’s Afro-Asiatic speakers continued to utilize Mota as their favored ancient Sub-Saharan African proxy, with newly-analysed early Levantine populations (viz. Mesolithic Natufians, Pre-Pottery Neolithic makers) serving as their preferred stand-ins for West Eurasian ancestry.

In 2020, Wang et al. released an archaeogentics paper that included a number of never before analysed ancient specimens from eastern Africa. These newly-published samples helped unveil several layers of ancestry in the Mota forager, which had previously been hidden. Mota’s ancestral makeup was revealed to actually consist of various hunter-gatherer elements (Hadza, Mbuti and Khoisan-related components), as well as minor Niger-Congo/Nilo-Saharan-related admixture and considerably higher Eurasian admixture than previously had been realized (~25%). Additionally, genome analysis found that the earliest Afro-Asiatic-speakers yet to be analysed in eastern Africa (i.e. the Cushitic settlers of the Pastoral Neolithic) carried a predominant West Eurasian ancestry related to ancient North African/Levantine groups, with ancillary Sub-Saharan African admixture. The analysis also showed that a 300 BP individual from the Kakapel site in Kenya bore the most such Sub-Saharan African ancestry, thus supplanting Mota as an ideal proxy (cf. Supplementary Material).

Thanks to these new samples, we can now estimate with much greater accuracy than ever before the actual ancestral composition of the Afro-Asiatic-speaking populations from the Horn of Africa.

Admixture Analysis

To assist us in this endeavor, we will make use of the Vahaduo Admixture JS program, which interprets data from the official Global25 datasheets. Global25, or G25, is a powerful genetic system originally developed by the Eurogenes project. Based on Principal Coordinate Analysis (PCA) coordinate data, it allows users to compare the genome of any modern or ancient individual against that of well over 6000 ancient samples culled from around the world, as well as several thousand modern samples.

According to Genoplot:

Global 25 (G25) ancestry modeling is currently the most effective way to perform free-form discovery of ancestry. The set of coordinates used by Global 25 are a product of Eurogenes. They were created as a means to facilitate ancestral admixture modeling[…]

This type of ancestry modeling allows for very precise and granular determination of ancestry. Unlike admixture calculators which come locked-in to pre-defined ancestral components, G25 modeling allows for selection of any number of potential ancestral sources.

Hence, Global25 ancestry modeling is the best tool for our genome inquiry.

Step 1: Identify the “purest” Sub-Saharan African reference population available

As a first step in our genetic investigation, we will try and determine which ancient Sub-Saharan African population the contemporary Nilotic peoples share the most affinity with. We are specifically interested in such individuals because genome analysis by Prendergast et al. (2018) and Wang et al. (2020) shows that the Cushites of the Pastoral Neolithic absorbed an African population carrying ancestry similar to that borne by modern Nilotes.

We begin by running a Vahaduo Admixture JS Distance analysis on the ancient African samples listed on the Global25_PCA datasheet. In order to not invalidate our findings, these Source populations must exclude any ancient specimens possessing substantial Eurasian ancestry (viz. the Pastoral Neolithic, Kulubnarti, Pastoral Iron Age, Kenya Iron Age, ancient Egyptian, ancient Moroccan, Guanche and Zanzibar Euro specimens). For our Target populations, we will employ all of the modern Nilote samples listed on the Global25_PCA_modern datasheet. The resulting Vahaduo Distance analysis, shown here, indicates that every single Nilotic sample (except for one heavily mixed Datog individual) shares greatest genetic affinity with the Kakapel 900BP cohort from Kenya.

In Wang et al.’s Figure S1-B below, we can further see that this Kakapel 900BP sample primarily bears Nilo-Saharan/Niger-Congo-related ancestry (purple component), similar to that which defines the contemporary Dinka Nilote sample from Sudan. Kakapel 900BP thus seems to be the earliest appearance of a modern Dinka-like specimen in the archaeogenetic record. However, like the Dinka of today, Kakapel 900BP also bears a non-trivial amount of West Eurasian admixture (red component). This makes the sample an unsuitable proxy for inferring “pure” ancient Nilotic ancestry.

Genome analysis of ancient and modern African specimens. The Kakapel 300BP sample from Kenya bears the same majority Nilo-Saharan/Niger-Congo-affiliated ancestry (purple component) as the Kakapel 900BP sample from the same site. However, Kakapel 300BP carries less West Eurasian admixture (red component) than both Kakapel 900BP and the Mota hunter-gatherer from Ethiopia (labeled Ethiopia_4500BP). This makes Kakapel 300BP the best available representative of ancient Nilotic ancestry (Wang et al. (2020), Figure S1-B).

To find a less admixed Sub-Saharan African reference sample, we turn instead to the Kakapel 300BP sample from the same site. As with Kakapel 900BP, we note that the Kakapel 300BP cohort appears among the top eight ancient African specimens with whom the modern Nilote samples show the closest genetic ties on Vahaduo’s Distance parameter. We know that this affinity is due to shared ancient Nilotic ancestry rather than shared non-African admixture since, in Wang et al.’s Figure S1-B above, Kakapel 300BP carries only a small proportion of the West Eurasian red component, unlike both Kakapel 900BP and the Mota forager from Ethiopia (labeled Ethiopia_4500BP).

As an additional precaution, in order to ensure that Kakapel 300BP is indeed the most optimal source of “pure” Sub-Saharan African ancestry available, we will conduct a Vahaduo Multi analysis (process described below). We shall use the Kakapel 300BP sample as a Source population to infer ancient Nilo-Saharan ancestry in all of the contemporary Nilotic samples listed on the Global25_PCA_modern datasheet. Our resulting genetic model, displayed here, is successful; it produces plausible admixture levels for all of the examined Nilotic individuals and at acceptable Distance fits of <9%. By contrast, tests using other ancient Sub-Saharan African specimens, which have the highest levels of the Nilo-Saharan/Niger-Congo purple component above, are all failures. These experiments either grossly exaggerate the non-African admixture levels in the modern Nilotic samples and/or do not capture any Natufian admixture, which these specimens are known to possess (since they assimilated some Cushitic peoples, who bear such West Eurasian ancestry).

Finally, we will consult Wang et al.’s height data on the Kakapel 300BP sample (cf. Supplementary Material). Since the Sidamo and Sab, respectively, are both the most African-admixed and shortest of the Afro-Asiatic-speaking populations in Ethiopia and Somalia (see Ancient DNA from Ethiopia), this will enable us to determine whether the Kakapel 300BP specimen represents the main ancient Sub-Saharan African peoples whom the early Afro-Asiatic speakers in Northeast Africa absorbed. Kakapel 300BP, a young adult woman, is listed by Wang et al. at a diminutive stature of 156 cm or 5’1.5″, confirming that she likely does represent that ancient Sub-Saharan African contact population.

Step 2: Identify which Eurasian ancestries the modern Afro-Asiatic speakers of the Horn carry

Next, we will try and ascertain which specific Eurasian ancestries the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn region actually bear. To accomplish this, we will avail ourselves of the Vahaduo Admixture JS program’s Single tab and compare these modern samples (which are listed on the Global25_PCA_modern datasheet) with all 6000+ ancient Eurasian samples listed on the Global25_PCA datasheet. To this official G25 datasheet we shall add the coordinates for the newly-analysed EGY_1879BCE sample, which belong to the Middle Kingdom ancient Egyptian aristocrat Nakht-Ankh:

EGY_1879BCE:Nakht-Ankh,0.0012,0.129,-0.044,-0.0965,-0.0031,-0.0534,-0.017,-0.0078,0.0551,-0.0049,0.0138,-0.0172,0.0306,-0.0015,0.0069,-0.0072,-0.0111,0.0053,-0.004,0.0042,-0.0012,0.0046,-0.0078,0.0026,-0.0013

Before proceeding, we will also make sure to exclude any ancient samples that have non-trivial Sub-Saharan African admixture. The end result, shown below, has identified four principal non-African ancestries, three of which are West Eurasian (ancient Egyptian component, European-related Steppe component, and Levantine Natufian component) and one which is East Eurasian (East Asian component).

In order to verify our preliminary findings, we will again run Vahaduo’s Single analysis. However, now we shall include our “pure” early Nilotic sample (the Kakapel 300BP specimen) as a Source population alongside all of the ancient Eurasian populations from the Global25_PCA datasheet, while keeping our modern Afro-Asiatic-speaking individuals from the Horn as our Target populations.

As an additional cautionary measure, we shall again conduct a Vahaduo Single analysis. Now we will add all of the other ancient Sub-Saharan African samples that have the least Eurasian admixture. These samples represent the “purest” Niger-Congo (COG_Kindoki_230BP:KIN002), East African Hunter-Gatherer (MWI_Chencherere:I4421_new_all), Pygmy (CMR_Shum_Laka:I10874_new_all), and Khoisan (ZAF_2000BP:bab001) specimens. Appending these samples will help us ascertain whether our Target Horn populations realistically carry any extra Sub-Saharan African admixture and from which sources.

As can be seen above, all of the aforementioned Eurasian ancestries appear once more, confirming their authenticity. Among the West Eurasian elements, the ancient Egyptian component is best represented by the EGY_1879BC sample, which is also the oldest Egyptian sample whose Global25 coordinates are available; the European-related Steppe component is best represented by the RUS_Baikal_BA specimens from Bronze Age Russia; and the Levantine Natufian component is best represented by the Levant_Natufian_EpiP specimens, which date to the Mesolithic. The East Eurasian element is best represented by the CHN_Huatuyan_500BP sample from late medieval China. We can also, for the first time, observe robust estimates of the actual ancestral proportions that characterize the Afro-Asiatic speakers analysed. On average, modern Cushitic, Ethiosemitic and North Omotic-speaking individuals appear to carry over 70% Eurasian ancestry (most of which is West Eurasian, with a significant East Eurasian element), with around 25% Sub-Saharan African admixture (primarily derived from early Nilo-Saharan speakers like Kakapel_300BP, and secondarily derived from ancient East African Hunter-Gatherers like MWI_Chencherere) and under 5% Epipaleolithic North African ancestry (i.e. Iberomaurusian/Taforalt component).

Step 3: Quantify these ancestral proportions

To further break down the apportionment of these ancestral elements, we will now make use of the Vahaduo Admixture JS program’s Multi function. In order to efficiently interpret our findings, we shall utilize the five ancient Eurasian and two ancient Sub-Saharan African “best representative” samples, which we have just identified above. As expected, the end result (shown below) appears very similar to Vahaduo’s Single analysis:

With regards to the table above, we may note that:

• The ancient Egyptian component (EGY_1879BCE) is found at highest frequency in a Somali individual from southern Somalia (21.2%), and at lowest frequency in an Ethiopian Oromo individual (13.6%). The southern Somali samples also have the highest average percentage of this Egyptian ancestral element (19.3%), whereas the Eritrean samples bear this component at the lowest average frequency (16.7%). Overall, this ancient Egyptian component occurs at an average frequency of 18% among our Afro-Asiatic-speaking samples.
• The European-related Steppe component (RUS_Baikal_BA) is found at highest frequency in a southern Somali individual (18%), and at lowest frequency in an Ethiopian Oromo individual (5.6%). The southern Somali samples also have the highest average percentage of the Steppe ancestral element (13.1%), whereas the Rendille carry this component at the lowest average frequency (8.5%). Overall, this Steppe component occurs at an average frequency of 11.3% among our Afro-Asiatic-speaking samples.
• The Levantine Natufian component (Levant_Natufian_EpiP) is found at highest frequency in an Ethiopian Jew individual (35.2%), and at lowest frequency in an Iraqw individual from Tanzania (1.8%). The Eritrean samples have the highest average percentage of this Natufian ancestral element (30%), whereas the Iraqw samples bear this component at the lowest average frequency (5.2%). Overall, this Natufian component occurs at an average frequency of 20.9% among our Afro-Asiatic-speaking samples.
• The ancient East Asian component (CHN_Huatuyan_500BP) is found at highest frequency in a southern Somali individual (27.2%), and at lowest frequency in an Ethiopian Amhara individual (17.6%). The Rendille samples have the highest average percentage of this East Asian ancestral element (25.6%), whereas the Eritrean samples carry this component at the lowest average frequency (20.4%). Overall, this ancient East Asian component occurs at an average frequency of 22.6% among our Afro-Asiatic-speaking samples.
• The ancient Nilo-Saharan component (KEN_Kakapel_300BP) is found at highest frequency in a Rendille individual (25.8%), and at lowest frequency in an Ethiopian Amhara individual (9.4%). The Rendille samples also have the highest average percentage of this Nilo-Saharan ancestral element (25.7%), whereas the Ethiopian Agaw samples bear this component at the lowest average frequency (13.9%). Overall, this ancient Nilo-Saharan component occurs at an average frequency of 17.1% among our Afro-Asiatic-speaking samples.
• The ancient East African Hunter-Gatherer component (MWI_Chencherere) is found at highest frequency in an Iraqw individual and an Ethiopian Oromo individual (both 18.8%), and at lowest frequency in an Eritrean individual (1.8%). The Iraqw samples also have the highest average percentage of this East African Hunter-Gatherer ancestral element (18.3%), whereas the Eritrean samples carry this component at the lowest average frequency (4.5%). Overall, this ancient East African Hunter-Gatherer component occurs at an average frequency of 8.6% among our Afro-Asiatic-speaking samples.
• The ancient Pygmy component (CMR_Shum_Laka) is found at highest frequency in an Eritrean individual (3.4%), and at lowest frequency among most samples in our dataset (0%). The Eritrean samples also have the highest average percentage of this Pygmy ancestral element (1.1%), whereas the southern Somali, Rendille and Iraqw samples bear this component at the lowest average frequency (0%). Overall, this ancient Pygmy component occurs at an average frequency of 0.2% among our Afro-Asiatic-speaking samples.
• The ancient Niger-Congo component (COG_Kindoki_230BP) was not detected in any of our Afro-Asiatic-speaking samples.
• The ancient Khoisan component (ZAF_2000BP) was not detected in any of our Afro-Asiatic-speaking samples.
• The North African Iberomaurusian component (MAR_Taforalt) is found at highest frequency in a southern Somali individual (6.2%), and at lowest frequency (0%) among various Ethiopian and Eritrean individuals (except the Agaw and Wolayta, who all have some percentage of this component). The southern Somali samples have the highest average percentage of this Iberomaurusian ancestral element (3%), whereas the Eritrean samples carry this component at the lowest average frequency (0.2%). Overall, this Iberomaurusian component occurs at an average frequency of 1.2% among our Afro-Asiatic-speaking samples.

Tables of ancestral proportions for each Afro-Asiatic-speaking population (derived from the Vahaduo Admixture JS program’s Multi function):

Afar (Ethiopia)

Agaw (Ethiopia)

Amhara (Ethiopia)

Eritrean

Ethiopian Jew

Iraqw (Tanzania)

Oromo (Ethiopia)

Rendille (Kenya)

Somali (Kenya)

Somali (South Somalia)

Tigray (Ethiopia)

Wolayta (Ethiopia)

Summary Vahaduo Multi table of the averages of each genome component for all the examined Horn populations:

	Ancient East Asian (CHN_Huatuyan_500BP)	Ancient Pygmy (CMR_Shum_Laka)	Ancient Niger-Congo (COG_Kindoki_300BP)	Ancient Egyptian (EGY_1879BCE)	Iran Neolithic (Ganj_Dareh_N)	Ancient Nilo-Saharan (KEN_Kakapel_300BP)	Natufian (Levant_Natufian_EpiP)	Iberomaurusian (MAR_Taforalt)	East African Hunter-Gatherer (MWI_Chencherere)	European Steppe (RUS_Baikal_BA)	Anatolian Neolithic (TUR_Marmara_Barcin_N)	Ancient Khoisan (ZAF_2000BP)	Average non-African Ancestry	Average Sub-Saharan African Ancestry	Average Ancient North African Ancestry
Afar (Ethiopia)	23.9%	0.8%	0%	18.2%	0%	14.4%	24.3%	0.9%	5.5%	12.1%	0%	0%	78.4%	20.7%	0.9%
Agaw (Ethiopia)	21.9%	0.2%	0%	19%	0%	13.9%	23.1%	1.0%	8.1%	12.8%	0%	0%	76.8%	22.2%	1.0%
Amhara (Ethiopia)	22.2%	0.2%	0%	18.1%	0%	14.7%	24.9%	1.0%	7.7%	11.3%	0%	0%	76.4%	22.6%	1.0%
Eritrean	20.4%	1.1%	0%	16.7%	0%	16.7%	30.0%	0.2%	4.5%	10.3%	0%	0%	77.5%	22.3%	0.2%
Ethiopian Jew	22.6%	0.3%	0%	17.6%	0%	15.1%	26.4%	0.3%	7.5%	10.3%	0%	0%	76.8%	22.9%	0.3%
Iraqw (Tanzania)	22.9%	0%	0%	18.2%	0%	21.7%	5.2%	2.4%	18.3%	11.3%	0%	0%	57.6%	40.0%	2.4%
Oromo (Ethiopia)	22.9%	0.1%	0%	17.2%	0%	17.6%	19.4%	0.8%	11.6%	10.4%	0%	0%	69.9%	29.3%	0.8%
Rendille (Kenya)	25.6%	0%	0%	18.1%	0%	25.7%	10.7%	1.8%	9.6%	8.5%	0%	0%	62.9%	35.3%	1.8%
Somali (Kenya)	23.6%	0.2	0%	18.5%	0%	20.4%	14.1%	2.1%	9.1%	12.1%	0%	0%	68.2%	29.7%	2.1%
Somali (South Somalia)	23.6%	0%	0%	19.3%	0%	20.0%	13.3%	3.0%	7.7%	13.1%	0%	0%	69.3%	27.7%	3.0%
Tigray (Ethiopia)	21.7%	0.1%	0%	17.8%	0%	15.5%	26.3%	0.8%	6.4%	11.5%	0%	0%	77.2%	22.0%	0.8%
Wolayta (Ethiopia)	21.7%	0.9%	0%	16.8%	0%	17.5%	15.6%	1.8%	14.7%	10.9%	0%	0%	65.1%	33.1%	1.8%

Step 4: Corroborate these findings with other scientific evidence

As a fourth step in our analysis, we shall further establish the veracity of our findings by corroborating them with other scientific evidence gathered from different disciplines. We will focus on the Steppe element because the ancient Egyptian component is fully discussed on Punt: an ancient civilization rediscovered.

In regards to the European-related Steppe ancestry, which we have just identified above, uniparental markers (both Y-DNA and mtDNA) support the existence of such an influence in Northeast Africa. Gad et al. (2020) report that the 18th Dynasty ancient Egyptian Pharaoh Amenhotep III, his son Pharaoh Akhenaten and his grandson Pharaoh Tutankhamun, who governed from the Amarna site in Upper Egypt, belong to the Y-DNA haplogroup R1b (cf. Gad et al. (2020a); Gad et al. (2020b)). iGENEA further specifies that these Amarna royals fall under the clade’s M269 branch, the most common paternal lineage carried today by European males. Yatsishina et al. (2021) likewise divulge that one of the ancient Egyptian mummies they analysed at the Kurchatov Institute bears the R1b-M269 haplogroup. Maternally, Khairat et al. (2013) state that a mummified ancient Egyptian individual they studied belongs to the I2 mtDNA haplogroup. This mitochondrial lineage has been detected among various early Steppe cultures of Europe. It is nowadays quite rare (typically under 5%), attaining a global frequency peak of 23% among Cushitic-speaking remnant groups in the Great Lakes region (Castrì et al. (2008)). Moreover, the basal I* haplogroup has only been observed among three persons worldwide; two of these individuals are from Somalia and the other is from Iran (Olivieri (2013)). White et al. (2023) also detected the rare H4a1 mtDNA clade in the mummy of Takabuti, an ancient Egyptian noblewoman from Thebes, Upper Egypt. The scientists note that this maternal lineage has been “described in antiquity only in Central Europe,” and propose that the haplogroup is “suggestive of the introduction of new gene pools during the Late Period of ancient Egyptian history.” 

Y-DNA haplogroups of the ancient Egyptian Pharaoh Amenhotep III, his son Pharaoh Akhenaten, and his grandson Pharaoh Tutankhamun, who were ruled from the Amarna site in Upper Egypt. These 18th Dynasty kings belong to the R1b clade, which today is the most common paternal lineage borne by Europeans. This finding supports an ancient presence in the Nile Valley of peoples bearing European-related Steppe ancestry (Gad et al. (2020a)).

Autosomal DNA analysis of the Amarna kings has also unveiled a clear Steppe-related ancestral affinity. Hawass et al. (2010) typed these ancient Egyptian monarchs for short tandem repeats (STRs). The genetic testing company DNA Tribes then compared these specimens’ microsatellite markers against those belonging to various modern populations contained within its internal database, and reported that they showed greatest genetic affinity with those of contemporary Sub-Saharan African individuals. However, a cross-analysis of the Amarna royals’ autosomal STRs with the microsatellites listed on the more extensive Allele Frequency Database (ALFRED) demonstrates instead a close affiliation with populations in South Asia and Europe (see our study Autosomal STR Analysis of the Ancient Egyptian Amarna Royal Family, Pharaoh Ramesses III, and Unknown Man E (Prince Pentawere). We know that this affinity is specifically tied to ancient Steppe-bearing peoples because the alleles with a primary South Asian affiliation also often include among their top results ALFRED’s eastern European samples, and eastern Europe is where the Steppe component is believed to have ultimately originated (e.g. 22.50% of Croatians carry the Pharaoh Akhenaten’s FGA=23 allele, which peaks at 40% in a Reddy/Vanne sample from South Asia). The reverse is also true. That is, the alleles with a primary European affiliation likewise frequently include South Asian groups among their top results (e.g. 48% of the Drokpa in South Asia carry the courtier Thuya’s D7S820=10 allele, which peaks at 52.60% in a Croatian sample). This finding agrees with our Vahaduo Admixture JS analysis, as well as with the Steppe-associated uniparental markers that these ancient Egyptians carry.

Autosomal STR analysis of the 18th Dynasty ancient Egyptian Amarna royal family (which includes the Pharaohs Amenhotep III, Akhenaten and Tutankhamun), as well as the Pharaoh Ramesses III and the prince Unknown Man E/Pentawere. These monarchs share greatest genetic affinity with populations in South Asia (Affinity Index: 37.58) and Europe (Affinity Index: 18.79). This concurs with a suggested diffusion of peoples bearing European-related Steppe ancestry into both Northeast Africa and South Asia (LOP (2023)).

Autosomal STR analysis of the Amarna royals indicates that these individuals bear a predominant Eurasian ancestry (~87.50% on average). Of these monarchs, the Pharaoh Amenhotep III carries the most total Eurasian ancestry, estimated at 100% (LOP (2023)).

What’s more, analysis of limb proportions is suggestive of contact with populations inhabiting the temperate zone. Holliday (2013) examined various old and recent global samples, including an ancient Egyptian cohort (dating from the Predynastic to Middle Kingdom), a Kerma sample (dating from the Middle Kingdom i.e., the same time period as the Global25 sample EGY_1879BCE, which belongs to Nakht-Ankh), and a Christian-era Nubian sample (dating from the 4th to 7th centuries CE). He reports that his Middle Ages Nubian cohort had a more cold-adapted body plan, similar to his medieval European samples. On the other hand, Holliday’s ancient Egyptian cohort and Kerma sample had more linear, tropically-adapted limbs, similar to the “leptosome tendency” which Coon (1939) affirms is typical of Bedouin Hadhramis in southern Arabia. This is consistent with our analysis below, which indicates that the Christian period inhabitants of Kulubnarti in Nubia bore some Steppe-related admixture. It therefore appears that during Nakht-Ankh’s lifetime, Steppe ancestry, although already present since the Neolithic period, had not yet spread throughout the Nile Valley.

The cephalic indices (CI) of the ancient Egyptian Amarna monarchs also attest to a European Steppe affiliation. Kemp and Zink (2012) report that, with the exception of the courtier Yuya, who is markedly dolichocephalic (long-headed, with a CI of 70.3), all of these royal mummies are either mesocephalic (medium-headed) or brachycephalic (broad-headed). That is, they possess cephalic index values of 75 or greater. Akhenaten and Tutankhamun are, in fact, brachycephalic, with high cephalic indices of 81.0 and 83.9, respectively. This is atypical for both ancient and modern Egyptians, who for the most part tend toward dolichocephaly (cephalic indices under 75). However, brachycephaly is common in eastern Europe, where frequencies of the Steppe ancestral component are today maximized (cf. Godina (2011)).

Additionally, philological evidence backs a Steppe connection. For example, Bahadur (1917) notes that “Eusebius states that Ethiopians [Meroites] emigrating from the River Indus settled in the vicinity of Egypt [Meroe].” Nilus similarly relayed to Apollonius Tynaeus that “the Indi are the wisest of all mankind. The Ethiopians [Meroites] are a colony from them: and they inherit the wisdom of their forefathers.” The Indus river mostly traverses Pakistan, an area that historically was settled by Indo-European speakers, who carried Steppe ancestry.

Craniometric analysis likewise points to a close association between Afro-Asiatic speakers in Northeast Africa, Indo-European-speaking and Dravidian-speaking populations of South Asia, and Europeans. This affinity extends back in time to subsume early groups in these areas, including the ancient Egyptians and post-Neolithic Nubians. Brace (1993), for instance, asserts that “insofar as India has metric ties with any other populations, it combines with Nubia [Bronze Age/X-Group and Medieval/Christian Era samples] and then the Somalis to join Europe and the Egyptians [Predynastic and Late Dynastic samples] as a last link before that set of branches ties in with the rest of the world.” Multiple other studies have also observed a similar affiliation (e.g. Morton (1854), Stoessiger (1927), Coon (1939), Sergent (1997), Brace et al. (2006)). This aligns well with a diffusion of ancient Steppe-bearing peoples into Northeast Africa and South Asia, either indirectly from a common waypoint near Central Asia or directly from Europe.

Craniometric analysis of ancient and contemporary global populations. The modern Afro-Asiatic-speaking populations in Northeast Africa, the ancient Egyptians, the Bronze Age Nubians (X-Group) and Medieval Nubians (Christian period), modern Indo-European-speaking and Dravidian-speaking groups of India, and modern and ancient Europeans cluster together. This is consistent with a spread of Steppe-bearing peoples from Europe to these areas, either directly or indirectly via Central Asia (Brace (1993)).

Furthermore, hair morphology supports an early European-associated presence in Northeast Africa. Lazaridis et al. (2022) conducted a comprehensive analysis of phenotypic traits borne by ancient individuals exhumed in Europe and Asia. The scientists indicate that blond hair was most common among their ancient European specimens and that red hair was exclusively found among these samples. This is key since Brothwell and Spearman (1963), employing reflectance spectrophotometry, observed a number of authentically blond ancient Egyptian individuals; their hair samples were not affected by either hair dye or cuticular damage. Strikingly, Griggs (1988) reports that excavations he led at a Roman-Christian era cemetery in Seila, located in the Fayum region of Egypt, yielded the remains of many individuals with blond or red hair. He affirms that “of the 37 adults whose hair was still preserved[…] there were 4 redheads, 16 blondes, 12 with light or medium brown hair, and only 5 with dark brown or black hair. Of those whose hair was preserved 54% were blondes or redheads, and the percentage grows to 87% when light-brown hair color is added.” Similarly, Janssen (1978) writes that “330 graves were excavated in cemetery 221 (Meroitic) and a proportion of blond individuals of Caucasoid type found.” Hrdy (1978), also analysing Meroitic remains, notes that many ancient individuals buried at Semna South in Sudanese Nubia had blond or red hair. He suggests that this “probably points to a significantly lighter-haired population than is now present in the Nubian region.”

Correspondingly, several of the ancient Egyptian mummies belonging to the Amarna royal lineage, including the aristocrats Yuya, Thuya and Tiye as well as the Pharaoh Ramesses III, also have blond or red hair. These are the same monarchs who, as we have just seen, carry some European-affiliated autosomal STR markers. In the case of Yuya, Hawass and Saleem (2016) argue that his blondism was caused by either the fading of henna dye on white hair or the interaction of embalming materials and applied henna. However, the Egyptologist Janet Davey of the Victorian Institute of Forensic Medicine later demonstrated through laboratory experimentation that natron used in the mummification process has no effect on hair color, regardless of whether or not a specimen’s hair had been dyed with henna during embalming. This finding was confirmed by a followup microscopic analysis conducted by Gale Spring of RMIT (cf. Smith (2016)). Hamed and Maher (2021), using various analytical processes (viz. microscopic examination, FTIR spectroscopy, gas chromatography and raman spectroscopy), also observed that Yuya’s natural hair color is indeed a reddish-blond. Elemental analysis of his hair shafts showed a high concentration of sulphur, an element that occurs in greater quantities in blond or red hair than in black hair. Tiye and the other royal mummies likewise reportedly have naturally red or blond hair. What’s more, a tomb painting of the Pharaoh Amenhotep III depicts him with a light reddish mane. This altogether underlines the fact that blond and red hair were prevalent among the ancient Egyptian Amarna nobles.

In summary, the existence of an old European Steppe ancestral component in Northeast Africa, analogous to that which we have detected through our Vahaduo Admixture JS genome analysis, is supported by studies on the Amarna royal family. These ancient Egyptian monarchs ruled from the Amarna site in Upper Egypt during the 18th Dynasty. Their mummies have been found to bear Steppe-related autosomal STR markers, uniparental haplogroups (notably, the R1b Y-DNA clade and the I mtDNA clade), primarily mesocephalic or brachycephalic skulls, and blond or red hair, much like populations in eastern Europe where the Steppe component originally dispersed from. Moreover, craniometric examination of modern Afro-Asiatic speakers and Nubians in Northeast Africa reveals close ties with groups in South Asia and Europe, consistent with population movements from the European Steppe into Central Asia and from there into both the Nile Valley/Horn and the Indian subcontinent. Such early migrations are also backed by ancient texts, which assert that peoples from the Indus river vicinity settled near Egypt, in the Meroë area situated in present-day Sudan.

Step 5: Confirm whether the ancient Pastoral Neolithic and Kulubnarti specimens share this ancestral composition

Fifthly, we shall explore if the ancient Cushitic settlers of the Pastoral Neolithic and the Christian-era Kulubnarti specimens from Nubia carry these same ancestral components and at similar frequencies. This will help us determine whether the Eurasian elements, which we have just identified, are legitimate ancestries or mere statistical constructs. It will also give us some insight as to which of these components are the original ancestries of the Afro-Asiatic speakers and which components are instead intrusive (i.e., elements acquired later through interbreeding).

We start off by launching another Vahaduo Single run, this time using the Pastoral Neolithic samples as our Target populations. The “pure” ancient Sub-Saharan African specimens (Kakapel_300BP, MWI_Chencherere, COG_Kindoki), CMR_Shum_Laka, ZAF_2000BP) and the 6000+ ancient Eurasian specimens listed on the Global25_PCA datasheet will once more serve as our Source populations. The end result is displayed below. It again primarily shows the same assortment of West Eurasian (viz. ancient Egyptian, Steppe and Natufian components) and East Eurasian (East Asian component) ancestries, which occur at similar total frequencies as before (over 70%). The remaining minority of the Pastoral Neolithic individuals’ ancestral composition consists of Sub-Saharan African admixture (~25%) and North African Iberomaurusian admixture (under 5%), just like the modern Afro-Asiatic speakers from the Horn region.

When we repeat this process for the Kulubnarti samples, we encounter the same ancestral components occurring again at practically identical percentages. However, one key difference between the Kulubnarti individuals on the one hand, and the Pastoral Neolithic and modern Horn samples on the other, is that the Kulubnarti specimens have little East African Hunter-Gatherer admixture. Almost all of their ancient Sub-Saharan African admixture instead consists of the Nilo-Saharan Kakapel300BP element. 

Lastly, when we run a Vahaduo Multi analysis on both our Pastoral Neolithic and Kulubnarti ancient samples, here too we come away with similar ancestral components and at comparable percentages:

Pastoral Neolithic

Kulubnarti

With regards to the Pastoral Neolithic table above, we may note that:

• The ancient Egyptian component (EGY_1879BCE) is found at highest frequency in a Pastoral Neolithic individual from Molo Cave in Kenya (23.4%), and at lowest frequency in a Savanna Pastoral Neolithic individual from Tanzania (14.2%). The singleton Pastoral Neolithic samples (i.e., Lukenya Hill, Molo Cave and Hyrax Hill in Kenya and Luxmanda in Tanzania) have the highest average percentage of this Egyptian ancestral element (20.1%), whereas the Tanzanian Savanna Pastoral Neolithic samples bear this component at the lowest average frequency (18.1%). Overall, this ancient Egyptian component occurs at an average frequency of 19% among our Pastoral Neolithic samples.
• The European-related Steppe component (RUS_Baikal_BA) is found at highest frequency in a Kenyan Savanna Pastoral Neolithic individual (17.4%), and at lowest frequency in a Kenyan Savanna Pastoral Neolithic individual (3.6%). The singleton Pastoral Neolithic samples also have the highest average percentage of the Steppe ancestral element (11.3%), whereas the Tanzanian Savanna Pastoral Neolithic samples and Early Pastoral Neolithic individuals from Kenya carry this component at the lowest average frequency (both 9.6%). Overall, this Steppe component occurs at an average frequency of 10.7% among our Pastoral Neolithic samples.
• The Levantine Natufian component (Levant_Natufian_EpiP) is found at highest frequency in a Kenyan Savanna Pastoral Neolithic individual (28%), and at lowest frequency in a Pastoral Neolithic individual from Molo Cave (0%). The Kenyan Early Pastoral Neolithic samples have the highest average percentage of this Natufian ancestral element (19.6%), whereas the singleton Pastoral Neolithic samples bear this component at the lowest average frequency (5.3%). Overall, this Natufian component occurs at an average frequency of 13.7% among our Pastoral Neolithic samples.
• The ancient East Asian component (CHN_Huatuyan_500BP) is found at highest frequency in a Kenyan Pastoral Neolithic individual from Lukenya Hill (27.2%), and at lowest frequency in a Tanzanian Savanna Pastoral Neolithic individual (18.6%). The Kenyan Early Pastoral Neolithic samples have the highest average percentage of this East Asian ancestral element (23.9%), whereas the Tanzanian Savanna Pastoral Neolithic samples carry this component at the lowest average frequency (21.4%). Overall, this ancient East Asian component occurs at an average frequency of 22.7% among our Pastoral Neolithic samples.
• The ancient Nilo-Saharan component (KEN_Kakapel_300BP) is found at highest frequency in a Kenyan Pastoral Neolithic individual from Molo Cave (28.6%), and at lowest frequency in a Kenyan Early Pastoral Neolithic individual (8%). The singleton Pastoral Neolithic samples have the highest average percentage of this Nilo-Saharan ancestral element (18.8%), whereas the Kenyan Early Pastoral Neolithic samples bear this component at the lowest average frequency (8.5%). Overall, this ancient Nilo-Saharan component occurs at an average frequency of 17% among our Pastoral Neolithic samples.
• The ancient East African Hunter-Gatherer component (MWI_Chencherere) is found at highest frequency in a Kenyan Pastoral Neolithic individual from Molo Cave (22.8%), and at lowest frequency in a Kenyan Savanna Pastoral Neolithic individual (0%). The singleton Pastoral Neolithic samples have the highest average percentage of this East African Hunter-Gatherer ancestral element (15.4%), whereas the Kenyan Savanna Pastoral Neolithic samples carry this component at the lowest average frequency (10.9%). Overall, this ancient East African Hunter-Gatherer component occurs at an average frequency of 12.4% among our Pastoral Neolithic samples.
• The ancient Pygmy component (CMR_Shum_Laka) is found at highest frequency in a Kenyan Savanna Pastoral Neolithic individual (5.6%), and at lowest frequency among most samples in our dataset (0%). The Kenyan Savanna Pastoral Neolithic samples also have the highest average percentage of this Pygmy ancestral element (1.4%), whereas the singleton Pastoral Neolithic samples and Kenyan Early Pastoral Neolithic samples bear this component at the lowest average frequency (0%). Overall, this ancient Pygmy component occurs at an average frequency of 0.6% among our Pastoral Neolithic samples.
• The ancient Niger-Congo component (COG_Kindoki_230BP) was not detected in any of our Pastoral Neolithic samples.
• The ancient Khoisan component (ZAF_2000BP) was not detected in any of our Pastoral Neolithic samples.
• The North African Iberomaurusian component (MAR_Taforalt) is found at highest frequency in a Kenyan Pastoral Neolithic individual from Hyrax Hill (9.2%), and at lowest frequency among two Kenyan Elmenteitan Pastoral Neolithic individuals and one Kenyan Savanna Pastoral Neolithic individual (0%). The singleton Pastoral Neolithic samples have the highest average percentage of this Iberomaurusian ancestral element (6.1%), whereas the Kenyan Elmenteitan Pastoral Neolithic samples carry this component at the lowest average frequency (2%). Overall, this Iberomaurusian component occurs at an average frequency of 1.2% among our Pastoral Neolithic samples.

Tables of ancestral proportions for each Pastoral Neolithic group:

Early Pastoral Neolithic (Kenya)

Elmenteitan Pastoral Neolithic (Kenya)

Savanna Pastoral Neolithic (Kenya)

Savanna Pastoral Neolithic (Tanzania)

Singleton Pastoral Neolithic (Kenya and Tanzania)

Step 6: Confirm whether modern Egyptians share this ancestral composition

Sixthly, we will examine whether contemporary Egyptian individuals have the same ancestral makeup as just outlined. As our Target population on Vahaduo Admixture JS, we shall use the Egyptian samples listed on Eurogenes’ official Global25_PCA_modern datasheet. For our Source populations, we will again utilize the Eurasian samples on the Global25_PCA datasheet, alongside the five “pure” ancient Sub-Saharan African representatives. With our Target and Source populations now loaded, we will tap into Vahaduo’s Single function, letting the program sift through Global25’s massive 6000+ samples to pinpoint for us the most optimal sources of ancient Eurasian ancestry.

From the above, it is apparent that modern Muslim Egyptians (i.e. non-Coptic Egyptians) do generally share the same ancestral composition as the Afro-Asiatic-speaking populations in the Horn of Africa. West Eurasian elements (ancient Egyptian, European-related Steppe, and Levantine Natufian components) and an East Eurasian element (East Asian component) are most prominent here too, and minor Sub-Saharan African admixture and a minute North African Iberomaurusian admixture can again be detected. That said, many of the analysed Muslim Egyptian individuals also show an affinity with the contemporary Levant/Arabia, as exemplified by the Levant_Tell_Qarassa_Early_Antiquity component. This West Eurasian ancestral element — which mainly consists of Natufian ancestry, with some later acquired Anatolian Neolithic and Caucasus Hunter-Gatherer/Iran Neolithic admixtures — is most typical of modern Arabic speakers, as well as many Yemeni Jews and some Mahra individuals (see Vahaduo Single analysis here).

Like before, to re-confirm the main ancestries that we have just identified and organize them into table format for easier interpretation, we will end with a Vahaduo Multi analysis. We shall include the Levant_Tell_Qarassa_Early_Antiquity sample to capture the modern Arabian admixture that is present in Egyptians. Next, we shall re-run our Multi analysis and include G25’s TUR_Marmara_Barcin_N and IRN_Ganj_Dareh_N samples among our Source populations so as to account for, respectively, the Anatolian Neolithic and Iran Neolithic elements that are inherent in the Levant_Tell_Qarassa_Early_Antiquity component:

Egyptian (with Levant_Tell_Qarassa_Early_Antiquity)

Egyptian (with Levant_Tell_Qarassa_Early_Antiquity broken down into its constituent elements)

As can be seen in the tables above, the Muslim Egyptian individuals still bear the same ancestries as other Afro-Asiatic speakers in the Horn of Africa and at comparable frequencies, confirming the observed affinities. On average, modern Egyptians carry around 84% non-African ancestry, the majority of which consists of West Eurasian elements (viz. primarily ancient Egyptian, Steppe and Natufian components, as well as some extra Anatolian Neolithic and Iran Neolithic admixtures) and a minority of which comprises an East Eurasian element (East Asian component). Furthermore, they also harbor around 13% Sub-Saharan African admixture (primarily consisting of the Nilo-Saharan element, and secondarily of the Niger-Congo element) and a very minor North African Iberomaurusian admixture (3%).

Coptic Egyptians are not yet included on the official Global25 datasheets, but they seem to have a somewhat different ancestral composition. This is suggested by the Coptic samples on IllustrativeDNA, a service which uses G25 technology to process its own coordinates (not official Global25 coordinates). When these coordinates are run through Vahaduo Admixture JS’s Single function, the Coptic individuals appear to derive over 99% of their ancestry from the EGY_1879BCE ancient Egyptian sample. However, since IllustrativeDNA’s samples are often low coverage, producing bloated fits on Vahaduo’s Distance parameter of >15%, they frequently do not allow for precise identification of all the ancestral components an individual might bear nor can they accurately quantify those elements (e.g. when used as Target populations against Global25’s ancient Eurasian Source populations, IllustrativeDNA’s Afro-Asiatic-speaking samples from the Horn have Vahaduo Distance fits which are around three times higher than Eurogenes’ official Global25 Horn samples; compare this with this). We must therefore perform an additional Vahaduo Distance analysis on our Coptic samples to make sure that they are reliable. When this is done, our Copts and other Egyptian samples from IllustrativeDNA wind up showing almost identical Distance fits as Eurogenes’ official Global25 Egyptian samples (see here and here).

This confirms that Coptic Egyptians indeed descend directly from Egyptians dating from at least the earlier Dynastic period — something which was already strongly implied by their traditional language, Coptic, a later iteration of the ancient Egyptian tongue. As such, Coptic Egyptians seem to have been largely unaffected by the aforementioned gene flow into the Nile Valley, which we have detected in both the ancestral Cushites of the Pastoral Neolithic and the later Dynastic period Egyptians. Having said that, besides the Y-DNA haplogroup E1b1b common among Afro-Asiatic speakers, some modern Coptic individuals also bear the R1b and J paternal clades (E1b1=74% and J1=1% among Copts in Upper Egypt according to Crubézy et al. 2010; E1b1b=21%, J=45% and R1b=15% among Copts in Sudan according to Hassan et al. (2008)). The R1b and J lineages were first brought to the Egypt area by newcomers bearing, respectively, European-related Steppe ancestry (seemingly introduced as early as the Neolithic) and Caucasus Hunter-Gatherer/Iran Neolithic ancestry (introduced during the later Dynastic period). Hence, there is genetic evidence of contact between Coptic Egyptians and foreigners. Our Vahaduo Single analysis below, however, demonstrates that this gene flow was ultimately also of negligible importance because, unlike Muslim Egyptians, Copts (both in Sudan and Egypt) for the most part do not bear these ancestral components.

We will finish by conducting a Vahaduo Multi analysis on all of the Coptic and Egyptian samples discussed above. To these we shall add Hollfelder et al. (2017)’s Coptic sample, as well as that paper’s Nubian cohort and other Sudanese Afro-Asiatic-speaking groups. The resulting data table, shown below, indicates that Hollfelder et al.’s samples, including their Coptic representative, are unreliable since they have the tell-tale inordinately high Distance fits (on average >15%; one Sudanese “Arab” Shaigia sample has an absurd Distance fit of 47%), few identified ancestral elements (usually 2 to 3 maximum), and skewed component frequencies typical of low coverage samples. However, it is interesting to note that the Egyptian samples from Cairo and Mansoura share an almost identical genetic profile as Coptic Egyptians, albeit with a small Sub-Saharan African admixture. Both of these samples are from IllustrativeDNA and have acceptable Distance fits of <9%. Since Cairo and Mansoura are cities located in northern Egypt, where the EGY_1879BCE specimen was excavated from at Deir Rifeh, we therefore now have, for the first time, genetic evidence substantiating the existence of Upper Egyptian/southern Egyptian and Lower Egyptian/northern Egyptian types.

Anthropologists have long observed such a cleavage in the Nile Valley’s skeletal record. For example, Batrawi (1946) remarks that the ancient Egyptians appeared to have been divided into two distinct but related physiognomies, and that “the study of the available measurements of the living, however, apparently suggests that the modern population all over Egypt conforms more closely to the southern type” (also see G. Billy (1975)). We can now state that the primary distinguishing factor between these two osteological types seems to have been gene flow from the European Steppe and later also from the Arabian peninsula rather than Sub-Saharan African admixture. This is because the contemporary Egyptian samples from Global25 and the northern Egyptian samples from IllustrativeDNA have almost the same low level of Sub-Saharan African admixture (13% and 11%, respectively). Ergo, after the early Dynastic period, foreign influences from Europe and Asia significantly impacted northern Sudan and southern Egypt as compared to northern Egypt.

Step 7: Confirm whether modern Sudanese “Arabs” also share this ancestral composition

For the seventh step in our analysis, we shall inquire whether Sudanese “Arabs” share the same ancestral composition as the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa. We will follow the exact same procedure as just described above for Egyptians, using Kababish as our Sudanese “Arab” cohort. To these we shall add two other samples from Sudan, of Rashaayda Arabs and Baggara “Arabs.” In addition, we will examine Daza (Gorane or southern Toubou) individuals and other Baggara “Arabs,” both from Chad. All of these samples were originally published in Fortes Lima et al. (2022) and later converted to Global25 coordinates for use in the Vahaduo Admixture JS software program (see here for the unscaled or raw G25 coordinates; though not official Global25 samples, they are high coverage/decent quality).

Our resulting Vahaduo Single analysis is as follows:

Judging by the Single analysis above, it is apparent that the Kababish “Arabs” generally bear the same ancestral makeup as the Horn’s Afro-Asiatic speakers.

To better organize our thoughts and strengthen our interpretation, we will finish by conducting a Vahaduo Multi analysis:

From the data table above, it is clear that the Kababish “Arabs” of Sudan do have the same overall ancestral composition as the Afro-Asiatic speakers from the Horn of Africa. The Kababish individuals bear a predominant Eurasian ancestry (averaging almost 70%), comprising majority West Eurasian elements (ancient Egyptian, European Steppe, and Levantine Natufian components) and a minority East Eurasian element (East Asian component). Furthermore, these individuals carry some Sub-Saharan African admixture (close to 30%) and a trace Iberomaurusian admixture (under 1%). One characteristic difference, however, is that the Kababish’s Sub-Saharan African admixture almost entirely consists of the “pure” ancient Nilo-Saharan component (KEN_Kakapel_300BP). Their comparatively trivial frequencies of the East African Hunter-Gatherer component (MWI_Chencherere), averaging just 1%, are instead more congruent with our modern Egyptian and ancient Kulubnarti results above, as well as our results for contemporary Libyans below. All of these samples have negligible frequencies of this forager element, which emphasizes that this component is indeed autochthonous to eastern Africa rather than the Nile Valley.

For their part, the Baggara “Arab” samples from Sudan and Chad are very similar to the Sudanese Kababish “Arab” cohort. These populations, in fact, appear to be of the same origin. However, it is evident from the figures above that the Baggara have intermixed more with their Nilo-Saharan-speaking neighbors since they harbor greater average percentages of the KEN_Kakapel_300BP component (40.2% for the Baggara in Chad and 47.3% for the Baggara in Sudan). 

The samples belonging to the Daza (Gorane), or southern Toubou, are almost identical to those of the Baggara “Arabs.” Just one key difference separates these two groups, and that is the Daza’s appreciable frequencies of the North African Iberomaurusian component (averaging 14.5%). In this respect, the Daza individuals appear more similar to the modern Libyans (discussed below), who have a comparable average percentage of this Taforalt element. It may be that the Daza and Teda or northern Toubou — as hypothesized successors of the ancient Garamantes/Garamantians, whose old territory they currently occupy — were originally Afro-Asiatic speakers of Libyan stock. Hence, as Kirwan (1934) observes, the etymological connection between the ethnonyms Goran and Garamantes. However, since the Daza and other Toubou intermingled significantly with their Nilo-Saharan neighbours, it is conceivable that they eventually adopted the latter’s language. This ultimately would have served to obscure their Berber origins.

The Rashaayda Arabs (Rashaida) of Sudan and Eritrea are relative newcomers to Northeast Africa. Their arrival from the Hejaz region of Saudi Arabia during the 19th century is well-documented. It is, therefore, completely expected that they should mostly bear Natufian-related ancestry. Nevertheless, just to confirm that these individuals are indeed of peninsular Arab origin, we shall run a final Vahaduo Multi analysis with all of our other Sudanese and Chadian “Arab” samples, but this time include the Levant_Tell_Qarassa_Early_Antiquity cohort to capture any such recent ancestry. We will also include the TUR_Marmara_Barcin_N and IRN_Ganj_Dareh_N specimens to see if our Rashaayda individuals and other samples carry any extra Anatolian Neolithic and Iran Neolithic admixture, respectively. The resulting analytical table below shows that, unlike the Kababish “Arab”, Baggara “Arab” and Daza Toubou samples, the Rashaayda Arabs clearly are of recent peninsular Arab origin. They are the only Arabic-speaking population of Sudan and Chad in our dataset that mostly belongs to the associated Levant_Tell_Qarassa_Early_Antiquity component (68.6% on average). Among the Kababish and Baggara, Arabian admixture is instead restricted to a handful of individuals (notably, the Chadian Baggara individual ABA032, who has an elevated 41.4% frequency of the Levant_Tell_Qarassa_Early_Antiquity element). These outliers are likely descendants of peninsular Arab Muslims, who introduced the Islamic faith and the Arabic language to the Sudan area during the medieval period.

Tables of ancestral proportions for each Arabic-speaking Sudanese and Chadian group as well as the Daza Toubou:

Baggara “Arab” (Chad)

Baggara “Arab” (Sudan)

Daza Toubou (Chad)

Kababish “Arab” (Sudan)

Rashaayda Arab (Sudan)

Rashaayda Arab (with Levant_Tell_Qarassa_Early_Antiquity)

Step 8: Confirm whether modern Maghrebis also share this ancestral composition

As an eighth step in our analysis, we shall explore whether contemporary Afro-Asiatic speakers of the Maghreb region in northwestern Africa also share the ancestral composition described above. We will begin, as previously, by conducting a Vahaduo Distance test on all of Global25’s ancient African samples that possess the least Eurasian admixture. This should help us determine which population mainly contributed the Sub-Saharan African admixture that modern Maghrebis carry.

Of the top eight results listed above, the Congo Kindoki specimens are the most suitable Niger-Congo proxies for our Maghrebi samples. This is because, along with the Congo NgongoMbata 220BP cohort, they are the “purest” available ancient specimens bearing Niger-Congo-related ancestry (see Step #9 below on how we know that), and Bekada et al. (2015) have found that contemporary Maghrebis harbor such Yoruba-like admixture. However, since the COG_Kindoki_230BP:KIN004 sample belongs to the Indo-European-associated Y-DNA haplogroup R1b1 (cf. Wang et al. (2020), Table S10), we shall avoid using it. We will instead utilize COG_Kindoki_230BP:KIN002 as our reference sample, for it bears the E1b1a paternal clade common among modern Niger-Congo speakers.

Moving forward, we shall now perform a Vahaduo Single analysis on our Maghrebi samples. The non-African specimens listed on the Global25_PCA datasheet will, alongside Congo_Kindoki and the other “pure” ancient Sub-Saharan African samples, again serve as our Source populations. Such a test leverages Vahaduo Admixture JS’s processing capabilities, allowing the program to find for us the exact ancestries our Target populations carry.

From the above, we can see that Maghrebis do generally share a similar ancestral makeup as other Afro-Asiatic speakers in the Horn and Nile Valley. Here too we may note the now-familiar array of majority West Eurasian elements (ancient Egyptian, European-related Steppe, and Levantine Natufian components) and a minority East Eurasian element (East Asian component), with a low Sub-Saharan African admixture (primarily derived here from the ancient Niger-Congo sample Congo Kindoki 230BP, with ancillary gene flow from the ancient Nilo-Saharan sample Kakapel 300BP). However, a major difference between these populations is that the Iberomaurusian/Taforalt component forms a large portion of the ancestry of virtually all modern Maghrebi individuals, whereas this element is found at very low frequencies toward the east (typically under 5%). Anatolian Neolithic-related ancestry (represented by TUR_Marmara_Barcin_N) is also an important admixture element, particularly among coastal populations in the north, with Iran Neolithic-related admixture (represented by IRN_Ganj_Dareh_N) also present. Furthermore, one population, the Arabic-speaking Rbaya of Tunisia, seems to be descended from recent settlers from the Arabian peninsula rather than Arabized Berbers. These Rbaya individuals carry a predominant Natufian ancestry like many peninsular Arabs, and (notwithstanding Sub-Saharan African admixture) low percentages of said quintessential Maghrebi ancestral elements.

To better marshal the findings above and more easily observe the identified trends via table format, we shall conclude by running a Vahaduo Multi analysis on our Maghrebi Target populations:

Fregel et al. (2018) studied Late Neolithic individuals excavated at the Kelif el-Boroud site in Morocco, and report that these ancient specimens bore ancestry comprised of roughly equal Natufian and Anatolian Neolithic genome elements. Given this discovery, we must conduct a Vahaduo Multi test using Global25’s MAR_LN ancient sample as an additional Source population. This will help us determine whether the Anatolian Neolithic ancestry, which we have just observed above in our Maghrebi samples, was primarily 1) inherited from these Late Neolithic Moroccans, or 2) acquired later through absorption of peoples arriving from southern Europe or western Asia. From the data table below, it is apparent that scenario #2 is correct; most Maghrebi groups did not derive their Anatolian Neolithic admixture from the Late Neolithic specimens from Kelif el-Boroud. Contemporary Maghrebi individuals carry the MAR_LN component at a low average of 4.4%, with little change in average frequencies of the Anatolian Neolithic-related TUR_Marmara_Barcin_N component (23.4% vs. 25.8%). This is also evidenced by the fact that haplogroup T, the only paternal clade that Fregel et al. observed among their Late Neolithic Moroccan specimens, is rare among just about all modern Maghrebi groups. The latter populations instead largely belong to the E1b1b lineage, as do most Epipaleolithic Iberomaurusians, Mesolithic Natufians, Pre-Pottery Neolithic makers, Early Neolithic specimens exhumed from the Ifri n’Amr or Moussa site in Morocco, ancient Cushites of the Pastoral Neolithic, and ancient Egyptian individuals.

When Libyans are added to our Maghrebi dataset, they appear most similar to Muslim Egyptians inhabiting the Nile Valley; they also share appreciable ties with the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn. The Libyan individuals have the same basic ancestral makeup as these Muslim Afro-Asiatic speakers to their immediate east, carrying majority West Eurasian ancestries (viz. ancient Egyptian, European-related Steppe, and Natufian components) and a minority East Eurasian ancestry (East Asian component), as well as a bit of Sub-Saharan African admixture and a small North African Iberomaurusian/Taforalt admixture. However, Libyans (13.5%) have a higher average frequency of the Iberomaurusian component than Egyptians (2.9% among Muslims, 0% among Copts) and Horn populations (1.2%), though significantly lower than Maghrebis (28.5%). Like Muslim Egyptians and to a lesser extent Maghrebi groups, Libyans also sustained recent gene flow from the Arabian peninsula. This is evidenced by the presence of the Levant_Tell_Qarassa_Early_Antiquity component in our Libyan dataset, an ancestral element which again is typical of modern Arabic speakers.

Libyan (with Levant_Tell_Qarassa_Early_Antiquity)

Libyan (with Levant_Tell_Qarassa_Early_Antiquity broken down into its constituent elements)

Step 9: Repeat analytical steps above with a control population to ensure accuracy and replicability

So as to ensure the accuracy and replicability of our admixture analysis, we will broadly repeat the steps above with a control population. For this purpose, we will utilize peninsular Arab samples from the Global25_PCA_modern datasheet as our Target group, including Yemeni Jews and Mahra individuals.

To start, we shall aim to identify the “purest” Sub-Saharan African reference population available for our Arabian Target population. We will achieve this by first conducting a Distance analysis on the Vahaduo Admixture JS program, using as our Source populations the ancient African samples listed on the Global25_PCA datasheet (again excluding the aforementioned ancient African samples with substantial Eurasian ancestry). We then take note of the top eight African samples with whom our Target population shares the closest genetic ties. We are only interested in the top eight results because these are the groups that are most likely to have contributed genes to our Target population.

Next, we scour the existing genetic literature to find out which of these eight African proxy groups has the least documented non-African admixture. This necessary step will help us avoid depressing Eurasian ancestry/inflating Sub-Saharan African admixture in our Arabian cohort. According to Wang et al. (2020)’s admixture analysis, the COG_Kindoki_230BP:KIN002 sample from the Democratic Republic of the Congo has the least Eurasian admixture (red component):

We have thus found our “pure” Sub-Saharan African proxy sample for our examined Arabian individuals. This discovery informs us that the ancient contact population which contributed most of the Sub-Saharan African admixture in the Arabian peninsula (as represented by Congo Kindoki 230BP) was different from that which did the same in the Horn of Africa and Nile Valley (as represented by Kakapel 300BP) — a fact which is especially clear when we perform a two-way Vahaduo Multi analysis with peninsular Arab individuals, Afro-Asiatic speakers from the Horn, and Maghrebis, using the COG_Kindoki_230BP sample as our Sub-Saharan African Source population and the ancient Egyptian EGY_Late_Period sample as our ancient Eurasian Source population. The peninsular Arab samples wind up showing the highest average Niger-Congo ancestry in comparison to the other examined Afro-Asiatic-speaking groups, confirming their preference for this component as their main source of ancient Sub-Saharan African admixture:

Now, we will carry out a Vahaduo Single analysis, using as our Source populations all of the ancient non-African samples listed on the Global25_PCA datasheet, except those with non-trivial Sub-Saharan African admixture. This step identifies the Levant_Tell_Qarassa_Early_Antiquity sample as the predominant Eurasian ancestry borne by virtually all of the examined Arabian individuals (see here).

We will end by running a Vahaduo Multi analysis, using Levant_Tell_Qarassa_Early_Antiquity as our “pure” ancient non-African reference sample and Congo Kindoki 230BP as our “pure” ancient African reference sample. The analysis produces acceptable Distance fits of <9%, with a sensible estimated average African admixture of ~17%. We may also note that the Mahra samples from Yemen have the least Sub-Saharan African admixture. This is consistent with previous research, which has established that Mahra individuals are on average the “purest” living Semites, having retained the most ancient Natufian ancestry and the lowest extraneous genetic influences (cf. Vyas (2017)).

Conversely, when a Vahaduo Multi analysis is conducted using KEN_IA_Deloraine — the ancient African sample with whom our Arabian individuals showed the greatest genetic affinity in the Vahaduo Distance analysis above (except Emiratis, most of whom preferred instead the COG_NgongoMbata_220BP ancient African sample) — the Arabian individuals appear to have a more elevated Sub-Saharan African admixture of ~19% on average (see here). If we consult again Wang et al.’s genome analysis, it is clear why that is: the early Bantu sample from the Deloraine farm in Kenya harbors substantial Eurasian admixture (red component) specifically related to Arabians, which, compared to other ancient African samples, is bringing it genetically closer to the modern Arabian individuals. This again highlights the importance of using ancient African proxy groups that have as little Eurasian admixture as possible.

Step 10: Re-confirm our findings using other ancient Egyptian samples 

As a penultimate step, we will repeat our Vahaduo Admixture JS analysis using other ancient Egyptian samples in lieu of the EGY_1879BCE cohort. Although all of our modern Afro-Asiatic-speaking samples from the Horn demonstrated a clear preference for EGY_1879BCE in the Vahaduo Single analysis in Step #3 above, EGY_1879BCE  is not listed on Eurogenes’ official Global25_PCA datasheet. We must therefore re-confirm our findings, this time using Global25’s official ancient Egyptian samples.

To start, we shall carry out a Vahaduo Distance analysis on all of the Eurasian samples listed on the Global25_PCA datasheet. Doing so will help us identify which of these ancient specimens our modern Cushitic, Ethiosemitic and North Omotic-speaking individuals share the nearest affinity with. The Distance analysis indicates that our Afro-Asiatic speakers show a preference for the Levant_Beirut_IAIII_Egyptian:SFI-44 cohort followed by EGY_Late_Period:JK2134, which are ancient Egyptian samples dating from the Iron Age and later Dynastic epoch, respectively (see here).

We will now perform a Vahaduo Multi analysis, utilizing the Iron Age Levant_Beirut_IAIII_Egyptian:SFI-44 sample in place of the earlier Dynastic period EGY_1879BCE sample:

As can be seen in the table above, our Afro-Asiatic-speaking samples again wind up with almost the same average non-African ancestry (just over 70%), with approximately 27% Sub-Saharan African admixture and around 3% North African Iberomaurusian/Taforalt admixture. The average Distance fit is also similar. However, the apportionment of the Eurasian ancestries differs appreciably from before. The frequency of the ancient Egyptian component increases about 10 percentage points, going from an average of 18% to 28.1%. Additionally, the average frequency of the Levantine Natufian component rises over 10 percentage points, spiking from 20.9% to 31.3%. These boosts ultimately come at the expense of the European-related Steppe component and the East Asian component, which, respectively, drop from an average of 11.3% to 0% (~11 percentage points) and 22.6% to 12.6% (10 percentage points). Hence, the Steppe and East Asian components appear to be embedded within the Iron Age Levant_Beirut_IAIII_Egyptian cohort, representing constituent elements of that sample.

These changes inform us that:

1. The northern Egyptian population to which the earlier Dynastic period specimen EGY_1879BCE (i.e., the Middle Kingdom nobleman Nakht-Ankh) belonged had not yet interbred with the peoples who brought the European Steppe and East Asian-related ancestries to the Nile Valley, nor with the folks responsible for the Sub-Saharan African admixture element. This is also suggested by Vahaduo Multi analysis of ancient Egyptian individuals, which reveals that EGY_1879BCE only bore embedded Natufian (~81%) and Anatolian Neolithic ancestry (~19%):

2. By the time of the Iron Age Egyptian specimen Levant_Beirut_IAIII_Egyptian:SFI-44, these newcomers had largely been absorbed. From the cumulative data available, we may presume that this assimilation process was concentrated in northern Sudan and southern Egypt since the older Cushites of the Pastoral Neolithic — who seem to have originated from northern Sudan; see Wang et al. (2022) — already bore Steppe and East Asian components, as well as a minor Sub-Saharan African admixture element and a tiny Iberomaurusian admixture.

We will finish by conducting the same Vahaduo Multi analysis on the later Dynastic-era EGY_Late_Period:JK2134 sample, which the Afro-Asiatic speakers of the Horn also appear to favor. Predictably, the end result is virtually identical to the Levant_Beirut_IAIII_Egyptian:SFI-44 Multi analysis, with only incremental differences in Distance fit and ancestral component frequencies (see here). This apprises us that the Iron Age Egyptian profile actually dates earlier, to at least the later Dynastic period. It also lets us know that our interpretations vis-a-vis the EGY_1879BCE sample are correct.

When we perform the same confirmatory Vahaduo Multi tests on the Coptic Egyptian samples and northern Egyptian (Cairo and Mansoura) samples from IllustrativeDNA and the Muslim Egyptian samples from Eurogenes, alternately using the later Dynastic period EGY_Late_Period:JK2134 sample and Iron Age Levant_Beirut_IAIII_Egyptian:SFI-44 sample as our ancient Egyptian Source population in place of the earlier Dynastic period EGY_1879BCE cohort, the Coptic and northern Egyptian samples have ballooned Distance fits approaching 15%. By contrast, the general Muslim Egyptian samples maintain acceptable Distance fits of <9%. Hence, Coptic Egyptians and northern Egyptians indeed appear to derive most of their ancestry specifically from the earlier Dynastic period Egyptians, as represented by the EGY_1879BCE sample:

Egyptian (using Levant_Beirut_IAIII_Egyptian)

Egyptian (using EGY_Late_Period)

Step 11: Consolidate our findings for all local Afro-Asiatic speakers 

Finally, to conclude our admixture study, we shall distil our findings by grouping all local Afro-Asiatic speakers (Horn African and North African alike) into one Vahaduo Multi table. This will allow us to more easily observe and describe broad trends in the data, and to spot any patterns or relationships that we may have overlooked.

From the data table above, we can discern three general ancestry patterns:

• Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa have a similar ancestral composition as Muslim Egyptians and Libyans. When we consult the data table for the Kababish “Arabs” from Sudan in Step #7, we can see that the Kababish also possess the same overall ancestral makeup. All of these groups share an assortment of majority West Eurasian ancestries (ancient Egyptian, European Steppe, and Levantine Natufian components) and a minority East Eurasian ancestry (East Asian component), as well as a minor Sub-Saharan African admixture and a small North African Iberomaurusian/Taforalt element. On average, Muslim Egyptians (13%) and Libyans (16%) carry slightly less Sub-Saharan African admixture than Afro-Asiatic speakers from the Horn (27%). Additionally, Muslim Egyptians and Libyans harbor extra Anatolian Neolithic (12% and 13%, respectively) and Iran Neolithic admixtures (9% and 4%, respectively), which are not borne by the Horn’s Afro-Asiatic speakers.
• Coptic Egyptians and northern Egyptians (from Cairo and Mansoura) have a common ancestral makeup. Both groups trace almost all of their ancestry to the EGY_1879BCE cohort, which currently is the oldest Egyptian sample whose Global25 coordinates are available. Northern Egyptians also bear a slight Sub-Saharan African admixture (~11% on average), comparable to the small amount harbored by other Muslim Egyptians.
• Maghreb populations carry similar ancestral components as Muslim Egyptians, Libyans and Afro-Asiatic speakers from the Horn. However, Maghrebis also bear considerable Iberomaurusian ancestry (28.5%). They likewise have significant Anatolian Neolithic admixture (23.4%), and a very small Iran Neolithic gene flow (1.9%). Additionally, Maghrebis have minor Sub-Saharan African admixture (~17% on average).

Besides the foregoing, we may also note that the Elmolo, a vestigial Cushitic-speaking group inhabiting Kenya, carry similar ancestral elements as the Horn’s Afro-Asiatic-speaking populations. They are distinguished by a substantially higher Sub-Saharan African admixture (~52% on average), which primarily consists of the “pure” ancient Nilo-Saharan element (Kakapel 300BP) followed by the “pure” ancient East African Hunter-Gatherer element (MWI_Chencherere). This is consistent with a heavy absorption of local Nilotic and forager individuals. Furthermore, the South Omotic-speaking Ari seem to derive the bulk of their ancestry from the Sub-Saharan African components (98%). This proportion is probably an overestimation since the Ari sample (taken from IllustrativeDNA) has a grossly unrealistic Distance fit of ~40%.

We will end by performing another Vahaduo Multi analysis on our Afro-Asiatic-speaking samples. This time, we shall employ the Levant_Tell_Qarassa_Early_Antiquity cohort as a Source population so as to quantify the amount of modern Arabian admixture present in our Target populations:

The data table above affirms that the Afro-Asiatic-speaking populations of the Horn, as well as Coptic Egyptians and northern Egyptians, do not bear any recent admixture from the Arabian peninsula. All of the examined Cushitic, Ethiosemitic and North Omotic-speaking individuals and Coptic and northern Egyptian individuals have a 0% frequency of the Levant_Tell_Qarassa_Early_Antiquity component, an ancestral element typical of contemporary peninsular Arabs. This suggests that most of the gene flow from Arabia into Northeast Africa predates the Islamic era. On the other hand, Muslim Egyptians and Libyans do harbor this Arabian component at low frequencies of around 17% and 19%, respectively. In the Maghreb, average frequencies of this Arabian element are a bit lower, except among the Arabic-speaking Rbaya of Tunisia. Rbaya individuals on average carry the Levant_Tell_Qarassa_Early_Antiquity component at an elevated percentage of 44%. This strongly supports their traditions of descent from Arab forefathers. Intriguingly, most persons from the Arabic-speaking Douz community in Tunisia also have high frequencies of this Arabian ancestral component, in keeping with their own traditions of descent from Arab settlers.

Conclusion

The admixture analysis above tells us a number of things about the biogenesis of the modern Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa. We may summarize these key findings as follows:

• The contemporary Afro-Asiatic speakers of the Horn carry a predominant non-African ancestry, which, on average, comprises over 70% of their ancestral makeup. This non-African ancestry can be further broken down into majority West Eurasian elements (ancient Egyptian, European-related Steppe, and Levantine Natufian components) and a minority East Eurasian element (ancient East Asian component). Additionally, the Afro-Asiatic speakers bear some low-to-moderate Sub-Saharan African admixture (~27%), as well as a very minor North African Iberomaurusian admixture (under 3%).
• As of late 2022, admixture studies that have focused on said Afro-Asiatic speakers have typically under-reported their Eurasian ancestry and inflated their Sub-Saharan African admixture. This error is mainly caused by either reliance on admixed modern reference populations (such as the Dinka Nilotes, who bear some Eurasian ancestry) or admixed ancient reference populations (such as the Mota specimen, which also bears Eurasian ancestry). To correct this mistake, “purer” ancient Sub-Saharan African samples must be used as proxies since these specimens can unveil previously hidden Eurasian ancestral components. Case in point, utilizing the Kakapel 300BP cohort — the best available surrogate for unadmixed ancient Nilotic ancestry — helped us uncover hitherto obscured Steppe and East Eurasian affinities in our admixture analysis above.
• The fact that the modern Afro-Asiatic-speaking populations of the Horn have genetic ties with ancient Egyptians is entirely expected. These affiliations have long been documented, and range from craniometric and anthropometric affinities to deep cultural links (see Punt: an ancient civilization rediscovered for a synopsis). Moreover, Egyptian-related ancestry is ancient and not something recently acquired. This is clear given that every single one of the modern Cushitic, Ethiosemitic and North Omotic-speaking individuals on the Global25 dataset carries such ancestry and at significant frequencies, as do the ancient Cushitic settlers of the Pastoral Neolithic.
• Natufian ancestry peaks among the Ethiosemitic-speaking samples, which is consistent with known facts. Y-DNA haplogroup analysis indicates that the Agaw-speaking ancestors of Abyssinians interbred with neighboring Mota-related foragers. This is also supported by our genome analysis above. Despite today not living in a forager inhabited area, the Amhara Abyssinians of northern Ethiopia have the same average frequency of the “pure” East African Hunter-Gatherer component (MWI_Chencherere) as the southern Somali individuals, who, by contrast, do dwell in a forager occupied locale (both 7.7%). Ergo, the Amhara appear to have received some extra gene flow from indigenous hunter-gatherers in the northern Ethiopian highlands. Later contacts with Sabaean settlers from Arabia would serve to both introduce Semitic languages to the Abyssinians’ Agaw forebears and offset their earlier, more elevated hunter-gatherer admixture. This would restore the Abyssinians’ Eurasian ancestry, raising it back up to a level similar to that of their Cushitic-speaking neighbors (see Ancient DNA from Ethiopia). Having said that, it is also important to note that Natufian ancestry was not first brought to eastern Africa by the Sabaeans. This is evident considering that the Cushites of the Pastoral Neolithic, who are substantially older than the Sabaeans, already harbored a Natufian element, though it is ancillary to their ancient North Africa-associated ancestry (viz. ancient Egyptian, European Steppe and East Asian components). 
• The fact that the southern Somali samples have the highest average frequencies of both the ancient Egyptian and Steppe genome components speaks to a close association with the Egypt area. This is because most ancient Egyptian individuals analysed to date have been found to bear paternal haplogroups that are either of North African ascription (E1b1b clade) or Indo-European affiliation (R1b clade) (refer to Punt: an ancient civilization rediscovered for details). 18th Dynasty Egyptian royal mummies of the Amarna dynasty have also been found to carry some European-related autosomal DNA (cf. LOP (2023)).
• The discovery of a previously undetected East Eurasian genome component among our Global25 Afro-Asiatic-speaking samples, with a peak among the Cushitic speakers, resolves many longstanding questions. It, at once, explains why: 1) Cushitic speakers in the Horn tend to have higher rates of non-kinky hair than their Abyssinian neighbors (cf. Charpin and Georget (1977); Coon (1939)), 2) Cushitic speakers also bear unusual genetic variants of East Asian affiliation, such as the EDAR allele, 3) many Afro-Asiatic speakers in the Horn have oblique eye folds, similar to populations in central and eastern Asia (Gallo (1979)), 4) the Y-DNA haplogroup F-M89, which today is most prevalent in South/Central Asia, has been found among Christian-era specimens on Meroe Island and along the 4th Cataract in Sudan, areas not far from the Kulubnarti site discussed above (cf. Yousif and Eltayeb (2009)), and 5) the 18th Dynasty ancient Egyptians Pharaohs of the Amarna lineage have autosomal STRs that share a significant affinity with those of individuals from Europe, South Asia and Northeast Asia (see our microsatellite marker study here). If it can be proven that the East Eurasian and Steppe ancestral components arrived in Northeast Africa together, it may be that they were brought to the area by an ancient population(s) originating from a Steppe-enriched zone in South/Central Asia (such as the Swat Valley or Turan), with whom the ancient Egyptians and Cushites would have interacted. An alternative source location for these components is eastern Europe, where the Steppe element is ultimately thought to have originated. According to genome analysis by Eurogenes, many old East Germanic-speaking peoples in the Global25 dataset carry Central Asian-related admixture, which was probably acquired through interaction with nomadic Asiatic groups such as the Avars, Huns and Sarmatians. The East Germanic-speaking early Goths of the Chernyakhiv culture in Ukraine were, for example, found to harbor ~14% Hunnic-affiliated ancestry (see Asiatic East Germanics). While most of this Central Asian intermixture seems to have taken place quite recently, similar population contacts likely occurred many centuries earlier, during the ancient Egyptian period. This is supported by the fact that the haplogroup R1b-M269 — which today constitutes the most prevalent Y-DNA clade among males in Europe — is so far the only Steppe-associated paternal lineage that has been observed among ancient Egyptian individuals (cf. Yatsishina et al. (2021); iGENEA). Likewise, the mtDNA haplogroup I, a maternal clade that has been detected among various ancient Steppe cultures in Europe, presently occurs at highest frequencies among Cushitic-speaking populations. In the archaeogenetic record, the I2 subclade has also been reported among ancient Egyptian mummies (cf. Khairat et al. (2013)).
• Sub-Saharan African admixture among Afro-Asiatic-speaking groups in Northeast Africa appears to be intrusive, having likely been picked up through contact with early Nilo-Saharan speakers and local foragers. This is suggested by the fact that these components are minority admixture elements in all of our Cushitic, Ethiosemitic and North Omotic-speaking Global25 samples, and vary in frequency independently from all of the other observed components. Accordingly, the Kulubnarti sample I18517, which, among the Christian-era Nubian specimens, bears the highest percentages of all three old Nile Valley-associated elements (i.e. the ancient Egyptian, Steppe and East Asian components), has a 0% frequency of the “pure” ancient Nilo-Saharan component Kakapel_300BP. The Early Pastoral Neolithic samples from Kenya, which represent the oldest Cushitic settlers in eastern Africa that have been analysed, likewise have a low average percentage of this “pure” Nilo-Saharan element (8.5%). Conversely, a different ancient contact population (represented in “purest” form by the Congo Kindoki 230BP sample) seems to have contributed most of the Sub-Saharan African admixture carried by both modern Maghrebis and modern Arabians.
• The fact that the Iberomaurusian component peaks among the southern Somali individuals is another aspect linking this population with other Afro-Asiatic speakers in the Nile Valley. Every single examined Agaw and Wolayta individual likewise bears at least trace levels of this North African ancestral element. Tellingly, these are the Ethiopian samples in the Global25 dataset who also happen to have the lowest average frequencies of the Natufian component. This suggests that, at least in the case of the Agaw (who have the second highest average percentage of the ancient Egyptian component), their original North Africa-derived ancestry was less affected by later migrations from the Arabian peninsula than their Abyssinian neighbors.
• Modern Muslim Egyptians generally share the same ancestral composition as other Afro-Asiatic speakers in the Horn region. Previous genome analyses have not been able to detect the full scope of this affinity for the reasons just outlined above (i.e., use of admixed modern and ancient reference samples; lack of appropriate ancient proxies). On average, Muslim Egyptian individuals carry around 84% non-African ancestry, which consists of majority West Eurasian elements (mainly ancient Egyptian, European-related Steppe, and Levantine Natufian components, as well as some later acquired Anatolian Neolithic and Iran Neolithic admixtures) and a minority East Eurasian element (East Asian component). Moreover, Muslim Egyptians bear minor Sub-Saharan African admixture (~13%) as well as a tiny North African Iberomaurusian admixture (~3%).
• During the early Predynastic period, a West Eurasian population seems to have occupied Egypt and northern Sudan. Archaeologically, in Lower Egypt/northern Egypt, this culture is known as the Merimdian; in Upper Egypt/southern Egypt, it is referred to as the Tasian. Based on the genetic affinities of the oldest Egyptian individual to be genomically analysed (namely, the EGY_1879BCE sample belonging to the aristocrat Nakht-Ankh), the early Predynastic Egyptians appear to have been closely related to the Pre-Pottery Neolithic makers of the Levant, with both groups defined by a common heritage consisting of Natufian and Anatolian Neolithic ancestral elements. During the later part of the Predynastic era, some new settlers, who bore European Steppe and East Asian components, seem to have arrived in the Nile Valley from the south. This is suggested by the fact that modern northern Egyptians (like Coptic Egyptians) appear to lack the Steppe and East Asian genetic signals, whereas southern Egyptians and Cushitic, Ethiosemitic and North Omotic speakers in the Horn carry them. The folks who introduced these ancestral components, therefore, likely entered the Nile Valley through the Bab el-Mandeb rather than the Isthmus of Suez. In Sudan and southern Egypt, local Predynastic Egyptians (viz. the Badarians and Naqadans) and Egyptian-related groups (the ancestral Cushites and ancient Libyans) would have assimilated these newcomers, apparently as early as the Neolithic. They also would have absorbed in situ some minor Sub-Saharan African and Iberomaurusian admixture. As a result, most Egyptian individuals in the later Dynastic period (as represented by the official Global25 samples EGY_Late_Period:JK2134 and EGY_Late_Period:JK2911) and ensuing Iron Age (as represented by the official Global25 samples Levant_Beirut_IAIII_Egyptian:SFI-44 and Levant_Beirut_IAIII_Egyptian:SFI-43) and Hellenistic era (as represented by the official Global25 sample EGY_Hellenistic_contam:JK2888) would now intrinsically harbor all of these elements. Modern Muslim Egyptians, Afro-Asiatic speakers from the Horn, Kababish “Arabs” from Sudan, and Libyans appear to largely descend from the later Predynastic period Egyptians, ancient Cushites and ancient Libyans. Muslim Egyptians (~17%) and Libyans (~19%) also have some minor admixture from contemporary Arabians, as exemplified by the Levant_Tell_Qarassa_Early_Antiquity component. On the other hand, Coptic Egyptians seem to almost exclusively derive their ancestry from the early Predynastic Egyptians.
• Contemporary Maghrebis also significantly share the same ancestral composition as Muslim Egyptians, Libyans and other Afro-Asiatic speakers from the Horn. However, Maghrebi individuals are distinguished by considerable North African Iberomaurusian/Taforalt ancestry (~29% on average). This element was probably acquired when the first Berber speakers moved westward from the Nile Valley and absorbed some relict populations related to Levantine Natufians and indigenous Aterians. Modern Maghrebis, particularly in the northern coastal areas opposite Iberia, also have substantial Anatolian Neolithic admixture (around 23%); Iran Neolithic admixture is likewise present at residual frequencies (under 2% on average). Moreover, Maghrebis have some minor Sub-Saharan African admixture (~17%), gene flow which mostly seems to date to the medieval slave trade. Furthermore, one population, the Arabic-speaking Rbaya of Tunisia, appears to consist of descendants of recent settlers from the Arabian peninsula as opposed to Arabized Berbers. These Rbaya individuals carry a predominant Levant_Tell_Qarassa_Early_Antiquity component like peninsular Arabs and have low frequencies of the typical Maghrebi ancestral components.

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Punt: an ancient civilization rediscovered

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Abdel Monem A. H. Sayed, Adulis, AECR, Afro-Asiatic, Ahmed El-Batrawi, Ahmed Ibrahim Awale, Alula, Amelia Edwards, ancient DNA, Ancient Egypt, ancient inscriptions, Antiquities Service of Egypt, Arrian of Nicomedia, Ati, Auguste Mariette, Axumite Kingdom, Édouard Naville, Barbaria, Bia-Punt, Book of Gates, Boswellia frereana, Carleton Coon, Caterina Cozzolino, Caucasoid, Cushitic, D'mt, Dalbergia melanoxylon, David O’Connor, Deir el-Bahri, Dimitri Meeks, Diodorus Siculus, Egyptian pantheon, El-Osbolé, Emmett Sweeney, Epiphanius of Constantia, Eric Robson, Ernest-Théodore Hamy, Ernesto Schiaparelli, F. Nigel Hepper, Flinders Petrie, frankincense, G. Billy, G. W. B. Huntingford, Gaston Maspero, George A. Hoskins, George Andrew Reisner, Georges Révoil, Giuseppe Sergi, Grafton Elliot Smith, Grand Procession, Hamitic, Hathor, Hatshepsut, Heinrich Karl Brugsch, Horus, Hyphaene thebaica, James Bruce, Johannes Maria Hildebrandt, John Desmond Clark, Kathryn Bard, Kenneth Kitchen, Laas Geel, Lady of Punt, Land of Punt, Lionel Casson, Medri Bahri, Meroitic culture, Mersa Gawasis, myrrh, Nathaniel Dominy, Neville Chittick, Northeast Africa, Palermo Stone, Papio hamadryas, Perahu, Periplus of the Erythraean Sea, Precambrian, PROTA, Red Sea, Richard Pankhurst, Robert Bennett Bean, Robert Hoyland, Rodolfo Fattovich, Saww, Solomonid Dynasty, Stanley Balanda, stela, Ta netjer, Theodor von Heuglin, Toby Wilkinson, Wadi Gawasis, Zoscales

The Land of Punt was a major civilization in the ancient world. Located to the south and east of the Nile Valley, it was Dynastic Egypt’s main trading partner and the source of much of the frankincense, myrrh and other coveted products that were used by the Pharaohs in their traditional rituals and ceremonies. According to the Egyptian First Dynasty rulers or Horus-Kings, Punt (Ta netjer or “God’s Land”) was also their ancestral homeland.

Given its historical importance, Egyptologists have long debated just where exactly this mysterious territory was situated. The riddle appeared to have been finally solved in 2010, when preliminary isotopic analysis narrowed down the prospective locations to present-day Eritrea. However, follow-up isotopic work as well as DNA studies conducted since then, analysis of clay from pots that were brought to Egypt from Punt, and little-known botanical evidence and epigraphs firmly locate the ancient land in a broader region stretching from northern Somalia, Djibouti and the Eritrea/Ethiopia corridor to northeastern Sudan. The recent discovery of the first actual Puntite artifacts and their similarity to those of ancient Egypt has, in particular, confirmed the close ties between both areas.

Route to Punt

One of the key factors in pinpointing the location of the Land of Punt is its geographical proximity to ancient Egypt. In this regard, scholars have often indicated that the territory was situated to the south and east. But what exactly do they base this on?

In the 1850s, the Antiquities Service of Egypt discovered hieroglyphic texts in the vicinity of Thebes (Luxor) in Upper Egypt. These inscriptions identify Punt as a source of aromatics found to the east of Egypt. This, in turn, would prompt the Egyptologist Heinrich Karl Brugsch to postulate that the ancient land was located in the Arabian peninsula. A few years later, his colleague the archaeologist Auguste Mariette came upon geographical lists at the Karnak Temple, which had been left by the Pharaoh Thutmose III of the Eighteenth Dynasty (r. 1458–1425 BCE). These hieroglyphics include Punt among the territories that lay to the south of Egypt. The Egyptologist Abdel Monem A. H. Sayed explains:

The first lists of this kind, and the most comprehensive, are those of Thutmoses III, where the regional and site names are arranged in a manner coinciding with their geographical locations.

The list of toponyms of the African side of the Red Sea begins with the heading Kush, the Egyptian name for Upper Nubia. Under this heading are recorded 22 toponyms. Then comes the regional name Wawat or Lower Nubia, with 24 toponyms listed under it. After that, the list begins again from the south, recording regional and site names closer to the Red Sea shore. The regional name Punt is mentioned as a heading for 30 toponyms. After Punt comes Mejay as a heading of 17 toponyms. Lastly comes the regional name Khaskhet extending along the Red Sea shore of Egypt, with 22 toponyms listed (Schiaparelli 1916, 115-9).

This clear hieroglyphic account allows the following important deductions[…] The relation between Punt and the other regional names in the list (Kush, Wawat, Mejay and some of the toponyms under the heading Khaskhet), of which the African locations are agreed among Egyptologists, shows clearly that in the time of Thutmoses III Punt was the most southerly region and adjacent to the Red Sea coast. This is of great value for locating Punt during the New Kingdom in general, and the time of Queen Hatshepsut in particular, with which I deal later.

A 26th Dynasty stela was also recovered from the ancient site of Dafnah (Daphnae) near the Egyptian Delta, which contains an inscription stating that “when rain falls on the mountain of Punt, the Nile floods.” This is a clear allusion to the northern Ethiopian highlands, around Lake Tana where the Blue Nile rises (cf. Sayed (1989)). The Papyrus of Hunefer, a 19th Dynasty document by an Egyptian royal scribe, strengthens this association, for it too includes the Blue Nile within the confines of Punt. Van Auken (2011) notes:

The Greek historian Herodotus wrote, “Egypt was the gift of the Nile.” Three tributaries created this amazing river. The first is the White Nile, a long gentle river flowing from Lake Victoria — a high mountain lake bordered by Kenya, Tanzania, and Uganda. This tributary joins with the shorter but more voluminous and nutrient-richer Blue Nile, springing from Lake Tana in Ethiopia. And in ancient times, a third tributary joined these two, the Yellow Nile flowing from the eastern highlands of Chad. The Yellow Nile is now dry but was once a part of this trinity of rivers creating the ancient Nile.

Each year during the rainy season, the ancient Nile River would overflow its banks and inundate Egypt; as it retreated, it left behind nutrient-rich black silt that made Egypt one of the most fertile lands in recorded history. Today, two dams now control the Nile — there is no flooding and no rich silt fertilizer.

Around this river of life-giving water grew one of the greatest cultures on the planet. The ancient Egyptians called the river Iteru, meaning “Great River”; the modern name comes from the Greek Neilos (Nilus in Latin), transliterated to Nile.

The Edfu Text, found in the Horus Temple in Edfu, and the Papyrus of Hunefer tell the story of a “hill people” who became the first settlers of this region. “We came from the beginning of the Nile where god Hapi dwells at the foothills of the Mountains of the Moon.” The Mountains of the Moon are likely those that contain Lake Tana in ancient Abyssinia (modern day Ethiopia), the origin of the Blue Nile. This name may be traced back to a Greek ruler of late Egypt, Ptolemy, and the use of the name “Mountains of Selene,” the moon goddess of the Greeks.

Coupled with some of the floral and faunal evidence discussed below, Mariette’s discovery and the Dafnah tablet helped shift scholarly opinion as to where Punt was situated (including eventually that of Brugsch himself) away from a hypothesized Arabian location to the adjacent Horn of Africa.

The Palermo Stone contains the earliest hieroglyphic description of an ancient Egyptian expedition to the Land of Punt, during the Fifth Dynasty (Sci-News).

Cozzolino (1993) enumerates over 50 other hieroglyphic inscriptions relating to the Land of Punt, and a few additional engravings have subsequently been discovered. The earliest of these writings is the Palermo Stone. It informs us that an ancient Egyptian expedition to Punt brought back 80,000 measures of ‘ntiyw (a particular type of incense), among other items, during the thirteenth regnal year of Sahure (ca. 2445 BCE), the second Pharaoh of the Old Kingdom’s Fifth Dynasty. Unfortunately, the Palermo Stone does not specify where Punt itself was located. We do, however, have an idea of how Sahure’s men got there. In 2002, an inscribed block was found at the pyramid of Sahure in the Abusir necropolis, with two of its registers depicting the arrival of ancient Egyptian cargo vessels transporting goods from Punt. From this, we know that the Sahure expedition was carried out by sea rather than overland. Punt was therefore not a landlocked territory.

A Sixth Dynasty inscription provides an even clearer indication of the route that the ancient Egyptians took to get to Punt during the Old Kingdom. Phillips (1997) notes that Pharaoh Pepi II or Neferkare (2278/2269–2184/2175 BCE) dispatched one of his expedition leaders, Pepinakht, to retrieve the body of the official Anankhti, who had been killed by bedouins in the Eastern Desert (the “desert of the Asiatics”) while overseeing the construction of a ship intended for another commercial expedition to Punt. Thus, the particular water route that was favored by the ancient Egyptian rulers appears to have been via the Red Sea. This is confirmed by a later, Middle Kingdom rock inscription at Wadi Hammamat from the reign of Pharaoh Mentuhotep III or Senekhkere (r. 2004–1992 BCE) of the Eleventh Dynasty. According to the chief treasurer Henu, he was ordered by the king to build a vessel destined for Punt along the Red Sea littoral:

[My lord, life, prosperity] health[…] sent me to dispatch a ship to Punt to bring for him fresh myrrh from the sheiks over the Red Land, by reason of the fear of him in the highlands. Then I went forth from Koptos upon the road, which his majesty commanded me…

I went forth with an army of 3,000 men. I made the road a river, and the Red Land (desert) a stretch of field, for I gave a stretch of field, for I gave a leathern bottle, a carrying pole[…], 2 jars of water and 20 loaves to each one among them every day. The asses were laden with sandals[…]

Then I reached the (Red) Sea; then I made this ship, and I dispatched it with everything, when I had made for it a great oblation of cattle, bulls and ibexes.

Now, after my return from the (Red) Sea, I executed the command of his majesty, and I brought for him all the gifts, which I had found in the regions of God’s-Land. I returned through the ‘valley’ of Hammamat, I brought for him august blocks for statues belonging to the temple. Never was brought down the like thereof for the king’s court; never was done the like of this by any king’s-confidant sent out since the time of the god.

In 1971, the Egyptologist Kenneth Kitchen demonstrated the feasibility of such ancient travel down the Red Sea coast by charting an actual itinerary to get to Punt. This maritime gazetteer includes 80 possible anchorage points, as well as the intervening distances between them. It stretches from the Port of Sudan to northern Eritrea, a broad region that Kitchen suggests was coextensive with the Land of Punt.

So we know from the existing hieroglyphic texts that the ancient Egyptians preferred to reach Punt by water, and through the Red Sea specifically. We also know that this navigation was doable. The question is, what actual port did the ancient Egyptians use for these trading expeditions once they had finished constructing their vessels? A stela that was discovered at Wadi Gawasis (Wadi Gasus) provides an answer. Erected by Khentkhetwer, an official under the Twelfth Dynasty Pharaoh Amenemhet II or Nubkaure (r. 1922–1878 BCE), it contains an engraving that explicitly identifies Saww as the port where Khentkhetwer and his men arrived after their voyage to Punt. The Khentkhetwer stela inscription reads:

Giving divine praise and laudation to Horus[…], to Min of Coptos, by the hereditary prince, count, wearer of the royal seal, the master of the judgement-hall Khentkhetwer[…] after his arrival in safety from Punt; his army being with him, prosperous and healthy and his ships having landed at Sewew (Saww). Year 28.

Wooden cargo boxes labeled “wonderful things of Punt”, which were discovered at Mersa Gawasis, the ancient Egyptian port of Saww (Traveltoeat).

In 2004, archaeological excavations led by the Egyptologists Kathryn Bard and Rodolfo Fattovich at Mersa/Wadi Gawasis in Egypt identified this harbor as the old port of Saww, which the ancient Egyptians used during their expeditions to Punt. The excavators found a number of commodities at the site that may have been brought back from Punt, including fragments of carbonized ebony wood (Diospyros sp.) and obsidian. Since the latter volcanic glass does not occur naturally in Egypt, it was clearly imported from elsewhere. Lucarini et al. (2020) sought to identify the exact provenance of these artifacts, so they conducted a geochemical analysis comparing six obsidian fragments, which Sayed et al. had gathered from Mersa Gawasis some years prior, to those from various source areas in the Horn of Africa and Arabian peninsula (viz. sites in Eritrea, Ethiopia and Yemen). However, the scientists did not examine any obsidian culled from Djibouti or Somalia. Of the sites they did sample, Kusrale in Eritrea was found to be the most likely procurement location for five of the six analysed Mersa Gawasis obsidian artifacts. The other obsidian fragment appeared instead to have been obtained from the Dhamar Reda volcanic region in Yemen.

Moreover, the archaeologists working at Mersa Gawasis also discovered actual shipbuilding materials dating to the Middle Kingdom, such as anchors, timbers and huge steering oars, as well as 26 well-preserved coils of vessel-rigging rope that were lying on the floors of a cave. Most intriguingly, they came upon 43 cargo boxes from the reign of Pharaoh Amenemhat IV (r. 1990–1800 BCE). Two of these boxes were engraved with a package label, which had been recorded by the scribe Djedy. It included inscriptions for his name, a cartouche of Amenemhat IV and regnal Year 8, and the phrase “wonderful things of Punt” in hieroglyphics. The cargo boxes were made of sycamore wood and were all empty since their contents, which are believed to have included frankincense, were apparently unloaded into containers or bags for later transport via caravan across the Eastern Desert. Additionally, Bard found a limestone stela with hieroglyphic text on it that commemorates two royal maritime expeditions to Punt and Bia-Punt (“Mine(s) of Punt”) during the reign of Pharaoh Amenemhet III (r. 1831–1786 BCE).

Researchers exploring the ancient seafaring vessels at Wadi Gawasis would later find ceramic fragments inside. These sherds once formed pots, which were used to hold goods for transportation from Punt to Egypt. The scientists also analyzed the actual clay that was used to make this pottery. They discovered that it came from the eastern coast of Africa, further proving that this area was indeed part of the Land of Punt (Hoare (2020)). More specifically, of the main prospective locations for the ancient territory, this finding points to Djibouti, Eritrea and Somalia since Ethiopia is landlocked and Yemen is in the Arabian peninsula.

That the ancient Egyptians journeyed to and from Punt through a Red Sea route, and via the old port of Saww in particular, has thus been confirmed. What we shall now see is that the main landing point of these trading expeditions, at least during the New Kingdom, was in northern Somalia. As such, Punt was located in a more expansive area between Cape Guardafui and the Port of Sudan.

Flora and fauna of Punt

Mural from Pharaoh Hatshepsut’s temple showing the Puntites and Egyptians transporting frankincense trees from inland to the shore (Sayed (1989)).

Besides the route taken to get there, another key aspect in situating the Land of Punt is the flora and fauna of the various proposed locations for the ancient territory. Specific plants and animals, which are said to have been native to Punt, are depicted on Egyptian temple walls and murals. Some of these “wonderful things of Punt” were also brought back to Egypt as gifts and offerings. Combined, this leaves us with invaluable information as to what kind of habitat the Puntites actually lived in.

Plants

Primary distribution of the doum palm or Hyphaene thebaica in Africa (PROTA).

In 1858, Mariette discovered a wall in the funerary temple of the Pharaoh Hatshepsut (r. 1479–1458 BCE) at Deir el-Bahri, which depicts an Egyptian expedition to Punt during the queen’s reign. The temple reliefs show in detail the flora and fauna of Punt, as well as the Puntites themselves. Among the clearly identifiable plants are doum palms (Hyphaene thebaica), tree species that were regarded as sacred in ancient Egypt. Kitchen argues that on the Somali coast, the doum palm is restricted to the southernmost areas, far from the suggested Puntite nucleus in the north. In actuality, the doum palm grows throughout the Somali territories. The traditional gourd used by Somali pastoralists (who historically expanded from the north) is, in fact, crafted in part from doum palm fibers. Accordingly, the Plant Resources of Tropical Africa (PROTA) foundation describes the geographical distribution of Hyphaene thebaica as follows:

Hyphaene thebaica is distributed from Senegal and Gambia eastwards to Somalia, and is especially common between latitudes 8°N and 12°N. It also occurs in Libya, Egypt, Israel, the Arabian Peninsula and western India. Hyphaene thebaica is often planted. It was already cultivated in ancient Egypt, where it was considered sacred.

One of the main products that the ancient Egyptians traveled to Punt to obtain was ebony. Through hieroglyphic inscriptions, which indicate that the Egyptians themselves chopped down the plant while in Punt (“cutting ebony in great quantity”), ebony is known to have grown wild in the territory. The Puntites apparently did not import it from elsewhere for later resale to the Egyptians.

An Oromo woman holding a traditional gourd. Among Cushitic pastoralists, doum palm fibers were often used to make their gourd containers. The doum palm (Hyphaene thebaica) is one of the clearly identifiable plant species native to Punt, which are depicted at Hatshepsut’s temple in Deir el-Bahri.

A Somali woman holding another example of the traditional Cushitic gourd.

Barnett (1999) notes that analyses of plant specimens found in tombs have confirmed that the particular variety of ebony that was used in ancient Egypt is Dalbergia melanoxylon. This species is endemic to Eritrea, Ethiopia and Sudan alike, according to PROTA. In Somalia, ebony today has a limited distribution. Archaeological evidence, however, suggests that the plant was more abundant there too in Pharaonic times. On this likelihood, Ahmed Ibrahim Awale, a scholar who recently led excavations in northern Somalia (more on that below under Traces of ancient civilization), writes:

[Over] the past several millenia, so much has changed in the composition of vegetation in the Somali peninsula. The discovery of crocodile artifacts in Hargeisa valley suggest that a tropical riparian ecosystem existed in those areas. Therefore, it cannot be discounted that ebony, one of the chief exports from Punt, was sourced from the area. Diospyros spp., locally known as ‘Kolaati‘, is still found to a limited extent in riparian formations in Somalia.

The incense-yielding hills around Alula in northeastern Somalia, which correspond with “the frankincense terraces of Punt” (Sayed (1989)).

Of all the items that were exported from the Land of Punt to ancient Egypt, frankincense was by far the most important. Sayed (1989) notes that the Deir el-Bahri murals record Pharaoh Hatshepsut as specifically commanding her party “to fetch (as the texts say) ‘fresh incense’, and ‘frankincense living trees’ from ‘the frankincense terraces of Punt’.” The main purpose of that Egyptian voyage to Punt — the largest sojourn of its kind to the ancient territory — was, therefore, to retrieve the prized aromatic resin. Indeed, the very reason why Hatshepsut organized such a massive expedition was because she wanted her men to bring back live frankincense trees for later transplantation in Egypt. Her temple reliefs show that each of the 31 heavy incense trees required 4 to 6 men to transport them to the cargo ships, or 124 to 186 Egyptian and Puntite carriers in total. Since there were around 150 crewmen on the expedition’s five vessels (30 per ship), this would mean that “the frankincense terraces of Punt” had to have been situated near the shore.

Frankincense-growing areas on the northern Somali littoral and their hieroglyphic, classical and modern toponyms (Sayed (1989)).

Sayed asserts that this incense-yielding locale, “the frankincense terraces of Punt”, was the northern Somali littoral. Specifically, the northeastern corner extending from Bandar Qasim to Cape Guardafui. He bases this in part on historical texts, which hail this region as an early center of incense production and exportation. Chief among these old documents is the Periplus of the Erythraean Sea (Periplus Maris Erythraei), a travelogue written in the 1st century CE by an Alexandrian merchant. It indicates that a top-grade libanos peratikos or “incense from beyond the straits” (Bab el-Mandeb straits) was exported from ancient city-states that dotted this part of the Red Sea area, including Avalites, Malao, Mundus, Mosyllum, the Market and Cape of Spices, Pano (Panon), Opone (Opun) and Akannai (see map on the left). The Periplus specifies that the laurel-grove of Akannai/Acannae is “where alone is produced the far-side frankincense, in great quantity and of the best grade.” Likewise, the historian and philosopher Arrian of Nicomedia testifies that the best frankincense of his day was exported from the same area around Ras Fiel/Ras Filuk (Cape Elephant/Cape Elephas), just off the Acannae harbor in present-day Alula.

View of Ras Filuk (Cape Elephas) from the Acannae/Akannai/Alula harbor (Sayed (1989)). According to the 1st century CE Periplus of the Erythraean Sea, Acannae is “where alone is produced the far-side frankincense, in great quantity and of the best grade.” 

Sayed (1989) remarks that the ancient Egyptians imported two types of frankincense: a lower grade variety called sntr, and a higher grade variety known as ‘ntiyw or nty. According to inscriptions from the Sixth Dynasty travelers Harkhuf and Sebni, the lower grade sntr type was obtained from the Nile Valley or in Punt and was transported overland to Egypt. The higher grade ‘ntiyw incense was, on the other hand, exclusively acquired from Punt and was typically imported by sea. F. Nigel Hepper of the Royal Botanical Gardens reports that botanists have identified this ‘ntiyw variety with Boswellia frereana. Along with Boswellia carteri, he indicates that these are the incense types that are prevalent on the northern Somali littoral (cf. Sayed (2002)). Both species of frankincense have also been found in actual ancient Egyptian tombs (Lucas (1945)). This is pivotal since, according to Hepper, northern Somalia is the only area where Boswellia frereana grows in close proximity to the seashore, and on the requisite rocky hills to boot. Although such “terrace” land formations also occur in other parts of the Red Sea region, in Djibouti, Eritrea and Sudan, frankincense here grows instead at a minimum of 100 kilometers inland. The tree varieties that are found in this hinterland are likewise different from Boswellia frereana.

Animals

As with its flora, the fauna of Punt that is depicted on the Egyptian frescoes and described in hieroglyphic texts is native (though not entirely exclusive) to the Red Sea region. Among these animals is the giraffe, which today is only found in Africa. Superficially, this seems to rule out an Arabian location for the Land of Punt. A closer reading of the ancient testimonials, however, reveals that the giraffe was apparently also present in parts of the Arabian peninsula and Levant during the classical period. The ancient Greek historian Diodorus Siculus refers to the species as “camel-leopards”, and notes that it used to roam the area between northern Arabia and Syria (cf. Scott (2012)).

Depiction of an uncertain species of Puntite rhinoceros at the Hatshepsut temple (Meeks (2012)).

In an analogous vein, the representation of what may be a one-horned rhinoceros on the Hatsheptsut temple reliefs has been suggested as being indicative of an Indian location for Punt. This is because two-horned rhino species are today limited to Africa, whereas the one-horned rhino is restricted to the Eastern Himalayas. However, as Kitchen (1971) observes, the rhinoceros figure in question, unlike the other animals depicted at Deir el-Bahri, is badly damaged, and this makes its identification difficult. Going by a similar “one-horned” rhino representation that was discovered at Kerma in Sudan, the depiction thus appears to have been an error. Kitchen writes:

That the beast seems only to have one horn (not two, as has the African rhino) is simply an error, analogous with that of one of the two Kerma representations of Middle Kingdom date (cf. Hilzheimer, ZÄS 67 (1931) 40), and with the stylized determinative of Louvre C. 14 accepted by Keimer (ASAÉ 48 [1948] 52 and fig. 5).

The archaeologist John Bimson also indicates that early Egyptian hieroglyphs included a pictogram of a one-horned rhinoceros. This, in turn, suggests that the species may have once inhabited the Nile Valley (cf. Sweeney (2006)). In short, the ultimate geographical origin of certain of the land-dwelling fauna of Punt is inconclusive.

A rather different situation exists with the fish and other aquatic creatures that are illustrated on the same murals. Sayed (1989) points out that the Hatshepsut temple walls show marine species whose natural habitat is saltwater, including the lobster (palinurus). The body of water that is depicted therefore could not have been the freshwater Nile river, but instead more likely the Red Sea. Correspondingly, an analysis of the aquatic fauna on the Puntite temple reliefs by Eva Danelius and Heinz Steinitz found that the bulk of the specimens are indeed Red Sea varieties. As Kitchen (1971) notes, only a handful appear to be freshwater species, a fact which can be easily explained:

One factor largely discounted by Herzog (pp. 27, 55) is that of the fishes in the Deir el Bahri reliefs. These are, almost throughout, Red Sea/Indian Ocean fauna, with only two or perhaps three fresh-water species; see Eva Danelius and H. Steinitz, JEA 53 (1967) 15-24. If Hatshepsut’s expedition had reached Punt solely by travelling up the Nile, the overwhelming majority of Red Sea fishes is totally inexplicable. Why not solely Nile fauna, as in other Nile scenes? On the other hand, the Red Sea fauna fit a Red Sea route to Punt. The very few fresh-water fishes (a turtle; catfish, able to go in salt water, anyway; tilapia, dubious) could reflect the Nile part of the journey (Koptos-Thebes) or even fauna in Punt (River Baraka into Tokar Delta?), and pose an infinitely less problem.

Deir el-Bahri mural showing a Puntite village surrounded by Red Sea aquatic species, myrrh trees and other flora and fauna native to Northeast Africa (Edwards (1891)).

An agrarian silo traditionally used by Oromo agriculturalists to store grain and other farming products. Note the resemblance to the conical huts, which the ancient Puntites built and placed atop stilts.

Furthermore, a mural at Deir el-Bahri shows a Puntite village next to a body of water containing Red Sea aquatic species. This settlement consists of domes or bee hive-shaped huts, which are raised above ground on stilts and accessible by ladder. Balanda (2005) points out that in Northeast Africa, such edifices are today mainly restricted to the Nile Valley itself. He argues that this particular scene, therefore, appears to represent a northerly part of the Land of Punt situated closer to Egypt, as opposed to the more distant sections of Punt which are clearly located in the Horn (namely, the Frankincense Terraces of Punt, the Mine(s) of Punt (Bia-Punt), and the Mountain of Punt). However, some Cushitic peoples in the latter area do, in fact, build similar structures for the storage of grain and other agrarian products. Oromo agropastoralists have traditionally constructed silos, which they place on poles, much like the ancient Puntites did (see image above). Hence, this depicted sequence could, on that basis, actually have taken place in the Horn.

A snippet of one of two secretary bird depictions on the Portico of Punt at Deir el-Bahri. The other bird figure is better preserved and displays the species’ distinctive head feathers, which allowed ornithologists to precisely identify it. Since the secretary bird is only found in Africa, and is a national emblem in Sudan, this finding supports a Northeast African location for Punt (Jadwiga Iwaszczuk).

Additionally, the walls of the Hatshepsut temple’s upper Portico of Punt feature bas-reliefs of a mysterious bird, which was among the animal species brought to Egypt from Punt. The bird was originally assumed to be a crane because only its rear could be seen. However, the Egyptologist Filip Taterka of the Polish Academy of Sciences found a well-preserved depiction of the same species on a nearby wall block. Thanks to its unique head feathers, Taterka was able to identify the animal as the secretary bird (Sagittarius serpentarius). This conclusion was also later confirmed by three ornithologists. Taterka’s finding is of particular importance vis-a-vis the debate on the whereabouts of Punt because the secretary bird only lives in open grassland in Africa. The species is endemic to Djibouti, Eritrea, Ethiopia, Somalia and Sudan alike; it actually serves as a national emblem in Sudan. This fact strongly tips the weight of evidence in favor of a Northeast African location for Punt (cf. Foundation PAP).

A Puntite man walking a Papio hamadryas baboon. Isotopic analysis of both bone and hair samples from baboon mummies that were brought to Egypt from Punt during the New Kingdom indicates that the specimens’ oxygen and strontium values most closely match those of baboons endemic to eastern Somalia and the Eritrea-Ethiopia corridor (Edwards (1891)).

The most definitive faunal data regarding where Punt was situated comes from baboons (Papio hamadryas). These are among the creatures that are depicted on the Hatshepsut temple walls at Deir el-Bahri, as well as on other ancient Egyptian murals. Baboon remains have also been found within actual tombs in the Valley of the Kings. Moreover, in the Egyptian pantheon, the deity Thoth is often shown with the head of a baboon.

In 2010, a research unit led by Salima Ikram of the Egyptian Museum and Nathaniel Dominy and Gillian Leigh Moritz of the University of California analyzed hairs from two such mummified baboons, which had been kept at the British Museum. To determine the place of origin of the specimens, the scientists compared the baboons’ oxygen isotopic values with those of living baboon specimens from various hypothesized Puntite locations, including Eritrea, Ethiopia, Somalia and Yemen. Although the isotope data of one of the baboons was distorted, initial results from analysis of the other specimen indicated that its oxygen isotopic values matched closest with those of modern baboons from Eritrea and eastern Ethiopia. This prompted Dominy to posit that “Punt is a sort of circumscribed region that includes eastern Ethiopia and all of Eritrea”. He also suggested that the port of Massawa in Eritrea may have been the landing point of the ancient Egyptians’ expeditions to Punt since a baboon specimen from that harbor matched well with their ancient baboon mummy.

In 2015, the same Egyptian and American researchers conducted a more comprehensive isotopic study to confirm their preliminary findings. This time they compared both hair and bone samples, which they had extracted from two New Kingdom baboon mummies, with those of living baboons from the primary hypothesized locations of the Land of Punt. Analyzing both oxygen and strontium values, the scientists found that the closest matches were with specimens endemic to eastern Somalia and the Eritrea-Ethiopia corridor. They thus concluded that this area was the likeliest source of the baboons that were exported from Punt to Ancient Egypt:

The tandem origins of maritime trade and international diplomacy have roots in the Red Sea region. Graphic and epigraphic accounts of this trade often provide specific place names, or toponyms, with unambiguous geographic locations. Yet the location of one crucial polity, Punt (or Pwnt), remains uncertain. Punt was a major emporium of gold, electrum, and biological materials such as myrrh, ebony, ivory, short-horned cattle, leopards, and baboons (Papio hamadryas). The importance of these materials is reflected in the 1200-year duration of trade between Ancient Egypt and Punt (Vth-XXth Dynasties; ca. 2458-1163 BC). The recovery of mummified baboons from several New Kingdom tombs, which was a period of thriving trade with Punt, raises the possibility of using stable isotope analysis to source their provenience. Here we report the oxygen and strontium stable isotope composition of two P. hamadryas mummies from XXth Dynasty tombs. We also analyzed the hair and bone of modern baboons in 106 habitats spanning five hypothesized locations of Punt: (1) Eritrea-Ethiopia; (2) Mozambique; (3) Somalia; (4) western Uganda; and, (5) Yemen. Isoscapes based on kriging interpolation of hair keratin δ¹⁸O values and bioapatite ⁸⁶Sr/⁸⁸Sr ratios were produced and an index of similarity was calculated based on the geometric mean of the two kriged maps. Our results reveal a high likelihood match with eastern Somalia and the Eritrea-Ethiopia corridor, suggesting that this region was the source of Papio hamadryas exported to Ancient Egypt.

In 2023, Dominy co-authored an archaeogenetic study which compared the mitogenome of a Late Period (c. 800-540 BCE) baboon specimen retrieved from Gabbanat el-Qurud (“Valley of the Monkeys”), Egypt, with those of other baboons recovered from various hypothesized Puntite sites in Africa and the Arabian peninsula. The scientists observed that the Gabbanat el-Qurud baboon carried the G3-Y mtDNA haplogroup, a baboon mitochondrial subclade whose present-day distribution is focalized around Eritrea and eastern Sudan, including the Adulis vicinity. Along with other lines of evidence (discussed below) — which indicate that, centuries before the establishment of the Axumite kingdom, Adulis was a key part of ancient Punt — this discovery further reifies that the Red Sea area in Northeast Africa was indeed the location of the old Puntite civilization (cf. Grathwol et al. (2023)):

Adulis, located on the Red Sea coast in present-day Eritrea, was a bustling trading centre between the first and seventh centuries CE. Several classical geographers––Agatharchides of Cnidus, Pliny the Elder, Strabo––noted the value of Adulis to Greco-Roman Egypt, particularly as an emporium for living animals, including baboons (Papio spp.). Though fragmentary, these accounts predict the Adulite origins of mummified baboons in Ptolemaic catacombs, while inviting questions on the geoprovenance of older (Late Period) baboons recovered from Gabbanat el-Qurud (“Valley of the Monkeys”), Egypt. Dated to ca. 800–540 BCE, these animals could extend the antiquity of Egyptian-Adulite trade by as much as five mummified baboon from Gabbanat el-Qurud and 14 museum specimens with known centuries. To explore this possibility, we analysed complete mitochondrial genomes from a provenance together with published georeferenced mitochondrial sequence data. Phylogenetic assignment connects the mummified baboon to modern populations of Papio hamadryas in Eritrea and eastern Sudan. This result, assuming geographical stability of phylogenetic clades, suggests that present-day Eritrea, and by extension Adulis, was a source of baboons for Late Period Egyptians. It also establishes geographic continuity with baboons from the fabled Land of Punt (Dominy et al., 2020), giving weight to speculation that Punt and Adulis were essentially the same trading centres separated by a thousand years of history.

Other products of Punt

Gold

In various hieroglyphic texts, the ancient Egyptians refer to Punt by another name: Bia-Punt. This roughly translates as “Mine(s) of Punt”, which indicates the primacy of gold among the imports from the old territory. A Sixth Dynasty inscription belonging to the Pharaoh Pepi II is more explicit, as it demands “more than the mining region of Punt” (Sagrillo (2014)). Punt, or at least some of the districts under its control, was thus a center of gold production. This fact is of considerable value in helping to narrow down its location since gold was and is only mined in select areas around the world.

Geological formations in Northeast Africa. The old metamorphic (Precambrian) rocks are associated with gold-yielding areas. Eritrea is the only territory in Northeast Africa and the Arabian peninsula whose entire geological structure consists of these Precambrian formations. As such, it is the most probable location of the gold-mining district(s) of Punt, which is identified in hieroglyphics as Bia-Punt or the “Mine(s) of Punt” (Scientific American).

The first mention of the new toponym comes from the Sixth Dynasty traveler Harkhuf (ca. 2250 BCE). In inscriptions recorded at Aswan, he asserts that he brought back products from “Bia-Punt”. Sayed (1989, 2002) notes that this is a clear allusion to gold, which Harkhuf had presumably imported overland through northern Sudan. In 1976-77, Sayed led a University of Alexandria expedition at Wadi Gawasis, where his archaeological team also found a Twelfth Dynasty stela “inscribed with a hieroglyphic text recording an order issued by King Sesostris I (Senusret I) to his vizier Antefoḳer to build ships to be sent to the region of Bia-Punt” (cf. Sayed (1978)).

Hence, Bia-Punt could be accessed through a water route. This implies that the region in question may have been coextensive with the Atbai desert in Sudan, which has long been a hub of gold mining. Other possibilities in the interior include the gold mines of western Ethiopia, as suggested by Eric Robson in his 2007 monograph In Search of Punt: Queen Hatshepsut’s Land of Marvels. Furthermore, Ibrahim (2013) reports that geologists have identified a zone in northwestern Somalia as potentially containing gold reserves. The Nubian Gold Corporation signed an agreement to prospect there, and the site has gold-quartz deposits with an estimated 13.5 gold parts per million. Since gold in Northeast Africa is associated with old metamorphic rocks — Precambrian geological formations that are found in all of these areas — Bia-Punt could conceivably have been situated anywhere within this traditional Puntite sphere. Eritrea would seem the most logical possibility, for it is the only territory in Northeast Africa and the Arabian peninsula whose entire geological structure consists of Precambrian rocks. On the other hand, Bressan (2013) notes that the geological formations of Yemen, Oman and other areas in Arabia are marked by recent sediments that are mostly bereft of gold. This makes the Arabian peninsula an unlikely location for Bia-Punt, the “Mine(s) of Punt.”

Slaves

Foreign tributaries on the top three registers of the Grand Procession mural at Thebes, Egypt. Top row=Puntites (left), Nilotes (far right); Middle row=Cretans; Bottom row=Hamitic-type Nubians, Nilote (center-right).

In addition to gold, slaves were among the main exports that the Puntites sent to their ancient Egyptian trading partners. Most of these captives appear to have been of “Negroid” ancestral stock. This is suggested by the Grand Procession mural in Thebes at the tomb of Rekhmire, a vizier under Pharaoh Thutmose III. The painting contains several registers or levels, which depict various foreign envoys submitting tribute to the ancient Egyptians, including Puntite, Cretan and Nubian emissaries. The Grand Procession’s uppermost register shows a couple of reddish-skinned, orthognathous Puntite delegates, who strongly resemble the mural’s similarly copper-toned Egyptian, Cretan and Hamitic-type Nubian figures. These Puntites are flanked to the right by jet black-skinned, prognathous men, who, except for their attire, are physically identical to the Nilotes in the Nubian panel. As Kitchen puts it, “beside the so called ‘Hamitic’ type (like Parahu) not very different from Egyptians in appearance, others represented were clearly of Negro stock” (cf. Balanda (2005)). The Grand Procession is paralleled by the Book of Gates mural in the tomb of Pharaoh Seti I, which similarly contrasts an Egyptian “Hamitic” type with a Nilotic “Negroid” type (Richardson (2003)).

Book of Gates mural in the Tomb of Seti I. From bottom left, clockwise: Reth (Ancient Egyptians, portrayed as copper-brown like the Puntites, Cretans and “red” Nubians); Aamu (Levantines, inhabitants of the Eastern Desert, portrayed as yellow-brown); Nehesu (Nilotes, the “black” Nubians); Temehu (Ancient Libyan group of European origin, portrayed as white; the original carriers of the paternal haplogroup R1b, they arrived directly from Europe (or indirectly from Central Asia) and were assimilated into the Nile Valley’s Afro-Asiatic-speaking populations (cf. Grugni et al. (2019))).

Closeup of the original single panel in the Tomb of Seti I. The mural depicts (from left) “black” Nubian, copper-brown Egyptian, yellow-brown Levantine, and white Temehu figures. (*N.B. This is supported by archaeogenetic analysis. Haber et al. (2017) note that Bronze Age Levantine individuals from Sidon generally looked like their modern descendants, but had a darker complexion: “SNPs associated with phenotypic traits show that Sidon_BA and the Lebanese had comparable skin, hair, and eye colors[…] but with Sidon_BA probably having darker skin than Lebanese today from variants in SLC45A2 resulting in darker pigmentation”.)

Erroneous artistic reproduction of the Tomb of Seti I single panel. The illustration mistakenly shows the Levantine figure as having a white complexion like the Temehu figure, when in actuality the Levantine figure is depicted as yellow-brown on the original mural.

Closeup of the top three registers on the Grand Procession mural. The “Hamitic” Puntite figures on the top row resemble the copper-toned Cretans and Hamitic-type Nubians, and correlate with the “red” peoples described in the early inscriptions. The “Negroid” figures to the right of the Puntites are identical to the very dark Nilote on the bottom panel, and are in all likelihood the “black” peoples of the engravings (Hoskins (1835)).

Dimitri Meeks of the French National Centre for Scientific Research, like many other Egyptologists, believes that the conspicuously Nilotic folks on the Grand Procession represent the Puntites’ slaves. As such, they would have been accompanying their masters on this tributary voyage. The Egyptologist Stanley Balanda, however, argues that the “Negroid” individuals may instead have been diplomatic envoys too because “both races are being represented in the same way without distinctions being made to indicate any social or legal differences”. By his reckoning, the Nilotic figures would therefore have also inhabited some districts of Punt alongside the Egyptian-related Puntites. Meeks’ position on the slave origin of the “Negroid” individuals that are standing near the Puntites is compatible with an Arabian location for Punt (a geographic theory of which he is one of the main proponents). Balanda’s postulation is not, though, since there appear to be no indigenous populations in the Arabian peninsula, relict or otherwise, that have a similar phenotype (cf. Coon (1939)). On the other hand, both arguments are in line with a Northeast African locus for the Land of Punt.

Distribution of global population groups. The “Hamitic” Caucasoids comprise Afro-Asiatic speakers (Berber, Cushitic and Egyptian branches), ancestrally related peoples who inhabit North Africa and the Horn of Africa.

“Negroid” groups — Nilotic and Bantu populations known in Djibouti and Somalia as jareer or adoon and in Eritrea and Ethiopia as shanqilla or barya (terms denoting “negro”) — have long constituted the bulk of the slave class in the Horn. In antiquity, most of these slaves were captured from the surrounding areas bordering South Sudan and the Great Lakes region. However, there is textual evidence pointing to an early presence of two separate ancestral stocks in Northeast Africa; one with “Hamitic” affinities, and the other of apparent “Negroid” origin. (*N.B. On a population level, the Afro-Asiatic speakers of the Horn generally do not intermarry with jareer/barya (“negroes”), whether at home or abroad. This is due to traditional beauty standards, which place a low value on “Negroid” features. These aesthetic preferences are how the Afro-Asiatic-speaking populations have managed to maintain their distinctive physiognomies to a remarkable degree, despite being flanked by Niger-Congo/Nilo-Saharan/Khoisan communities with markedly different phenotypes. The Afro-Asiatic speakers’ reluctance to interbreed with “negro” groups also stems from a desire to preserve their own ancestral heritage (cf. Mwakikagile (2009), Gwyn (2013), Folklore Institute (2003)). Correspondingly, ancient DNA analysis has found that the early Cushitic settlers of East Africa were of North African ancestral stock, and that their modern descendants in the Horn share close affinities with them; see Ancient DNA from Ethiopia.)

“Red Nubians” from a Nile Valley mural, bearing a close resemblance to the ancient Egyptians. Ancient DNA analysis has confirmed ties between these Meroitic & X-Group (Post-Meroitic) period inhabitants of Nubia and the Afro-Asiatic-speaking populations.

Nubian artist Mohamed Mounir retaining the physiognomy of the “red Nubians,” the Egyptian-related inhabitants of ancient Nubia.

Young Somali man retaining the physiognomy of the Puntites, relatives of the “red Nubians” and ancient Egyptians.

This racial dichotomy was reported as far back as the kingdom of D’mt/Da’mat in Eritrea and northern Ethiopia, which flourished around 3,000 years ago during the pre-Axumite period. According to Robert Hoyland, who conducted archaeological excavations in the area in 2013, inscriptions attributed to the kings of that polity describe its rulers as lords of “Da’mat, its east and its west, its Sabaeans and its immigrants, its red people and its black people”. Tibebu (1995) likewise notes that “the distinction between the saba qayh (red men) and tsalim barya (dark slave) was also made during the Aksumite period”.

“Black Nubians” bound together, as reproduced from an ancient Egyptian mural. One of the individuals is covered in red ochre, a custom that is still practiced by the Noba/Nuba of the Kordofan Mountains and certain Nilotic populations.

Nilote woman retaining the physiognomy of the “black Nubians,” the Nilotic inhabitants of ancient Nubia.

A Noba/Nuba woman doused in red ochre, closely resembling the red ochre-covered “black Nubians.” Such painted individuals are distinct from the Egyptian-related “red Nubians,” whose actual skin color was a copper-brown tone.

In that regard, in keeping with the Grand Procession and other ancient Egyptian murals, the Asiatic Society (1968) reports that epigraphs belonging to the Axumite King Ezana differentiate between “red” Nubians and “black” Nubians; the former correspond with Hamito-Cushitic peoples related to the Egyptians, and the latter are associated with Nilotes:

The Nubians at that time also (as in previous centuries) were divided into the Red People or the Kasu or Cushites (Hamites like the Egyptians) and the Black People or Sudanian Negroids[…] these two peoples evidently were contrasted as “Red” and “Black” from their skin-colour; and as late as the fourth century A.D., the great Ethiopian King ‘Ezana, who conquered Nubia, differentiated between these two classes of Nubian.

A Somali queen, recalling the ancient Puntite figures depicted on the Deir el-Bahri and Thebes murals (French-Sheldon (1892)).

Thanks to the medieval chronicle of the Ethiopian Emperor Susenyos I, we are able to precisely identify the descendants of the “red” and “black” populations in the Horn. The royal court historian refers to the Afro-Asiatic-speaking non-slave populations as qayh (red) and the “shanqilla” groups as tsalim (black) (cf. Pankhurst (1976)). In short, whether the “Negroid” figures that are standing beside the Puntites on the Grand Procession mural represent emissaries or slaves, either possibility is consistent with a Northeast African center for the Land of Punt. This is because there was both an early presence in the area of distinct “Hamitic” and “Negroid” populations (as depicted on said fresco), and a well-established slavery tradition involving Nilotic captives.

A slave of the queen, recalling the ancient “Negro” figures portrayed on the Grand Procession at Thebes (French-Sheldon (1892)).

Besides the foregoing, other ancient Egyptian inscriptions indicate that the Puntites also exported a number of Pygmy slaves. Harkhuf writes that during the second regnal year of the Pharaoh Pepi II (r. 2278–2184 BCE), he brought back a dancing pygmy as a royal gift for the child-king, which he had acquired from Punt by way of the kingdom of Yam in the Sudanese region. The traveler also avers that another pygmy had been imported from Punt at an earlier date, during the reign of Pharaoh Djedkare-Isesi of the Fifth Dynasty (r. 2414–2375 BCE).

This begs the question, from where did the Puntites capture the Pygmy slaves to begin with? Perhaps somewhere in the central African hinterland, where they in fact have long been concentrated. Based on recent archaeological finds in an inland valley in northwestern Somalia (discussed below), Ibrahim (2013) argues that the Puntites had intermittently ventured even further in the interior, far beyond the boundaries of Punt and toward the Congo Basin and the gold mines of Mashonaland. There, they would have accessed slaves, additional gold reserves, and other commodities in the trans-regional trade networks for later barter with the ancient Egyptians. It would appear that such mercantile contacts persisted for centuries, as Leo Africanus testifies that the Sultanate of Mogadishu (Magadazo) originally controlled the gold trade at Sofala in present-day Mozambique (“this golden trade [at Sofala] was first in the power of the Moores of Magadazo”).

More parsimoniously, Lunde and Porter (2004) report that the so-called “Pygmies” brought back to Egypt might instead have been natural dwarves. This raises the possibility that these captives were simply short-statured individuals, and thus, plausibly drawn from the native hunter-gatherer communities of the Horn (as represented by the diminutive Chabo, Eyle and Ribi foragers) or Great Lakes regions (as represented by the small Hadza and Sandawe foragers). In support of these scenarios, Scozzari et al. (1999) observed a moderately high incidence of B-M60 haplotypes among individuals in northern and southern Egypt; Scozzari et al. (2014) also report that ~28% of Berbers in Egypt’s Siwa Oasis, a medieval hub of the slave trade, carry the B2a subclade (Table S7). However, this paternal lineage has not been found in ancient samples from either Egypt or Sudan (cf. this essay; Ancient DNA from Sudan). It instead today occurs at greatest frequencies among both the Hadza and Mbuti hunter-gatherers of southeastern and central Africa. Furthermore, genome analysis of modern Afro-Asiatic speakers in the Horn of Africa indicates that these individuals bear a predominant non-African ancestry (over 70%), with minor Sub-Saharan African admixture (~27%) that was in part derived from ancient East African foragers. This East African hunter-gatherer component is, however, rare among the contemporary Egyptian and Libyan samples (see Genetic affinities of the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa). Ergo, the presence of haplogroup B in Egypt is indeed likely a legacy of the captured “Pygmies,” who — considering the absence of this clade from the Nile Valley’s archaeogenetic record — seem to have been imported in significant numbers only after the Graeco-Roman period.

Henna

Mural at Deir el-Bahri depicting ancient Egyptian men loading henna onto vessels for transportation from Punt to Egypt. Henna was and is ubiquitous in Egypt, where traditionally it has been used for cosmetic, medicinal and ritualistic purposes (Dreamstime).

During the Hatshepsut expedition to Punt, one of the key products that her party brought back with it to Egypt was henna (Lawsonia inermis) (IPA (1967)). A mural at Deir el-Bahri (shown below) depicts this queen’s men loading the plant onto their vessels alongside other cargo. The ancient Egyptians required the henna for cosmetic, medicinal and ritualistic purposes. To this end, actual mummies have been found in Egypt with traces of the dye on their hands, feet, nails and hair. Grafton Elliot Smith, for instance, states that the 18th Dynasty official Henttawi had his hair dyed a bright reddish color. This practice seems to date to at least the predynastic era, for Guy Brunton writes that a Badarian old woman apparently had henna-dyed hair of a light brown-red hue (Lucas and Harris (1999)). (*N.B. Brothwell and Spearman (1963) also observed authentically blond ancient Egyptian individuals; their hair samples were not affected by either hair dye or cuticular damage.)

The custom of using henna to decorate the body was, therefore, of some importance in ancient Egypt. It is also still adhered to by modern Egyptians. Moreover, henna is a cultural staple of the Afro-Asiatic-speaking populations in the Horn of Africa. Among Somalis, Afars, Oromos, Saho, Beja, Tigre, Jebertis and Hararis, the dye is used on a weekly basis for cosmetic adornment. More elaborate designs are reserved for special occasions such as wedding ceremonies, Eid celebrations and birthdays. Although usage of henna in the Horn is closely linked with Islam, the plant’s exportation from Punt suggests that, as in Egypt, this tradition is actually a holdover from remote times.

A Somali woman with henna designs on her arms. Henna application is an ancient custom among the Afro-Asiatic-speaking populations in Northeast Africa, a tradition which apparently dates to the Puntite era.

A Cushitic-speaking Saho woman from Eritrea with traditional henna designs on her arm.

A Cushitic-speaking Bilen (northern Agaw) woman with henna designs on her hands and nails.

A Nubian girl with henna designs on her hand (Aswan, Upper Egypt). Like their Egyptian, Cushitic and other Afro-Asiatic-speaking neighbors, henna application has long been a staple of Nubian culture. Genetic analysis also suggests that Nubians themselves were originally Afro-Asiatic speakers, as they are closely related to adjacent Afro-Asiatic-speaking populations.

A Somali woman with henna designs on her hands, feet and nails. In the Horn, henna is used on a weekly basis for cosmetic decoration, with more elaborate designs reserved for special occasions.

Mummified hand of a 19th Dynasty ancient Egyptian princess from Thebes. The appendage has darkened due to necrosis. However, the specimen’s fingernails are painted red with henna.

Kohl

Kohl is another one of the “wonderful things of Punt” that were brought back to Egypt. The ancient Egyptians usually mined malachite and galena (lead sulphide) — the main elements used to make, respectively, the earlier green and later black varieties of kohl — at Sinai and the Eastern Desert, as well as in various areas in Upper Egypt. However, they would sometimes also import these cosmetic ingredients from the Arabian peninsula through Punt in the Horn region (Hardy et al. (2006)). During the New Kingdom, the Egyptians would procure kohl itself directly from Punt (Bard and Fattovich (2018)).

In ancient Egypt, kohl was liberally applied as eye-paint on both men and women. The predynastic Egyptians stored it in cosmetic palettes. These later evolved to small containers, and eventually to tubes, pots and spoons during the dynastic era. Besides kohl’s obvious aesthetic function, scholars have proposed that it may have also served a ritualistic or protective purpose insofar as its use was an attempt to symbolize the Eye of Horus (wadjet) (Mendoza (2017)). Likewise, the C-Group pastoralists of Lower Nubia, whom Oric Bates and George Andrew Reisner have identified as ancient Libyans, were known to apply the kohl eye cosmetic (E. S. Thomas (1926) notes: “the “C” Group people dressed in skins ; they used black eye paint and tatued their bodies, proving that they had light skins”).

Ancient Egyptian figures depicted with the ubiquitous kohl eye-paint, from the Nebamun Tomb-Chapel c. 1350 BCE (British Museum).

An ancient Egyptian triple kohl tube made of faience, dating from the New Kingdom or later (ca. 1550 BCE or later) (Johns Hopkins Archaeological Museum).

Gold burial mask of the ancient Egyptian Pharaoh Psusennes I, 21st Dynasty. The kohl eyeliner serves to both enhance the sculpture’s aesthetic appeal and protect the eyes from baleful influences.

Gold masks of the ancient Egyptian courtier Yuya (right) and his wife Thuya (left), maternal great-grandparents of the 18th Dynasty Pharaoh Tutankhamun. Note the habitual kohl eye-paint (Ministry of Tourism and Antiquities).

Painted limestone statue of the ancient Egyptian Prince Rahotep, from the Mastaba of Rahotep at Meidum, Lower Egypt. This sculpture dates from the Old Kingdom’s 4th Dynasty (c. 2613-2498 BCE), showing the early usage of the kohl eyeliner in the Nile Valley.

The omnipresence of kohl in old Egypt is clearly reflected in dynastic period artwork. Monument walls and temple murals, such as at the Nebamun Tomb-Chapel, routinely show Egyptian figures wearing the eyeliner. Statues are likewise often depicted with painted eyes. This fact is especially interesting given that some ancient Puntite sculptures — which were recently excavated in northern Somalia; see discussion below — similarly feature contouring of the eyes, as if with kohl. Besides visual art, kohl is mentioned in the ancient Egyptian fable the Tale of the Shipwrecked Sailor. This story describes an encounter between a stranded Egyptian merchant and a talking snake, the latter of whom calls himself the “Prince of Punt.” The serpent offers to the trader a number of gifts to take back to Egypt, including kohl (Westling (1999)).

As with henna, kohl remains today in wide usage among Egyptians. The eye-paint is also a traditional fixture among the Afro-Asiatic-speaking populations in the Horn of Africa. This fact serves as yet another compelling reason why the ancient Land of Punt was almost certainly located in Northeast Africa.

A Somali woman with kohl eyes (indha kuul). Kohl is a commonly applied eye-paint among the Afro-Asiatic-speaking populations in Northeast Africa. The cosmetic’s usage dates from antiquity, for it was one of the “wonderful things of Punt” that were imported to ancient Egypt during the New Kingdom.

Somali artist Hamdi Bilan wearing the traditional kohl eye cosmetic.

Oromo artist Duni Mame wearing the traditional kohl eyeliner.

Berber connection

Hieroglyphic signs for brbrta, the ancient Egyptian ethnonym for the Puntites (AECR (1976)).

One of the most insightful clues as to the location of the Land of Punt involves the etymology of the word Berber. It has often been assumed — incorrectly — that the appellative originated with the ancient Greeks as a cognate of barbaros (“barbarian”). However, the first mention of the term actually dates earlier to the New Kingdom of Egypt (c. 1500 BCE), when it served as an ethnonym for the Puntites. Specifically, during the Hatshepsut expedition to Punt, the ancient Egyptians identified their Puntite counterparts as brbrta in hieroglyphic symbols. This is believed to have been an onomatopoeic imitation on the Egyptians’ part of the “bar” or “ber” sound that was apparently common in the Puntite language (cf. AECR (1976); Bowersock (2013)). In view of these hieroglyphics, the Egyptologist Ernesto Schiaparelli suggests that the Puntites inhabited a region coinciding with northern Somalia, Eritrea (then part of northern Ethiopia), and the Atbara zone in northeastern Sudan (AECR (1976)):

In the “Dictionnaire des noms geographiques contenus dans les textes hiéroglyphiques” by H. Gauthier, the Italian Egyptologist Schiaparelli is quoted as identifying the inhabitants of Punt during the Hatshepsut expedition with the people living in the northernmost part of Ethiopia, what is now Eritrea, and in two cities named Berbera. One is situated just north of Atbara, the town at the confluence of the Blue and White Niles, the other on the coast of Somaliland. Schiaparelli based his conclusion on the hieroglyphic signs which stood for the Puntites, namely [brbrta]. I believe that these signs brbr were an onomatopoeic attempt on the part of the Egyptians in the expedition to imitate the language of the people with whom they were dealing. The actual occurrence of brbrta as identifying the people of Punt, a historical people of ca. 1500 B.C., gives weight to the theory that it was here in the Egyptian New Kingdom that the word Barbar originated, rather than in the land of the Sumerians, or the Semites, or the Indo-Europeans.

Ancient Egyptian statue of the Pharaoh Sesostris I (Senusret I). According to a stela found at Wadi Gawasis, the king ordered an expedition to Punt. Pliny the Elder specifies that Sesostris’ party therein traveled as far as the cinnamon emporium of Mosylon (Mossylum), located in present-day northeastern Somalia (Aldred (1970)).

Schiaparelli also bases his argument on the aforementioned Periplus of the Erythraean Sea, a document which repeatedly alludes to “Berbers” living in these same areas. As a result, this territory was known to the ancient Greeks as “Barbaria” or “Barbara”, meaning the “land of the Berbers” (Huntingford (1980)). The Periplus indicates that there were Berber commercial settlements all along the Red Sea coast during the 1st century CE, with two such concentrations: one in the “Barbaria” in the Nile Valley around southern Egypt and northern Sudan, and the other in the “far-side” ports of the “other Barbaria” in the Horn (viz. “there are other Berber market-towns, known as the ‘far-side’ ports”). These Berbers/Puntites were therefore still trading in frankincense and other commodities in the southern part of their territory, just as they had over a millennium before in Pharaoh Hatshepsut’s time. This is confirmed by the Roman scholar Pliny the Elder, who tells us that the Pharaoh Sesostris I — a ruler that, as seen on the Wadi Gawasis stela, ordered at least one expedition to Punt during his reign — led his men to the “far-side” Berber port of Mosylon (Mossylum), a cinnamon emporium located in the present-day Bosaso area in northeastern Somalia.

Map of select ancient market towns and their principal exports described in the Periplus of the Erythraean Sea (c. 1st century CE). Many of these localities are in the Northeast African territories of the “Berbers”, situated in the Nile Valley and Horn of Africa (viz. the “other Berber market-towns”). Among the ports listed are Adulis, Avalites, Malao, Mundus, Mosyllum, the Market and Cape of Spices, Pano and Opone. Not shown on the map are the market-towns of the southern Azania coast (including Nikon, Sarapion and Rhapta), as well as the emporium of Acannae on the northeastern Barbaria littoral. The Periplus specifies that Acannae is “where alone is produced the far-side frankincense, in great quantity and of the best grade” (Wickramasinghe (2018)).

Another key aspect of the Barbaria connection is the form of governance that the territory’s denizens were said to have adhered to. The Periplus indicates that the Berbers were divided into tribal communities, each ruled by its own chief. These independent city-states in the greater Barbaria were, in turn, overseen by a learned king or paramount chief named Zoscales (Zoskales):

On the right-hand coast next below Berenice is the country of the Berbers. Along the shore are the Fish-Eaters, living in scattered caves in the narrow valleys. Further inland are the Berbers, and beyond them the Wild-flesh-Eaters and Calf-Eaters, each tribe governed by its chief; and behind them, further inland, in the country towards the west, there lies a city called Meroe.[…]

These places, from the Calf-Eaters to the other Berber country, are governed by Zoscales; who is miserly in his ways and always striving for more, but otherwise upright, and acquainted with Greek literature.[…]

The voyage to all these farside market-towns is made from Egypt about the month of July, that is Epiphi. And ships are also customarily fitted out from the places across this sea, from Ariaca and Barygaza, bringing to these far-side market-towns the products of their own places; wheat, rice, clarified butter, sesame oil, cotton cloth, (the monache and the sagmatogene), and girdles, and honey from the reed called sacchari. Some make the voyage especially to these market-towns, and others exchange their cargoes while sailing along the coast. This country is not subject to a King, but each market-town is ruled by its separate chief.

Fine ceramics recovered from tomb excavations at Heis (Xiis) in northwestern Somalia, a site corresponding with the ancient “Berber” emporium of Mundus. 1-4=Mesopotamian Glazed Ware; 5 and 6=Italian terra sigillata; 7=Eastern Terra Sigillata; 8=Egyptian fine ware (González-Ruibal et al. (2022)).

Skeleton of a child excavated from a cairn at Heis (Xiis) in northwestern Somalia. The individual (c. 7.5 to 9.5 years old) was interred with several grave goods, including a Roman glass flagon dated to the 3rd century CE. Since this Tomb 120 is contemporaneous with ancient Mundus, the person buried within it appears to be one of the “Berbers” (Barbaroi) described in the Periplus (González-Ruibal et al. (2022)).

As in the Berber period, the various Puntite districts were apparently governed by separate leaders. This is clear from Egyptian hieroglyphics, which Balanda (2005) notes repeatedly allude to the “chiefs” of Punt in the plural. For example, an inscription at Deir el-Bahri reads: “pitching tents for the king’s representative and his (the king’s) expedition to the myrrh terraces on both sides of the sea[…] in order to receive the chiefs of this land.” Likewise, an inscription at Sinai, which dates from the 36th regnal year of the Pharaoh Amenophis III (r. 1390–53 BCE), records an official indicating that: “I went forth by the sea coast (pr.n=j hr-gs wtd-wr) to announce the marvels of Punt to receive aromatic gums which the chiefs had brought (jn.n wrw) in their Khementy-boats as revenue from unknown lands.” The loosely centralized governmental structure of the Berbers/Puntites, therefore, also appears to have remained essentially unchanged since the New Kingdom.

(*N.B. From the Deir el-Bahri hieroglyphic text above, we also learn that there were “myrrh terraces on both sides of the sea,” which the ancient Egyptians visited during their sojourns in Punt. This statement appears to give some credence to Balanda’s assertion that the Puntites inhabited both the Horn of Africa and the neighboring parts of the Arabian peninsula. Other evidence to that effect includes linguistic analysis by Alexander Militarev, who identified a Cushitic substratum in the Modern South Arabian languages. Militarev, an advocate of a Levantine origin for the Afro-Asiatic language family, suggests that this signifies that a) Cushitic speakers originally dwelled in Arabia, in an area adjoining that of the speakers of the MSA languages, b) most Cushitic speakers later migrated to Northeast Africa, and c) the Cushites who stayed behind in the Arabian peninsula were assimilated by their Semitic neighbors (cf. Blažek (2013)). Since the ancient Himyarites occupied the Hadramout governate and southwestern areas in Yemen near the domain of the MSA speakers, it is relevant to note that “in the 5th century the Himyarites, in the south of Arabia, were styled by Syrian writers Cushaeans and Ethiopians” (Baynes (1878)). Additional evidence supporting Balanda’s contention includes genetic and anthropometric analysis: Non (2010) observed close mtDNA ties between various Cushitic/Ethiosemitic-speaking populations of the Horn and Yemenis from the Hadramout governate, and Billy (1988) reported that his Cushitic and Ethiosemitic-speaking samples shared anthropometric affinities with Yemenis.)

Ancestral and spiritual homeland

Rock art at Laas Geel in northern Somalia, which appears to depict cow worshiping in honor of the ancient Egyptian deity Hathor (Phys).

The ancient Egyptians held a special reverence for the Land of Punt. Known to them as Ta netjer or Ta nuter (“God’s Land”), they regarded it as both their ancestral homeland and a spiritual center. Thus, whenever the ancient Egyptians depicted the Puntites on their temple walls, they consistently showed them as being similar to themselves in appearance and size (unlike other non-Egyptians, who were instead frequently caricatured). Punt was likewise always identified in the hieroglyphic texts without the determinative symbolizing a foreign territory.

The Egyptologist Gaston Maspero summarizes these conventions as follows:

The legends which seem to bring the ancestors of the Egyptians from the Red Sea coast have already been mentioned. They are closely connected with the worship of the Sky and Sun god Horus of Edfu. Hathor, his nurse, the “House of Horus,” the centre of whose worship was at Dendera, immediately opposite the mouth of the Wadi Hammamat, was said to have come from Ta-neter, “The Holy Land,” i.e. Abyssinia or the Red Sea coast, with the company or paut of the gods. Now the Egyptians always seem to have had some idea that they were connected racially with the inhabitants of the Land of Punt or Puenet, the modern Abyssinia and Somaliland. In the time of the XVIIIth Dynasty they depicted the inhabitants of Punt as greatly resembling themselves in form, feature, and dress, and as wearing the little turned-up beard which was worn by the Egyptians of the earliest times, but even as early as the IVth Dynasty was reserved for the gods. Further, the word Punt is always written without the hieroglyph determinative of a foreign country, thus showing that the Egyptians did not regard the Punites as foreigners. This certainly looks as if the Punites were a portion of the great migration from Arabia, left behind on the African shore when the rest of the wandering people pressed on northwards to the Wadi Hammamat and the Nile. It may be that the modern Gallas and Abyssinians are descendants of these Punites.

Correspondingly, George Rawlinson reports that hieroglyphic inscriptions variously describe Amun, the king of the ancient Egyptian gods, as the Hak or King of Punt. The sky deity Horus is also venerated as “the holy morning star which rose to the west of the land of Punt.” Moreover, a Ramesside monument inscription at Sinai identifies the lunar god Thoth as the “Lord of Punt” (cf. Shaheen (1998)). As the historian Amelia Edwards further notes, the greatest and one of the oldest of the ancient Egyptian female deities, Hathor, was in fact styled as the “Lady of Punt”:

The Egyptians entertained an extreme reverence in the abstract for the Land of Punt, which apparently formed part of a larger district known generally as Ta-nuter, or the Land of the Gods. Hathor and Bes, two of the principal deities worshipped by the Egyptians had their divine origin in Punt, and Hathor was adored under a special form as “The Lady of Punt.” Bes, in his grotesque features and general characteristics, is clearly a barbaric divinity, and is occasionally represented as nursing or devouring the large cynocephalus apes depicted in the wall-sculptures of Dayr-el-Bahari as indigenous to the Land of Punt. The Egyptians appear to have cherished a vague tradition of their own origin as natives of Ta-nuter at some extremely remote period ; and it is interesting to note that the curved beard characteristic of these natives of the Land of the Gods is a special attribute of divinities as well as of deified personages in Egyptian art.

Statue of the ancient Egyptian female Pharaoh Hatshepsut. The Queen believed that she was of Puntite origin, and ordered an expedition to the Land of Punt during her 18th Dynasty reign (Met Museum).

Ancient Egyptian bust of the goddess Hathor, the “Lady of Punt.”

The respect that the ancient Egyptians had for Punt, and its associated goddess Hathor in particular, is perhaps best expressed by Pharaoh Hatshepsut herself. Hieroglyphic inscriptions attributed to this monarch remark (Manley (1996)):

It is the sacred region of God’s Land; it is my place of distraction; I have made it for myself in order to cleanse my spirit, along with my mother, Hathor… the lady of Punt.

Ancient Egyptian figures performing a ritual dance (Nebamun Tomb-Chapel, c. 1350 BCE).

Afar women performing a traditional dance, closely resembling the ancient Egyptian dancers. This is consistent with ancestral descent from the Puntites, who were relatives of the ancient Egyptians.

Modern stamp from Somalia depicting a folklore dance like that of the ancient Egyptians.

Somalis performing a traditional dance, similar to that of the ancient Egyptians.

Given the above, we can better situate ancient Punt by examining whether or not the various hypothesized Puntite locales once had an established spiritual cult devoted to deities from the Egyptian pantheon. To this end, the Roman scholar Pliny the Elder refers to the area near present-day Bulhar in northwestern Somalia as the “Port of Isis”, so named after the Egyptian goddess Isis (Österreichische Leo-Gesellschaft (1941)). Certain pastoral-themed rock art in northern Somalia, such as at the Laas Geel site, likewise seems to depict worshipers honoring the deity Hathor, the presiding “Lady of Punt” and figurative “mother” of Queen Hatshepsut (cf. Ibrahim (2013)).

Biological affinities

Egyptologists have long acknowledged that whichever geographical location truly conforms with the Land of Punt, it should have populations that share close biological ties with the ancient Egyptians; or, at the very least, with the ancient Egyptians’ lineal descendants, the modern Egyptians. This rules out Mozambique and Uganda since their Bantu and Nilotic majorities are fairly recent settlers, and these groups also do not have any significant affinities with the ancient and modern Egyptians. The Afro-Asiatic (Hamitic-Semitic) speaking populations of the Horn, Sudan, Maghreb and the Arabian peninsula, on the other hand, are in an altogether different position. Anthropological studies have confirmed that they share close physical and genetic ties with Egyptians as a whole. This perhaps should not come as a surprise, for the ancient Egyptians were Afro-Asiatic speakers too.

Puntite carriers, from a mural at Deir el-Bahri. Note the “Caucasoid” craniofacial profile, lithe build, reddish-brown complexion, long wavy hair and chin-tuft typical of this ancient population.

Illustration of a Somali warrior. The semblance to the ancient Puntite figures in terms of physiognomy and attire is conspicuous.

An Eritrean man with the mariin phenotype. Egyptologists have long recognized Eritrea as one of the key areas in the ancient Land of Punt, due in no small part to the close physical resemblance between the ancient Puntites and Eritrean individuals with a mariin/amrani physiognomy.

A Somali man with the mariin phenotype. Somali individuals with a mariin/amrani physiognomy closely parallel that of the ancient Puntites, as they have a lithe build, fine-features, a reddish-brown complexion, soft-textured hair, and are usually of moderately tall height.

A Mahra man. South Arabian individuals also often have a physiognomy that approximates that of the ancient Puntites. However, the southern Arabs are usually brachycephalic (broad-headed), whereas the Puntites’ siblings the ancient Egyptians were primarily dolichocephalic (long-headed).

An Afar man with the mariin phenotype, bearing a close resemblance to the ancient Puntites. Along with coastal Eritrea, Somalia and Sudan, Djibouti is also thought to have been part of the ancient Land of Punt.

An admixed Nilotic man, client of the Cushitic Afar. Cushitic populations traditionally had various Bantu/Nilotic/hunter-gatherer individuals attached to them on a client basis (called “sheegad” or “pretenders”). These non-Cushitic, acculturated clients do not resemble the ancient Puntites/Egyptians, owing to their “Negroid” physiognomy.

Morphology

As seen at Deir el-Bahri, among other archaeological sites, the ancient Egyptians consistently show the Puntites on their temple walls as being very similar to themselves in physical type — just as though these groups were sibling populations. The Puntites are depicted as moderately tall and of gracile build, with “Caucasoid” features and reddish-brown skin; they also frequently wear their hair long. John Desmond Clark writes:

The Puntites are depicted in several Eighteenth Dynasty scenes. Typically, the men have dark reddish skins and fine features; characteristic negroid types are not shown, although they occur amongst depictions of riverine southerners (of Wawat, Kush, Irem, etc.). Other Puntite features are also not found amongst other southerners. Long hairstyles are typical for Puntites until the reign of Amenhotep II; during his reign and earlier, in that of Tuthmosis III, an intermediate ‘bobbed’ hairstyle appears, and thereafter Puntites have close-cropped hair similar to that of the chief of Punt under Hatshepsut. A long or medium dressed goatee is found at all periods

Such external morphological traits are relatively common among the Afro-Asiatic-speaking populations on either side of the Red Sea (see, for example, the anthropometric studies Leguebe (1981) and Billy (1988) below). For our purposes, then, the skeletal characteristics of these groups are more useful in locating Punt.

Anthropometric analysis of Afro-Asiatic and Nilo-Saharan-speaking populations. The Cushitic-speaking samples (Galla (G) from central Ethiopia and Oromo (O) from west-central Ethiopia) group with Egyptians from the Kharga Oasis (K1, K2). The Nilo-Saharan-speaking samples form their own seperate cluster. This agrees with the view that the Land of Punt was situated in the Horn region (Leguebe (1981)).

Anthropometric relations between ethnolinguistic groups in Africa and the Arabian peninsula. The Cushitic and Ethiosemitic-speaking populations in the Horn of Africa cluster with other Afro-Asiatic speakers in North Africa (northern Libyans and Egyptians) and the Arabian peninsula (Yemenis). Nubians also group with the Afro-Asiatic-speaking samples rather than with the Nilo-Saharan and Niger-Congo-speaking populations. This again supports a Red Sea area location for ancient Punt (Billy (1988)).

In terms of height, the Egyptologist Édouard Naville states that the Puntite chief Perahu (Parahu) is depicted on the Deir el-Bahri temple walls as “a tall well-shaped man.” This portrayal concurs with the estimated stature of an ancient individual excavated at Heis (Xiis), a site in northwestern Somalia corresponding with the old “Berber” port of Mundus (discussed further below). Measurement of the total length of this adult male skeleton (c. 21 to 46 years in age), which was exhumed from Tomb 75, produced a height of around 1.68 m (cf. González-Ruibal et al. (2022)). When adjusted for flesh covering the bones in the living and minor osteological shrinkage from dehydration, this gives a stature close to the averages of 1.729 m and 1.723 m, respectively, which Boughey (1971) reported for his Dir male sample from northwestern Somalia and Puccioni (1931) reported for his Darod male sample from northeastern Somalia.

Craniometric relations between various global populations. The Afro-Asiatic-speaking groups of the Horn of Africa cluster with Egyptians from all periods, from the predynastic era through to the dynastic and modern epochs. This concurs with the theory that Punt, a brotherly civilization to ancient Egypt, was located in the Horn (Kemp (2006)).

Additionally, Kemp (2006) found that the ancient and modern Egyptians are craniometrically closest to other Afro-Asiatic speakers inhabiting Northeast Africa. They are also more distantly related to populations in the Near East, but share no significant affinities with the ancient and modern “Negroid” populations in Africa. Spradley (2006) compared the skulls of recent populations from northern Somalia and Egypt with those of various Subequatorial African groups and recently mixed African Diaspora populations, including African Americans (who are descended from Niger-Congo speakers, with ancillary European and Native American admixture). She similarly observed that the individuals from “Somalia and Egypt are closest to one another.” Likewise, Terrazas Mata and Benavente (2013) report that their Horn of Africa and Dynastic Egypt samples craniometrically cluster together, separately from their Niger-Congo, Nilo-Saharan and Khoisan-speaking samples. The scientists attribute this shared affinity between the Horn and Egyptian groups to common descent from ancestral Afro-Asiatic-speaking populations, whom they suggest ultimately arrived from the Middle East. In the same vein, Adel et al. (2021) note that:

Craniofacial features are considered one of the most unique features of populations with different ethnic backgrounds. The Egyptians present facial features close to those of Northeast Africans, Mediterranean Asians, and Europeans, all of them sharing Caucasian ancestry.

The biological ties between the Afro-Asiatic-speaking groups in Northeast Africa are, in fact, so well established that researchers have moved on to exploring which specific ancient “Hamitic” series in the region they share the most immediate affinities with (e.g. Batrawi (1946); Mukherjee (1955); Billy (1977); Billy (1981b); Rösing (1990)). G. Billy (1975) summarizes these findings thusly:

During the dynastic era, this last [Upper Egyptian] variety covered a wide central zone of the Nile valley, stretching well beyond towards East Africa, as shown by the similarity which persists with the present-day Ethiopian populations (Tigre) or even Somali. By virtue both of its diffusion and its perenniality, they deserve to be assimilated to the basic population type of the Egypto-Nubian complex.

Osteological relations between Galla, Somali and Tigre populations and other “Hamitic” series from early Northeast Africa as well as the ancient Near East. Batrawi (1946) notes that “the affinities of the Galla and Somali to the A-group, C-group and Meroitic populations of Lower Nubia : these are very close, and they may suggest the extension of the Predynastic Upper Egyptian type over a very wide area in north-east Africa. It cannot be said with any certainty, however, whether the people of that type existed over all that area since Predynastic times, or whether they were pushed from their earliest known home in Egypt southwards” (Batrawi (1946)).

Altogether, this highlights the close relatedness of the Puntites and ancient Egyptians, ancestral populations whose apparent descendants have remained biologically proximate.

In addition to the preceding, Egyptologists have noted a sporadic occurrence of blondism in the Land of Punt. This can serve as a helpful hint as to where the territory was situated, for blond individuals were relatively uncommon in the ancient world. The Hatshepsut expedition murals show the Egyptians being received by a chief of Punt, the aforementioned Parahu/Perahu, who Édouard Naville writes is depicted as “flaxen” or blond-haired.

A Deir el-Bahri temple mural depicting the Puntite chief Parahu (right) and his wife Ati, the latter of whom was afflicted with the Queen of Punt syndrome.

Illustration of the fabled Somali queen Araweelo. Note how the headbands on the female figures behind her resemble that worn by the Puntite ruler Ati.

A Somali woman wearing a traditional headband. Notice the similarity with the headband donned by the Puntite queen Ati.

An Oromo woman wearing a traditional headband. Observe again the similitude with the headband worn by the Puntite chieftess Ati.

Sculpture of the ancient Egyptian Princess Nofret (c. 2613-2498 BCE, 4th Dynasty, Old Kingdom). Like their Puntite relatives, ancient Egyptians were also known to wear traditional headbands (Egyptian National Museum).

Sweeney (2006) argues that this precludes both the Horn and Southern Arabia as prospective locations for the Land of Punt since there are few blond individuals today among the Afro-Asiatic-speaking populations in these areas. He asserts that the blondism points instead to an Indo-European source centered in the Near East; either the Indo-Iranian mariyanna elites of the Levant, or the Phoenicians (whom he suggests may have acquired such an element through intermarriage in western Europe). However, ancient blond individuals did, in fact, exist in the Nile Valley itself. Archaeologists working in burial sites associated with the Meroitic culture have unearthed a number of clearly blond specimens. Janssen (1978) reports that “330 graves were excavated in cemetery 221 (Meroitic) and a proportion of blond individuals of Caucasoid type found” (refer to Hrdy (1978) for additional examples). Given these finds, the minor incidence of blondism among the Puntites more likely reflects a Meroitic strain in this population than a direct Indo-European one (for empirical evidence of such an influence, see Batrawi diagram above). This, too, is in agreement with a Northeast African locus for Punt.

Mummy of the ancient Egyptian Pharaoh Hatshepsut. Like the Puntite chief Parahu, queen Hatshepsut had blondish hair.

Mummy of the ancient Egyptian noblewoman Takabuti, with her natural auburn hair visible (Ulster Museum). Archaeogenetic analysis indicates that this aristocrat belonged to the H4a1 mtDNA sublineage, which is “a predominantly European haplogroup” (Drosou et al. (2020)). The H maternal clade has also been observed at moderate frequencies among Afro-Asiatic speakers in Northeast Africa, supporting the view that this area was the Punt of old.

Exterior of the ancient Egyptian noblewoman Takabuti’s coffin (Ulster Museum).

Mummy of the ancient Egyptian aristocrat Yuya, great-grandfather of the 18th Dynasty Pharaoh Tutankhamun. Notice Yuya’s straight reddish-blond hair; elemental analysis has revealed that this was his natural hair color (cf. Hamed and Maher (2021)).

Mummy of the ancient Egyptian aristocrat Thuya, great-grandmother of the Pharaoh Tutankhamun. Note Thuya’s wavy blond hair.

(*N.B. Lazaridis et al. (2022) conducted a comprehensive analysis of phenotypic traits borne by ancient individuals exhumed in Europe and Asia, and report that blond hair was most common among their early European samples (viz. 62.5% in Early Medieval Germany, 42.9% in Pre-Christian Iceland, 40% among ancient Saxons of England, and 40% among the Motala hunter-gatherers of Sweden; cf. Supplementary Materials). By contrast, the scientists did not observe instances of blond hair in any of their examined ancient Levantine samples, except for a low frequency of 14.3% among specimens from Chalcolithic Israel — a situation clearly ascribable to foreign influx since no blond individuals have been found among both earlier Levantine samples from Mesolithic and Neolithic Israel and later Levantine samples from Middle-to-Late Bronze Age Israel. In brief, archaeogenetic analysis has confirmed that the blondism documented among the Meroites and ancient Egyptians is almost certainly affiliated with early European populations, as are the instances of red hair in the Nile Valley (refer to Ancient DNA from Sudan). For details on these ancient peoples, who introduced the Steppe genome component to Northeast Africa, see Genetic affinities of the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa.)

Genetics

Along with comparative morphology, genetic analysis provides much information on the likely location of ancient Punt. Examination of uniparental lineages, which include both Y-DNA (paternal) and mtDNA (maternal) haplogroups, has revealed strong ties between the Afro-Asiatic-speaking populations in the Horn and Nile Valley.

Phylogenetic tree of the E1b1b paternal haplogroup. Notice how the V32 subclade that is frequent in the Horn immediately descends from V12, the most common lineage today among southern Egyptians (Eupedia).

Trombetta et al. (2015) observed that around 74.5% of southern Egyptians are haplogroup E1b1b-V12* or E3b1a1 carriers (cf. Supplementary Table 7). According to Hirbo (2011), this clade is next most prevalent among Cushitic-speaking populations in East Africa (Garreh=74.1%, Gabra=58.6%, Borana Oromo=50%). E1b1b-V12 is also immediately ancestral to the V32 subhaplogroup that constitutes the main paternal lineage among ethnic Somalis from Somalia (80%) and Tigre individuals in Eritrea (60%) i.e., in the core ancient Puntite area. (*N.B. While the Tigre nowadays speak a Semitic tongue, their language contains a North Cushitic (Beja) substratum. This suggests that they were originally Cushitic speakers, who later adopted a Semitic language from South Arabian settlers in the Eritrean highlands. Accordingly, Hirbo (2011) reports that his sampled Beja individuals overwhelmingly belong to the E1b1b paternal haplogroup (100%). Hassan et al. (2008) further indicate that most of their Beja male samples, like the Tigre, fall under the clade’s V32 subhaplogroup.)

Antonio et al. (2019) identified E1b1b-V12 in two Imperial and Medieval Roman individuals, remarking that “this haplogroup is present at high frequency across present-day North Africa, especially in Egypt (up to 74.5%)” (cf. Supplementary Materials). Moreover, Sirak et al. (2021) observed a prevalence of the Y125054 subclade of V12 among Christian-era Nubian individuals from Kulubnarti in Sudan. These specimens also had considerable West Eurasian ancestry, which the scientists propose was likely derived from Egypt. Prendergast et al. (2018) further indicates that an ancient Cushitic individual (ca. 3350-3180 BP) excavated at Cole’s Burial, Kenya, a site associated with the Pastoral Neolithic cultural complex, bears the CTS3282 sublineage of V32. As of 2021, this is the earliest reported instance of E1b1b-V32 in the archaeogenetic record.

Similarly, mitochondrial analyses by Stefflova et al. (2011) and Boattini et al. (2013) found that the maternal haplogroups that are common among the Cushitic and Semitic-speaking Afro-Asiatic populations in the Horn are also frequent among the Afro-Asiatic speakers in Egypt. These shared clades include the M1 haplogroup, whose earliest occurrence has been detected among Epipaleolithic Iberomaurusian specimens excavated at Taforalt (Loosdrecht et al. (2018)) and early Neolithic individuals buried at Ifri n’Amr or Moussa (Fregel et al. (2018)), both located in Morocco. Loosdrecht et al. (2018) note that the M1 and U6 mtDNA lineages are “mostly confined to present-day populations in North and East Africa” and that “U6 and M1 have been proposed as markers for autochthonous Maghreb ancestry, which might have been originally introduced into this region by a back-to-Africa migration from West Asia.” Stevanovitch et al. (2004) also report that M1 is now particularly common in Egypt’s Gurna Oasis, suggesting an ancestral connection between the Gurna population and other Afro-Asiatic-speaking communities in the Horn of Africa.

Two “Hamitic” -type Nubian men (Bean (1935)).

As discussed on Ancient DNA from Ethiopia, the Afro-Asiatic-speaking populations in Northeast Africa also appear to share the same autosomal DNA (auDNA) signature. Hodgson et al. (2014) observed that ethnic Somalis, Afar, Amhara, Tigray and Oromos are defined by a West Eurasian-affiliated ancestral component, which they refer to as “Ethio-Somali”. Dobon et al. (2015) found that roughly the same ancestral element defines Egyptian Copts, Beja, Afro-Asiatic-speaking Ethiopians, Sudanese Arabs, and many Nubians (evidently, individuals descended from the Hamitic Kasu or “red” Nubians). By contrast, Hodgson et al. discovered that the Omotic-speaking Ari are defined by a separate, Nilo-Saharan-affiliated ancestral component, which the researchers call “Ethiopic”. Thus, the Ethio-Somali/Coptic and Ari components appear to correspond rather closely with the “red” (“Hamitic”) and “black” (“Negroid”) ancestral populations, respectively, that are depicted on the ancient temple walls and mentioned in the hieroglyphic inscriptions as having inhabited Punt. This is also confirmed by López et al. (2021), who compared the genomes of the Afro-Asiatic-speaking groups in Ethiopia with those of other global populations, both ancient and modern. The scientists identified a West Eurasian ancestral component among the local Afro-Asiatic speakers, which they suggest is Egypt-related and traces back to the inhabitants of the Land of Punt:

Ethiopians in the southwest, typically NS speakers plus a few non-NS speaking groups (Chabu, Dasanech, Karo), are more related to Bantu and Nilotic speakers relative to AA speakers in the northeast that instead show more ancestry related to Egyptians and West Eurasians (Fig 3, Fig S12). The inferred timing and sources of admixture related to Egypt/W.Eurasian-like sources, starting around 100-125 generations ago (~2800-3500 years ago; Fig 3, Fig S12) as in previous findings (Pickrell et al., 2014; Pagani et al., 2012), is consistent with significant contact and gene flow between the peoples of present day Ethiopia and northern Africa even before the rise of the kingdom of D’mt and interactions with the Saba kingdom of southern Yemen which traded extensively along the Red Sea (Currey, 2014; Phillipson, 2012). This timing is also consistent with trading ties between the greater Horn and Egypt dated back only to 1500 BCE, when a well-preserved wall relief from Queen Hateshepsut’s Deir el-Bahari temple shows ancient Egyptian seafarers heading back home from an expedition to what was known as the Land of Punt (SI Section 1A).

Coffins of the ancient Egyptian aristocrats Nakht-Ankh & Khnum-Nakht. The Two Brothers were found to belong to the M1a1 haplogroup, a signature maternal clade among Afro-Asiatic-speaking populations in Northeast Africa (Drosou et al. (2018)).

Ancient DNA analysis provides the most direct genetic evidence that the Land of Punt was located in Northeast Africa.

In 2013, a research unit led by Rabab Khairat of the University of Tübingen completed the first genetic study utilizing next-generation sequencing techniques to gauge the ancestral lineage of an ancient Egyptian. The scientists extracted DNA from the heads of five Egyptian mummies dating from the Late Dynastic to Ptolemaic periods (806 BCE–124 CE). They found that one of the mummified individuals belonged to the I2 mtDNA haplogroup. This discovery is especially interesting for a number of reasons. Firstly, the I maternal clade is closely associated with the spread of Indo-European speakers because the lineage has been detected among various ancient cultures on the European Steppe. This implies early migrations from this area into Northeast Africa; either directly from Europe or indirectly through Asia. Secondly, haplogroup I is today quite rare globally and exceeds 5% in few populations. The clade is by far most common among the Rendille and other Cushitic-speaking remnant groups inhabiting the Great Lakes region, where it has been observed at frequencies as high as 23% (cf. Castrì et al. (2008)). Thirdly, the basal or ancestral I* haplogroup has only been identified in three persons worldwide. Of these individuals, two are from Somalia and the other is from Iran (Olivieri (2013)). Lastly, I2 (formerly known as N1e) is a subclade of N1. Yatsishina et al. (2021) indicate that the haplogroup N is the most frequently occurring maternal lineage among the ancient Egyptian mummies they examined at the Kurchatov Institute (2 out of 3 specimens or ~67%). Similarly, Kılınç et al. (2016) report that N1 is the most commonly borne maternal haplogroup among the central Anatolian Neolithic individuals they studied (5 out of 9 or 55.56% of the examined specimens). This mitochondrial lineage is nowadays also rare but likewise peaks in frequency among Afro-Asiatic speakers in the Horn. (*N.B. The Rendille proper (who are known as asil or original Rendille) are distinct from the Ariaal (or assimilated Rendille). The Ariaal are instead people of Nilotic Samburu origin and “Negroid” appearance, most of whom still speak their native Nilo-Saharan language.)

A Rendille woman with the amrani/mariin phenotype (asil or original Rendille). Note the close resemblance with the ancient Puntite figures depicted on the Egyptian temples. mtDNA analysis has found that the Cushitic-speaking Rendille, who today inhabit the Great Lakes region, have among the highest global frequencies of the I haplogroup. This West Eurasian maternal lineage has also been observed among ancient Egyptian mummies. Since the Rendille are believed to have originated in Ethiopia, this finding aligns well with the hypothesis that ancient Punt was located in the Horn.

Closeup of the asil Rendille woman.

An assimilated Rendille woman of Nilotic origin (Ariaal group). The Ariaal are people of Samburu extraction and “Negroid” physiognomy, most of whom still speak their native Nilo-Saharan language. As such, the Ariaal do not descend from the ancient Puntites/Egyptians.

In 2018, a research unit led by Konstantina Drosou of the Manchester Institute of Biotechnology again used next-generation sequencing to examine the DNA of ancient Egyptian individuals. The samples were culled from a tomb at Deir Rifeh and were dated to the Middle Kingdom (1985 BCE–1773 BCE), making them the second oldest Egyptian specimens so far to be genetically analyzed. They comprised the mummies of Nakht-Ankh and Khnum-Nakht, a pair of 12th Dynasty aristocrat siblings, who shared a mother but had different fathers. The Two Brothers were found to belong to the M1a1 haplogroup. As mentioned above, this maternal lineage is today most common among the Afro-Asiatic-speaking populations inhabiting the Horn of Africa and Nile Valley. (*N.B. The oldest Egyptian specimen thus far analyzed, the 4000-year old mummy Djehutynakht, Overlord of the Hare (15th) nome of Upper Egypt, belongs to the U5b2b5 mtDNA haplogroup. This is an early European maternal lineage, which has been found among Early Bronze Age Sardinian individuals (cf. Olivieri et al. (2017); Marcus et al. (2020)). It is also borne today by Berbers in Egypt’s Siwa Oasis. Ergo, we see here again that the population affinities of the earliest Egyptians are not Semitic (in the modern sense), much less Nilo-Saharan/Niger-Congo/Khoisan (cf. Loreille et al. (2018)).)

Interestingly, Schuenemann et al. (2017) also observed both the M1 and I mitochondrial clades as well as the E1b1b-V22 paternal haplogroup in their analysis of later New Kingdom to Roman Period (c. 1388 BCE–426 CE) Egyptian samples from Abusir el-Meleq. The researchers, moreover, identified some J clade bearers. However, it is unlikely that older Egyptian individuals from the Early Dynastic (c. 3000 BCE–2650 BCE) and Predynastic (before 3000 BCE) epochs belong to this Y-DNA lineage. This is because, although haplogroup J arrived in Egypt from the Middle East, the earliest reported example of this clade in the Levant/Arabia is quite recent, being first attested there in a 3700 year old (c. 1680 BCE) Bronze Age specimen (Haber et al. (2017)). Furthermore, the nobleman Nakht-Ankh, who is the oldest Egyptian individual to have his Y-DNA successfully identified, appears to belong to the H2m clade (cf. HaploTree; Open Genomes). In the paleogenetic record, H2 is a patrilineage mainly affiliated with populations bearing Anatolian Neolithic ancestry; particularly Neolithic Europeans (e.g. Cassidy et al. (2020)). The H2 paternal clade has also been detected in an individual linked with the Pre-Pottery Neolithic B, a culture in the Levant dating from an era marked by the arrival of new settlers carrying Anatolian Neolithic ancestry (Lazaridis et al. (2016), Table S6.1). In addition, Gad et al. (2020a) affirm that the ancient Egyptian aristocrat Yuya, the maternal great-grandfather of the Pharaoh Tutankhamun, belongs to the G2a clade. Like the H lineage, the Y-DNA haplogroup G is primarily associated with early populations bearing Anatolian Neolithic ancestry.

(*N.B. Gad et al. (2020b) report that the 18th Dynasty Pharaoh Amenhotep III (b. 1411 BCE), his son Pharaoh Akhenaten, and grandson Pharaoh Tutankhamun carried the R1b haplogroup, a typical European paternal lineage (also see Gad et al. (2020a)). iGENEA specifies further that they belonged to the clade’s M269 subhaplogroup, which now accounts for over half of all Y-DNA lineages in western Europe. What’s more, according to DNA Consultants, the 20th Dynasty Pharaoh Ramesses III (b. 1217 BCE) and his son Prince Pentawere (“Unknown Man E”) bore the V22 sublineage of the E1b1b haplogroup. The V22 subhaplogroup is today most common among the Cushitic-speaking Saho population inhabiting Eritrea (cf. Trombetta et al. (2015), Supplementary Table 7). Ramesses III and Pentawere were initially thought to have belonged to the E1b1a clade, an error caused by an incomplete analysis of their Y-STR markers: Whit Athey’s Haplogroup Predictor, the tool that Hawass et al. (2012) indicate they used to determine the rulers’ paternal lineage, does not have an option for GATAH4, one of the markers that Ramesses III and Pentawere were originally analysed for; when GATAH4 and the other Y-STR markers are inputed into the Nevgen Haplogroup Predictor, these men are instead assigned to the E1b1b-V22 clade. Additionally, Yatsishina et al. (2021) examined ancient Egyptian mummies at the Kurchatov Institute, and found that the specimens likewise carried the E1b1b-V22 and R1b-M269 haplogroups (see Ancient DNA from Sudan for hair morphology analysis conducted on the Kurchatov Institute’s ancient Egyptian mummies). All in all, this suggests that ancient Egyptian individuals may have borne the common North African E1b1b lineage, as well as R1b and Anatolian Neolithic-associated haplogroups (e.g. the T, H and G clades) before the haplogroup J first entered the Egyptian gene pool. It is known that the J clade was introduced to the Semitic-speaking areas of the Levant and Arabia during the Bronze Age, by outsiders from the Caucasus/Iranian plateau who carried the Caucasus Hunter-Gatherer genome component. However, when exactly this western Asian admixture spread to the Egypt area is uncertain. Morez (2023) proposes that this introgression first occurred during the Second Intermediate Period (c. 1650-1550 BCE), an epoch marked by the Hyksos invasion of Egypt, since genomic analyses of an earlier, Old Kingdom Egyptian individual from Nuerat (dated to c. 2868-2492 BCE) did “show a strong genetic affinity of this sample to Levantine Natufians.” By contrast, “the Nuerat sample did not carry the Caucasus Hunter-Gatherer genetic component that started to spread across West Asia ~4000 years ago and is widely spread in present-day populations.”)

Ancient DNA analysis has revealed that the Egyptian Pharaoh Amenhotep III, his son Akhenaten, and grandson Tutankhamun bore the R1b haplogroup, the most common paternal clade among modern Europeans. Maternally, Pharaoh Tutankhamun belonged to the European Neolithic-associated K lineage, which he inherited from his mother “The Younger Lady”, his grandmother Queen Tiye (“The Elder Lady”), and his great-grandmother Thuya (Gad et al. (2020a)). The oldest examined Cushitic settler in East Africa was likewise found to belong to the K mtDNA haplogroup, in agreement with the idea that the Horn region was coextensive with the Land of Punt (Prendergast et al. (2018)).

Granite statue of the 18th Dynasty ancient Egyptian Pharaoh Amenhotep III (r. 1390-1353 BCE), excavated at Al-Qurnah, Egypt (Luxor Museum of Ancient Art). Autosomal STR analysis suggests that Amenhotep III and other members of the Amarna royal family carry a predominant non-African ancestry, with a close genetic affinity to populations in South Asia and Europe (LOP (2023)).

Mummy of the 20th Dynasty Egyptian Pharaoh Ramesses III. Ancient DNA analysis indicates that Ramesses III and his son Prince Pentawere (“Unknown Man E”) belonged to the E1b1b-V22 paternal lineage (cf. DNA Consultants; Nevgen Haplogroup Predictor). V22 is today most common among the Cushitic-speaking Saho population of Eritrea, who have an 88.3% frequency of the subhaplogroup according to Trombetta et al. (2015) (Supplementary Table 7). This fact further validates the theory that ancient Punt was situated in the Horn of Africa.

 

Additionally, Schuenemann et al. analyzed phenotype alleles carried by several of their ancient Egyptian samples. They reported that two of the individuals bore the derived allele of the SLC24A5 gene, a variant that is associated with lighter skin coloration (this mutation has also been found among ancient Cushitic pastoralists in East Africa; cf. Wang et al. (2020), Table S7). However, the specimens carried ancestral alleles at the Europe-specific SLC45A2 locus and other pigmentation-related genes. Altogether, this suggests that they had a light brown complexion. These findings are consistent with notarized contracts from the Pathyrite and Latopolite nomes. In these legally-binding documents, almost all of the ancient Egyptian signatories indicated that they had a “honey-coloured complexion”, with a “long face”, “straight hair” and a “straight nose” (Van Dorpe (2004)).

An excerpt of notarized contracts from the Pathyrite and Latopolite nomes, wherein almost all of the ancient Egyptian signatories indicated that they had a “honey-coloured complexion”, with a “long face”, “straight hair” and a “straight nose”. This is consistent with ancient DNA analysis, which has detected that the examined Egyptian specimens bore the derived allele of the SLC24A5 gene (Van Dorpe (2004)). This mutation is associated with lighter skin pigmentation, and has also been found among the early Cushitic settlers of East Africa (Wang et al. (2020), Table S7).

In 2020, Ester Oras of the University of Tartu and colleagues examined two ancient Egyptian child mummies, which likewise dated from the Late/Graeco-Roman Periods. They found that one of the individuals bore the HV haplogroup, an mtDNA lineage that nowadays occurs most frequently among Afro-Asiatic speakers; particularly Egyptians from El-Hayez oasis (Kujanova ́ et al. (2009)), Somalis from Somalia (Musilová et al. (2011)), and Asni, Bouhria, Figuig and Siwa Berbers (Coudray et al. (2009)).

Urban Christian et al. (2021) conducted a comprehensive archaeogenetic study of ancient Egyptian individuals. The samples were culled from six different archaeological sites across Egypt, a time transect spanning 4000 years of Egyptian civilization. According to the researchers, the analyzed specimens carried mtDNA lineages similar to those previously identified at Abusir. This, in turn, indicates that almost all of the examined ancient Egyptian individuals bore derivatives of the Eurasian M and N maternal lineages.

Distribution of the mtDNA macrohaplogroup L in Northeast Africa and the Arabian peninsula. Most of the Afro-Asiatic speakers in northern Somalia, Djibouti, Eritrea, Egypt, Yemen and Oman carry derivatives of the Eurasian M and N maternal lineages (60%-84%); the remaining individuals bear derivatives of the Africa-centered L macroclade (16%-40%). This accords well with the hypothesis that ancient Punt was located in the Red Sea area (Non (2010)).

Frequency map of the HV1 mtDNA haplogroup (Musilová et al. (2011)). Oras et al. (2020) observed the HV maternal lineage among ancient Egyptian individuals dating from the Graeco-Roman period. Among modern populations, Musilová et al. (2011) detected the HV1 subclade at highest frequencies in Somalia and Egypt, bolstering the view that the Land of Punt was situated in the Horn region.

Y-DNA and mtDNA haplogroups of ancient Egyptian mummies analysed at the Kurchatov Institute. One of the individuals belongs to E1b1b1a1b2a4b5a, a derivative of the V22 sublineage of E1b1b, a signature paternal clade among Afro-Asiatic-speaking populations; the other specimen carries the R1b1a1b or M269 subclade of R1b, which is the most common Y-DNA haplogroup today among Europeans. Maternally, 2 out of the 3 examined Egyptian individuals (~67%) bear the macrohaplogroup N (Yatsishina et al. (2021)). The N1 sublineage is relatively common among Afro-Asiatic speakers in the Horn of Africa, whereas the N5 subclade is today primarily restricted to the Indian peninsula.

Almarri et al. (2021) compared the DNA of ancient Egyptian individuals from the Pre-Ptolemaic era with that of the modern Afro-Asiatic-speaking populations in the Horn of Africa. Analysing single nucleotide variants (SNVs), the scientists found that their Pre-Ptolemaic Egyptian specimens provided the best-fitting model for the source of the West Eurasian ancestry borne by the Horn groups, whereas their ancient Levantine sample from Sidon appeared to have contributed most of the West Eurasian ancestry carried by the present-day Arabian and Levantine populations. These results represent a significant advancement over other genomic analyses (e.g. Razali et al. (2021)), which by contrast insisted on employing Levantine or Arabian samples as reference populations in lieu of ancient Egyptian samples. As a consequence, these studies substantially undercounted the Horn groups’ actual West Eurasian ancestry. Thanks to Almarri et al.’s better designed and more logical analysis, we can now estimate that ancient Egyptian-related ancestry is present at frequencies of around 70% among Cushitic and Ethiosemitic-speaking individuals of the Horn, with a percentage climax in Eritrea and likely northern Somalia (cf. Table S4). (*N.B. Sirak et al. (2021) analyzed Christian-period individuals buried at Kulubnarti in Sudan, and similarly observed that “we obtain a fit only when Egypt_published is used as the West Eurasian-related proxy.” Sirak et al. (2022) also note that “ancient DNA data suggest that the African gene flow observed in present-day Egyptians occurred predominantly within the last 2000 years.” Thus, whenever ancient Egyptian samples have been utilized as a reference population, they have proven to be the best-fitting surrogate for the West Eurasian ancestry borne by the Nubian and Afro-Asiatic-speaking groups in Northeast Africa.)

Reconstruction of an ancient Egyptian man (Parabon NanoLabs). Archaeogenetic analysis has unveiled that the modern Cushitic/Ethiosemitic-speaking populations in the Horn of Africa on average bear around 70% Eurasian ancestry, which was mostly derived from the Egypt area (Almarri et al. (2021), Table S4). This observation all but confirms that the Land of Punt was situated in the Horn, as the Puntites were close relatives of the ancient Egyptians.

Somali man with the cad phenotype. Such individuals represent the closest living approximation to the early Cushites.

Oromo leader Haji Adam Sado with the cad phenotype.

Sheikh Bishir Bey of the Ababda Beja, with another example of the cad physiognomy found among the Cushitic peoples.

Almarri et al. indicate:

Kitchen et al. (2009) suggested that Semitic languages would have spread into East Africa with little gene flow, as Ethiosemitic-speaking populations share similar proportions of non-African ancestry and are genetically similar to Cushitic-speaking populations, confirmed by more recent analysis (Pagani et al., 2015). They proposed that the current distribution of Ethiosemitic languages reflect a language diffusion process through African populations, rather than gene flow. Our admixture tests Tables S3 and S4 also suggest an ancient Egyptian source of ancestry in East Africa, rather than from Arabia, although ancient DNA from Arabia is still missing to make a comparable analysis.

Estimated average non-African ancestry proportions among modern Afro-Asiatic-speaking populations of the Horn of Africa and Cushitic-admixed Nilo-Saharan-speaking populations of the Great Lakes region (Almarri et al. (2021), Table S4). Almarri et al. observed that ancient Egyptian individuals from the Pre-Ptolemaic era were the closest source of the West Eurasian ancestry borne by the Horn’s Afro-Asiatic speakers. The scientists estimate that such Pre-Ptolemaic ancestry peaks at around 70.1% among their Eritrean sample. This strongly supports the hypothesis that Punt was located in the Horn of Africa. (*N.B. Almarri et al.’s Eritrean sample comprises randomly selected individuals from Eritrea. Their Somali samples consist of the Simons Genome Diversity Project’s Kenya cohort. As of 2021, no genome-wide study has yet to analyse a sample of individuals from northern Somalia (Puntland and Somaliland regions). This is significant because northern Somalia, alongside Eritrea, is the other main prospective location of the Land of Punt and thus likely another frequency peak area for ancient Egyptian-related ancestry.)

Estimated average non-African ancestry proportions among modern Afro-Asiatic-speaking populations of the Horn of Africa (Hodgson et al. (2014), Supplementary Text S1). Hodgson et al. inferred that the Horn’s Afro-Asiatic speakers bear a predominant non-African ancestry of near 70%, with the Egypt area being the proximal source of most of that heritage. Almarri et al. (2021)’s paleogenetic study, using Pre-Ptolemaic Egyptian samples, has now confirmed that prescient analysis. (*N.B. Hodgson et al.’s Somali sample was borrowed from Pagani et al. (2012), who analysed individuals originating from the Mogadishu area in south-central Somalia. This South-Central Somali sample is distinguished by higher non-African ancestry (~66%) than Almarri et al.’s Kenyan Somali cohort (~51.8%-54.3%). A cline of ancient Egyptian-related ancestry therefore seems to exist, with such ancestry appearing to decrease the further one gets from the Puntite nucleus in northern Somalia and Eritrea.)

Genetic distance analysis on the Vahaduo Admixture JS program, comparing modern Cushitic, Ethiosemitic and North-Omotic-speaking individuals with ancient non-African specimens. The Cushitic/Ethiosemitic/North Omotic speakers’ West Eurasian ancestry is most similar to that of the ancient Egyptian samples. This is in agreement with uniparental marker (Trombetta et al. (2015), Suppplementary Table 7; Boattini et al. (2013)) and craniometric analyses (Batrawi (1941); Rösing (1990); Brace (1993); Spradley (2006); Terrazas Mata and Benavente (2013)), which have shown close ties between the Afro-Asiatic speakers in the Horn and Nile Valley.

Genome analysis on the Vahaduo Admixture JS program indicates that the contemporary Cushitic/Ethiosemitic/North Omotic speakers of the Horn carry a predominant non-African ancestry, which, on average, comprises over 70% of their ancestral makeup. This non-African ancestry can be further broken down into majority West Eurasian elements (ancient Egyptian, European-related Steppe, and Levantine Natufian components) and a minority East Eurasian element (ancient East Asian component). Additionally, these Afro-Asiatic-speaking individuals bear some low-to-moderate Sub-Saharan African admixture (~27%), as well as a very minor North African Iberomaurusian admixture (under 3%).

In summary, genetics strongly relates both the modern and ancient Egyptians with contemporary Afro-Asiatic-speaking groups elsewhere in Northeast Africa. This perfectly concords with Puntite origins for the latter populations. (*N.B. For detailed analysis, see Genetic affinities of the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa.)

Traces of ancient civilization

Stone ruins, inscriptions and coins

One of the principal challenges in locating the Land of Punt has been the absence of artifacts that could be definitively identified with an ancient Puntite civilization. Perhaps the closest thing to that were two v-shaped arm-clamps made of ivory, which were found in an Old Kingdom tomb at Shellal in Upper Egypt. Some writers initially proposed that the person buried within the grave may have been a Puntite envoy. However, the Egyptologist David O’Connor later demonstrated that the man was, in fact, an Upper Nubian emissary since an Upper Nubian figure is shown wearing a very similar armlet on the causeway of Pharaoh Sahure’s mortuary temple in Abusir (cf. Wilkinson (2002)).

Aside from this false positive, various early scholars and colonial officials discovered traces of an ancient civilization in the Horn; one apparently distinct from and older than the Axumite Kingdom. The explorer Georges Révoil encountered many stone ruins while in northern Somalia, as well as inscriptions in a mysterious writing script.

On this lost orthography, the Ministry of Information indicates that:

An important point which is often lost sight of is that the ancient Somalis had evolved their own script systems which existed for a considerable period in their history. Convincing historical evidence in this respect is the numerous inscriptions and rockpaintings on cave-walls, on granite rocks, old coins etc., that are found to this day in various parts of the country.[…]

An interesting point, however, is that this script system was apparently based on vowel sound, not a Word-Picture writing as in ancient Egypt.

The foregoing rules out the known Sabaean and Himyarite writing systems since they and other ancient Semitic scripts, except Ge’ez, have no vowels (for details on Sabaean finds in northern Somalia, see Prioletta et al. (2021)). Likewise, it seemingly disqualifies the Libyco-Berber orthography, for it too is an abjad (examples of this ancient script, known as Tifinagh, have recently been found in Somalia). The above also precludes Meroitic hieroglyphs because they were derived from ancient Egyptian hieroglyphics. However, Meroitic cursive remains a possibility; especially since, as an abugida, it has inherent vowel representation. In this regard, the scholar Muhammad Shamsaddin Megalommatis (2021) notes that “even today both [the Afar and Somali] languages retain ample Ancient Cushitic vocabulary that was written in Meroitic hieroglyphic and cursive writing before 2000 years. The Somali word ‘boqor’ (king) is identical to the title of the Cushitic kings of Meroe: ‘Qore’.”

(*N.B. Another plausible candidate is Linear A, the undeciphered second script used by the ancient Minoans of Crete (the other two writing systems being Cretan Hieroglyphs and Linear B). Several of the characters etched on the cave walls and granite rocks in northern Somalia, where most of the examples of the old Somali orthography have been found, can clearly be identified with Linear A symbols. Among these are the cross-filled circle or encircled cross (represented as the ka syllabogram in Linear A, such as on the Tablet ARKH 3a discovered at Arkhanes), the three open circles (similar to Linear A characters carved into Tablet HT 31, found at Haghia Triada), as well as various signs which Ester Salgarella of St. John’s College — who created the SigLA online database for Linear A — refers to as being “more like Chinese ideograms.”)

Ancient inscriptions discovered by Georges Révoil at El-Osbolé in northeastern Somalia. The “TH” initials on the upper-right were apparently left by the explorer Theodor von Heuglin during an earlier visit (Révoil (1882)).

Some other sites in northern Somalia where examples of the ancient Somali writing script have been found (MOI).

A stone block from the Berbera excavation (discussed below), featuring inscriptions in an unknown orthography. This is likely another instance of the ancient Somali writing script. The inscriptions have been tentatively dated to 2000 years ago, making them contemporaneous with the old “Berber” city-states described in the Periplus (Kluijver (2018)).

Sabaean script on an ancient tablet, retrieved from a site on the northern Somali coast. The inscriptions have been dated to the 7th-8th centuries BCE, in line with the known mercantile contacts between the local “Berber” emporiums of the Horn region and their counterparts in the Arabian peninsula (Prioletta et al. (2021)).

Stones engraved with symbols in the ancient Himyarite script. These petroglyph incriptions were discovered in coastal south-central Somalia.

Tablet found at Haghia Triada, Crete, inscribed with symbols in Linear A. This undeciphered orthography was used by the Minoans, a people whom the ancient Egyptians depicted as resembling themselves and the Puntites. The script appears to match rather closely with the old writing system of northern Somalia. Note in particular the tablet’s three open circles and Chinese-like ideograms, which are akin to the symbols Georges Révoil discovered (see El-Osbolé signs above) (University of Melbourne).

Cave painting at the Dhawaale site in northwestern Somalia featuring a cross-in-circle design (also known as the cross-filled circle or encircled cross). This symbol appears on the Haghia Triada tablet, where it represents the Linear A script’s ka syllabogram. The cross-filled circle is also found at various other locales in Northeast Africa.

Other examples of cross-filled circle symbols (#4-6), which have been observed on rock art at Harurona in Ethiopia and Abka in Sudan, as well as on material objects belonging to the C-Group culture. This symbol also still features prominently in Egyptian Coptic magic (Bachechi (2005)).

During excavations of one of the tumuli at Salweyn (Salwine), Révoil found ceramic fragments of apparent Macedonian origin. These objects and other recovered items, which include Ptolemaic and Roman era artifacts, are presently kept at the Musée de l’Homme in Paris (cf. Desanges (1992)). Révoil was also able to discern a definite ancient Egyptian and Classical influence in the local culture and populace, notably in terms of physiognomy, customary law, attire, weaponry and vocabulary. These findings inspired him to declare that Auguste Mariette was indeed right, and that he had in fact stumbled upon the Punt of antiquity. The Geographical Society of Marseilles explains:

Being detained by bad weather near Hais, in a small creek named the Salwine, M. Revoil landed to get ballast, and found on the banks of the creek a great number of tumuli, similar in every respect to those which he had met with in all parts of the country, and had photographed in the course of his expedition. For the first time, and not without danger, he succeeded in partially excavating one of these tumuli, and brought to light a tomb and close alongside some remains denoting the former existence of a very advanced civilisation, including some superb enamels, fragments of pottery from Samos, and a mask, indicative of a Greek colony. Taking the observations of Dr. J. C. Prichard, who described a type, in connection with the information he obtained himself in regard to the existence of a white Galla race living farther south on the borders of Webi, M. Revoil put forward the suggestion that the present Somali race bears the marks of the existence of a white colony, very probably Macedonian, and that this colony, according to the traces he met with in the interior, has been preserved almost intact in this white tribe of Gallas. M. Revoil found besides in their idiom, arms, and dress, strong arguments in support of his opinion, which he further corroborated by an important series of profile photographs.

The scientist Johannes Maria Hildebrandt would likewise remark that:

We know from ancient authors that these districts, at present so desert, were formerly populous and civilised. I also discovered ancient ruins and rock-inscriptions both in pictures and characters. These have hitherto not been deciphered.

Over the ensuing years, Ernest-Théodore Hamy, George Andrew Reisner, Grafton Elliot Smith and many other prominent Egyptologists would echo these sentiments on similar grounds, insisting that Punt was to be found in the Horn.

A cairn with standing stones at Salweyn in northern Somalia (BIEA).

Another large cairn at Salweyn, again flanked by standing stones. This particular funerary structure is rectangular (BIEA).

In a remarkable coincidence, the Alexandrian merchant Cosmas Indicopleustes records a Greek inscription, which he had seen on a stela in Adulis, Eritrea. The basalt slab was apparently erected there by the Egyptian king Ptolemy III Euergetes (246-221 BCE) to commemorate his conquest of various kingdoms in the Near East. Phillips (1997) suggests that this signifies that Adulis itself and environs were at the time under the control of Ptolemaic Egypt:

The location of the stela observed by Kosmas, at Adulis, suggests the king had ordered it to be erected somewhere around there, possibly in gratitude for providing the means to conquer (he boasts) virtually all of  Western Asia; it could hardly have been brought there by chance. This suggests, in turn, that Adulis (or the nearby place where it originally was erected) and by extension the area immediately inland, was sufficiently controlled by Egypt that its king could erect a self-laudatory stela there.

During the early 1920s, C. W. Hayward also uncovered a hoard of old coins at Port Dunford, a site in southern Somalia that is thought to correspond with the Periplus’ ancient market-town of Nikon. H. Mattingly later published these numismatic finds in 1932. Among the pieces were 22 Ptolemaic mints (c. 3rd-1st century BCE), 6 of Imperial Rome, 46 of Byzantium (primarily 4th century CE), 6 of Mamluk Egypt, and 7 of Ottoman Egypt.

An amphora excavated from a grave at Ras Hafun in northeastern Somalia. This site corresponds with the ancient “Berber” emporium of Opone (BIEA).

A Roman glass flagon retrieved from Tomb 120 at Heis (Xiis) in northwestern Somalia. This site corresponds with the ancient “Berber” emporium of Mundus (González-Ruibal et al. (2022)).

A predynastic grave from Abydos, Egypt, dating from the Naqada I or Amratian period (c. 4000-3500 BCE). The entombed ancient Egyptian individual rests near a vase, which is similar to containers found within old “Berber” burials in the Horn of Africa.

A predynastic grave from the Naqada site in Upper Egypt, dating from the Naqada II or Gerzean period (c. 3500-3300 BCE). The ancient Egyptian individual buried within the tomb is surrounded by grave goods, which are akin to the amphorae, flagons, bowls and vases exhumed from old “Berber” sites in the Horn.

A grave dating from the Naqada III period (c. 3300-3000 BCE), the last phase of predynastic Egypt. The ancient Egyptian individual buried within the tomb, an adult woman, is again flanked by containers and pots — grave goods like those recovered from old “Berber” burials in the Horn region.

In 1975, the archaeologist Neville Chittick more fully explored some of the visible ancient structures at Ras Hafun (the Periplus’ Opone) and other areas in northeastern Somalia. He described a number of heretofore obscure ruins, including stone platform monuments near Alula and sherds of unglazed Roman pottery at Damo (the Market and Cape of Spices described in the Periplus). No actual Puntite material objects, though, had yet been excavated, and most of the Egyptian imports that had been discovered were of Ptolemaic age or younger. Consequently, supporters of a Levantine or Arabian location for Punt would often cite this archaeological void as a primary reason why the ancient territory could not have been situated in the Horn. As Sweeney (2006) concluded (somewhat prematurely), “nor was there in Eritrea or Somalia, in the time of Hatshepsut or Thutmose III, any civilization or culture of the type portrayed at Deir el Bahri that the Egyptians could have traded with[…] this topic [is] of fundamental importance to the whole debate”.

Puntite artifacts

Stone bust excavated in a valley in northwestern Somalia. Depicts a Puntite king in royal nemes headdress, wearing the divine Puntite/Osiris beard, and wielding the sacred crook and flail (Ibrahim (2013)).

Bust of the Pharaoh Tutankhamun excavated in Egypt. The king is in regal nemes headdress, wearing the divine Puntite/Osiris beard, and wielding the sacred crook and flail (Tour Egypt).

In 2013, the scholar Ahmed Ibrahim Awale led excavations at Gol Waraabe, a site in Hargeisa valley in northwestern Somalia, where his archaeological team unearthed what appear to be the first actual artifacts belonging to the Land of Punt. As discussed in greater detail on The Mystery of the Land of Punt Unravelled – book review, the recovered objects include stone statuettes and bowls of considerable antiquity. The human figurines, in particular, bear an uncanny resemblance to those produced in ancient Egypt and by other early Afro-Asiatic-speaking populations in the Sudan area. These commonalities range from similar headdress styles, oval face shape, keen facial features and Puntite beard (Osiris beard), to analogous cobra and vulture headdress emblems, and crook and flail symbolism. Ibrahim describes the busts’ likeness thusly:

our Puntite personages tell a different and more reliable story[…] The oval face, thin lips, aquiline nose and the slender feature are all typically Somali.[…]

Of the many convincing features to be seen in our Puntite artifacts, I want to present the below figurine (fig. 6) which carries two symbols of authority among ancient Egyptians. The crook (heka) and the flail or flabellum (nekhaka), are two of the most prominent items in the royal regalia of ancient Egypt.[…] Now let us compare it with the next picture (fig. 7) which stands for King Tutankhamun. Both figurines display the two sticks. Again both of them carry on their heads the cobra snake and the vulture as a symbol of the deities Wadjet and Nekhbet. The royal cobra (uraeus) was worn by the pharaohs over their brows. It was thought to spit fire at the pharaoh’s enemies. Another great similarity of the two figurines is the divine osird beard which in death, the kings were frequently portrayed wearing it.[…]

Another common similarity between the Puntites and Egyptians is the headgear which is clearly seen in the below Puntite statuette found in Hargeisa. Again the cobra snake and vulture are mounted on their forehead while the osird beard is attached to the chin.

Statuette of what appears to be a Puntite queen, shown donning the royal cap-crown.

Bust of the ancient Egyptian Queen Nefertiti, which depicts her wearing the cap-crown (Egyptian Museum Berlin).

Most of the statuettes that were dug up appear to depict male personages. However, at least one is manifestly that of a woman. The bust in question (shown above) has the same standard “Caucasoid” features and oval face shape, but her head is more narrow and her nasal bridge and visage are exaggerated in length. This figure is also wearing a headpiece that looks very similar to the cap-crown donned by the Egyptian female Pharaoh Nefertiti (r. 1370–1330 BCE), which suggests that she may represent a Puntite queen. Other conspicuous similarities between the excavated Puntite statuettes and ancient Egyptian figurines include the practice of artificial cranial deformation (which was evident on certain other busts), and worship of deities from the Egyptian pantheon, like Sobek.

Another of the excavated Puntite busts. Note the “Caucasoid” features and hyper-leptoproscopic (very long and narrow) face.

Northern Somali man with a very similar countenance as the excavated Punt statuettes. This is consistent with ancestral descent from the “Hamitic” Puntites of yore.

An anthropomorphic ancient Puntite statue excavated at Gol Waraabe, northwestern Somalia. The sculpture depicts a male wearing what appears to be the hedjet or White Crown of Upper Egypt.

Ancient Egyptian statue of a man wearing the hedjet. The sculpture, whose nose broke off, was found at the Western Gate/Door of the Pharaoh Shoshenq III (r. 837-798 BCE, 21st Dynasty), located in Tanis, Nile Delta, Lower Egypt.

Illustration of Oromo/Galla men, with one figure wearing a traditional cone-shaped hat. Note the close resemblance between this headdress, the conical headdress of the excavated Puntite statue, and the hedjet of ancient Egypt.

Although Ibrahim did not manage to date the artifacts, particular headdress styles present on several of the figurines give us a rough idea of when they were likely made. For starters, one of the sculptures, an anthropomorphic statue of a male, is wearing what appears to be the hedjet or White Crown of Upper Egypt. This headdress predates the unification of Upper and Lower Egypt by the Pharaoh Narmer (Menes), the last king of the predynastic period and founder of ancient Egypt’s First Dynasty. Several of the male statuettes are also donning the nemes, a headcloth topped on the brow by the cobra (uraeus) and vulture (nekhbet) emblems. The nemes was the most commonly depicted royal headdress in ancient Egyptian art from the Old Kingdom onwards (cf. Russman (1997)). Ergo, these Puntite busts seem to have been hewn either during the predynastic epoch or in the Early Dynastic period, though later manufacture cannot be definitively ruled out.

Aerial view of three of the Puntite statues excavated at Gol Waraabe. The bust in the center is the same one as shown above from the front (BBC).

In 2018, Robert Kluijver, curator of the Museum of Contemporary Ancient Arabia, announced the discovery of a second batch of ancient statues in northwestern Somalia. Kluijver apparently procured the artifacts from a private seller, who had come across the objects while digging on his farm near Berbera. The excavated materials include realistic busts of a white hue, which appear to have been made of limestone; abstract figures of a reddish color, possibly crafted from sandstone; and blocks of stone containing inscriptions. According to Kluijver and specialists who he showed the objects to, the Berbera statues (like those previously found in Hargeisa valley) do not correspond with any of the known styles in ancient Yemeni art, nor do they resemble the figurines produced by the Axumites. He estimates that the artifacts are 2000 years old. This would make them contemporaneous with the ancient “Berber” city-states described in the Periplus of the Erythraean Sea, including the northwestern port of Malao. The latter market-town was located in the vicinity of present-day Berbera.

Among the recovered artifacts, the limestone busts feature most of the artistic elements first seen in the Gol Waraabe statues: stoic figures with long faces, orthognathous profiles and narrow, moderately projecting noses. At least one of the statues also appears to have had the Osiris or Puntite beard attached, though this Pharaonic appendage has since broken off. Kluijver postulates that this figure may therefore represent a prince. With regard to the inscriptions, they are in an unknown script. Kluijver speculates that the writing may be an early form of Arabic or Phoenician. However, it is more probable that these engravings are yet another instance of the mysterious ancient Somali orthography, which Révoil and others encountered in northern Somalia.

(*N.B. J. H. Patterson (1907) reported the finding of similar Egyptian-related antiquities in Mombasa, a coastal town in Kenya, which, before the arrival of Bantus/Nilotes from the interior, was part of the realm of the Cushitic Azanians (see Who were the ancient Azanians?): “The town of Mombasa[…] is supposed to have been founded about A.D. 1000, but the discovery of ancient Egyptian idols, and of coins of the early Persian and Chinese dynasties, goes to show that it must at different ages have been settled by people of the very earliest civilisations.”)

One of the realistic limestone sculptures from the second batch of ancient Puntite statues, excavated near Berbera in northwestern Somalia. The figure has the same phlegmatic expression, long face and “Caucasoid” features as the Gol Waraabe statues. He is also wearing an ornate headdress, which possibly indicates that he is royalty.

Closeup of the princely limestone bust from the Berbera excavation. Notice the kohl-like eyeliner and the chin stub, left after the Puntite/Osiris beard broke off.

Another of the realistic Berbera limestone statues. The figure is almost identical to the Sobek bust that was found at Gol Waraabe, pointing to a recurring artistic theme. Also note again the cobra emblem (uraeus) that is wedged in the personage’s headdress.

One of the sandstone sculptures excavated near Berbera. Although abstract in design, we can nonetheless faintly make out the Pharaonic symbols of the crook and flail, Osiris beard, and what may be the royal nemes headcloth.

Another of the abstract sandstone sculptures exhumed from the Berbera vicinity. This statue displays the same elements as the aforementioned sandstone figure, except for the crook and flail. The scales on the nemes headdress are also more deeply incised.

Stone bust of an 18th Dynasty ancient Egyptian woman, recovered from a site near Tombos. The stylistic resemblance to the limestone Puntite statues is striking, particularly the long face, narrow features and contouring of the eyes/eyebrows with kohl.

Legacy

A Galla woman (Sergi (1901)).

Considering the importance of the Land of Punt within the ancient Egyptian ethnocultural complex, the territory left behind a substantial legacy. Quite understandably, it has figured prominently in most anthropological and linguistic reconstructions that attempt to better understand the ancestral relations between the Afro-Asiatic-speaking populations in Northeast Africa. This scholarly tradition is exemplified in the work of Flinders Petrie, leader of the Archaeological Survey of Egypt. The pioneering Egyptologist maintained that the dynastic Egyptians may have originated from an ancient “Hamitic” population centered in the Horn:

The Gala are the remnant of an ancient Hamitic people who appear to have come from North-east Africa, now Somaliland, the region which is most probably to be identified with the land of Punt. It seems, also, that from the same stock which produced the Gala came the dynastic Egyptians, as I have suggested (ANCIENT EGYPT, 1926, p. 10). This is attested, among other things, by the proofs of the Gala origin of the XIIth dynasty (ANCIENT EGYPT, 1924, pp. 38-42).

In addition, Punt has been commemorated in state insignia, literature and philately. The government of Somalia accordingly indicates in its official documentation that:

Somalia was called «Land of Punt» by the Pharaohs, who believed it to be the land of the gods they then used to worship[…]

Ethnically, the Somali people belongs to the Hamitic group, which is further subdivided into:

a) the so-called «Northern Hamites», i.e. the inhabitants of North Africa, namely Libya, Tunisia, Algeria and Morocco;

b) the so-called «Eastern Hamites», i.e. the inhabitants of Somalia and Egypt.

Egyptian stamp commemorating Pharaoh Hatshepsut’s expedition to Punt during the New Kingdom (Tour Egypt).

Along with the Egyptian government, the colonial authorities in Italian Somaliland also issued stamps in honor of Pharaoh Hatshepsut’s expedition to Punt during the New Kingdom. In 1998, an autonomous region in northeastern Somalia, Puntland, was likewise named after the territory.

Perhaps the most salient legacy of Punt is the impact that the ancient land has had on the Eritrean national consciousness. It has sometimes been hypothesized that the seeds of the independence movement in Eritrea date back to the medieval kingdom of Medri Bahri, which was a distinct polity from the Solomonid dynasty based in northern Ethiopia. However, textual evidence suggests that these roots actually trace their origin much earlier, to the Puntite era. Because the king Zoscales held sway over Adulis in Eritrea, which in later centuries became the main port of the Axumite kingdom, certain scholars have conflated him with one Za-Haqale, a ruler of Axum. This association is unlikely, though. As George W. B. Huntingford remarks, the Abyssinian king list where Za-Haqale appears was composed retroactively, during the Middle Ages, and is generally apocryphal (e.g. several of the kings on the list are said to have reigned for over a hundred years, which biologically-speaking is doubtful). Moreover, as already seen, the Periplus only indicates that Zoscales was a paramount chief in Barbaria; not in Axum per se. It also differentiates between Adulis and “the city of the people called Auxumites.” The former was a three-days’ journey from the interior town of Coloe (present-day Qohaito), whereas the latter was a five-days’ journey from there. Epiphanius of Constantia further bears witness to this when he explicitly distinguishes between the Adulites and Axumites. Lionel Casson writes:

There is a third possibility — that Zôskalês was king not of Axum but of an independent realm centered on Adulis and embracing the coastal areas to the north and south. In a paper presented at the Colloque de Strasbourg, 24-27 juin 1987: L’Arabie préislamique, G. Fiaccadori, on the basis of the later history of Adulis and its environs, argued that the area previously must have been independent; it follows that Zôskalês would have been its ruler at the time the Periplus was written. Epiphanius of Constantia (4th century A.D.), in a list of peoples living along the African shore of the Red Sea in the third century A.D., includes Azomitorum cum (A)dulitibus, “the Axumites along with the Adulitans” (Corpus Scriptorum Ecclesiasticorum Latinorum 35, p. 478; cf. Desanges 346); this would indicate not only that Axum and Adulis were separate but that they long remained so.

That Adulis (Aduliton) was, at its inception, not yet under Axumite control is additionally confirmed by Pliny the Elder. The Roman scholar avers that the city was founded by ancient Egyptian deserters, who had moved southwards and established a new settlement thereabouts:

Five days journey from Ptolemais is Aduliton, a city built by the Egyptian deserters.

A Tigre girl from Eritrea (At-Temariam clan). The Tigre today inhabit the Adulis vicinity, one of the Periplus’ “far-side” ports of the “other Barbaria” in the Horn region.

A Bisharin Beja girl. Although Tigre individuals now speak a Semitic tongue, their language contains a North Cushitic substratum. This suggests that they originally spoke a Beja language (Bedawi) like the neighboring Beni Amer Beja in Eritrea and the Bisharin Beja further north in the Nile Valley.

Zoscales thus governed from a seat at Adulis, which, like the rest of Barbaria, was originally independent from Axum. Correspondingly, the dominant paternal haplogroup among the Tigre, who are the present-day inhabitants of the Adulis vicinity, is the same Egyptian-affiliated E1b1b-V32 clade that is common elsewhere in the former Berber/Puntite area. In fact, due to their Cushitic origins, most Ethiosemitic speakers (especially those inhabiting Eritrea) belong to the E1b1b paternal haplogroup: Tigre (up to 100%), Tigray-Tigrinya (up to 72%), Amhara (45%) (cf. Trombetta et al. (2015), Supplementary Table 7). The Semitic-mediated J lineage is instead more frequent toward the southern interior in Ethiopia, where it climaxes among North Omotic-speaking populations: Shekecho (52%), Kefa (38%), Yem (32%) (Plaster (2011)). This clade reaches its next highest prevalence in Ethiopia’s erstwhile Axum region, in agreement with a Sabaean origin for the separate Axumite empire. Having said that, there is evidence that at least some Pharaonic cultural elements did penetrate the latter kingdom; likely via Adulis or Meroë. The 18th century explorer James Bruce reported having witnessed stelae in Axum that were engraved with figures of the ancient Egyptian deity Horus (cf. van de Walle (1953)). Although these stone slabs unfortunately no longer exist, the revelation that they once did serves to further highlight the bonds between the Afro-Asiatic-speaking populations in the Horn and Nile Valley.

A predynastic Egyptian ivory carving excavated at Hierakonpolis, Upper Egypt. The figure’s long face, high-domed skull, narrow eye slits and moderately projecting nose closely resemble the Puntite statues (Petrie (1901)).

An ancient Libyan man depicted on an Egyptian stone engraving. Flinders Petrie states that the “precise resemblance” of the predynastic Egyptian and ancient Libyan figures “is beyond question,” which indicates a common origin for these “allied tribes of a European character” (Petrie (1901). (*N.B. This affinity has been confirmed by ancient DNA analysis. Muslim Egyptians share a similar genome profile as modern Libyans (direct descendants of the ancient Libyans) and Afro-Asiatic speakers from the Horn. These populations also bear some European Steppe-derived ancestry — see Genetic affinities of the Cushitic, Ethiosemitic and North Omotic-speaking populations of the Horn of Africa.)

Another ancient Libyan figure, displaying again what Oric Bates calls the Libyans’ original “brun Hamitic type” (i.e., a swarthy Caucasoid physiognomy, like the Minoans). Later Egyptian representations of Libyan figures instead appear pale white, often with blond or red hair and blue eyes. This signals the arrival in the Nile Valley of haplogroup R1b-V88 carriers from Europe, where the oldest example of this paternal lineage has been found (Bates (1914)).

Closeup of an ancient Cushitic figure dating from the 12th Dynasty. The man closely resembles both the predynastic Egyptian and brun-type ancient Libyan figures (Seligman (1913)).

Engraving of a Philistine man from the temple of Medinet Habu, Egypt (c. 11950-1164 BCE), bearing a close resemblance to the ancient Libyan, Cushitic and Egyptian figures. The Philistines were among the Sea Peoples, who settled in the eastern Mediterranean. Ancient DNA analysis has revealed that the Philistines were of European origin, sharing affinities with the early Cretans. The ancient Israelites (mortal enemies of the Philistines), the modern Palestinians and other Semitic peoples were instead found to derive most of their ancestry from the Levant (Feldman et al. (2019)).

A 4th century CE Kingdom of Axum bust excavated in Ethiopia. The figure’s greatly projecting nose and large eyes are leitmotifs in Axumite art, reflecting the Sabaean origins of Axum’s founders. These Sabaeans settled amongst Cushitic-speaking Agaws (ancestors of the Abyssinians) and introduced to them Semitic languages (Artkhade).

Bronze statue of the Himyarite king Dhamar Ali Yahbur II (c. 179-180 CE). The ruler’s sharp, “Mediterranean” features are akin to those of the predynastic Egyptian, Cushitic, ancient Libyan and Philistine figures. Compared to the Sabaeans, this suggests that the Himyarites retained more Pre-Pottery Neolithic ancestry, which was substantially Anatolian Neolithic (i.e. Mediterranean or Sardinian-like) in affinities. (*N.B. According to Baynes (1878), “in the 5th century the Himyarites, in the south of Arabia, were styled by Syrian writers Cushaeans and Ethiopians.” The polytheistic Himyarites would eventually convert to Judaism (c. 380 CE), two centuries after Yahbur II’s reign.)

Stone engraving of an ancient Hittite man and his modern Armenian equivalent. Note the resemblance with the Axumite figure above. This suggests that the Axumites’ Sabaean forebears received marked Caucasus Hunter-Gatherer/Iran Neolithic gene flow, superimposed on their earlier Pre-Pottery Neolithic ancestry.

A slate carving dating from the Early Dynastic period, excavated in Upper Egypt. Petrie indicates that the figure most closely resembles those of a deity and worshipper found at Ibriz in West Asia. The personage’s curly hair is also quite similar to some portrayals of ancient Semitic figures, which altogether suggests that he represents a foreign people. According to Petrie, this physiognomy is characterized by “close curly hair, a plaited hanging beard, thick straight nose rounded at the end, rather thick lips, and receding chin”, and is “extremely different” from the predynastic Egyptian type (Petrie (1901)).

A Libyan-Negro figure from a stone engraving found at Hierakonpolis. Petrie asserts that the personage represents a crossing of ancient Libyan with Negro, as evidenced in particular by the somewhat kinky hair and prognathous visage. This stands in stark contrast to the ancient Libyan, Cushitic and Egyptian figures from the same monuments. The Libyan-Negro figure thus likely comprises an early Fulbe type (Petrie (1901)).

Early terracotta bust of the Nok culture (c. 500 BCE-200 CE), bearing the distinctive “Negroid” features of the Niger-Congo/Nilo-Saharan peoples. The statue’s broad and flat nose, everted lips and prognathism are markedly unlike the “Caucasoid” countenances of the sculptures made by the ancient Egyptians, Puntites and other Afro-Asiatic-speaking populations. This points to different ancestral origins for the Nok culture bearers.

Ancient Benin Bronze masks (c. 13th century CE-17th century CE), retaining the “Negroid” features of their Nok predecessors.

Ancient terracotta sculpture of a woman from the Ife culture of West Africa (c. 6th century CE) and her modern Hausa equivalent. The Hausa and other Chadic-speaking populations inhabiting the Sahel in the past assimilated some Afro-Asiatic speakers, from whom they also adopted their present Chadic languages. Consequently, many Chadic speakers today carry the R1b haplogroup — a paternal clade whose earliest occurence in Africa has been observed among ancient Egyptian specimens (cf. Yatsishina et al. (2021)) — while their maternal DNA and autosomal DNA has largely remained the same as that of Niger-Congo/Nilo-Saharan-speaking populations. This Afro-Asiatic-related gene flow is also reflected in the physiognomy of the contemporary Chadic speakers (as represented by the ancient Ife statues), who tend to have less strongly accentuated Negroid features than their “purer” Niger-Congo/Nilo-Saharan-speaking congeners (as represented by the ancient Nok and Benin statues).

The way forward

In conclusion, a holistic examination of the data on Punt emphatically locates it in Northeast Africa. That is, the hieroglyphic, botanical, craniometric, genetic, cultural and geological evidence indicates that the territory was situated in a broad region encompassing northern Somalia, Djibouti, the Eritrea/Ethiopia corridor and northeastern Sudan, with the ancient Egyptians visiting or writing about different parts of this expansive area at different times.

The famous 18th Dynasty Egyptian expedition to Punt organized by the Pharaoh Hatshepsut clearly alighted on the incense-bearing hills of Alula (Acannae) in northeastern Somalia, as this is the only place where the higher grade of frankincense known as ‘ntiyw (Boswellia frereana) grows on “terrace” land formations near the seashore (i.e., these are the “frankincense terraces of Punt” alluded to on the edifices at Deir el-Bahri). Likewise, Pliny the Elder informs us that the Pharaoh Sesostris I (Senusret I) ordered an expedition to the port of Mossylum; we know from the Periplus of the Erythraean Sea that this cinnamon emporium was located in the present-day Bosaso area in northeastern Somalia. Moreover, the Puntite tributaries shown on the Grand Procession at Thebes likely arrived from Eritrea or Ethiopia since, other than Nubia, these are the only locales today where Egyptian-related peoples (viz. Cushitic/Ethiosemitic speakers) and Nilotes like those depicted on the mural can still be found living in close proximity to each other. Eritrea is also the most probable location of Bia-Punt (“Mine(s) of Punt”), the gold-mining district(s) of Punt, for it is the lone territory in Northeast Africa and the Arabian peninsula whose entire geological formation consists of old metamorphic (Precambrian) rocks, which are associated with gold-yielding areas. Additionally, a 26th Dynasty stela recovered at Dafnah, close to the Egyptian Delta, states that “when rain falls on the mountain of Punt, the Nile floods” — a clear allusion to the northern Ethiopian highlands, near the source of the Blue Nile at Lake Tana.

Archaeological excavations at Ras Hafun, northeastern Somalia. This site corresponds with the Periplus’ ancient emporium of Opone (Opun), which is thought to be the etymological source of the earlier toponym “Punt” (BIEA).

Archaeological excavations in Adulis, Eritrea. According to Pliny the Elder, Adulis was founded by ancient Egyptian deserters. The city would later fall under Axumite control, obscuring its Puntite origins.

With the above established, archaeological excavations on a larger scale must hereafter be conducted in order to begin to understand ancient Punt’s history. Who, for instance, are the kings and queens that appear to be represented on the Puntite statuettes, which were exhumed at Gol Waraabe and near Berbera? For how long did these nobles reign and under what circumstances? What was their royal order of succession and was it hereditary? Was Adulis their original seat? Or were they alternately, at different times, domiciled in Alula and other cities within the greater Barbaria?

Ransom (1978) indicates that Pharaoh Hatshepsut drew inspiration from a monument that her expedition had observed while in Punt, and used that shrine as a basis for her own temple at Deir el-Bahri:

When Hatshepsut returned, she built a temple patterned after the one she had seen in Punt. She even referred to the construction as building a “Punt”; and the reliefs on one wall were devoted to describing the trips to Punt. The temple was called “The Most Splendid of Splendors” and the remains are still located at Deir el-Bahari near Thebes. Many comments have been made concerning the apparent fact that the architecture does not fit the standard traditional Egyptian style.

According to Trigger et al. (1983), Hatshepsut’s party constructed another temple during their two or three month sojourn in Punt itself, and dedicated that shrine to the queen and the deity Amun. All this considered, more extensive digging in the Puntite area may eventually also yield the remains of monuments that are similar, if not identical, to those that were erected in ancient Egypt.

Ancient DNA from Ethiopia

Tags

A-Group, Afro-Asiatic, Ala111Thr, ancient DNA, Ancient Egypt, Badarian, biogeographical analysis, Brenda Stoessiger, C-Group, Capsian, Carleton Coon, Cushitic, Daniel Stiles, EDAR, Ethiopia, G. P. Rightmire, Hamitic, Harold C. Fleming, Iberomaurusian, Indus Valley, Kiffian, lactose tolerance, Linearbandkeramik, Mediterranean, Meroe, Mota, Nella Puccioni, Omotic, Out-of-Africa, Pastoral Neolithic, Richard Leakey, Robert Gayre, Samuel George Morton, Savanna Pastoral Neolithic, Semitic

Scientists often regard Ethiopia as the cradle of humanity. In the 1960s, an archaeological expedition under Richard Leakey discovered skeletal remains at the Omo-Kibish sites near the Omo river. Since these fossils show some modern features and have been tentatively dated to almost 200,000 years before present, many paleontologists argue that they represent the earliest anatomically modern humans (Homo sapiens sapiens) found so far. Other scholars dispute this association, remarking that the skulls also possess archaic characteristics; particularly the Omo II specimen, which has retained the robusticity of earlier, non-modern hominids.

Various evolutionary theories on the origins and dispersal of modern humans (Groucutt et al. (2015)).

The “Out-of-Africa” (OOA) or “Recent African Origin” (RAO) theory emerged as one of several competing hypotheses seeking to explain the prehistoric peopling of the world. Although initially born out of a hoax, complete with false dating, the OOA model gained popularity in the 1990s with the development of the human paternal (Y-DNA) and maternal (mtDNA/mitochondrial DNA) phylogenetic trees. Researchers observed that the deepest or oldest uniparental lineages on the respective trees, paternal haplogroup A and maternal haplogroup L0, are mainly restricted to small Khoisan groups inhabiting Southern Africa. They also found that most populations outside of Africa carry younger maternal lineages that were prehistorically derived from the L3 macroclade (“Eurasian Eve”). Although widely diffused both within and outside of Africa, this haplogroup today has its greatest diversity in Ethiopia. Consequently, L3 is assumed to have been in the area for at least several millenia i.e. long enough to have evolved various sublineages, and thus likely to have originated in the region. Ethiopia is therefore often considered the most probable starting point of the suggested Out-of-Africa colonization.

For these and other reasons, ancient DNA from human fossils in the area holds the potential to greatly improve our understanding of global prehistory.

Mota

In 2015, a genetic research team led by M. Gallego Llorente and E. R. Jones managed to successfully extract ancient DNA from a human skeleton found in Mota Cave, located in the Gamo highlands of southwestern Ethiopia. The Mota remains belonged to a middle-aged male hunter-gatherer, and were radiocarbon dated to around 4,500 years before present:

Low contamination rates were observed, confirming the authenticity of the extracted DNA. Further examination of the fossil’s Y-DNA and mtDNA assigned him to the paternal haplogroup E1b1 and the maternal haplogroup L3x2a, respectively:

To more closely gauge Mota’s population affinities, the scientists also ran a principal component analysis comparing his DNA against that of various contemporary Ethiopian populations from different ethnolinguistic groups. The specimen was most similar to the South Omotic-speaking Ari and the Khoisan-speaking Sandawe populations:

The close association between Mota and the modern Ari was also supported by f3 statistical analysis, which showed that they formed a clade unto themselves.

In order to ascertain whether Mota harbored any West Eurasian ancestry like modern Ethiopian populations, the researchers ran an admixture analysis using the Yoruba and Druze as the African and West Eurasian reference samples, respectively, against which Mota’s DNA and that of other contemporary populations was compared. The results suggested that Mota lacked any West Eurasian ancestry. This was also supported by the fact that the specimen did not carry the derived SLC24A5 (Ala111Thr/rs1426654) allele linked with lighter skin pigmentation, nor any lactase persistence variants, nor apparently any Neanderthal-associated alleles.

So what can be concluded from this ancient DNA analysis? Are the findings significant, or is Mota simply an early Ari individual and little beyond that?

The results are quite illuminating in that they suggest, among other things, that:

• Mota’s nearest contemporary relatives are the Ari.
• A biological division exists between speakers of the South Omotic languages and other local Afro-Asiatic-speaking populations (including North Omotic speakers).
• Mota co-existed in the region with physically and genetically distinct early Cushitic populations. Hodgson et al. (2014)’s inferred “Ethio-Somali” (ancestral Afro-Asiatic) and “Ethiopic” (ancestral Ari) components are therefore real.
• There also appears to be as yet unidentified East Eurasian ancestry in the Horn, and likely elsewhere in Northeast Africa.
• Using ancient DNA samples as reference groups in lieu of modern samples can potentially uncover hitherto obscured population affinities.
• The prehistoric Out-of-Africa colonization, if any, probably did not emanate from Ethiopia.

Limitations of biogeographical analysis

Before proceeding further, let us briefly note some of the principal limitations of biogeographical analysis, such as that around which the Mota study is centered. BGA/admixture testing is at its core speculative, for it is based on probability. That is, such analysis estimates where or in which geographical area given stretches of DNA known as SNPs likely originated according to which reference populations today carry those SNPs at highest frequencies. This is problematic for a number of reasons, some quite obvious:

• BGA testing is entirely dependent on the quality of the modern reference populations that the SNPs are compared against. For example, if a modern reference population with multiple ancestries is included in the analysis (like, say, the Maasai, who are Nilotes with some Cushitic influence), the SNPs could theoretically be most closely associated with any of that mixed reference population’s various ancestries (in this case, they could be associated with either the early Nilotes or the early Cushites).
• Where a reference population resides today is not necessarily where it resided in the past.
• Just because a reference population today has the highest frequencies of a particular SNP does not necessarily mean it always did. For one thing, many ancient populations have died off (early Cushitic populations in particular) or gone through population bottlenecks, and they easily could have had higher frequencies of that SNP than any modern reference population.
• Just because a reference population today has the highest frequencies of a particular SNP does not necessarily mean that that SNP actually originated with that proxy group. This SNP could have been passed on to that reference population’s ancestors by interbreeding with an unrelated, now extinct population. Through linguistics and haplogroup analysis, we know for a fact that such contacts happened many times in the past and over a wide area between now extinct Cushitic groups and early Nilotic and Bantu populations.
• Certain modern populations have high frequencies of private alleles, which are genetic variants that are only found today in that population. These are quite common among contemporary Afro-Asiatic-speaking groups in Northeast Africa, who have among the most private alleles on the continent. In other words, many SNPs for these individuals cannot be matched to any modern reference population. They are therefore not factored into the biogeographical analysis, which in turn gives a misleading estimate as to where most of these individuals’ overall SNPs truly cluster.
• Ancient reference populations, though certainly preferable to modern proxy groups, are also subject to many of these same caveats; particularly if they have not been carefully selected. An example of this is shown below, where it is demonstrated that neither the Mota specimen nor the Neolithic LBK sample used in the Mota analysis are representative of the ancestral Afro-Asiatic speakers in the Horn. More appropriate ancient proxy groups are instead suggested (under final observations and recommendations).

Besides the points above, perhaps the biggest limitation of biogeographical analysis is the fact that it can only at best capture a small fraction of an individual’s total ancestry i.e. that contained within the genetic tree, not that within the exponentially larger genealogical tree. The Genetic Genealogist explains:

In reality, everyone has two family trees.  The first is a Genealogical Tree, which is every ancestor in history that had a child who had a child who had a child that ultimately led to you.  Every decision made by every person in that tree contributed to who and what you are today.

However, not every person in that tree contributed a segment of your DNA sequence (because of random inheritance, as discussed above).  As a result, we have a second family tree – a Genetic Tree – which is a tree that contains only those ancestors who contributed to our DNA.  No one has yet been able to construct their Genetic Tree, but soon it will be a reality thanks to advances in genetic sequencing and comparison such Relative Finder.  These tools are using relatedness between people living today to deduce the inheritance of DNA from people who have been dead for centuries.[…]

The Genealogical Family Tree contains ALL of your biological ancestors[…] The Genetic Family Tree contains a small subset of your biological ancestors[…] Due to the nature of the Genealogical versus the Genetic Family Tree, entire populations, ancestors, and ethnicities are regularly lost entirely from your DNA! [They] therefore would not be detected by a DNA test.

Uniparental markers and Out-of-Africa

The Mota specimen’s paternal haplogroup E1b1 is today relatively rare, and is mainly restricted to a few Afro-Asiatic speakers in Ethiopia and environs. It has been found amongst 18% of Ethiopian Jews, 11%-12.8% of Oromos, 11% of Iraqw, 6%-10.4% of Amhara, 10% of Ethiosemitic speakers generally, and in 18.2% of Ethiopians as a whole. Given the clade’s close association with Afro-Asiatic-speaking populations in Ethiopia, it appears that Mota’s ancestors obtained the E1b1 haplogroup through contact with early Afro-Asiatic male settlers in the area.

Mota’s L3x2a maternal lineage points to a similar, if more ambiguous, affiliation. It too is today mainly concentrated among some Afro-Asiatic speakers in East Africa, and is also present in Egypt and among Yemeni Jews. How exactly Mota’s hunter-gatherer culture acquired the haplogroup is uncertain, for Babalini et al. (2002) found a comparably-aged L3 carrier in their ancient DNA study of early human specimens from the Fezzan in Libya (dated to around 3,000-1,500 BCE). Fernández et al. (2014) likewise identified an even older L3-bearing individual in their examination of skeletal remains from Pre-Pottery Neolithic B (PPNB) sites in the Near East. Dated to between 8,700-6,600 BCE, the PPNB specimen predates Mota and the Fezzan individual by over four thousand years. This highlights the early global distribution of the L3 haplogroup, if not an ultimately Middle Eastern origin for the clade, as Farrell et al. (2013) propose:

Here we present the first high-coverage whole genome sequences from a Middle Eastern population consisting of 14 Eastern Province Saudi Arabians. Genomes from this region are of interest to further answer questions regarding “Out-of-Africa” human migration. Applying a pairwise sequentially Markovian coalescent model (PSMC), we inferred the history of population sizes between 10,000 years and 1,000,000 years before present (YBP) for the Saudi genomes and an additional 11 high-coverage whole genome sequences from Africa, Asia and Europe.

The model estimated the initial separation from Africans at approximately 110,000 YBP. This intermediate population then underwent a long period of decreasing population size culminating in a bottleneck 50,000 YBP followed by an expansion into Asia and Europe. The split and subsequent bottleneck were thus two distinct events separated by a long intermediate period of genetic drift in the Middle East. The two most frequent mitochondria haplogroups (30% each) were the Middle Eastern U7a and the African L. The presence of the L haplogroup common in Africa was unexpected given the clustering of the Saudis with Europeans in the phylogenetic tree and suggests some recent African admixture. To examine this further, we performed formal tests for a history of admixture and found no evidence of African admixture in the Saudi after the split. Taken together, these analyses suggest that the L3 haplogroup found in the Saudi were present before the bottleneck 50,000 YBP. Given the TMRCA estimates for the L3 haplogroup of approximately 70,000 YBP and the timing of the Out-of-Africa split, these analyses suggest that L3 haplogroup arose in the Middle East with a subsequent back migration and expansion into Africa over the Horn-of-Africa during the lower sea levels found during the glacial period bottleneck.

These results are consistent with the hypothesis that modern humans populated the Middle East before a split 110,000 YBP, underwent genetic drift for 60,000 years before expanding to Asia and Europe as well as back-migration into Africa. Examination of genetic variants discovered by Saudi whole genome sequencing in ancestral African populations and European/Asian populations will contribute to the understanding human migration patterns and the origin of genetic variation in modern humans.

Thus, the prehistoric “Out-of-Africa” colonization, assuming one occurred at all, does not appear to have emanated from the Horn. The finding that the L3 haplogroup likely originated in and spread from the Middle East points instead to some other center of evolution. (*N.B. For the latest evidence on the suggested non-African origin of the mtDNA macrohaplogroup L3, see Cabrera (2022) and Cabrera et al. (2017).)

North Omotic vs. South Omotic

Kawo Tona, the last King of the Wolayta. Prior to assimilating Mota-related foragers, most Omotic speakers had a Cushitic physiognomy like that of this late ruler. Nowadays, this phenotype is mainly confined to North Omotic speakers.

The Omotic branch of Afro-Asiatic is divided into two subgroups: North (also known as Nomotic) and South (or Somotic). South Omotic consists of the Ari, Dime, Hamar, Gayil and Karo languages. Of these South Omotic idioms, the first three are sometimes collectively known as “Aroid”.

Anthropologists and linguists working in the Ethiopian region have long observed a marked physical and linguistic cleavage between, on the one hand, the speakers of the Aroid Omotic languages, and on the other, the non-Aroid Afro-Asiatic-speaking populations. Harold C. Fleming, who coined the term “Omotic” and helped establish the validity of the phylum as an independent branch of the Afro-Asiatic family, remarks that the Ari are generally “Negroid” in physiognomy, in contrast to the “Ethiopid” northern Cushitic and Ethiosemitic groups:

The Ari peoples have been described extensively by scholars of the Frobenius tradition, especially A. Jensen, Eike Haberland, and others, as well as observed and described more informally by various anthropologists (e.g., Herbert Lewis, Jean Lydall, Ivo Strecker, myself) and Ethiopian government officials. One of our colleagues, Ayyalew Mitiku, is an Amhara who grew up among the Ari and speaks their language fluently. Among all these observers there is a consensus that the Ari and many of the Banna and Hamar represent a variety of African Negro, rather than an Ethiopid or “Afro-Mediterranean” variety. However, the Ari variety of Negro is distinctive and is not very much like the neighbouring Nilotic or Surmic peoples to the west and south; nor particularly like the Bantu of East Africa. Some resemblance is noted to the Koman of the Ethiopia-Sudan border areas and some Sudanese populations. Above all this aspect of the Ari, while it has earned them the label of “blacks” or “Shanqillas”, strikes many of us as being the appearance of a distinctive kind of African, a population that has evolved on its own to a considerable extent.

Due to the Ari’s aberrant morphology and the divergent nature of the Aroid languages themselves, Fleming further indicates that Ari and the other Aroid languages were regarded by earlier scholars as non-Afro-Asiatic idioms possessing Nilo-Saharan affinities:

The three main branches of my Somotic, viz, Dime, Hamar and the Ari cluster are what [Lionel Bender] calls Aroid; they are so different from the rest of Omotic that older German and Italian scholars thought of them as ‘Negroid’ or Nilotic or the like. It was a struggle to get them accepted as a branch of Omotic or West Cushitic. All you have to do is work on a Dizoid (Maji, Na’o, Shako) language and then on Dime or Galila (Ari), as I did, to see that they are very different in phonology and morphology. Yes, there has been some borrowing across the Omo river. Dime informants will tell you that “Maji” used to rule them; the borrowings are not massive, however. Dizoid and ‘Aroid’ simply do not belong in the same moiety in opposition to the rest of Omotic.

Correspondingly, in the ethnological literature, the traditional explanation for the Ari’s differing physiognomy and culture as well as the divergent nature of their South Omotic language is that they are descendants of Nilo-Saharan-speaking peoples (the Pre-Nilotes), who settled in the parts of Ethiopia bordering South Sudan around 4,000 years ago. These Pre-Nilote groups are then thought to have interbred with early Omotic populations from the Sahara and gradually adopted the latter’s Afro-Asiatic languages, thereby giving rise to the Ari and related groups. Per the Centre National de la Recherche Scientifique:

Negroid people from the Sudan, speaking languages ancestral to those classified as the four branches of the Nilo-Saharan family settled in West and South West Ethiopia about the third millenium B.C. (Pre-Nilotes). They became ancestors of peoples living on the western border and intermixed with Omotic speakers to form the Ari, Basketo, Dimi and Gimira-Maji groups of tribes. The languages spoken in Ethiopia in the third millennium B.C. are derived from a single stock (Hamito-Semitic or Afro-Asiatic) originating in the Eastern Sahara.

Shinasha young women (North Omotic speakers). DNA analysis of Shinasha, Shekkacho, Wolayta and other North Omotic-speaking individuals has revealed that they are closely related to other Afro-Asiatic speakers in Northeast Africa. The anthropologist/linguist Harold C. Fleming, who coined the term “Omotic”, could already deduce this from their physical resemblance to their Cushitic and Ethiosemitic-speaking neighbors. This affinity suggests that the Shinasha and other North Omotic speakers directly descend from the original Omotic settlers of the Horn (Gopalan et al. (2019); López et al. (2021)).

An Ari woman (South Omotic speaker). In contrast to the North Omotic-speaking groups, the Ari and other South Omotic-speaking individuals are both phenotypically and genetically distinct from other local Afro-Asiatic speakers. The South Omotic speakers are instead similar to Niger-Congo and Nilo-Saharan-speaking populations inhabiting the Great Lakes region. This suggests that the Ari and other South Omotic speakers are language shifters i.e., their forager ancestors originally spoke non-Afro-Asiatic tongues (Gopalan et al. (2019); Boattini et al. (2013)).

Dermatoglyphic affinities of Afro-Asiatic and Nilo-Saharan-speaking populations in Ethiopia. Fingerprint patterns, which are genetically inherited, indicate that the North Omotic-speaking Shinasha share ties with the other sampled Afro-Asiatic-speaking individuals (Cushitic-speaking Oromo and Ethiosemitic-speaking Amhara and Tigray) rather than with the Nilo-Saharan-speaking individuals (Berta). This again suggests that the Shinasha and other North Omotic speakers directly descend from the original Omotic settlers of the Horn (Yohannes and Bekele (2015)).

Genomic analysis of various populations in Africa and Europe. The North Omotic-speaking Shekkacho sample has a similar level of West Eurasian ancestries (Afro-Asiatic & Iberian-related components) as the other Afro-Asiatic-speaking populations and Nubian groups in Northeast Africa. Although bearing some Mota-related admixture like the Ethiosemitic-speaking samples (Amhara & Tigray), the Shekkacho primarily belong to the Afro-Asiatic ancestral component, which peaks among Cushitic-speaking Somalis. This element is analogous to Hodgson et al. (2014)‘s “Ethio-Somali”, an inferred ancestral component that the scientists demonstrated via a battery of tests to be essentially West Eurasian. The foregoing supports the view that the earliest Omotic settlers in the Horn region were, like the ancient Cushitic pastoralists in the Great Lakes area, transplants from North Africa. As also observed by López et al. (2021), the North Omotic-speaking Shekkacho, Shinasha and Wolayta thus represent pockets of Omotic speakers who retained much of their original Afro-Asiatic ancestry, whereas this ancestry was largely diluted in South Omotic-speaking areas through intermixture with and assimilation of local hunter-gatherers. Since Omotic is regarded by most linguists as the first diverging branch of the Afro-Asiatic language family, this analysis holds implications for the population affinities of the Proto-Afro-Asiatic speakers (Gopalan et al. 2019)).

Genetic differentiation

Besides morphology and language, the postulation that the Pre-Nilote forebears of the Ari (who are presumably represented by the Mota specimen) were of a different ancestral stock than the progenitors of the Afro-Asiatic-speaking Ethiopian groups is strongly supported by genetic studies on these contemporary populations.

For starters, researchers have observed a high frequency of the derived SLC24A5 allele (Ala111Thr or rs1426654) among various Cushitic- and Semitic-speaking Afro-Asiatic populations in Ethiopia. This mutation is closely associated with lighter skin pigmentation, and is believed to have originated in or near West Asia. Almost 60% of Ethiopian Jews and ethnic Somalis from Somalia carry the variant. Tekola-Ayele et al. (2015) found a similarly high percentage of the allele among the North Omotic-speaking Wolayta. By contrast, only 12% or so of the South Omotic-speaking Ari ironworkers possess the Ala111Thr polymorphism. Since the Mota specimen does not harbor the mutation, this suggests that the ancestors of the Afro-Asiatic-speaking groups in the Horn were responsible for having introduced the allele into the Ari gene pool. This, in turn, implies that these early Afro-Asiatic settlers were of a lighter complexion than the Ari’s Mota-like forebears.

Lactase persistence (LP) frequencies among various Afro-Asiatic-speaking Ethiopian populations and adjacent groups (Jones et al. (2015)).

Further evidence that the Mota specimen was clearly not ancestral to the local Afro-Asiatic-speaking populations can be seen through comparative lactase persistence (LP) analysis. While Llorente et al. observed that Mota does not carry any lactose tolerance alleles, such LP mutations are found at high frequencies among the region’s main pastoral groups. To this end, Jones et al. (2015) note that over 60% of Beja, Afar and Borana Oromos are lactase persistent, carrying several different LP variants. In their large study of lactose tolerance in eastern Africa, Tishkoff et al. (2007) likewise find widespread lactase persistence among not only the Afro-Asiatic-speaking populations, but also among certain Nilo-Saharan and Niger-Congo pastoralist groups (like the Datog Nilotes) that are known to have absorbed some early Southern Cushites in the Great Lakes region.

Various analyses showing negligible-to-low autosomal DNA affinities between the Ari and adjacent Afro-Asiatic-speaking populations (Vandorp et al. (2015)).

Most tellingly, the Afro-Asiatic-speaking populations in the Horn appear to have generally different autosomal DNA (auDNA) signatures than the Ari. Hodgson et al. (2014) observed that ethnic Somalis, Afar, Amhara, Tigray and Oromos are defined by a West Eurasian-affiliated ancestral component, which they refer to as “Ethio-Somali”. On the other hand, the Ari are defined by a separate, Nilo-Saharan-affiliated ancestral component, which the researchers call “Ethiopic”. The Wolayta, despite possessing comparatively greater Mota-like admixture, were again found to be closer overall to the Cushitic- and Semitic-speaking populations than to the Ari. Dobon et al. (2015) further confirmed the existence of a defining West Eurasian ancestral element among the Afro-Asiatic speakers in Northeast Africa. Vandorp et al. (2015), in turn, reaffirmed the lack of close ties between the Afro-Asiatic-speaking populations and the neighboring Ari.

Ethnolinguistic distribution of maternal lineages in the Horn, Nile Valley, Sahara, Maghreb, Great Lakes and the Arabian peninsula (Boattini et al. (2013)).

Similarly, Boattini et al. (2013) observed that the mtDNA of the South Omotic-speaking Dawro-Konta and Hamer in southern Ethiopia, who are closely related to the Ari, is tied to that of Nilotic and Bantu populations in the Great Lakes region as well as the Ongota (who are believed to have once spoken a Nilo-Saharan language). On the other hand, the maternal lineages of the Cushitic- and Ethiosemitic-speaking groups of the Horn cluster instead with those of other Afro-Asiatic-speaking populations in the Nile Valley, Yemen and Sahara.

Altogether, this is consistent with the aforementioned tradition that the Ari’s “Shanqilla” ancestors (i.e. Mota) were originally Nilo-Saharan speakers, who at some point in antiquity adopted an Omotic language from early Afro-Asiatic-speaking settlers.

Afro-Asiatic ancestral population

In their study of the Mota remains, Llorente et al. note that contemporary Ethiopian populations (specifically, the Afro-Asiatic speakers) have substantial West Eurasian affinities that the Mota specimen does not appear to possess. They therefore conclude that that ancestry likely arrived after Mota’s lifetime, and originated from a Sardinian-like population most similar to the early Neolithic farmers who settled Europe (according to f3 statistical analysis).

In lieu of modern reference populations, the researchers ran an admixture test using the Mota specimen and a Neolithic Linear Pottery culture or Linearbandkeramik/LBK sample (represented by the Stuttgart specimen) as the baseline African and West Eurasian samples, respectively, against which the DNA of the Ari and that of the neighboring Afro-Asiatic-speaking populations was compared. This alone constitutes something of a breakthrough in biogeographical analysis, where disparate, admixed modern groups are instead frequently used as stand-ins for ancient populations (e.g. Yoruba and Utah denizens versus early Africans and West Eurasians). Nonetheless, there remain several problems with utilizing these particular Mota and Linearbandkeramik samples as the ancient proxy groups. Perhaps the most conspicuous issue is that, despite their antiquity, neither the Mota fossil nor the makers of the Neolithic LBK industry are representative of the ancestral Afro-Asiatic speakers in the Horn. We already examined above why that is vis-a-vis the Ari and their apparently Nilo-Saharan-speaking Mota progenitors, so let us now turn to the Linearbandkeramik agriculturalists.

While the LBK farmers may very well have prehistorically contributed some genes to the populations in Northeast Africa (and/or elsewhere on the continent), they do not appear to have been responsible for the majority of the West Eurasian affinities that are found today in the Horn. There are a number of reasons why we can be confident of this. Firstly, although the mtDNA haplogroup N1a, which is quite common today among the Afro-Asiatic-speaking populations in the Horn, is found at high frequencies among Neolithic LBK samples from Central Europe, the particular 7,000 year old Stuttgart sample from Germany that Llorente et al. utilized in their own analysis belongs to the T2 clade (cf. Lazaridis et al. (2013)). This latter maternal haplogroup is, by comparison, relatively rare in Northeast Africa. Unfortunately, since the Stuttgart sample is that of a woman and females do not inherit a Y chromosome, it is unclear whether the situation is the same with regard to the paternal side of things. Haak et al. (2010) did, however, successfully type three Neolithic LBK males for their Y-DNA. These individuals were assigned to haplogroups G2a3 and F*, both of which are also uncommon in Northeast Africa.

Another clue that the Linearbandkeramik agriculturalists are not the main source of the West Eurasian ancestry in the Horn is the fact that local rock art, such as at Laas Geel in northern Somalia, clearly depicts both herders and their domesticated cattle prior to the ~3,000 year old date that Llorente et al. propose as the arrival period of the LBK people. Those cave paintings also have stylistic precedents in the Arabian Peninsula (as explained further here, under ecology, rock art and genetics). Moreover, the Stuttgart woman, like the Mota man, was apparently unable to digest lactose. Lazaridis et al. remark that she lacks any alleles associated with lactase persistence. This in itself is not especially unusual for members of non-herding populations (whether farmers or hunter-gatherers) since they often do not drink cow milk and thus their bodies have no need to continue producing the lactase enzyme passed the breast-feeding infant age. Nevertheless, the finding is at odds with the aforediscussed high frequency of lactose tolerance among the pastoralist Afro-Asiatic-speaking groups and also contrary to the great diversity of the LP alleles present in the region.

The ~3,500 year old Cairn 4 burial excavated by Daniel Stiles, containing the 190 cm/6’4″ skeleton of an early Cushitic male settler (Stiles and Munro-Hay (1981)).

Aside from differing genetic markers and pastoral rock art, archaeology provides the most obvious indication that a West Eurasian-affiliated population — one likely distinct from the LBK farmers — co-existed in the region at around the same period as the Mota man and his kinfolk. In the 1980s, at various oases on the eastern margin of the Chalbi desert, the anthropologist and archaeologist Daniel Stiles excavated a number of cairns belonging to the Cushitic-associated Savanna Pastoral Neolithic (Stone Bowl Culture). The burials yielded the remains of tall individuals of “Caucasoid” physical type, with the oldest such skeleton, a 190 cm/6’4” male, radiocarbon-dated to around 3,500 years before present. By contrast, Llorente et al. estimate the roughly coeval Mota specimen’s stature at only 154.8 cm/5’1” i.e., a whopping 35.2 cm/13.9 inch difference in height! As explained in detail on The Elongated African fallacy (under physiognomy and exotic influences), indirect evidence has also established that, unlike Mota, these early Cushitic settlers possessed both the Ala111Thr allele for lighter skin pigmentation and a lactase persistence mutation as well as non-kinky (cymotrichous) hair texture.

Approximate difference in height between the Savanna Pastoral Neolithic Cairn 4 specimen and the coeval Mota hunter-gatherer specimen (MrInitialMan.com).

Thus, with the discovery, biological examination and dating of the Mota fossil, we now have concrete evidence of the existence of at least two genetically and physically distinct populations residing in the region during the Neolithic: one population ancestral to the Afro-Asiatic-speaking groups and linked with West Eurasians, and the other population ancestral to the Aroid groups and possibly linked with Nilo-Saharans (though the Mota specimen’s diminutive stature, his hunter-gatherer lifestyle, and his and the Ari’s genetic ties with the Sandawe may point to deeper Khoisan relations).

Unidentified East Eurasian elements

In addition to unrepresentative reference populations, another problematic aspect of the Mota biogeographical analysis is its intrinsic assumption that two proxy groups — an African sample and a West Eurasian sample — are sufficient to accurately capture the ethnic composition of the populations in Northeast Africa and elsewhere on the continent. A closer, multidisciplinary look at the broader data, however, points to the presence of at least a third ancestral element; one with apparently East Eurasian affinities.

Morphology and ancient testimonies

Craniometric relationships between various ancient and modern populations (Brace (1993)).

Almost two centuries’ worth of craniometric and anthropometric studies contradict the suggestion in the Mota paper that the Afro-Asiatic-speaking populations in the Horn may have been ancestrally formed through interbreeding between an early Sardinian-like population (the LBK makers) and a Mota-like population. In actuality, rather than morphologically clustering somewhere halfway between these two ancient reference groups — as one would expect for peoples that are supposedly 50% European and 50% African — the Afro-Asiatic speakers show few of the osteological characteristics of actual biracial populations. They instead appear “skeletally Mediterranean” (see, for instance, Brace (1993) to the right; also Kemp (2006) and the other studies here).

Sidamo men of relatively “pure” Cushitic type, closely resembling many Oromos.

Hadiya Sidamo leader Gaaxi Ani Fit. Geejja Garbo with the mariin (“red-brown”) phenotype widespread among the Cushitic peoples.

A Sidamo man of mixed Cushitic and South Omotic ancestry. The South Omotic or Ari-like forager influence is particularly evident in the kinky hair texture and broader/flatter nasal bones and cartilage, as well as what Carleton Coon refers to as “an enlargement of both sagittal and lateral diameters of the face.”

The anthropologist Carleton Coon observed this firsthand in his detailed examination of physical types in the Horn, “The Mediterranean Race in East Africa”, a chapter in his influential 1939 work The Races of Europe. By analyzing the Sidamos of southern Ethiopia in particular, who are the actual product of recent intermixture between Cushitic peoples and adjacent Pre-Nilotes, he was able to see what exact morphological changes such hybridization produces. Coon thus concluded that the local “Hamitic” populations were essentially “Caucasoid” and that “Negroid” influence, while also present, was on the whole minor.

Furthermore, Coon was able to identify an additional “non-Negroid” ancestral element, which was especially important among Somalis, Afars/Danakils, Agaus and other Cushitic groups. This swarthy “Veddoid” component, he postulated, may have arrived in antiquity from the Indus Valley by way of Southern Arabia along with the zebu cattle (Bos indicus):

Later than the development of highland agriculture in East Africa was the introduction and diffusion of pastoral nomadism. The cattle complex, with its elaborate set of social restrictions and of social differentiation on the basis of wealth in herds, was introduced from India by way of southern Arabia, along with the humped zebu, at some none too distant period, probably as late as the first millennium B.C.[…]

Our survey of the metrical characters of the inhabitants of the Hamitic racial area has brought several facts to light; the agricultural population of the Ethiopian highlands, both indigenous and imported from Arabia, belongs to a tall, dolichocephalic to mesocephalic, leptoprosopic, moderately leptorrhine race, which is Mediterranean in metrical position and cannot be distinguished, on the basis of the more commonly taken measurements, from blond and brunet Mediterraneans of Europe and North Africa. The Somalis, on the other hand, belong to an extreme racial form; extremely linear in bodily build, extremely narrow-headed and narrow-faced, with a special narrowness of the jaw. The relationship of the Somalis, on metrical grounds, is with some of the peoples of India as much as with the Mediterraneans elsewhere. The leptosome tendency, and the narrowness of the face, remind one of the same tendency found among the mixed Bedawin group of the Hadhramaut. It cannot be attributed to negro-white mixture, for that phenomenon, as witnessed among the Sidamos, has produced a heaping of characters, resulting in an enlargement of both sagittal and lateral diameters of the face, in some cases in excess of either the Hamitic white or the negroid parent. Upper face height and nose height are especially affected. The Somali face and nose are not long, they are merely narrow.

Royal effigy of the Meroitic King Asharramon (Fig. 191) and heads of ancient Egyptian commoners of similar “Austral-Egyptian” type (Morton (1854)).

Coon’s assertion is nothing new, for various early Greek, Roman, Egyptian and Brahmin writers, including Strabo and Philostratus, inform us of ancient colonies of Indus Valley peoples in Northeast Africa. For example, Bahadur (1917) notes that “Eusebius states that Ethiopians emigrating from the River Indus settled in the vicinity of Egypt [Meroë].” Nilus similarly relayed to Apollonius Tynaeus that “the Indi are the wisest of all mankind. The Ethiopians [Meroites] are a colony from them: and they inherit the wisdom of their forefathers”.

Herodotus (c. 440 BCE) indicates that different populations — both light-skinned and dark-skinned — lived in ancient Aethiopia, an area in Africa roughly corresponding with the territory to the south of Egypt and Libya. Among these inhabitants were (cf. Herodotus: The Histories):

• the “Ethiopians nearest to Egypt”, who were centered in the “great city called Meroe, which is said to be the capital of all Ethiopia” i.e., the ancient Meroites of Nubia (Book II: chapters 1‑98, Book III: chapters 89‑117); ancient DNA analysis indicates that the Meroites were closely related to the ancient Egyptians, with both populations carrying a predominant West Eurasian ancestry — see Ancient DNA from Sudan
• the “nomad Ethiopians”, who lived along a great lake near Elephantine island in Upper Egypt i.e., early Beja Cushites (Book II: chapters 1‑98)
• the “long-lived Ethiopians”, who “dwelt on the Libyan coast of the southern sea” and to whom the Persian king Cambyses sent envoys; they were “said to be the tallest and fairest of all men” and the “tallest and fairest and longest-lived of all men” i.e., the ancient Macrobians (Book III: chapters 1‑38, Book III: chapters 89‑117); ancient DNA analysis has confirmed that these early Cushitic settlers in East Africa were of North African origin, carrying a predominant West Eurasian ancestry (including a derived allele associated with lighter skin pigmentation) — see discussion below
• the “black-skinned” Ethiopians, who in complexion resembled the “Indians [that] dwell far away from the Persians southwards” (Book III: chapters 89‑117)
• the Ethiopians “who dwell about the holy Nysa”, located in the mountains of Upper Nubia (Book III: chapters 89‑117)
• the “Ethiopians from the east”, who lived in Asia (in or near Balochistan) and “are straight-haired” (Book VII: chapters 57‑137)
• the “Ethiopians of Libya”, who dwelled “in the south of Libya” and “have of all men the woolliest hair” i.e., Niger-Congo & Nilo-Saharan-speaking peoples/negroes (Book IV: chapters 145‑205, Book VII: chapters 57‑137)
• the “cave-dwelling Ethiopians”, whose “speech is like none other in the world[…] it is like the squeaking of bats” i.e., click-speaking Khoisan (Book IV: chapters 145‑205)

Other anthropologists have likewise proposed that an ethnographical tie exists between early Afro-Asiatic-speaking populations in Northeast Africa and the makers of the Indus Valley civilization. Following detailed examination of the skulls and murals of the ancient Meroites in the Nile Valley, Samuel George Morton asserted that “the Austral-Egyptian or Meroite communities were an Indo-Arabian stock, engrafted on the primitive Libyan inhabitants”. He further explained that, while such an influence was also present among commoners in Egypt, it was strongest in Nubia, including among the ruling class:

I observe, among the Egyptian crania, some which differ in nothing from the Hindoo type, either in respect to size or configuration. I have already, in my remarks upon the ear, mentioned a downward elongation of the upper jaw, which I have more frequently met with in Egyptian and Hindoo heads than in any other, although I have seen it occassionally in all the races. This feature is remarkable in two of the following five crania (A, B), and may be compared with a similar form from Abydos[…]

It is in that mixed family of nations which I have called the Austral-Egyptian that we should expect to meet with the strongest evidence of Hindoo lineage; and here, again, we can only institute adequate comparisons by reference to the works of Champollion and Rosellini. I observe the Hindoo style of features in several of the royal effigies; and in none more decidedly than in the head of Asharramon (Fig. 191), as sculptured in the temple of Debod, in Nubia. The date of this king has not yet been ascertained; but, as he ruled over Meroe, and not in Egypt, (probably in Ptolemaic times [B. C. 200-300],) he may be regarded as an illustration of at least one modification of the Austral-Egyptian type[…]

Another set of features, but little different, however, from the preceding, is seen among the middling class of Egyptians as pictured on the monuments, and these I also refer to the Hindoo type. Take, for example, the four annexed outlines (Fig. 192), copied from a sculptured fragment preserved in the museum of Turin. These effigies may be said to be essentially Egyptian; but do they not forcibly remind us of the Hindoo?

The Badarian factor

A typical Badarian male skull (Stoessiger (1927)).

Of all the ancient populations in Northeast Africa, the Badarians of Upper Egypt were most often regarded as the likeliest link between the local Afro-Asiatic-speaking groups and the Indus Valley peoples.

The Badarian culture flourished between 4400-4000 BCE. It consisted of small villages of semi-nomadic agropastoralists, who kept domesticated animals, cultivated grain, produced the first glazed objects, and also used metal. The Badarians interred their dead in cemeteries on the outskirts of their living area. Within the actual graves, the deceased were laid out in the fetal position, facing the setting sun toward the west. They were buried with some clothing items, pottery, jewelry and a fertility idol. Despite its brief existence, the culture is considered archaeologically important since Badarian sites have yielded the earliest evidence of agriculture in Egypt.

In Coon’s examination of Badarian skeletal remains, he observed that they were on the whole quite similar to those of other predynastic Egyptians. He described the Badarians as essentially “Mediterranean” in the anthropological sense, possessing cranial affinities with both the Afro-Asiatic-speaking populations of the Horn (although the Horn groups are ultimately closer to the later Naqadans) and the Dravidian populations of southern India:

From the type site, Badari, come the earliest skulls of a definitely Egyptian group which have yet been discovered. These Badarians lived about 4000 B.C., after the climate had become considerably drier than it was in Tasian times, so dry, in fact, that in many cases the skin and hair of their dead have been naturally preserved. The skin was apparently brunet white, while the hair was black or dark brown in color, thick, of fine texture, and usually wavy in form.

Although the Badarians, like the Tasians and Merimdians, still hunted and fished to enhance their larders and vary their diet, they lived primarily by agriculture and by herding cattle and sheep. Unlike the Merimdians they raised no pigs. By hammering copper they were entering the transition from the Neolithic to the Metal Age. They navigated the Nile in ships, whose shapes are revealed by pottery models, but we cannot be sure that they sailed them. These Badarians were undoubtedly newcomers to Upper Egypt who displaced the Tasians and perhaps other predecessors.[…]

The Badarian type represents a small branch of the Mediterranean racial group. The head is unusually high in comparison to the other dimensions, and the facial skeleton is in the absolute scale unusually small; the mandible is small, narrow and light. Its mean male bicondylar diameter is the smallest known, while the bigonial diameter of 91.6 mm. is also extremely low.[…]

Morant shows that the Badarian cranial type is closely similar to that of some of the modern Christians of northern Ethiopia, who incidentally do not show negroid characteristics in the skull, and also to the crania of Dravidian-speaking peoples of southern India. One might add that living Somalis show a close approximation to this physical type in most respects, and the extremely narrow jaw in which the Badarians seem to reach a world extreme may be duplicated among both Somalis and the inhabitants of southern India. In Europe, the closest parallel to the Badarian type is found among modern Sardinians, but this is not as close as their relationships to outer and later Egyptians.

Coon indicates that the Badarians seem to have eventually been absorbed by the ensuing predynastic Egyptians of Naqada. He also asserts that a Badarian strain persists in the Horn. Despite the prevailing “Mediterranean” element, this lingering influence, he suggests, manifests itself in various ways; particularly through attenuation of the distal or remote segments of the limbs (i.e., small wrists, hands, ankles and feet), as is common among the populations of southern India:

The bodily build of the African Hamites is typically Mediterranean in the ratio of arms, legs, and trunk, but the special attenuation of the extremities among the Somalis is a strong local feature, which finds its closest parallels outside the white racial group, in southern India and in Australia.

In her comprehensive study of Badarian skeletal remains, the anthropologist Brenda Stoessiger (1927) confirmed that the Badarians were closely related with other predynastic Egyptian series, but also bore relations with Dravidian populations in the Indian peninsula. She attributes these bonds to parallel population movements, westward into Northeast Africa and eastward into South Asia, from a common center in or near the ancient Caucasus:

Anthropologists have frequently drawn attention to the similarity in the appearance of the skulls of the Hindu races of India and the Early Egyptians. In a paper “Sur l’Origine de l’Ancienne Race Egyptienne,” published in the first volume of the Mémoires de la Société d’Anthropologie de Paris, pp. 410-422, Pruner-Bey notes this similarity only to reject it; each race, he says, has a skull, small and oval in shape; the body and extremities are for both races beautifully proportioned; but there is a marked difference in the fleshy parts, the Ancient Egyptian resembling the modern Berber, while the Hindu is bronze to bistre in colour. Finally he dismisses the idea of direct relationship on the grounds of linguistic differences, an argument which would scarcely now-a-days be advanced.[…]

From skull measurements alone it would be difficult to choose between the primitive Indian and Egyptian series as the group to which the Badarians are closer. Unfortunately it is not possible to carry the analogy further and find low coefficients between the later Egyptian series and the Indian series as the types diverge in different directions.[…]

This study confirms the conclusions based on cultural and topographical evidence that the Badarian skulls are early Predynastic Egyptian but if anything more primitive in type than the other series of this period, though the mean direct measurements differ very little from them. The early and late Predynastic types however do show a significant difference which, if we may assume the races to be divided by a period of four or five thousand years or more, may be accounted for by slight evolutionary changes or a gradual infusion of races.

How far do these results confirm Sir Flinders Petrie’s theory of a Caucasian origin? When we compare the Badarian race with others outside Egypt, it is not the Mediterranean or any Negro type which it resembles most closely but the primitive Indian, the Dravidian and the Veddah. Thus they do not oppose the suggestion of a common origin in the Caucasus from a race sending one branch westward to Egypt and Europe and another south-eastward to India. To confirm this, however, we should need series of ancient skulls from Palestine, Persia, and Western India.

Genetic/phenotypic oddities & linkage disequilibrium bias

Hair form and anthropometric means of the Afars and Issa Somalis (Charpin and Georget (1977)).

According to Coon (1939), ethnic Somalis (86%), Afars and other lowland Cushitic groups possess significantly higher rates of non-kinky hair texture than do the Amhara (40%), Tigray and other highland Abyssinian Semitic speakers. He asserts that the Sidamo, despite their Omotic admixture, also have a higher rate of non-kinky hair texture than do the Abyssinians. Puccioni (1931) reported comparable findings for the Somali clans in Somalia. Charpin and Georget (1977) similarly observed that only 3.8%-4.9% of the Issa Somalis and the Afars of Djibouti had hair in the kinky/ulotrichous class (cheveux crépus). Conversely, the Mota study and a few other biogeographical/admixture analyses, which use only African and West Eurasian samples as reference populations, assert that the Abyssinian groups possess slightly higher non-African ancestry than do the Cushitic groups (e.g. Pagani et al. (2012), who indicate that their Somali DNA samples were collected by S. Qasim Mehdi (S.Q.M.) for the earlier study Li et al. (2007); as such, these samples primarily consist of individuals originating from the Mogadishu area in south-central Somalia – cf. D.I.P.). This intuitively makes no sense, for Abyssinians, being the group with allegedly higher non-African ancestry, should logically also have the higher rates of cymotrichous hair (unless some of their non-African ancestry is, say, of Melanesian origin, which does not appear to be the case). Yet, they apparently do not. This discrepancy lends further credence to the idea that the Cushitic populations carry an appreciable East Eurasian genetic component, which rudimentary biogeographical testing using West Eurasian samples as the non-African baseline is unable to detect. This East Eurasian element is either not found at all in the Abyssinian plateau groups or exists at lower frequencies among them, and is one of the main factors behind the differing rates of non-coiled hair texture.

Estimated non-African ancestry proportions among populations of the Horn of Africa. After correcting for linkage disequilibrium bias, most of the Cushitic and Ethiosemitic-speaking samples fall within the 60%-70% range (right-most column): Afar (69%), Tygray (68%), Somali (66%), Amhara (65%), Ethiopian Somali (64%), Oromo (55%), Wolayta (44%), and Ari (20%) (Hodgson et al. (2014)). (*N.B. These estimates increase even further when the extra non-African ancestry that is embedded within the African reference sample’s gene pool is factored in.)

Greater genetic variability among the Cushitic groups also in part accounts for these counterintuitive results. For instance, other Somali samples have shown higher West Eurasian ancestry than the Abyssinian samples (e.g. Steele et al. (2014); Kidd et al. (2011)). Hodgson et al. (2014) provide the best explanation for this discrepancy between the morphological and autosomal SNP data, when they note that genomic analyses based on linkage disequilibrium (LD) are strongly affected by bias toward recent admixture events (such as the adoption of South Semitic languages by Abyssinians). When this LD bias is corrected for by removing SNPs that are in high linkage disequilibrium, the Cushitic and Ethiosemitic speakers instead show almost identical estimated non-African ancestry levels, in the 60%-70% range. (*N.B. This non-African ancestry estimate is close to that of Dobon et al. (2015) (viz. “the main component (~70%) is that detected in North Africa and Middle East”) as well as that of Ragsdale et al. (2022), although the latter researchers did not adjust their dataset for linkage disequilibrium bias: “We further find that Back-to-Africa gene flow at the beginning of the Holocene primarily affected the ancestors of the Ethiopian agricultural populations, comprising over half of their genetic ancestry, estimated to be 64–65%.”)

Overall, the biological studies indicate that West Eurasian affinities in the Horn seem to peak in the northern parts of the region. This is logically well-founded since these areas correspond with the former Land of Punt in northern Somalia and Eritrea (established by the Egyptian-related Puntites) and the Axumite Kingdom in northern Ethiopia (established by the South Arabian Sabaeans).

Principal Component Analysis of Afro-Asiatic, Niger-Congo, Nilo-Saharan and Khoisan-speaking populations from the African Genome Variation Project (AGVP). When the dataset is not corrected for linkage disequilibrium bias, the clustering pattern often shows the Afro-Asiatic-speaking Amhara sample slightly less shifted towards the Sub-Saharan samples than the Afro-Asiatic-speaking Somali sample (e.g. in PC1 above). This is primarily because genome analyses based on linkage disequilibrium are strongly affected by bias toward recent admixture events, such as the adoption of Semitic languages by the Amhara and other Abyssinians (Gurdasani et al. (2015)).

Principal Component Analysis of Afro-Asiatic, Niger-Congo, Nilo-Saharan and Khoisan-speaking populations from the African Genome Variation Project, Human Heredity and Health in Africa, 1000G, and 1000 Genome Project. When the dataset is corrected for linkage disequilibrium bias by pruning/masking SNPs that are in strong linkage disequilibrium, the clustering pattern instead shows most of the same Afro-Asiatic-speaking AGVP Somali sample slightly less shifted towards the Sub-Saharan samples than the Afro-Asiatic-speaking AGVP Amhara sample (Choudhury et al. (2020)). (*N.B. Choudhury et al. indicate that “we performed linkage disequilibrium pruning on our merged dataset using PLINK (v.1.90) to remove correlated (r2 > 0.15) single nucleotide polymorphisms (SNPs)”.)

Principal Coordinate Analysis of Afro-Asiatic, Niger-Congo, Nilo-Saharan and Khoisan-speaking populations from the African Genome Variation Project, Human Heredity and Health in Africa, 1000G, and 1000 Genome Project. When the dataset is corrected for linkage disequilibrium bias, the clustering pattern here too shows the Afro-Asiatic-speaking AGVP Somali sample slightly less shifted towards the Sub-Saharan samples than the Afro-Asiatic-speaking AGVP Amhara sample (Choudhury et al. (2020), Supplementary Information). (*N.B. Gurdasani et al. indicate that many of the individuals in their AGVP Somali sample are from the Mogadishu area in south-central Somalia: “although these samples were collected from Ethiopia, many of these individuals are from Somalia (Mogadishu)”; cf. Gurdasani et al. (2015), Supplementary Information.)

Principal Component Analysis of select Afro-Asiatic-speaking populations from the Horn of Africa (Northern Somalis, Ethiopian Oromos, Ethiopian Jews) and various Niger-Congo and Nilo-Saharan-speaking populations from East and West Africa. Notice how many of the Northern Somali individuals (black circles) cluster with the Ethiopian Jew individuals (pink triangles), whereas others cluster with the Ethiopian Oromo individuals (red triangles) (Ali et al. (2020)). Scheinfeldt et al. (2019) and López et al. (2021) similarly observed that their Cushitic-speaking Beja and Agaw samples, respectively, clustered with their Ethiosemitic-speaking Abyssinian samples. This is consistent with Almarri et al. (2021), who note that “Ethiosemitic-speaking populations share similar proportions of non-African ancestry and are genetically similar to Cushitic-speaking populations” and that their “admixture tests[…] also suggest an ancient Egyptian source of ancestry in East Africa.” (*N.B. Ali et al.’s Northern Somali sample consists of individuals born in the northeastern Puntland region of Somalia. The study utilized SNP genotyping rather than whole genome analysis, and represents the first genetic analysis to examine Northern Somali individuals. As of 2021, no genome-wide study has yet to analyse Northern Somali (Puntland and Somaliland regions) or Djiboutian Somali individuals.)

Besides the osteological work, ancient testimonials, zebu cattle complex and hair morphology, there are a couple of other indications that an East Eurasian ancestral component likely exists among the Afro-Asiatic-speaking groups in Northeast Africa. Narasimhan et al. (2019) report a high prevalence of the Afro-Asiatic-linked E1b1b paternal haplogroup among Late Bronze Age/Early Iron Age individuals from the Swat Valley in northern Pakistan, specimens which also exclusively bore M and N mtDNA derivatives. This points to ancient ties between this area, Mesopotamia, the Levant, the Arabian peninsula, North Africa and the Horn of Africa (cf. Table S1-S5). More specifically, the presence of haplogroup E1b1b in South/Central Asia this early in time likely reflects eastward incursions by Neolithic and/or Bronze Age Levantines (the original Elamo-Dravidian settlers, perhaps?). These newcomers possibly interbred with local populations, before eventually returning to the Afro-Asiatic fold along with their newly-acquired East Eurasian genes. Such early connections between Afro-Asiatic-speaking populations and groups bearing East Eurasian ancestry are likewise supported by Witas et al. (2013), who analyzed Early Bronze Age to Roman era specimens excavated at Tell Ashara (Terqa) and Tell Masaikh (Kar-Assurnasirpal) in Mesopotamia. The researchers found that these ancient individuals (dated to 2500BCE-500CE) belonged to the mtDNA clades M4b1, M49 and/or M61, maternal lineages that are today concentrated and believed to have evolved in the Indian subcontinent. Various autosomal DNA analyses have also observed an East Eurasian component in their Somali samples (e.g. Kidd et al. (2011); Kidd (2011b); Truelsen et al. (2017); Pereira et al. (2017)). Other factors supporting this association are the elevated frequency of the B blood group among Ethiopian Somali males (44.44%) and Afar males (33.33%) (cf. Abegaz (2021)) as well as among Beni Amer Beja (31%; Corkill (1949)) — a serological system that is also common among Egyptians (24.1%; Swelem et al. (2018)) and Riverain & Shaigiya Sudanese “Arabs” (25% and 24%, respectively; cf. Corkill (1949)) and which globally peaks among populations in South Asia (Kocak et al. (2017)); the high mean number of private alleles that are found today in certain Cushitic groups (cf. Babiker et al. (2011)); as well as the presence in these populations of unusual genetic variants of apparent East Eurasian origin (e.g. the EDAR gene’s derived allele, which is associated with hair thickness among populations in eastern Asia; around 12.5% of ethnic Somalis bear the mutation, whereas it is largely absent in Subequatorial Africa, the Maghreb, West Asia and Europe).

Autosomal SNP analysis detecting the presence of a notable South/Central Asian component (blue) in the Somali sample in contrast to the Ethiopian Jew and Mozabite samples (Kidd et al. (2011)). (*N.B. Kidd (2011b) indicates that this Somali sample is from the Yale collection, which ALFRED notes was originally gathered by Dr. Qasim Mehdi. This is the same cohort that Pagani et al. (2012) used in their analysis, and thus likely mainly consists of Hawiye Somali rather than Benadiri Somali individuals.)

Autosomal SNP analysis again detecting a South/Central Asian component (purple) in the Somali sample. Oddly, this component is found at lower frequencies in the Iranian, Turkish and Druze samples, although these populations border Central Asia (Truelsen et al. (2017)).

Autosomal SNP analysis yet again detecting a South/Central Asian component (orange) in the Somali sample. This component is also found in the Libyan sample, albeit at lower frequencies (Pereira et al. (2017)).

Genome analysis of modern Emirati individuals detecting the presence of a South/Central Asian component. Researchers have usually ascribed this element among contemporary Arabians to recent admixture with persons from South/Central Asia. However, the absence of the Ancestral South Indian component among Afro-Asiatic speakers in general, coupled with the presence of a South/Central Asian component among some Afro-Asiatic-speaking individuals, suggests deeper associations, perhaps linked to the dispersal of the original Elamo-Dravidian speakers (Elbait et al. (2021), Figure S2).

Ancestral composition of modern populations in South and Central Asia. The Onge or Ancestral South Indian genome component is today widely distributed across this region. However, it has not been observed among the Afro-Asiatic-speaking populations in Africa. This suggests that the South/Central Asian inferred element, which in some analyses has been detected among modern Cushitic, Berber and Arabic speakers, was either a) derived from an area in South/Central Asia, such as Balochistan, where the Ancestral South Indian component is not found at appreciable frequencies, or b) introduced early on by South/Central Asian settlers, such as the makers of the Indus Valley civilization, at a time period when the latter had not yet interbred with the original bearers of the Ancestral South Indian component (Lazaridis et al. (2016)). (*N.B. Distance analysis on the Vahaduo Admixture JS program indicates that, besides the recent IND_Great_Andamanese_100BP sample on Eurogenes’ official Global25 datasheet, the Onge share the nearest genetic affinity with the LAO_Hoabinhian specimen (see here). Ergo, the latter ancient individual is currently the best available stand-in for “pure” Ancestral South Indian ancestry.)

Final observations and recommendations

Another interesting facet of the Mota analysis concerns Llorente et al.’s assertion that they were able to detect West Eurasian affinities in every African population that they examined. While such ancestry is not unexpected for certain groups like the Maasai, Sandawe, and Khwe and Nama Khoi (who are known to have assimilated some early Cushitic pastoralists), it is less clear how isolated hunter-gatherer populations like the Xun/!Kung San and Mbuti Pygmies would have acquired such an influence. It is tempting to suggest that the spread of haplogroup E may have had something to do with this. However, the fact that the Neolithic LBK farmers apparently did not carry the paternal clade rules them out as the disseminating ancient population. So does the fact that the Stuttgart LBK woman possesses the derived SLC24A5 allele for lighter skin pigmentation, whereas most African populations, other than the Afro-Asiatic-speaking groups in the Horn and North Africa, do not.

Given the foregoing, better potential reference populations for future ancient DNA tests would be:

• For the source of the West Eurasian ancestry in the Horn – The oldest skeletons in the Savanna Pastoral Neolithic mound cairns that were excavated by Daniel Stiles. These remains belong to early Southern Cushitic settlers. The A-Group, C-Group and Kerma peoples of ancient Nubia and the predynastic Egyptians of Naqada are also interesting possibilities, as they are craniometrically quite close to present-day Afro-Asiatic speakers in the Horn. A tertiary option is the medieval-period KulR17 infant from Kulubnarti in Sudan, which Sirak et al. (2015) found to possess Middle Eastern affinities.
• For the source of the unidentified East Eurasian ancestry in the Horn – The ancient Badarians of the Nile Valley. Osteological analysis by Stoessiger (1927) suggests that they are as closely related to other predynastic Egyptian groups as they are to modern Dravidian populations in South Asia.
• For the source of the putative West Eurasian ancestry in Subequatorial Africa – The makers of the Iberomaurusian industry of Northwest Africa. They lived before the derived mutations for lighter skin pigmentation evolved, and also appear to have been lactose intolerant. As such, the Iberomaurusians easily could have spread West Eurasian genes to the similarly dark-skinned, lactose intolerant early hunter-gatherer populations in the adjacent subequatorial areas. The makers of the Capsian culture are also an intriguing alternative for comparable reasons, as are the Kiffians and Tenerians of the Gobero in the Sahara (who are presently being typed for ancient DNA, according to paleontologist Paul Sereno).

For related archaeogenetics, see Ancient DNA from Sudan. Also stay tuned for new aDNA work from Egypt.

*Update #1

In January 2016, Llorente et al. published an erratum online pertaining to their Mota study. The announcement (summarized here by Scientific American) indicates that there was a software-related oversight on the researchers’ end, which caused them to unknowingly overlook some chromosomal affinities that do apparently exist between the Mota specimen and their West Eurasian reference sample. The scientists also write that the proposed large ancient migration from West Eurasia was instead mainly confined to East Africa:

Erratum to Gallego Llorente et al. 2015

The results presented in the Report “Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent“ were affected by a bioinformatics error. A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as missing data (the analysis of admixture with Neanderthals and Denisovans was not affected). When those positions were included, 255,922 SNP out of 256,540 from the contemporary reference panel could be called in Mota. The conclusion of a large migration into East Africa from Western Eurasia, and more precisely from a source genetically close to the early Neolithic farmers, is not affected. However, the geographic extent of the genetic impact of this migration was overestimated: the Western Eurasian backflow mostly affected East Africa and only a few Sub-Saharan populations; the Yoruba and Mbuti do not show higher levels of Western Eurasian ancestry compared to Mota.

We thank Pontus Skoglund and David Reich for letting us know about this problem.

First off, the researchers are to be commended for their professionalism; both for having the courtesy to admit to a mistake (which happens) and then promptly trying to redress that, and for having the vision to conduct such an ancient DNA analysis in the first place.

That said, what are the implications of the Mota erratum? Not much since, as explained above, Mota was not an adequate African proxy to begin with. His uniparental lineages already pointed to gene flow from an early Afro-Asiatic-speaking settler group(s), as is the situation with his contemporary Ari relatives. This introgression is now also supported by Llorente et al.’s revised analysis, which has apparently detected minor West Eurasian ancestry in Mota’s genome.

A better and older African reference population than Mota would, therefore, perhaps be Schepartz (1987)’s hunter-gatherer sample from the Gogoshiis Qabe Rockshelter in southern Somalia (8,100-5,400 BP). Sellers (2008) compared these skeletons’ dental metric affinities to those of modern ethnic Somali pastoralists and Final Paleolithic Nubian hunter-gatherers, Sudanese agriculturists (3,400-1,200 BP) and Sudanese intensive agriculturists (1-1,500 BCE), and found that the ethnic Somali individuals were much more closely related to the more recent Sudanese intensive agriculturalists (viz. the Meroitic, X-Group and Christian period populations) and Sudanese agriculturalists (viz. the A-Group and C-Group populations) than to the Gogoshiis Qabe Rockshelter hunter-gatherers and Final Paleolithic Nubian hunter-gatherers. As explained on Ancient DNA from Sudan, this is because ethnic Somalis and other Afro-Asiatic-speaking populations that today inhabit the Horn did not actually evolve there. Their ancestors — ancient Cushitic speakers; not the Gogoshiis Qabe Rockshelter hunter-gatherers or Mota or the LBK makers — arrived instead from the Sahara and Nile Valley. The latter area is the likely Afro-Asiatic urheimat or “original homeland”.

For a comprehensive overview of these early “Hamitic” settlers in the Horn, see Punt: an ancient civilization rediscovered.

*Update #2

It is 2020, a good four years since our last update, and much has happened in the world of palaeogenetics. We now have genomic data from both the Iberomaurusians in Northwest Africa and early Southern Cushitic settlers in East Africa, as well as more extensive testing of ancient Egyptian specimens of the Nile Valley. These ancient DNA analyses, amplified by studies on modern groups, have gone a long way towards helping to clarify existing and past population relationships and inheritance patterns.

Anatolian Neolithic component & ancestral deconvolution

As discussed above, various SNP-based autosomal DNA analyses have suggested that the modern Afro-Asiatic speakers in the Horn of Africa (and to a lesser extent the Afro-Asiatic speakers in North Africa) harbor two distinct ancestries: one non-African and the other African.

Non-African ancestral composition of the Oromo. This NAF component is estimated to be comprised of 85% Anatolian Neolithic and 15% CHG for the Oromo, Amhara and Wolayta, and 92% Anatolian Neolithic and 8% CHG for the Somali (Molinaro et al. (2019), Supplementary Information).

Researchers have hypothesized that this non-African component is associated with either Neolithic Europe (as represented by the LBK culture), the Mesolithic Levant (Natufian culture), or the Neolithic Levant (Pre-Pottery Neolithic culture). According to Molinaro et al. (2019), when the whole genome of the Cushitic and Semitic-speaking individuals is analyzed (that is, when both the non-African and African components are examined together), their West Eurasian ancestry appears to be primarily derived from the Neolithic Levant. However, when the non-African component (NAF) is isolated through a process of ancestry deconvolution, it instead appears to be largely composed of the Anatolian Neolithic component, with minor admixture from the Caucasus Hunter-Gatherer (CHG) component. Among populations in Ethiopia, Molinaro et al. estimate this non-African component ratio at 85% Anatolian Neolithic and 15% CHG for the Amhara, Oromo and Wolayta, and 92% Anatolian Neolithic and 8% CHG for the Somali.

What are the merits of this biogenesis scenario?

• Molinaro et al. (2019) is the first study to attempt isolating the non-African component from the African component. As the scientists point out, this is a necessary analytical step because in whole genome analysis, the African component (due to its highly divergent nature) skews the overall allele frequency spectrum. Molinaro et al.’s thesis is strengthened by the fact that it has been successfully replicated by Aneli et al. (2021), the second and only other study so far that has applied ancestral deconvolution to the question. Like Molinaro et al., Aneli et al. found that the distal source of the West Eurasian ancestry borne by the Horn’s Afro-Asiatic-speaking populations is largely Anatolian Neolithic-related. The researchers call this ancestral signature “Pan-Mediterranean” since they found it to be characteristic of earlier groups throughout the Mediterranean, including the ancient Daunians of Apulia and the Minoans of Crete (*N.B. Recent studies have found pre-Ptolemaic Egyptian samples to be the best-fitting surrogate for the proximal source of the Horn groups’ West Eurasian ancestry (cf. Almarri et al. (2021), Table S4; Sirak et al. (2021)). This, in turn, implies that Anatolian Neolithic ancestry would have been abundant in Egypt too prior to the spread of haplogroup J carriers into the Nile Valley.)
• Among modern populations, the researchers identify Tunisian Jews as the closest in terms of ancestral composition to the non-African component borne by the Afro-Asiatic speakers in the Horn of Africa. This is supported by Serra-Vidal et al. (2019), which, like Molinaro and colleagues, found the Anatolian Neolithic component to be the defining non-African component among the Afro-Asiatic-speaking populations of the Maghreb.
• Among ancient populations, the researchers identify the Minoans of Crete as the closest in terms of ancestral composition to the non-African component borne by the Afro-Asiatic speakers in the Horn. This is supported by ancient Egyptian iconography such as the Grand Procession mural at the tomb of Rekhmire, which, on adjacent panels, depicts quite similar-looking ancient Puntite and Cretan figures (see Punt: an ancient civilization rediscovered).
  

  Meshwesh, one of the ancient tribes of Sea Peoples. Note the braided hairstyle, which is still maintained by some Afro-Asiatic speakers in Northeast Africa (Salimbeti).

• It explains why in whole genome statistical modeling Levantine Neolithic samples are often a better proxy for the non-African ancestry present in the Horn region than are Mesolithic Natufian samples (e.g. Skoglund et al. (2017)). According to Schuenemann et al. (2017), the Levantine Neolithic component is itself composed of Natufian ancestry and later-arriving Anatolian Neolithic admixture. Hence, the Levantine Neolithic signal that is being picked up could in reality be associated with that component’s Anatolian Neolithic element rather than its Natufian element. This appears to be why, after ancestral deconvolution, Molinaro et al. primarily detected an Anatolian Neolithic affinity for the Horn’s West Eurasian ancestry but no Natufian affinity.

• It is supported by data on Neanderthal admixture. Schaefer et al. (2021) compared Neanderthal genomes to those of various modern populations, identifying haplotype block lengths that are indicative of Neanderthal genetic introgression. The scientists observed that their Somali, Mozabite Berber and Sahrawi samples were distinct from their other African samples and instead had haplotype block lengths similar to their non-African samples. This indicates that the early Cushitic settlers in the Horn region descended from a non-African population, though not the Natufians since the Natufians have been found to be devoid of Neanderthal admixture. More specifically, Schaefer et al. suggest that “these Neanderthal haplotype blocks may have originated in ancient European migrants to eastern Africa,” in agreement with the view that Minoan-related settlers (viz. the early Cushites) introduced the Anatolian Neolithic component to the Horn.
  

  Mean Neanderthal haplotype block lengths, which identify Neanderthal admixture in various modern populations. The Somali sample has haplotype block lengths similar to those of the North African (Mozabite Berber and Sahrawi) and non-African samples. Schaefer et al. (2021) suggest that this is because “these Neanderthal haplotype blocks may have originated in ancient European migrants to eastern Africa.” This is consistent with the view that the early Cushitic settlers in the Horn of Africa descended from a population bearing Anatolian Neolithic ancestry (Schaefer et al. (2021)).

• It is supported by serological data on Rh-negative blood. Rhesus negative persons are nowadays quite rare, with around 89%-95% of examined individuals worldwide being Rh-positive. Rhesus negative blood has been observed at highest rates among European populations (~17% in Britain), especially Basques (29%). Equally high Rh-negative frequencies have also been reported among Berbers in the High Atlas mountains of Morocco (29%; cf. Weinstock (2014)), as well as in Syria (30.5%; Kocak et al. (2017)) and Al-Jouf province in Saudi Arabia (29%; Eweidah et al. (2017)). Golassa et al. (2017) likewise observed a high frequency of Rh-negative blood (21.32%) among the Afro-Asiatic-speaking residents of Gambella town, a Nilotic majority area located in the Gambella woreda (district) of southwestern Ethiopia (cf. Table 1). Of these Afro-Asiatic-speaking inhabitants (locally known as degegna or ‘highlanders’), most are Cushitic Oromo individuals (20.13%) (MANR (2016)). Similarly, Abegaz (2021) found elevated Rh-negative frequencies among his Oromo (34.74%) and Tigray (28.57%) female samples collected in Ethiopia’s northern Amhara region. Since Basques and Berbers have been found to be defined by the Anatolian Neolithic ancestral component (cf. Sarno et al. (2017), Supplementary Fig. S3; Serra-Vidal et al. (2019)), these findings accord well with Molinaro et al.’s thesis that Minoan-related settlers introduced the Anatolian Neolithic component to the Horn.

• 
  

  Lactase persistence allele frequencies of Afro-Asiatic-speaking populations in the Nile Valley and East Africa. The Northeast African-affiliated G-13907 variant peaks among the Beni Amer Beja (25%), the Arabian-affiliated G-13915 variant climaxes among Somalis (50%), and the South Cushitic-affiliated C-14010 variant is prevalent among the Yaaku (53.6%) (Tishkoff et al. (2010)).

  It is supported by the lactase persistence (LP) alleles that are presently distributed in Northeast Africa. Tishkoff et al. (2010) and Hassan et al. (2016) note that the local Afro-Asiatic-speaking populations have high frequencies of various LP mutations, especially the pastoralist Cushitic groups. Of these derived alleles, the most commonly borne ones are: G-13907, which is centered in the Nile Valley and Horn of Africa and associated with cattle pastoralism; G-13915, which is centered in Arabia and associated with camel pastoralism; and C-14010, which is centered in the Great Lakes region and also associated with cattle pastoralism. The first two of these lactose tolerance variants are prevalent among North Cushitic and East Cushitic groups (G-13907 climaxes among Beni Amer Beja at 25%, and G-13915 peaks among Somalis at 50%), whereas C-14010 is typical of Southern Cushitic groups (the earliest occurence of this allele is among ancient Cushitic specimens of the Pastoral Neolithic; cf. Prendergast et al. (2018)). A fourth LP allele, T-13910, is most common in Europe and is also found among Tuareg Berbers, Mozabite Berbers and Fulani groups. According to Enattah et al. (2008):

  The European T-13910 and the earlier identified East African G-13907 LP allele share the same ancestral background and most likely the same history, probably related to the same cattle domestication event.

  Kulichová et al. (2017) indicate that the T-13910 LP allele was likely spread by pastoralists originating from outside Africa. Furthermore, Marcus et al. (2020) suggest that such population movement(s) from Europe into Africa also introduced both the R1b-V88 paternal haplogroup and Sardin