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Thread: West Asian source for Eurasian admixture in Ethiopians

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    West Asian source for Eurasian admixture in Ethiopians

    It's the Sea Peoples? Really?


    West Asian sources of the Eurasian component in Ethiopians: a reassessment

    "The presence of genomic signatures of Eurasian origin in contemporary Ethiopians has been reported by several authors and estimated to have arrived in the area from 3000 years ago. Several studies reported plausible source populations for such a signature, using haplotype based methods on modern data or single-site methods on modern or ancient data. These studies did not reach a consensus and suggested an Anatolian or Sardinia-like proxy, broadly Levantine or Neolithic Levantine as possible sources. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ~50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called “NAF” for Non African) and ancient and modern proxies. Our results unveil a genomic legacy that may connect the Eurasian genetic component of contemporary Ethiopians with Sea People and with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization."

    In the following paragraphs we will base our results on the assumption that the majority of the Eurasian component observed in contemporary Ethiopians is the result of a major admixture event that took place ~3 kya. An alternative or complementary contribution to the presence of West Asian components in contemporary Ethiopians, may involve the Neolithic Pastoralist population movements reported to have occurred in East Africa by Prendergast and collaborators9. We explored this possibility through MALDER and showed no multiple admixture events in the area (with the exception of Wolayta who show an additional signal for a more recent admixture wave). Even though the events reported by Prendergast and colleagues are at the edge of the MALDER detactability (See Table S2), the lack of admixture dates in Ethiopians prior to 3 kya may point to a reduced impact of this early migrations on Ethiopians, also in accordance with the ancestry modelling suggested for Ethiopian populations by Prendergast and colleagues themselves9."

    Just saying, but that's a pretty big assumption. The fixing of admixture times is often wrong.

    We then explored the Ethiopian NAF component through ADMIXTURE (Fig. S7) and projected PCA, and showed them to fall within the range of Eurasian populations, close to ancient populations with a high Anatolian Neolithic component (e.g. Anatolia_N and Minoans) and away from neighboring populations from the Arabian Peninsula (Figs. 2 and S2 for Amhara). The PCA position shown by Amhara in Fig. 2 is superimposable to the ones of Oromo, Ethiopian Somali and Wolayta NAF components (Figs. S3S5) accounting for overall homogeneity of the Ethiopian NAF components extracted by AD. Notably, several Jewish populations from North Africa cluster with NAF as well. The affinity between Anatolian Neolithic and NAF was further highlighted by Outgroup f3 statistic, in contrast to results obtained with the genomes before ancestry deconvolution (Supplementary Fig. S8). Overall, whole-genome sequences of all the Ethiopian populations appear closer to ancient broadly West Asian populations such as: Minoans, Natufian, Levant Neolithic and Anatolian Neolithic. On the other hand, their NAF components appear closer to populations with a high Anatolian rather than Levantine component (such as Minoans, Sardinians and Anatolia Neolithic). North African (Tunisian, Libyan and Moroccan) Jews (See Fig. S6), consistently with what seen in PCA (See Figs. 2 and S2S5), show the highest increase of Outgroup f3 affinity when replacing Ethiopian populations with their NAF counterparts. Importantly, other populations that could have served as good proxy for the Eurasian component in the Ethiopians due their chronological or geographical position (i.e. Sidon_BA10, Levant_BA3, Iranians3,11 (contemporary, Chalcolithic and Neolithic individuals), Egyptians, Yemeni and Saudis12), did not show high similarity to the NAF component based on the Outgroup f3 test and were not further investigated."

    Figure 1

    Frequency-based allele-sharing analyses. f4 statistic test on Amhara in form of (PopA,PopB;Test,Mbuti) to assess genetic similarity between Amhara and respective NAF genomes to pairs of several West Asian populations. A and B populations are listed in the right and left side of the plot, respectively. Values in x axis indicate the Z-Scores, we draw two lines to highlight |z-Scores| = 2 and 3. Points with |z-Score| > 3 indicate a clear affinity of the test population towards one of the other population. Amhara’s segments tested: Amhara whole-genome (Amhara, in blue), the Non African component (Amhara NAF, in yellow), Amhara AF and NAF components together (Amhara Joint, in violet) and Amhara NAF with X component (Amhara NAF + X, in orange).

    Figure 2

    Principal Component Analysis. Principal component analysis of modern West Eurasian populations used as a scaffold (grey points) on which ancient genomes and Amhara deconvoluted NAF were projected. To highlight reference populations we coloured European Hunther-Gatherers in brown, ancient genomes from Anatolia and Levant areas (orange and green respectively), Minoans in yellow, Iranians in purple and Jewish populations from North Africa in red. Amhara whole and NAF genomes are listed in blue and light blue. Variance explained by PC1 is 0.9% and PC2 is 0.3%.

    We further dissected the observed affinity between NAF and Anatolian Neolithic-like populations through a set of f4 tests aimed at refining through more and more stringent comparisons the best proxy population for the Eurasian layer (Fig. 1). The whole-genomes, with both African and Non-African components, are significantly closer to a Levantine ancestry rather than Anatolian (Z-Score −2.98), with them being closer to Levant_ChL individuals than Levant_N. On the other hand, NAF is shown to be closer to a Neolithic ancestry from Anatolia rather than any Levantine one (Z-score 2.847) and, among Levantine populations, notably closer to Levantine Chalcolithic than to Bronze Age groups or contemporary Lebanese. We further compared the best proxies for the Non African component using the top scoring populations from Outgroup f3 analyses. Minoans appear to be as close to NAF as Anatolian Neolithic individuals (Z-Scores < 1). When we delved into the North African Jews signals, they broadly show affinity with NAF with particular reference to Jews from Tunisian. Similar trends did not change when considering alternative combinations of deconvoluted components, such as NAF + X and Joint (Fig. 1). The similarity between the NAF and Anatolia_N samples, rather than Levantine, is maintained also when different proxy populations are used to extract the NAF component or a different deconvolution software is used (Fig. S9). The f4 results on the other Ethiopian populations are strongly comparable with Amhara results: Oromo, Ethiopian Somali and Wolayta show higher genetic affinity with Anatolian Neolithic group rather than any Levantine one (Fig. S10), with them being closer to Levantine Chalcolithic individuals rather than Neolithic ones, as seen for Amhara. Peculiarly, Ethiopian Somali and Wolayta when tested specifically with Minoans and Levant Chalcolithic samples show Z-Scores < 2. Given that our ability to pinpoint the actual source of the NAF component is inherently limited by the availability of ancient and modern populations, we used qpGraph (Supplementary Figs. S11S13) and qpAdm to model NAF as a mixture of the major axes of genetic diversity that best described the Mediterranean area at the time of the studied event, following Lazaridis et al.3. When looking at the global genomes, for all Ethiopian populations, our qpAdm results replicate a Levant_N origin for the Eurasian component of Ethiopians3 (Fig. 3, left column and Fig. S14, first row). The NAF component alone, on the other hand, can be described as a mixture of Anatolia_N and CHG. Particularly, Amhara, Oromo and Wolayta NAF components can be modelled as ~85% Anatolian_N and ~15% CHG, while Ethiopian Somali NAF is better characterized as 92% of Anatolia_N and 8% of CHG. In sum, similarly to Minoan and Tunisian Jewish populations, the non African component of Ethiopians can be best modelled as a mixture of ~85% Anatolian_N and ~15% CHG composition of ancestries (Fig. 3, columns 2, 3, 4 and Table S4), with small fluctuations across the various Ethiopian populations (see Table S4 and Supplementary Fig. S14)."

    And now to the biggest assumption of all:

    "Of the ones analyzed here, Minoans and Tunisian Jews seem to provide the two closest matches to NAF, adding on top of the genetic evidence a criteria of space/time compatibility. A tentative link between these three groups may be provided by the historical maritime trade routes connecting Crete (home to the Minoan culture) to the Levant13,14,15 and by the shuffling role played by a horde of nomads who navigated throughout the Mediterranean Sea 3 kya: the Sea People. These tribes are linked to Crete, Anatolia where they fought the Hittite Empire, Egypt and the Levant, and are told to have settled in the land of Canaan, known also as Palestine16. Interestingly, the Sea People tribes that settled in Palestine included, among others, Denyen and Peleset according to the Egyptian inscriptions of Merneptah and Medinet Habu17. Although there are different theories around the origin of each of these tribes, there are suggestions that link the Denyen with the tribe of Dan, from which Jews from Ethiopia have been said to descend, and the Peleset to the Philistines from the Levant18. The role of Sea People may therefore be crucial in explaining a temporary presence of a Minoan-like ancestry in the Levant, bringing Anatolian-like components to levels as high as 85%. A pulse of populations with Anatolian-rich ancestry has just been recently detected in Iron Age Levant, appearing and disappearing from the archaeological record within a range of few centuries, at the beginning of the 1st Millennium BCE19. These Levant Iron Age samples can indeed be modelled as having at least 80% Anatolian Neolithic ancestry (~20% CHG and ~80% Anatolia_N, see Supplementary Table S6) and surrogate Ethiopian NAF in relevant f4 analyses (Supplementary Table S5). Notably Ethiopian NAF is still closer than Levant IA to Tunisian Jews (Supplementary Table S5). Ethiopian NAF therefore offers a solution to the disappearance of the Levant IA component from the population record of the area, where their signal may have become erased as a consequence of major warfare after 1000 BCE20 or 3 kya, displacing these genetic components towards Ethiopia (an allegory of which can be read in the mythological account of the meeting between King Solomon and the Queen of Sheba) and North Africa Jewish communities (where such a signature is still detectable after the major population movements following the Alhambra Decree after 1492 CE)."

    If they want to stick to a 3,000 yr. ago arrival, they'd be better off with positing Jews.

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    In my opinion it's very unlikely that Sea People, whatever they were, had a so significant genetic impact that can still be found today in the contemporary population.

    When will geneticists stop pretending to be archaeologists and historians?

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