Wednesday, September 11, 2019

Modern Ethiopian Genetics

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with -- and shape -- genetic structure in human populations. Using primarily novel genetic variation data covering 1,268 Ethiopians representing 68 different ethnic groups, together with information on individuals’ birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors upon shaping the genetic structure of Ethiopians today. 
We provide examples of how social behaviours have directly -- and strongly -- increased genetic differences among present-day peoples. We also show the fluidity of intermixing across linguistic and religious groups. We identify correlations between cultural and genetic patterns that likely indicate a degree of social selection involving recent intermixing among individuals that have certain practices in common. 
In addition to providing insights into the genetic structure and history of Ethiopia, including how they correlate with current linguistic classifications, these results identify the most important cultural and geographic proxies for genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians.
Saioa López, et al., "The genetic landscape of Ethiopia: diversity, intermixing and the association with culture" bioRXiv (September 5, 2019) doi:

(There is excellent background information on Ethiopian history, anthropology and linguistics in the Supplementary Materials).

From the Results section (references omitted; emphasis outside of headings added):
Genetics broadly correlates with linguistic classifications but supports pervasive recent intermixing among ethnic groups speaking diverged languages 
Our study contained individuals from four different branches (second tier of classifications at within the Afroasiatic (AA) and Nilo-Saharan (NS) language families: the NS Satellite-Core (193 individuals), AA Cushitic (390 individuals), AA Omotic (565 individuals) and AA Semitic (95 individuals) branches. Reflecting a fluidity of genetics across these linguistic classifications, several fineSTRUCTURE-inferred clusters contain individuals from different ethnic groups that represent multiple language categories. For example, the AA Cushitic-speaking Agew cluster genetically with the AA Semitic-speaking Amhara. In addition, the AA Omotic speaking Shinasha, the AA Cushitic-speaking Qimant and the AA Semitic-speaking Beta Israel show very similar inferred ancestry and admixture dates to clusters predominantly containing AA Semitic speakers, with the Qimant and Beta Israel having been reported previously to be related linguistically to the Agew.  
The sample sizes are very impressive for groups like Omotic speakers that are historically undersampled. These are the main correlations. The Amhara language group was probably derived in significant part from language shift from Agew language speakers as do Cushitic Qimant and Beta Israel populations. One Omootic population is close to populations that are now Semitic speaking, also suggesting language shift. Continuing with the results section:
The observed blending of groups’ genetics across language classifications may be attributable in part to ethnic groups adopting their current languages relatively recently and/or to pervasive recent intermixing among distinct Ethiopian groups that reside near one another. To test for the latter, we applied GLOBETROTTER to each of the 78 Ethiopian clusters under the “Ethiopia-internal” analysis, which includes Ethiopians as surrogates for admixing sources and hence can identify intermixing that has occurred among Ethiopian groups. GLOBETROTTER inferred admixture events in 70 clusters in this analysis, 59 (84.3%) of which had estimated dates <30 generations ago (<900 years ago) Across clusters, inferred dates under the “Ethiopia-internal” analysis typically are much more recent than those inferred under the “Ethiopia-external” analysis that does not allow Ethiopian populations as surrogates for the admixing source. This indicates that the “Ethiopia-internal” analysis is identifying recent intermixing among Ethiopian groups rather than relatively older admixture involving non-Ethiopian sources; otherwise dates under the two analyses  would be similar. Supporting the possibility that geographically nearby Ethiopians are intermixing, the GLOBETROTTER “Ethiopia-internal” analysis infers intermixing among Ethiopian clusters that reside more geographically near to each other than expected by chance (p-value < 0.00002).  
Nonetheless, we also explored whether individuals from the same linguistic category are more genetically similar on average, which would reflect a general tendency to share more recent ancestry despite groups changing language and/or some degree of recent intermixing among groups. As an example, on average, individuals from the AA Cushitic, AA Omitic, AA Semitic, and NS classifications, as well as individuals from separate sub-branches within each of these categories, are genetically distinguishable from each other under both the “Ethiopia-internal” and “Ethiopia external” analyses (p-val < 0.01) Indeed, individuals from five of 14 NS-speaking ethnic groups are more genetically similar to the NS-speaking Dinka from Sudan than they are to Ethiopians from AA-speaking ethnic groups, with two of these five (Anuak, Nuer) most genetically similar to the Dinka overall. These observations suggest that the first three tiers of Ethiopian language classifications at are genetically -- in addition to linguistically -- separable on average, and that these genetic differences may not solely be attributable to recent isolation. Consistent with this, individuals from different language categories sometimes display substantially different inferred ancestry. For example, among clusters that predominantly consist of NS speakers, GLOBETROTTER infers admixture events typically occurring <50 generations (<1450 years) ago between EastAfrican/Somali-related sources and SSAfrican-related sources that carry some West/Central African-like ancestry. Markedly different to this, all clusters that predominantly consist of AA Semitic speakers show similar inferred ancestry proportions and admixture events occurring ~57-97 generations (~1600-2800 years) ago between a source related to present-day SSAfricans/Somalians and a source related to present-day Egyptians/W.Eurasians. Meanwhile AA Cushitic and AA Omotic speakers display a wide range of inferred dates and admixture proportions that fall between those inferred for NS and AA Semitic speakers.  
Nilo-Saharan genetic distinctiveness runs very deep, indicating relatively little admixture with Afro-Asiatic language speakers. The Ethio-Semitic speakers, consistent with expectations, so a star-like common ancestry at the expected source date for those languages that have a common source. The divide between Ethio-Semitic speakers and speakers of Afro-Asiatic speakers of non-Ethio-Semitic languages is pre-dates the Ethio-Semitic origin point (as expected), but has more recent common ancestry than the Afro-Asiatic speakers do with the Nilo-Saharan speakers (unsurprising but not as clearly expected). Continuing in the results section:
The Shabo, a hunter-gatherer group and linguistic isolate, show the strongest overall degree of genetic differentiation from other ethnic groups, consistent with the relatively high degree of isolation that has been previously suggested. Under the “Ethiopia-external” analysis, both the Shabo and the AA Omotic-speaking Karo show similar genetic patterns to those of individuals in clusters of predominantly NS speakers near which they both reside. The genetic similarity between the Shabo and NS speakers supports some conclusions based on linguistics  and has been suggested in a study of genetic data from other Shabo individuals. Our analysis finds the Shabo to be significantly most genetically similar to the NS speaking Mezhenger relative to any other ethnic group considered ; for example, merging with the Mezhenger prior to all other NS groups in the fineSTRUCTURE-inferred tree. The Shabo also share very similar inferred admixture events, dated to 300-900 years ago, and ancestry proportions, with the Mezhenger, whom have been suggested to share origins with the Shabo. These inferences are consistent with a high degree of intermarrying among the Shabo and Mezhenger, as has been proposed, and/or Shabo speakers having split from some other NS speakers more recently than 900 years ago, with some degree of current genetic differences between NS speakers and the Shabo attributable to recent isolation (e.g. due to social marginalisation of the Shabo).  
The other group with uncertain linguistic classification in our study, the NegedeWoyto, are significantly differentiable (p-val < 0.001) from all other ethnic groups under the “Ethiopian-internal” analysis, and cluster separately. However, under the “Ethiopia-external” analysis they are not significantly distinguishable from multiple ethnic groups representing all three AA branches and AA Semitic speakers as a whole (p-val > 0.01), consistent with the NegedeWoyto sharing ancestry most recently with AA speakers. Their relatively high amount of Egyptian ancestry (34%) is consistent with the group’s own origin narrative of a migration from Egypt by way of the Abay river. Scholars have also proposed possible genealogical relationships with the Beta Israel and/or Agaw; we observe a high genetic similarity between Negede Woyto and each of these groups though with some degree of recent isolation among them.  
Thus, the ambiguous linguistic classification of two groups is clarified by close genetic ties to the Nilo-Saharan Mezhenger population to the hunter-gather Shabo population in one case (as suspected but shown less clearly from prior investigations) and Egyptian origins consistent with oral traditions for the NegedeWoyto with the other. Continuing in the results section:
Recent intermixing among different groups is associated with shared culture  
For all pairwise combinations of 47 ethnic groups from the SNNPR where we had more detailed cultural information, we also calculated cultural distance as the number of 31 reported cultural practices, primarily related to marriage traditions, that were shared between each pair, with and without weighting by the relative rarity of each practice. In each case, we found a significant association between genetic similarity and reporting of shared cultural traits under the “Ethiopia-internal” analysis (Mantel-test p-value < 0.01), which remained after accounting for geographic or elevation distance (partial Mantel-test p-value < 0.025) or language group (partial Mantel-test p-value < 0.025). This association disappeared under the “Ethiopia-external” analysis, suggesting that ethnicities sharing cultural traits can be ancestrally quite different.  
As an illustration, we find strong genetic similarity -- beyond that explained by spatial distance -- between the Suri, Mursi, and Zilmamo, the only three Ethiopian ethnic groups that share the practice (not included among the 31) of wearing decorative lip plates, in a manner consistent with recent shared ancestry between these three groups and recent isolation from others. Among the 31 cultural traits, six out of the 20 reported by more than one ethnic group exhibited significantly higher (p-value < 0.05) genetic similarity among ethnic groups participating in the practice relative to those who did not participate or whose participation in the practice was unknown. These six cultural traits were male circumcision, female circumcision and four different marriage practices: arrangement by parents, abduction, sororate/cousin, and belt-giving.  
Assuming that individuals have not changed ethnic labels, these findings are consistent with some groups that share cultural practices splitting from one another relatively more recently and/or recently intermixing. To distinguish between these two possibilities, we determined whether two individuals from different groups showed evidence of sharing recent ancestors in a manner consistent with recent genetic exchange between the groups. In particular, only in the scenario where two groups have recently intermixed do we expect some pairings of individuals from the two groups to share a most recent common ancestor (MRCA) for atypically long segments of DNA relative to those shared among all other pairings of individuals from the two groups. Therefore, to test for evidence of recent intermixing between two groups, we assess whether some pairings of individuals, one from each group, have average inferred MRCA segments that are over 2.5 centimorgans (cM) longer than the median length of average inferred MRCA segments across all such pairings of individuals from the two groups. We see such a trend in 134 (12.9%) of 1035 (= 46 choose 2) total pairings of groups considered in this analysis, versus in 11 (20%) of 55 pairings involving male circumcision and 7 (23.8%) of 21 pairings involving Sororate/Cousin marriages. We also see this trend in the AA Cushitic-speaking Dasanech and NS-speaking Nyangatom, who share practices of arranged and abduction marriages. These two groups belong to different language families and show different genetic patterns on average under the “Ethiopia-external” analysis, which is inconsistent with them having recently split. However, they reside near each other, which can be conducive to intermixing and sharing culture, and occasionally cluster together, suggesting some individuals from the two groups are genetically inseparable by our approach. In addition, under the “Ethiopia-internal” analysis, GLOBETROTTER infers reciprocal admixture events 15 generations ago (95% CI: 11-19gen) between the cluster containing the majority of Dasanech (cluster 14) and the cluster containing the majority of Nyangatom (cluster 10). 
Thus, key cultural practices are associated with intermarriage across group lines even for genetically, ethnically and linguistically distinct populations that are geographically close to each other, again, an unsurprising result, but a result that now has more than a conjectural foundation.

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