Ethiopian Genetic Diversity

[Angela]

See: Luca Pagani (Mark Thomas, Chris Tyler-Smith)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3397267/

"Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool"

"[FONT=&quot]Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified “African” and “non-African” haplotypic components for each Ethiopian individual. The non-African component, which includes the [/FONT]SLC24A5[FONT=&quot] allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations."

We've had papers before finding "Non-African" in the horn. One paper dubbed it "Sardinian" like, which is clearly just a way of saying ancient "farmer" like. Here they point to the Levant.

The following is unusual. If the influx was from the Levant, why is the influence so much more on the mtdna? We usually see male mediated migrations.

"[/FONT][FONT=&quot]Similarly, genetic studies indicate that a major component of recent Ethiopian ancestry originates outside Africa: for example, half of the mtDNA haplotypes[/FONT][FONT=&quot]16[/FONT][FONT=&quot] and more than one-fifth of Y haplotypes[/FONT][FONT=&quot]17[/FONT][FONT=&quot] found in Ethiopia belong to lineages that, on the basis of phylogeographic criteria, have been attributed to a non-African rather than a sub-Saharan African origin."

I think they're getting thrown off because ROLL OFF like all these timing algorithms only picks up the last admixture. 3,000 years ago is only the last admixture, imo. They themselves recognize the problem to some extent: "[/FONT][FONT=&quot]Assuming that the African and non-African components of the Ethiopian genomes result from a single admixture event, we used ROLLOFF[/FONT][FONT=&quot]39[/FONT][FONT=&quot] to estimate the midpoint of the period of admixture. However, if there were multiple or continuous admixture events, as with the North African populations, this method detected[/FONT][FONT=&quot]39[/FONT][FONT=&quot] the most recent event or the admixture midpoint, respectively. " They should have included the last statement in the abstract or people will quote the abstract for an incorrect proposition.

[/FONT][FONT=&quot]"The first PC of the African samples separates sub-Saharan Africans from North Africans, with Ethiopians positioned between them ([/FONT]Figure 1[FONT=&quot]A), whereas the second and third components separate the hunter-gatherers (click speakers and Pygmies) and the East Africans, respectively ([/FONT]Figures 1[FONT=&quot]A and 1B). Both plots separate the Ethiopian samples according to their linguistic origin. This linguistic clustering appears to be more important than geographical structure, especially for the Semitic and Cushitic populations ([/FONT]Figure 1[FONT=&quot]D), and is also supported by the neighbor-joining tree of [/FONT]Figure S2[FONT=&quot]. Remarkably, the Ethiopian clusters, taken together, span half of the space delimited by all the African populations and surround the Maasai from Kenya."

[/FONT]

 

[Jovialis]

The Genetic Palimpsest Of The Horn Of Africa

https://www.gnxp.com/WordPress/2019/01/10/the-genetic-palimpsest-of-the-horn-of-africa/

 

[Ygorcs]

I wonder if they what they're identifying as a non-African component with more affinity to Levantines is actually an artifact of the lack of much more proximate admixture sources in Neolithic/Chalcolithic North Africa (where Levant_Neolithic ancestry probably met and mixed extensively with the already somewhat related North African indigenous people) and in the Bronze Age Arabian Peninsula (possibly a very Levant_Neolithic population later diluted by Iranian_Chalcolithic). I always find it a bit strange that most of these genomic studies on African populations seem to ignore the possibility of North African migration altogether or just presume that they were all basically "Levantines". Maybe due to the lack of sufficient ancient DNA for other areas, it seems North Africa is still kind of neglected, despite the decisive role of Egypt in that region's history and so on. Do you remember that recent study (was it the Dzudzuana one?) which concluded that in fact Natufians already carried North African ancestry, not just the other way around?

I happen to think, based on some genetic and linguistic evidences, that the Cushitic expansion probably came from North Africa with the hunter-gatherers indigenous to the region who learned agriculture and especially pastoralism from the Levantines, partially mixing with them (Natufian and descendants). That must've been the first non-African influx into the Horn of Africa, and later the non-African component was completed by the Semitic influx (which makes much more sense having come from South Arabia, because the Semitic Ethiopian languages are closely related to South Arabian Semitic languages, not to the Semitic languages of the Levant, unless the Levant was once populated by South Semitic speakers pushed southward later - but I really doubt that could've still be the case ~3000 years ago, when Canaanite languages were already attested there).

 

[Govan]

I wonder if they what they're identifying as a non-African component with more affinity to Levantines is actually an artifact of the lack of much more proximate admixture sources in Neolithic/Chalcolithic North Africa (where Levant_Neolithic ancestry probably met and mixed extensively with the already somewhat related North African indigenous people) and in the Bronze Age Arabian Peninsula (possibly a very Levant_Neolithic population later diluted by Iranian_Chalcolithic). I always find it a bit strange that most of these genomic studies on African populations seem to ignore the possibility of North African migration altogether or just presume that they were all basically "Levantines". Maybe due to the lack of sufficient ancient DNA for other areas, it seems North Africa is still kind of neglected, despite the decisive role of Egypt in that region's history and so on. Do you remember that recent study (was it the Dzudzuana one?) which concluded that in fact Natufians already carried North African ancestry, not just the other way around?

I happen to think, based on some genetic and linguistic evidences, that the Cushitic expansion probably came from North Africa with the hunter-gatherers indigenous to the region who learned agriculture and especially pastoralism from the Levantines, partially mixing with them (Natufian and descendants). That must've been the first non-African influx into the Horn of Africa, and later the non-African component was completed by the Semitic influx (which makes much more sense having come from South Arabia, because the Semitic Ethiopian languages are closely related to South Arabian Semitic languages, not to the Semitic languages of the Levant, unless the Levant was once populated by South Semitic speakers pushed southward later - but I really doubt that could've still be the case ~3000 years ago, when Canaanite languages were already attested there).

Indeed.

In fact alot of E1b1b lineages in Ethiopia moved down from North Africa alongside Eurasian mtDNAs.

I think they just lack Mesolithic /Neolithic Egypt and Sudan aDNA. They just stated the profile ressembles the Levant but they don't go into further complicated details not backup by ancient DNA.

 

[Ygorcs]

Considering the presence of 3 highly (really highly) divergent Afro-Asiatic families in or near Ethiopia, I think at least 3 admixture events with non-Subsaharan people should be considered: an earlier one bringing language groups such as Omotic, probably the first wave of North African Afro-Asiatic peolpe (Ehret places his "Afrasian" in Mediterranean North Africa and the Red Sea coastal hills); later, with pastoralists and farmers, the Cushites; and finally the Arabian Semites.

As Govan said, I think some of that Eurasian MtDna x African Y-DNA may be an artifact ofa situation that already existed in the homeland of the immigrants that later settled in Ethiopia, especially the earlier, non-Semitic Afro-Asiatic people. The Semites were a different thing altogether, a northern extension, with much more "Middle Eastern" Y-DNA haplogroups (J1, J2, G2 and so on) and autosomally much more shifted toward Anatolian_Neolithic and especially Iranian_Neolithic. I wonder how Egyptian would fit in that scenario, but I presume they'd originally be like a mid term between the more West Asian Semitic (northeast) and the more North African Berbers and early Cushites.

 

[Angela]

Considering the presence of 3 highly (really highly) divergent Afro-Asiatic families in or near Ethiopia, I think at least 3 admixture events with non-Subsaharan people should be considered: an earlier one bringing language groups such as Omotic, probably the first wave of North African Afro-Asiatic peolpe (Ehret places his "Afrasian" in Mediterranean North Africa and the Red Sea coastal hills); later, with pastoralists and farmers, the Cushites; and finally the Arabian Semites.

As Govan said, I think some of that Eurasian MtDna x African Y-DNA may be an artifact ofa situation that already existed in the homeland of the immigrants that later settled in Ethiopia, especially the earlier, non-Semitic Afro-Asiatic people. The Semites were a different thing altogether, a northern extension, with much more "Middle Eastern" Y-DNA haplogroups (J1, J2, G2 and so on) and autosomally much more shifted toward Anatolian_Neolithic and especially Iranian_Neolithic. I wonder how Egyptian would fit in that scenario, but I presume they'd originally be like a mid term between the more West Asian Semitic (northeast) and the more North African Berbers and early Cushites.

I think that makes a great deal of sense.

 

[Megalophias]

I do too. Moroccan aDNA from the Palaeolithic and Early Neolithic was all E-M35 + U6 and M1, and Palaeolithic Israel had E-M35 + R0, JT, and N1 (and a very large proportion of Horner uniparental markers are related to these). Not many sites tested, but it would make sense that Northeast Africa in between would also have this Eurasian mtDNA-African Y DNA mix before the Neolithic, likely people related to Taforalt and Natufians though who knows exactly how. Then some Levantine Neolithic gene flow together with domestic livestock and such, bringing back some more E-M35 again plus maybe T etc, and pastoralists spreading south during the Green Sahara to mix with Nilo-Saharan-type people and colonize the Horn from Sudan.

But very likely PPNB herders moved into Arabia at the same time they were spreading into North Africa; there may have been related populations on both sides of the Red Sea much of the time anyway, which makes it hard to distinguish routes into the Horn. The archaeology doesn't seem terribly clear, the Horn had contact with both Sudan and Yemen when pastoralism first appeared.

 

[Ygorcs]

I do too. Moroccan aDNA from the Palaeolithic and Early Neolithic was all E-M35 + U6 and M1, and Palaeolithic Israel had E-M35 + R0, JT, and N1 (and a very large proportion of Horner uniparental markers are related to these). Not many sites tested, but it would make sense that Northeast Africa in between would also have this Eurasian mtDNA-African Y DNA mix before the Neolithic, likely people related to Taforalt and Natufians though who knows exactly how. Then some Levantine Neolithic gene flow together with domestic livestock and such, bringing back some more E-M35 again plus maybe T etc, and pastoralists spreading south during the Green Sahara to mix with Nilo-Saharan-type people and colonize the Horn from Sudan.

But very likely PPNB herders moved into Arabia at the same time they were spreading into North Africa; there may have been related populations on both sides of the Red Sea much of the time anyway, which makes it hard to distinguish routes into the Horn. The archaeology doesn't seem terribly clear, the Horn had contact with both Sudan and Yemen when pastoralism first appeared.

I think that considering the date we have amassed until now what you say is the most plausible hypothesis. In a more bolder speculation, I tend to think that Afro-Asiatic languages were born in North Africa with the indigenous peoples who also seem to have contributed to the Natufians and possibly lent them their language, too. Later the descendants of Natufians migrated to North Africa and to other parts of West Asia north and east of the South Levant, possibly being the origin of Proto-Semitic and (who knows?) even Proto-Egyptian. And the Afro-Asiatic North African subgroups, mixed (but not nearly replaced as the WHG) with those Eurasian-enriched farmers and herders (maybe a bit of Southern European EEF inflow, at least in the Maghreb, too), absorbed the new economic package and then could expand southward into the Sahel and Horn of Africa.