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Presence of Ancient West Eurasian Ancestry in Southern, Eastern Africans Hints at Ancient Movements

NEW YORK (GenomeWeb News) – An analysis of genome-wide data suggests that genes from west Eurasian sources flowed into southern African populations through eastern African populations, according to a study appearing in the Proceedings of the National Academy of Sciences this week.

Southern Africa is home to a number of populations with diverse genetic as well as cultural and linguistic backgrounds that may have been influenced by mixture with other populations. In this study, researchers led by Harvard Medical School's David Reich focused on several southern African Khoisan populations — broadly defined as indigenous populations that speak non-Bantu languages with click consonants — and uncovered evidence of two admixture events, one of which traced back to a European or Middle Eastern population. Similarly, eastern African populations also showed a signal of west Eurasian ancestry.

"The most striking inference from this analysis is the presence of west Eurasian ancestry in southern Africa that we date to 900–1,800 [years] ago," Reich and his colleagues said. "Several lines of evidence suggest that the population that brought this ancestry to southern Africa was an already-admixed population from eastern Africa."

At the Biology of Genomes meeting last May, first author Joseph Pickrell, now at the New York Genome Center, noted that he and his colleagues had uncovered hints of ancestry from individuals resembling present-day populations in Italy in southern and eastern African populations, like the Ju|'hoansi. This apparent mixing, likely through an intermediate population in eastern African, underscored the effect of uncharacterized back-to-Africa gene flow.

For the PNAS study, Pickrell, Reich, and their colleagues turned to a dataset of some 1,040 people from 75 populations worldwide who were genotyped on the Affymetrix Human Origins array.

To characterize the extent and source of admixture in the Ju|'hoan_North population, the researchers compared weighted linkage disequilibrium between that group and the 74 other characterized populations using the software program ALDER. From this, the researchers found that Europeans appeared to be the likely source of the admixture signal, though some Middle Eastern populations also could be good proxies. By examining allele frequencies, the researchers confirmed that the signal likely originated from western Eurasians. They also estimated that this gene flow took place some 1,300 years ago.

This signal of relatedness to west Eurasian is found throughout other Khoisan populations, the researchers found. At the same time, they noted that there appeared to be multiple admixture signals.

Using a method they developed to study multiple admixture events, Reich and his colleagues found that a number of Khoisan populations, including the Xuun, G||ana, and Ju|'hoan_South, had evidence of two admixture waves.

Other populations, though, only appeared to have had a single admixture event, but the researchers pointed out that the fitted model didn't seem to fully explain the patterns they saw.

To increase their ability to detect admixture events by examining combined population sets, the researchers found further hints of secondary admixture events in additional populations. For instance, in a set combining Ju|'hoan_North and G|ui populations, they found evidence of a second, earlier admixture event, with the two events tracing back to about 30 generations ago and the other about 109 generations ago.

This, the researchers said, suggests that the population that introduced the west Eurasian ancestry into southern Africa was itself an admixed population, with its admixture dating back nearly 110 generations.

The researchers also calculated that Khoisan populations have varying levels of West Eurasian ancestry. For instance, they estimated that the Khoe-Kwadi-speaking groups had the highest levels of West Eurasian DNA, with the Nama population exhibiting about 14 percent West Eurasian ancestry.

Eastern Africans, especially Semitic and Cushitic-speaking groups, have even higher percentages of West Eurasian ancestry, especially Ethiopian populations, the researchers reported.

Using their approach for analyzing multiple admixture events, Reich and his colleagues noted evidence of multiple admixture events within eastern African populations, with most showing evidence for an admixture event dating back about 90 generations, or about 3,000 years ago.

As in the southern African populations, the west Eurasian admixture event with the eastern African populations was the more ancient admixture event.

"We conclude that the west Eurasian ancestry in southern Africa was likely brought by a migration of an already admixed population from eastern Africa," Reich and his colleagues said.

Still, they added that the ultimate source of this west Eurasian ancestry is an "open question."

While the archaeological record from that timeframe is limited, the researchers said that architecture in Ethiopia from this time period bears a strong resemblance to that of southern Arabia and the timing broadly coincides with the introduction of Ethiosemitic languages to Africa. Additionally, other linguistic evidence indicates that the predecessor to the Khoe-Kwadi languages of southern Africa arrived in that region from the influx of eastern African pastoralists.

Pulling together the genetic, archaeological, and linguistic data, Reich and his colleagues proposed that people from west Eurasia moved into Ethiopia some 3,000 years ago, distributing west Eurasian ancestry throughout the region. Then, that admixed population migrated from eastern Africa to southern Africa where another admixture event took place some 1,500 years ago.