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Evidence of Ancient Admixture Found in Genomes of Modern West Africans

NEW YORK – Researchers have uncovered hints of ancient admixture with an unknown archaic hominin within the genomes of four modern West African populations.

Archaic hominins interbred with the ancestors of modern humans, as Neanderthal genes have been found among modern non-Africans — and, recently, among modern Africans — while Denisovan genes have been noted in Oceanians and eastern non-Africans. A recent study also hinted that the ancestors of modern-day sub-Saharan Africans interbred with an archaic human group

A pair of researchers from the University of California, Los Angeles, examined whole-genome sequencing data from modern-day Yoruban, Esan, Gambian, and Mende populations to uncover evidence of archaic introgression from an unknown hominin population that likely split from the human lineage before Neanderthals did.

"The signals of introgression in the West African populations that we have analyzed raise questions regarding the identity of the archaic hominin and its interactions with the modern human populations in Africa," UCLA's Arun Durvasula and Sriram Sankararaman wrote in their paper, which appeared Wednesday in Science Advances.

The researchers calculated the conditional site frequency spectrum — the frequency of derived alleles in a modern population where the allele from an archaic individual was also derived — for Yorubans as compared to Neanderthals. Under a demographic model in which the ancestors of modern and archaic humans split with no subsequent gene flow and alleles are neutrally evolving, this spectrum is expected to be uniformly distributed. 

But in this case, the spectrum was U-shaped, the researchers reported. That shape held even when they performed the analysis using Denisovans. Similar U-shapes were produced when they analyzed data from the Esan, Gambian, and Mende populations.

The shape was also unchanged when they modeled variations in recombination rate, background selection, and biased gene conversion.

The researchers examined whether current human demographic models could account for this shape. For instance, they studied a model that included interbreeding events between Neanderthals, Denisovans, and modern humans, such as introgression from Neanderthals into non-Africans as well as from early modern humans into Neanderthals and into Denisovans from an unknown archaic hominin population. This model and other current demographic models they tested, though, did not account for the pattern observed.

Instead, a scenario in which modern West Africans can trace part of their ancestry to a population that split from the ancestors of modern humans and Neanderthals before the ancestors of Neanderthals and modern humans themselves diverged could account for this pattern.

This putative archaic hominin population likely split from the ancestors of Neanderthals and modern humans between 360,000 years and 1.02 million years ago and introgressed into the ancestors of West Africans between 0 and 124,000 years ago. They estimated that this archaic hominin population contributed between 5 percent and 19 percent of the ancestry of these West African populations and that the introgressing archaic hominin population had a large effective population size of about 25,000.

Variations on this model could also explain the U-shaped pattern they observed, the researchers noted. For instance, while this introgression event may have occurred recently, it also could have involved multiple archaic hominin populations over a longer stretch of time.

"A detailed understanding of archaic introgression and its role in adapting to diverse environmental conditions will require analysis of genomes from extant and ancient genomes across the geographic range of Africa," the researchers wrote in their paper.

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