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Researchers Map Out Neanderthal, Denisovan Ancestry in Modern Humans

NEW YORK (GenomeWeb) – A team of researchers from Harvard Medical School and University of California, Los Angeles have traced segments of the human genome back to Denisovan and Neanderthal origins, finding that South Asians have a little more Denisovan ancestry than expected.

As Harvard's David Reich and his team reported in Current Biology today, the genes that modern human populations inherited from archaic hominins have since been under both positive and negative selection. They further placed the timing of the human-Denisovan admixture event as occurring after the one that took place between the ancestors of modern humans and Neanderthals.

"There are certain classes of genes that modern humans inherited from the archaic [hominins] with whom they interbred, which may have helped the modern humans to adapt to the new environments in which they arrived," Reich said in a statement. "On the flip side, there was negative selection to systematically remove ancestry that may have been problematic from modern humans. We can document this removal over the 40,000 years since these admixtures occurred."

Reich and his team teased out spots in the genomes of modern-day, out-of-Africa humans that are derived from Denisovans by searching for derived alleles that are found in Denisovan genomes, but not in the genomes of Neanderthals or sub-Saharan Africans. Using the same approach, they likewise uncovered regions in the genomes of modern out-of-Africa humans that are derived from Neanderthals.

Based on this and decay rate data, they traced the timing of the admixture events between Denisovans and humans and between Neanderthals and humans. They pegged the Denisovan-human admixture event to have taken place about 1,000 generations ago, or between 44,000 years and 54,000 years ago. Similarly, they placed the Neanderthals-human admixture event to have taken place 1,121 generations ago.

Reich and his colleagues also applied their method to tease out the archaic hominin ancestry of 257 high-coverage genomes from 120 diverse human populations of the Simons Genome Diversity Project. This dataset, they noted, includes 20 Oceanian individuals from populations that are known to have high levels of Denisovan ancestry. For each individual, the researchers inferred archaic ancestry segments across their autosomes and chromosome X.

As expected, they found that Denisovan ancestry was higher in Oceanians like New Guineans and Australians than in other non-Africans and that higher levels of Neanderthal and Denisovan ancestry were present in eastern non-Africans than West Eurasians.

Intriguingly, though, Reich and his colleagues noticed increased Denisovan ancestry in South Asians from the Himalayas and from South and Central India. Sherpas, they reported, have an estimated 0.10 percent Denisovan ancestry. While this isn't entirely unexpected — as the EPAS1 allele that has enabled Tibetans to adapt to high-altitude life is likely of Denisovan origin — after accounting for that known gene of likely Denisovan origin, the researchers said that some South Asian groups still had a higher-than-expected amount of Denisovan ancestry.

Reich and his colleagues said that this could be due to a single Denisovan introgression into modern humans that was then diluted to different extents in Oceanians, South Asians, and East Asians. Alternatively, they said it could indicate that at least three distinct Denisovan introgressions into the ancestors of modern humans occurred.

Some parts of the modern human genome are more, and others less likely to harbor genes of archaic hominin origin, Reich and his colleagues found. They uncovered 38 regions of the human genome with increased levels of Neanderthal ancestry and 48 regions with increased Denisovan ancestry.

These regions with high Neanderthal ancestry include genes involved in skin and hair, while those with high Denisovan ancestry include genes involved in fat metabolism and the perception of subtle scents.

At the same time, four regions of the human genome conspicuously lacked both Neanderthal and Denisovan ancestry. One such desert, the researchers noted, encompasses the FOXP2 gene, which is thought to have a key role in modern human speech and language.

They also noted a reduction of both Neanderthal and Denisovan ancestry on chromosome X as well as in testes-related genes. This suggested to the researchers that admixture between archaic hominins and the ancestors of modern humans was likely associated with decreased male fertility.