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Study Tallies Human Adaptations Helped Along by Neanderthal, Denisovan DNA

NEW YORK (GenomeWeb) – A new study has identified potentially adaptive genome sequences that seem to stem from ancient admixture between humans and archaic hominins such as Neanderthals or Denisovans.

Researchers from the University of Washington examined genome sequences from more than 1,500 individuals around the world, alongside refined genome maps for Neanderthals and Denisovans. The study, published today in Current Biology, uncovered 126 loci stemming from archaic admixture that appear to remain at relatively high frequency in the human genome, suggesting they may have helped humans adapt to some of the environmental factors they faced when migrating out of Africa.

Among the archaic sequences found at higher-than-anticipated frequency in the human genome, the team highlighted Neanderthal or Denisovan sequences that appear to contribute to adaptive traits such as immunity and skin pigmentation.

"The ability to increase to such high population frequencies was most likely facilitated because these sequences were advantageous," senior author Joshua Akey, a researcher in the Department of Genome Sciences at the University of Washington, said in a statement.

Past studies indicate that roughly 2 percent of the human genome was passed down from ancient mixing with Neanderthals in individuals in populations living outside of Africa, while another 2 percent to 4 percent of human DNA seems to have originated from Denisovans in Melanesian individuals, the team noted.

In studies published earlier this year, two teams described potential roles for Neanderthal sequences in innate immunity, particularly those related to the Toll-like receptor genes TLR6, TLR1, and TLR10. In those studies, Neanderthal versions of these genes seemed to be maintained in the human genome, while other Neanderthal sequences had apparently been culled over time. Other research hints that Denisovan sequences may also contribute to adaptive traits, such as altitude tolerance in Tibetan populations.

To delve into additional adaptive traits related to archaic admixture, Akey and colleagues analyzed more than a billion bases of Neanderthal sequence and more than 300 million bases of Denisovan sequence in samples from 504 individuals from East Asia, 503 individuals from Europe, 489 South Asians, and 27 individuals from Island Melanesia.

Based on the presence or absence of SNP markers for known archaic sequences, the team narrowed in on 126 loci where the frequency of Neanderthal or Denisovan DNA was higher-than-anticipated for sequences with neutral adaptive effects — a set that included seven sites described in past adaptive introgression analyses.

Most of the potential adaptive archaic sequences were present in just one human population tested, the researchers explained, with high frequency archaic sequences in European, East Asian, and South Asian populations all corresponding to Neanderthal sequences. Neanderthal haplotypes also made up more than half of the suspected adaptive loci in Melanesians, even though Denisovan sequences tend to be more abundant overall in this population.

When the team took a closer look at four dozen high-frequency archaic haplotypes, it tracked down 13 apparent expression quantitative trait loci, which appear to influence the expression of at least 34 genes in one or more tissues. The archaic haplotypes tended to influence genes involved in everything from skin or hair pigmentation to immune activity, including response to viruses.

The researchers noted that the Neanderthal version of Toll-like receptor genes described in prior studies of adaptive sequences from archaic hominins was present in more than one third of individuals from East Asia, but found at lower frequency in populations from Europe and South Asia and in just 6 percent of Melanesians.

"Our results demonstrate that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments," the authors wrote, noting that "better geographic representation would accelerate efforts to understand adaptively introgressed loci, and more generally, human genomic diversity."