Genetic map shows how ancient interbreeding affects modern humans

The majority of Asians and Europeans possess at least some genetic material that originated from Neanderthals and another kind of ancient human known as Denisovans, and that DNA could help explain some of the differences that have evolved in modern humans, a new study claims.

In the latest edition of the journal Current Biology, researchers from Harvard Medical School and UCLA reveal new research suggesting that people of South Asian heritage may have more Denisovan DNA than Neanderthal, and proposing that the ancestors of modern humans interbred with the former approximately 100 generations after their liaisons with the latter.

Their research resulted in an new map of human ancestry, and using comparative genomics, they predicted where genes from Denisovan and Neanderthal could be affecting both the anatomy and physiology of modern humans. For example, they report that Neanderthal genes might contribute to tougher hair and skin, while Denisovan DNA could be why the peoples of Papua New Guinea have a more subtle sense of smell and those living in Tibet are adapted to high-altitude living.

As Harvard geneticist and lead author David Reich explained Monday in a statement, “There are certain classes of genes that modern humans inherited from the archaic humans with whom they interbred, which may have helped the modern humans to adapt to the new environments in which they arrived. On the flip side, there was negative selection to systematically remove ancestry that may have been problematic from modern humans.”

Oceania home to most ancient DNA; Asians have most Denisovan genes

Reich and his colleagues discovered evidence that past ancestry from both the Neanderthals and the Denisovans have been lost from the X chromosomes of modern humans, as well as in genes expressed in the male testes. This has likely resulted in reduced male fertility, which is common in hybrids between two highly divergent groups of the same species, they explained.

Their findings are based on a comparison of known Neanderthal and Denisovan gene sequences across more than 250 genomes from 120 non-African populations. The sequences were obtained through a public database and analyzed using a machine-learning algorithm capable of telling the difference between specific components of ancestral DNA.

Based on their analysis, Reich’s team reported that people living in Oceania have the highest percentage of archaic ancestry, and that south Asians have a higher amount of Denisovan DNA than previously believed, indicating the existence of instances of interbreeding which previously had not been identified. Western Eurasians were found to have the lowest concentration of non-modern human DNA among non-Africans, according to the study authors.

Reich said that the interactions between modern humans and their ancient ancestors throughout the years were “complex and perhaps involved multiple events.” His team’s research comes on the heels of a similar study, published earlier this month in the journal Science, which reported that there were at least three known encounters between modern people and their predecessors over a 60,000 year span, and that fossil evidence suggests there may have been two others.

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This map shows the proportion of the genome inferred to be Denisovan in ancestry in diverse non-Africans. The color scale is not linear to allow saturation of the high Denisova proportions in Oceania (bright red) and better visualization of the peak of Denisova proportion in South Asia. Credit: Sankararaman et al./Current Biology 2016

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