New Clues Reveal How Denisovan DNA Shaped Early Human Evolution

Scientists believe individuals of the most recently discovered “hominin” group (the Denisovans) that interbred with modern day humans passed on some of their genes via multiple, distinct interbreeding events that helped shape early human history.

In 2010, the first draft of the Neanderthal genome was published, and comparisons with modern human genomes revealed that Neanderthal and modern humans had interbred in the past.

A few months later, analysis of a genome sequenced from a finger bone excavated in the Denisova cave in the Altai mountains in Siberia revealed that this bone fragment was from a newly discovered hominin group that we now call Denisovans, who also interbred with modern humans.

“This was one of the most exciting discoveries in human evolution in the last decade,” said Dr Linda Ongaro, Postdoctoral Research in Trinity College Dublin’s School of Genetics and Microbiology, and first author of a fascinating new review article published in leading international journal Nature Genetics.

“It’s a common misconception that humans evolved suddenly and neatly from one common ancestor, but the more we learn the more we realise interbreeding with different hominins occurred and helped to shape the people we are today.

“Unlike Neanderthal remains, the Denisovan fossil record consists of only that finger bone, a jawbone, teeth, and skull fragments. But by leveraging the surviving Denisovan segments in Modern Human genomes scientists have uncovered evidence of at least three past events whereby genes from distinct Denisovan populations made their way into the genetic signatures of modern humans.”

Each of these presents different levels of relatedness to the sequenced Altai Denisovan, indicating a complex relationship between these sister lineages.

In the review article, Dr Ongaro and Prof. Emilia Huerta-Sanchez outline evidence suggesting that several Denisovan populations, who likely had an extensive geographical range from Siberia to Southeast Asia and from Oceania to South America, were adapted to distinct environments.

They further outline a number of genes of Denisovan origin that gave modern day humans advantages in their different environments.

Dr Ongaro added: “Among these is a genetic locus that confers a tolerance to hypoxia, or low oxygen conditions, which makes a lot of sense as it is seen in Tibetan populations; multiple genes that confer heightened immunity; and one that impacts lipid metabolism, providing heat when stimulated by cold, which confers an advantage to Inuit populations in the Arctic.

“There are numerous future directions for research that will help us tell a more complete story of how the Denisovans impacted modern day humans, including more detailed genetic analyses in understudied populations, which could reveal currently hidden traces of Denisovan ancestry. Additionally, integrating more genetic data with archaeological information – if we can find more Denisovan fossils – would certainly fill in a few more gaps.”

Reference: Ongaro L, Huerta-Sanchez E. A history of multiple Denisovan introgression events in modern humans. Nat Genet. 2024. doi: 10.1038/s41588-024-01960-y

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