Several Denisovan Populations Introgressed into Modern Humans Multiple Times: Study

The identification of a new hominin group called Denisovans was one of the most exciting discoveries in human evolution in the last decade. Unlike Neanderthal remains, the Denisovan fossil record consists of only several skeletal fragments. According to new research, several Denisovan populations, who likely had an extensive geographical range, were adapted to distinct environments and passed on some of their genes via multiple, distinct interbreeding events that helped shape early human history.

Denisovans are an extinct hominin group initially identified from a genome sequence determined from a fragment of a finger bone found at Denisova Cave in the Altai Mountains in southern Siberia.

“This was one of the most exciting discoveries in human evolution in the last decade,” said Dr. Linda Ongaro, a researcher at Trinity College Dublin.

Subsequent analyses of the genome have shown that Denisovans diverged from Neanderthals 400,000 years ago and that at least two distinct Denisovan populations mixed with ancestors of present-day Asians.

The only physical remains of Denisovans discovered so far are a fragmentary finger bone, three teeth, and a skull fragment from Denisova Cave; and a jawbone and a rib bone from Baishiya Karst Cave at the northeast margin of the Tibetan Plateau.

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

“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 their new paper, Dr. Ongaro and her colleague, Professor Emilia Huerta-Sanchez of Trinity College Dublin and Brown University, outlined 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 outlined a number of genes of Denisovan origin that gave modern day humans advantages in their different environments.

“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,” Dr. Ongaro said.

“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.”

The paper was published in the journal Nature Genetics.

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L. Ongaro & E. Huerta-Sanchez. A history of multiple Denisovan introgression events in modern humans. Nat Genet, published November 5, 2024; doi: 10.1038/s41588-024-01960-y