Scientists have successfully sequenced the genome of a man who was alive 45,000 years ago, which makes the resulting sequence the oldest one researchers have ever obtained from a modern human.
“The next oldest human for which we have genome sequence is the 24,000 year old Mal’ta boy,” says Janet Kelso, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and a co-author of the study published today in Nature. And the quality of the genome Kelso managed to produce is “as good as the genome sequences that are available for present-day people.”
In the study, researchers sampled bone material from a thigh bone that was found in 2008 on the banks of the river Irtysh, near Siberia’s Ust’-Ishim settlement. They used collagen taken from the bone to date it, and DNA samples to sequence the man’s genome. Once they had the full sequence, they were able to compare it to that of present-day humans, and count the “missing mutations” in the Ust’-Ishim man’s genome — mutations that had yet to occur in the human lineage.
“Given that we know that the Ust’-Ishim individual is 45,000 years old, we can calculate how many mutations accumulate per site per year,” Kelso says. And “we find between one and two mutations per year accumulated in the genomes of populations in Europe and Asia since the Ust’-Ishim man lived.”
Mapping this man’s genome helped the researchers gain a better understanding of the relationship between ancient Ust-Ishim human populations and present-day humans. “We found that this Ust’-Ishim individual is equally closely related to present-day Asians and to early Europeans,” Kelso says. This means that the population to which this man belonged probably diverged from Europeans and Asians around the same time, or slightly before, these two groups diverged from one another.
If that’s correct, the researchers write, it’s possible that this Siberian human population “failed to leave descendants among present-day populations.” Moreover, the presence of a human population in Siberia 45,000 years ago indicates that human migrations into Eurasia weren’t restricted to a southern route, as was previously suggested.
There’s more to this genome than its humanity, however. As it turns out, the Ust-Ishim man’s genome contains longer Neanderthal DNA segments than ours do today. This, Kelso says, doesn’t mean that he was “more Neanderthal” than we are — the amount of Neanderthal ancestry present in his genome is similar to ours — but it does hint that our own Neanderthal DNA segments were once longer than they are today and reduced in size over generations. In addition, dating the bone and producing a complete genome helped the researchers determine when his ancestors might have mixed with Neanderthals. Previous estimates have ranged from 37,000 years ago to 86,000 years ago, but Kelso and her colleagues think that a mixing event would have happened about 50,000 to 60,000 years ago — or about approximately 7,000 to 13,000 years before this individual was born. The genome didn’t provide evidence that this man or his ancestors had breed with Denisovans, however, a hominin population that’s thought to have bred with aboriginal people of Oceania.
Having this genome on hand provides a new, independent way of estimating human mutations rates, Kelso says. Usually, researchers either use phylogenetic trees — a method that allows researchers to count mutations between closely related species — or estimates of errors in DNA replication to determine mutation rates. Now, this genome can help researchers double-check their estimates. “By providing these genomes as public resources,” Kelso says, “we hope [to see] many more insights into the history of modern humans.”