A international team of researchers has completed one of the most detailed analyses of a Neanderthal genome to date. Among the many new findings, the researchers learned that Neanderthals first mated with modern humans a surprisingly long time ago, and that humans living today have more Neanderthal DNA than we assumed.
Image courtesy James Ives.
Before this new study, only four Neanderthal specimens have had their genomes sequenced. Of these, only one — an Altai Neanderthal found in Siberia — was of sufficient quality, where scientists were able to accurately flag variations in the genome. The new analysis, enabled by a remarkably well-preserved genome taken from a 52,000 year old bone fragment, is now the second Neanderthal genome to be fully sequenced in high fidelity. The resulting study, now published in Science, confirms a bunch of things we already knew about Neanderthals, while also revealing some things we didn't know.
The international research team that conducted this study — a group led by Kay Prüfer and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany — sequenced the genome of a female Neanderthal, dubbed Vindija 33.19, whose remains were uncovered at Vindija Cave in northern Croatia. By studying Neanderthal genomes in detail, and by comparing their DNA to those of modern humans, scientists can learn more about our evolutionary history and biology. And indeed, the researchers made some interesting discoveries.
Based on previous archaeological and genetic evidence, archaeologists and anthropologists suspected that Neanderthals were thinly dispersed across Europe and Asia. The lack of genetic diversity (low heterozygosity) in the Vindija 33.19 specimen affirms these earlier findings, showing that Neanderthals "lived in small and isolated populations" and "with an effective population size of around 3000 individuals," the researchers write in their study.
The earlier genomic analysis of the female Altai Neanderthal showed that her parents were half-siblings, which got scientists thinking that Neanderthals made it a habit of breeding with immediate family members. But the Vindija 33.19 genome is different; her parents were not as closely related, so we can no longer say that extreme inbreeding is a common fixture of the Neanderthals. That said, the Croatian Neanderthal shared a maternal ancestor with three other individuals found in the Vindija Cave (whose genomes aren't nearly as complete).
The previous Altai Neanderthal study also suggested that Neanderthals starting breeding with archaic modern humans around 100,000 years ago, but the new analysis pushes that back even further to between 130,000 to 145,000 years ago. The location of these sub-species encounters probably happened in the Middle East or the Arabian Peninsula, but before modern humans spread en masse into Europe and Asia.
A comparative analysis of the Vindija 33.19 DNA to living humans resulted in an uptick in the amount of genes retained by Homo sapiens. When our ancestors mated with Neanderthals, we absorbed and retained some of their genes — some good, and some bad (more on this in just a second). Some of these genes have been lost forever (due to natural selection weeding out unfavourable inherited traits), but some have stuck around. Prüfer and Pääbo say that, based on the new high-quality genome, modern populations carry between 1.8 to 2.6 per cent Neanderthal DNA — that's higher than the previous estimates of about 1.5 to 2.1 per cent. More specifically, East Asians have about 2.3 to 2.6 per cent Neanderthal DNA, while people from western Europe and Asia have retained about 1.8 to 2.4 per cent DNA. African populations have virtually none because their ancestors did not mate with Neanderthals.
Finally, the researchers were able to identify the functions of the gene variants that are still exerting a force on humans today. These include genes associated with plasma levels of LDL cholesterol and vitamin D, eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia, and response to antipsychotic drugs. "This adds to mounting evidence that Neanderthal ancestry influences disease risk in present-day humans, particularly with respect to neurological, psychiatric, immunological, and dermatological phenotypes [disease of skin, nails, hair]," write the researchers. Some of these inherited characteristics allowed modern humans to survive outside of Africa, but now make us susceptible to diseases today.
Anne Stone, an anthropological geneticist at Arizona State University who wasn't involved in the study, says the most surprising thing about the new research is that the scientists were able to acquire such a beautifully preserved genetic sequence.
"From that information, however, I think what was most interesting to me was the evidence that ancient modern humans interbred with Neanderthals really early (we see this in the Neandertal genomes) during a time that was prior to when we think the big movement out of Africa occurred (that resulted in the colonization of the rest of the world by modern humans)," Stone told Gizmodo. "The other surprising aspect was that the level of genetic diversity was similar to that seen in some isolated modern human populations. This is different from what was seen in the Altai Neandertal who was quite inbred."
An aspect of the study that did not surprise Stone — but one she found cool nonetheless — was that the Vindija 33.19 individual was more closely related to the population of Neanderthals that interbred with ancient modern humans who had moved out of Africa. "This is not surprising given the location of the cave [which is] much closer to the area where we think this happened," she said.
Pretty amazing what scientists can learn from a 52,000-year-old strand of DNA.