Two separate teams of researchers have used advanced DNA sequencing methods to analyze the 52,000-year-old remains of a Neanderthal woman from Vindija Cave in Croatia, and the 34,000-year-old remains of four anatomically modern humans from the Upper Paleolithic archaeological site of Sunghir. The findings are published in two papers in the journal Science.
Neanderthals are the closest evolutionary relatives of all present-day humans and therefore provide a unique perspective on human biology and history.
Five Neanderthal genomes have been sequenced to date, yet only one yielded high-quality data, an individual found in Siberia known as the ‘Altai Neanderthal.’ Three less well-defined genomes come from individuals found in Croatia’s Vindija Cave and one from Mezmaiskaya Cave in the Republic of Adygea.
The first research team — Max Planck Institute for Evolutionary Anthropology researcher Kay Prüfer and co-authors — successfully analyzed billions of DNA fragments sampled from a new individual in the Croatian cave, dubbed Vindija 33.19.
Similar to previous findings, the genetic data suggest that Neanderthals lived in small and isolated populations of about 3,000 individuals.
The previously sequenced Altai Neanderthal genome suggested that the individual’s parents were half-siblings, prompting scientists to wonder if Neanderthals commonly interbred with family members — yet the genome of Vindija 33.19 does not have similar incestual patterns, suggesting that the extreme inbreeding between the parents of the Altai Neanderthal may not have been ubiquitous among Neanderthals.
“Vindija 33.19 does appear to share a maternal ancestor with two of the three other individuals from the Croatian cave who were genetically sequenced, however,” Dr. Prüfer and colleagues said.
They also analyzed divergences and gene flow among Neanderthals, Denisovans (another extinct species of hominin), and modern humans.
Among many findings, they found that early modern human gene flow into Neanderthal populations occurred between 130,000 and 145,000 years ago, before the Croatian and Siberian Neanderthals diverged.
Based on the new high-quality genome, the scientists estimate that modern non-African populations carry between 1.8-2.6% Neanderthal DNA, which is higher than previous estimates of 1.5-2.1%.
They also identified a wealth of new gene variants in the Neanderthal genome that are influential in modern day humans, including variants related to plasma levels of LDL cholesterol and vitamin D, eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia and responses to antipsychotic drugs.
“Our analyses indicate that Vindija 33.19 was more closely related to the Neanderthals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Altai Neanderthal, allowing 10-20% more Neanderthal DNA to be identified in present-day humans, including variants involved in LDL cholesterol levels, schizophrenia and other diseases,” they said.
In a separate study, University of Copenhagen researcher Martin Sikora and co-authors sequenced and analyzed the genomes of four archaic, anatomically modern humans that were found at the Sunghir site.
“These genomes provide a rare glimpse into the social organization of humans during the Upper Paleolithic period,” the authors said.
“The individuals, who lived sometime between 34,600 and 33,600 years ago, are all male and unrelated to each other.”
“Furthermore, we did not find inbreeding signatures, as seen with the Altai Neanderthal.”
“Given the genetic diversity of these individuals, despite being a part of a small genetic population, they likely mated outside of their hunter-gatherer clans.”
Kay Prüfer et al. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science, published online October 5, 2017; doi: 10.1126/science.aao1887
Martin Sikora et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science, published online October 5, 2017; doi: 10.1126/science.aao1807