Three less well-defined genomes come from individuals found in a cave, Vindija, in Croatia, and one from Mezmaiskaya Cave, in Russia. Here, Kay Prüfer and colleagues successfully analyzed billions of DNA fragments sampled from a new individual in the Croatian cave, dubbed Vindija 33.19, a female who lived roughly 52,000 years ago. Similar to previous findings, the genetic data suggest that Neandertals lived in small and isolated populations of about 3,000 individuals.
The previously sequenced Altai Neandertal genome suggested that the individual's parents were half-siblings, prompting scientists to wonder if Neandertals commonly interbred with family members - yet the new Vindija genome does not have similar incestual patterns, suggesting that the extreme inbreeding between the parents of the Altai Neandertal may not have been ubiquitous among Neandertals. 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.
The authors use the Vindija 33.19 genome to analyze divergences and gene flow among Neandertals, Denisovans (another extinct species of hominin), and modern humans. Among many findings, they report that early modern human gene flow into Neandertal populations occurred between 130,000 and 145,000 years ago, before the Croatian and Siberian Neandertals diverged.
Based on the new high-quality genome, the authors estimate that modern non-African populations carry between 1.8-2.6% Neandertal DNA, which is higher than previous estimates of 1.5-2.1%.
Lastly, they identify a wealth of new gene variants in the Neandertal 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.