Comparisons of the Neandertal genome to present-day human genomes have revealed that ~1-2% of present-day genomes outside Africa come from Neandertals and it has been suggested that a major part of the admixture took place in the Levant between 47-65 kya [1, 2]. However, it has also been shown that a ~42,000-year-old modern human from Romania had a Neandertal ancestor four to six generations back in his family tree, indicating that the admixture between modern humans and Neandertals was not restricted to a single event in Near East . To better understand late Neandertal populations and the interactions between Neandertals and modern humans we are investigating the genomes of European Neandertals from the time when they or their immediate ancestors could have met modern humans.
We identified five late Neandertal specimens – from the Troisième caverne of Goyet and Spy in Belgium, Les Cottés in France, Vindija Cave in Croatia and Mezmaiskaya Cave in Russia – where the fraction of endogenous sequences are between 6% and 64% after depleting microbial contamination through hypochlorite treatment. We have sequenced the nuclear genomes of these individuals to an average coverage between 1- and 2.7-fold. Present-day human DNA contamination varies between ~1% and ~2.5% for the nuclear and mitochondrial DNA sequences, respectively.
Based on the number of DNA fragments recovered from the X chromosome and the autosomes, we determined that the specimens from Goyet, Les Cottés and Vindija were females, whereas the Spy and Mezmaiskaya 2 specimens were males. We further use these genomes to determine population structure among late Neandertals and their relationships to the Neandertals that contributed DNA to present-day humans, as well as to determine whether there was gene flow from early modern humans into these late Neandertals.