A high-coverage Neandertal genome from Chagyrskaya Cave

Abstract

<jats:p>We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655–658 (2017); Hajdinjak et al., Nature 555, 652–656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43–49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.</jats:p>

New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland)

“…Recently, comparisons of Neanderthal nuclear genomes suggest a population turnover from Western Europe to the Altai region after 90 ka 1 whereas the continuous gene flow between Neanderthals and Denisovan during the last 100 ka, and the almost complete absence of Denisovan ancestry in European Neanderthals suggests recurrent dispersals eastwards to Altai 45 . Furthermore, a long distance migration of Neanderthals carrying a Micoquian toolkit has been discovered at Chagyrskaya Cave in Altai 17,18 whereas movements of Micoquian groups (Keilmessergruppen) from Central Europe to other western regions have also been documented in the Netherlands, Belgium, and France [46][47][48] . These evidences suggest that the foraging radius of Neanderthals living in steppe/taiga environments could have been bigger than previously envisaged.…”

Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe

“…In these phases the tool is more likely the result of the achievement of a conceptual scheme and, perhaps, equipped with aesthetic and symbolic value. The cultural and possibly ethnic value of these industries has recently been reinforced with data from the early-MIS 3 Neanderthals from Chagyrskaya in the Altai mountains: here, techno-typological affinities with Central-and Eastern-European Micoquian come together with genetic similarities with European specimens, while the same groups were unquestionably different from earlier Altai Neanderthals bearing Mousterian assemblages [141,142].…”

A genetic variant protective against severe COVID-19 is inherited from Neandertals

“…To further investigate this locus, we used the round 4 (alpha) release of the COVID-19 Host Genetics Initiative (HGI) (covid19hg.org) to analyze 35 SNPs that are significantly associated with severe COVID-19 and have been scored in the archaic genomes (Table S1). A 60,000 to 80,000-year-old Neandertal from Chayrskaya Cave in southern Siberia (Mafessoni et al . 2020) carries the protective alleles at 34 of these SNPs in a homozygous form, while an approximately 50,000-year-old Neandertal from Vindija in Croatia (Prüfer et al .…”