# Population Genetics > Paleogenetics > Paleolithic & Mesolithic >  Third Neanderthal Genome Sequenced

## Angela

The paper:

Mafessoni et al
https://www.pnas.org/content/early/2.../15/2004944117

"*Significance*We present the third high-quality genome to be determined from a Neandertal. Patterns of variation in the genome suggest that her ancestors lived in relatively isolated populations of less than 60 individuals. When we analyze this genome together with two previously sequenced Neandertal genomes, we find that genes expressed in the striatum of the brain may have changed especially much, suggesting that the striatum may have evolved unique functions in Neandertals.

*Abstract*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.

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## ratchet_fan

Interesting. Also interesting that their uni-parental markers don't exist anymore.

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## Angela

"When analyzing genetic changes on the Neandertal lineage using the three Neandertal genomes, the number of changes in genes expressed in the striatum during adolescence stands out. One possibility is that these changes accumulated in Neandertals due to their small population size, perhaps in combination with a relaxation of selection on genes expressed in the striatum. Interestingly, genes expressed in the striatum overlap more frequently than expected with genomic regions where Neandertal introgressed fragments in modern human genomes are rare. We speculate that striatal genes may carry Neandertal-specific changes that were disadvantageous when introduced into modern humans. This, as well as positive selection for derived changes in the modern human lineage, may underlie so-called Neandertal deserts in present-day human genomes, i.e., regions that are depleted of Neandertal ancestry (20, 35)."

Some alleles for wound healing and immunity were helpful and so were not subject to negative selection.

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## bicicleur

complete turnovers happened not only in modern humans, also amongst Neanderthalers

all Neanderthals prior to the most recent split ca 150-120 ka went extinct and were replaced by 'modern Neanderthals'
even in the Denisova cave : the hybrid Denisovan-Neanderthal hybrid is not a mixture with the 120 ka 'Altaï Neanderthal', but with a 'modern Neanderthal'

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