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Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures

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After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1–2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10–20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.

OriginalsprogEngelsk
Artikelnummer5317
TidsskriftNature Communications
Vol/bind12
Nummer1
Antal sider11
ISSN2041-1723
DOI
StatusUdgivet - dec. 2021

Bibliografisk note

Funding Information:
We thank Felix Riede for advice on anthropological interpretations and Matthew Hurles for suggesting to contrast derived allele accumulation between X and autosomes. We thank Juraj Bergman and Marjolaine Rouselle for all discussions about the consequences of the Neanderthal dilution scenario in West Eurasian populations. We thank Priya Moorjani for commenting and providing feedback on the study and giving insightful suggestions. The study was supported by grants NNF18OC0031004 from the Novo Nordisk Foundation and 6108-00385 from the Research Council of Independent Research to M.H.S.

Publisher Copyright:
© 2021, The Author(s).

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