@article {321732,
	title = {The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes},
	journal = {Nature},
	year = {2020},
	month = {2020/04/22},
	abstract = {<p>Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2\% of their genomes to admixture from Neanderthals, which occurred 50{\textendash}60 thousand years ago1. Here we examine the effect of this event using 14.4\&nbsp;million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566\&nbsp;Icelanders, corresponding to a range of 56,388{\textendash}112,709 unique archaic fragments that cover 38.0{\textendash}48.2\% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5\% of fragments to an Altai or Vindija Neanderthal origin and 3.3\% to Denisovan origin; 12.2\% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500\&nbsp;thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types{\textemdash}perhaps due to different generation intervals for males and females. Finally, we assessed 271\&nbsp;phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.</p>
},
	isbn = {1476-4687},
	doi = {https://doi.org/10.1038/s41586-020-2225-9},
	url = {https://www.nature.com/articles/s41586-020-2225-9$\#$citeas},
	author = {Skov, Laurits and Coll Maci{\`a}, Mois{\`e}s and Sveinbj{\"o}rnsson, Gar{\dh}ar and Mafessoni, Fabrizio and Lucotte, Elise A. and Einarsd{\'o}ttir, Margret S. and J{\'o}nsson, H{\'a}kon and Halldorsson, Bjarni and Gudbjartsson, Daniel F. and Helgason, Agnar and Schierup, Mikkel Heide and Stefansson, Kari}
}
