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Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns
Rogers, Alan R.; Bohlender, Ryan J.; Huff, Chad D.
Abstract:
Mafessoni and Prüfer (1) (MP) make three points: ( i ) Low variation among Neanderthal genomes implies a small population, ( ii ) Neanderthal–Denisovan divergence is small relative to archaic-modern, and ( iii ) an analysis including singleton site patterns (in which the derived allele appears only once) supports a small Neanderthal population and a more recent Neanderthal–Denisovan separation. Point i assumes that sequenced Neanderthals are representative of all Neanderthals, yet samples come primarily from the north, where DNA preserves well. The global population may have been larger if some unsampled populations were distantly related to those sampled. Point ii is subsidiary to point iii , because divergences can be calculated from site pattern frequencies. We therefore focus on point iii . Our previous estimates (2) were biased, because our modern human data excluded invariant nucleotide sites (3). Mutations in an archaic lineage appear only if that lineage introgressed into moderns, leading … [↵][1]1To whom correspondence should be addressed. Email: rogers{at}anthro.utah.edu. [1]: #xref-corresp-1-1
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