• Submit Earth, Atmospheric, and Planetary Sciences Papers
  • Science Sessions: The PNAS Podcast Program

Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns

  1. Chad D. Huffb
  1. aDepartment of Anthropology, University of Utah, Salt Lake City, UT 84112;
  2. bDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030

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 …

?1To whom correspondence should be addressed. Email: rogers{at}anthro.utah.edu.

Online Impact

  • 864971864 2018-01-22
  • 258841863 2018-01-22
  • 957295862 2018-01-22
  • 553518861 2018-01-22
  • 983792860 2018-01-22
  • 539694859 2018-01-22
  • 956115858 2018-01-22
  • 730379857 2018-01-22
  • 346624856 2018-01-22
  • 201609855 2018-01-22
  • 72549854 2018-01-21
  • 795928853 2018-01-21
  • 752345852 2018-01-21
  • 566508851 2018-01-21
  • 615722850 2018-01-21
  • 689612849 2018-01-21
  • 846903848 2018-01-21
  • 674896847 2018-01-21
  • 11197846 2018-01-21
  • 986896845 2018-01-21