ancient structure

Sankararaman S, Patterson N, Li H, Pääbo S & Reich D 2012 The date of interbreeding between Neandertals and modern humans. PLoS Genet 8:e1002947.

  • Neandertals share more genetic variants with non-Africans than with Africans
  • this could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa
  • it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa
  • these hypotheses make different predictions about the date of last gene exchange between the ancestors of Neandertals and modern non-Africans
  • the date of 37,000–86,000 years BP is too recent to be consistent with the "ancient African population structure" scenario, and strongly supports the hypothesis that at least some of the signal of Neandertals being more closely related to non-Africans than to Africans is due to recent gene flow
  • these results are concordant with a recent paper by Yang et al [44] that analyzed joint allele frequency spectra in Africans, non-Africans and Neandertals, to reject the ancient structure scenario
  • Eriksson and Manica [45] showed, using an Approximate Bayesian Computation approach, that models of ancient substructure can produce a signal of Neandertals sharing more derived alleles with non-Africans than with Africans
  • that is, they can account for the observation that D-statistics are significantly different from zero
  • the new statistics we focus on here as well as the statistics focused on by Yang et al [44] show that ancient structure alone cannot explain these signals
  • one possibility that we have not ruled out is that both ancient structure and gene flow occurred in the history of non-Africans
  • in this scenario, the ancient structure will tend to make the date estimate older than the truth but by not more than 15%
  • we have not been able to differentiate amongst variants of the recent gene flow scenario
  • a single episode or multiple episodes of gene flow or continuous gene flow over an extended period of time
  • our date has a clear interpretation as the time of last gene exchange under a scenario of a single instantaneous gene flow event
  • in the other scenarios, the date is expected to represent an average over the times of gene flow and should be interpreted as an upper bound on the time of last gene exchange
  • our analysis cannot reject the possibility that gene flow did not involve Neandertals themselves, but instead populations that were more closely related to Neandertals than any extant populations are today
  • the date should be interpreted as the last period of time when genetic material from Neandertals or an archaic population related to Neandertals entered modern humans