ancient structure

Eriksson A & Manica A 2012 Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. PNAS 109:13956-12960.

  • the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations
  • African populations are more diverse than non-African ones
  • diversity declines progressively with increasing distance from Africa
  • all these lines of evidence point strongly to a recent out-of-Africa (OOA) expansion providing the largest contribution to the gene pool of anatomically modern humans
  • they cannot rule out small levels of hybridization with other hominins, as the signal left behind in modern populations would be very difficult to detect
  • some attempts to detect hybridization based on patterns of linkage disequilibrium have found a possible signal
  • these approaches rely on simplistic demographic models with assumptions that are not testable
  • Currat and Excoffier (5) used a spatial framework to investigate admixture with Neanderthals, but concentrated on the role of gene surfing during the expansion wave in affecting the distribution of polymorphisms unique to Neanderthals across Eurasia, provided admixture did happen
  • gene surfing leads to overestimates of admixture in nonspatially structured models
  • they assumed the ancestors of African modern humans to be unstructured and ignored the common ancestry between Neanderthals and modern humans
  • Currat and Excoffier (5) had already shown that models lacking spatial realism tend to overestimate the level of hybridization by ignoring gene surfing during the human expansion into Eurasia
  • including ancient structure in Africa further undermines the case for hybridization
  • our conclusion was robust to the use of different measures of shared polymorphism, clearly indicating the limitation of looking for polymorphisms that are only shared between a single ancient genome and a restricted group of modern populations
  • our results show the extent to which ignoring spatial population structure causes models to underestimate the geographic differences expected in the absence of hybridization
  • the issues raised in this paper should also apply to claims of admixture based on the distribution of linkage disequilibrium
  • we urge caution in inferring recent admixture from geographic differences in genetic overlap between ancient hominins and modern-day populations
  • we do not claim that anatomically modern humans never admixed with other hominins
  • our results imply that current evidence for such admixture events is inconclusive at best
  • future tests, to be convincing, will need to show that the genetic patterns used to invoke hybridization cannot be explained by population structure