Abstract

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Highlights

  • Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans

  • During excavations in 1937, it was found in a black clayey layer with Middle Paleolithic artefacts known as the Black Mousterian based on the sediment colour and the cultural assignment of the technocomplex retrieved in the stratigraphic unit, which is associated throughout Europe with Neanderthals[16]

  • The African introgression hypothesis suggests that Late Pleistocene Neanderthal mitochondrial DNA (mtDNA) originated through gene flow from an African source[8], which we constrain taking place more than

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Summary

Introduction

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. The closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. A genetic introgression event from African hominins into the early Neanderthal population that gave rise to the ‘Late Pleistocene’ Neanderthal mtDNA lineage has been proposed[8] This event must have occurred after archaic and modern human populations diverged. While genomic evidence showed that gene flow between lineages as divergent as modern humans and Neanderthals took place[12,13] in both directions[14], it is unclear whether such small-scale phenomena were sufficient to explain the complete replacement of the initial Neanderthal mtDNA pool (found in Sima de los Huesos) by a Middle Pleistocene human lineage from Africa. An assessment of the feasibility of such a replacement as well as the availability of more ancient specimens is required to conclude whether the African introgression hypothesis is a viable one and to refine its time boundaries

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