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Deeply Divergent Archaic Mitochondrial Genome Provides Lower Time Boundary for African Gene Flow Into Neanderthals


Deeply Divergent Archaic Mitochondrial Genome Provides Lower Time Boundary for African Gene Flow Into Neanderthals

Cosimo Posth et al. Nat Commun.


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.

Conflict of interest statement

The authors declare no competing financial interests.


Figure 1
Figure 1. Archaic and modern humans' mtDNA and nDNA evolutionary scenarios.
(a) Pictures of the HST femur, (b) map of archaeological sites where complete mtDNA from archaic humans were reconstructed, (c) maximum parsimony tree of 54 modern human (collapsed), 18 Neanderthal, 3 Denisovan and 1 Sima de los Huesos mtDNAs built with coding region only and 98% partial deletion. Grey node numbers refer to bootstrap support after 1,000 iterations. Tree rooted with a chimpanzee mtDNA (not shown). (d) Schematic comparison of the nDNA (wide lines) with the mtDNA (thin lines) phylogenies of Neanderthals, Denisovans and modern humans. In c,d, colour legend for individual symbols and node numbers is illustrated in the horizontal time line. Node numbers in rectangular boxes are divergence times estimated in this study (Table 1), while in oval boxes are dates estimated in Prüfer et al. and Meyer et al. in thousand years before present. Red and blue tree branches represent supposed African and Eurasian distribution, respectively.
Figure 2
Figure 2. Archaic and modern humans' mtDNA diversity.
The pairwise nucleotide distance over its frequency (in logarithmic scale) is measured among 311 worldwide modern human, 17 Neanderthal, 3 Denisovan and 18 Neanderthal (including HST) mtDNAs. Points on the x axis represent one sequence pair comparison.

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