Evidence for ancient human interbreeding from mitochondrial DNA genomics

3 November 2017

Konstantin Khrapko
Department of Biology
Northeastern University


mtDNA pseudogenes (NUMTs) are fragments of mtDNA that have been integrated into the nuclear genome during millions of years of our (and other species) evolutionary histories. NUMTs are sometimes called "mtDNA fossils" as they preserve ancient mtDNA sequences that existed at the time of NUMT integration into the protected, low mutation nuclear environment.

Intriguingly, some ancient mtDNA lineages preserved by NUMTs appear to be so divergent from our ancestral mtDNA of that time, that individuals who carried such mtDNA should have been separated from our ancestors for millions of years before returning back onto our evolution tree. Thus it appears that our species' history included episodes of interbreeding/hybridization with fairly distant species, far more distant than, for example, Neanderthals [1].

There are at least two possible scenarios of such interbreeding. In one, the NUMT (a nuclear DNA locus) is transferred from a distant species into our ancestral population. Alternatively, a similar phylogeny is produced when a "new" mitochondrial DNA from a distant species replaces the "old" mtDNA of our ancestral population, provided that that our population already carries a NUMT formed from the "old" mtDNA. Both scenarios have precedents in other taxa. We believe that there were multiple hybridization events and both scenarios might have been realized in our evolution history.

Intriguingly, the mtDNA replacement might have left a trace in what appears to be a remnant of ancient mtDNA recombinant marginally recognizable in the human and chimpanzee mitochondrial genomes. This finding reflects back on our study that has first demonstrated the existence of recombinants in human mtDNA [2].


  1. K Popadin, K Gunbin, L Peshkin, S Annis, G Kraytsberg, N Markuzon, R R Ackermann, K Khrapko, "Mitochondrial pseudogenes suggest repeated inter-species hybridization in hominid evolution", BioRxiv, 2017.
  2. Y Kraytsberg, M Schwartz, T A Brown, K Ebralidse, W S Kunz, D A Clayton, J Vissing, K Khrapko, "Recombination of human mitochondrial DNA", Science 304:981 2004. PDF

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