Abstract
Genetic contributions of Neanderthals to the modern human genome have been evidenced by comparative analyses of present-day human genomes and paleogenomes. Current data indicate that Neanderthal introgression is higher in Asians and Europeans and lower in African lines of descent. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and ancient Homo sapiens lineages, or archaic Anatomically Modern Humans (AMH) that migrated from Africa into the Middle East and Europe in the last 50,000 years. It has been proposed however that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that the modern human mitochondrial genome might contains potential 66 Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs) being 36 in coding regions (7 nonsynonymous), 5 in SSU rRNA, 4 in LSU rRNA, 3 in tRNAs and 18 in the D-loop. Also, 7 N-SNVs are associated with traits such as cycling vomiting syndrome and Alzheimers’ and Parkinsons’ diseases and 2 N-SNVs associated with intelligence quotient. Based on our results with bootscan recombination tests, Principal Component Analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes recombination events cannot explain the presence of N-SNVs in present-day human mitogenomes. These results suggest that homoplasies alone and convergent evolution can explain N-SNVs. Our data also shows that African mtDNAs have Neanderthal SNVs as has been suggested for nuclear genome. Based on our data we conclude that most intercrosses might have occurred between Neanderthal males and archaic AMH females, crosses between archaic AMH males and Neanderthal females would be extremely rare and recombination was negligible, which explains the few Neanderthal marks (66 out of 16,569bp) in present day mitochondrial genomes of human populations. These 66 signatures are probably the result of homoplasies and convergent evolution.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
↵* Both share first author status
Based on reanalysis of results of recombination tests and discussions with expert scientists in the field we provided a novel interpretation of our results. We agree that there is no need to invoke recombination to explain the data pattern observed.