Differential distribution of Neandertal genomic signatures in human mitochondrial haplogroups

Genetic contributions of Neandertals to the modern human genome have been evidenced by comparative analyses of present day human genomes and paleogenomes. The Neandertal introgression differs in European, East Asian and African lines of descent, and is higher in Asians and Europeans and lower in Africans. Neandertal signatures in extant human genomes are attributed to intercrosses between Neandertals and ancient Homo sapiens lineages, or 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 Neandertal mitochondrial DNA to contemporary human genomes. Here we show that the modern human mitochondrial genome contains 75 Neandertal signatures of which 11 are associated with diseases such as cycling vomiting syndrome and depression and 3 associated with intelligence quotient. Principal component analysis and bootscan tests suggest rare recombination events. Also, contrary to what is observed in the nuclear genome, African mitochondrial haplogoups have more Neandertal signatures than Asian and European haplogroups. Our results suggest that although most intercrosses occurred between Neandertal males and Anatomically Modern Humans (AMH) females, crosses between AMH males and Neandertal females were extremely rare with also rare recombination events thus leaving few marks (75 out of 16,565bp) in present day mitochondrial genomes of human populations.