@article {Ferreira190363, author = {Renata C. Ferreira and Camila R. Rodrigues and James R. Broach and Marcelo R. S. Briones}, title = {Neandertal signatures in modern human mitochondrial genome haplogroups?}, elocation-id = {190363}, year = {2018}, doi = {10.1101/190363}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Genetic contributions of Neandertals to the modern human genome have been evidenced by comparative analyses of present day human genomes and paleogenomes. The current data indicates that Neandertal introgression is higher in Asians and Europeans and lower in African lines of descent. Neandertal signatures in extant human genomes are attributed to intercrosses between Neandertals 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 Neandertal mitochondrial DNA to contemporary human genomes. Here we show that the modern human mitochondrial genome might contain potential 66 Neandertal signatures, or Neandertal single nucleotide variants (N-SNVs) of which 7 are associated with traits such as cycling vomiting syndrome and Alzheimers{\textquoteright} and Parkinsons{\textquoteright} diseases and 2 N-SNVs 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 potential Neandertal signatures than Asian and European haplogroups. Based on our results we hypothesize that although most intercrosses occurred between Neandertal males and archaic AMH females, crosses between archaic AMH males and Neandertal females were extremely rare and with rare recombination events thus leaving few marks (66 out of 16,569bp) in present day mitochondrial genomes of human populations.}, URL = {https://www.biorxiv.org/content/early/2018/09/18/190363}, eprint = {https://www.biorxiv.org/content/early/2018/09/18/190363.full.pdf}, journal = {bioRxiv} }