Human y chromosome variation and the peopling of the African continent

The analysis, by Next Generation Sequencing, of 1.5 Mb of the Male-Specific region of the Y chromosome (MSY), in a sample carefully selected to represent a wide range of diversity and antiquity among MSY lineages, led to the identification of 2,386 variable positions, 80% of which were novel. Many aspects of this pool of variants resembled the pattern observed among genome- wide de novo events, suggesting that in the MSY a large proportion of newly arisen alleles have survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. We used these markers to reconstruct a phylogenetic tree, which showed remarkable differences with the one known in literature, although recapitulating the previously known topology. The relative lengths of the tree branches have been notably altered, and the time estimates associated with the tree nodes have moved towards more ancient times. Keeping into account the present day distribution of patrilineages, and the fossil remains of Homo sapiens found to date, our data enabled us to draw hypotheses on the evolutionary events that involved the human species, since its origin, up to its migration out of the African continent.