A next generation sequencing analysis of the human Y chromosome provides new clues about ancient genetic events in Africa

The male-specific portion of the human Y chromosome (MSY) has been intensively studied for phylogeographic purposes. However, the deepest lineages of its phylogeny remained largely unexplored, resulting in a biased distribution of known markers over the phylogenetic tree. We characterized by high-coverage next generation sequencing a set of deep rooting lineages, framed in a larger collection of worldwide Y chromosomes; we identified 2,386 SNPs, 80% of which novel. Evidence for some degree of purifying selection emerged in the form of an excess of private missense variants. The resulting MSY tree recapitulated the previously known topology but showed drastically different relative branch lengths, with remarkably older node ages. Our dating results, together with phylogeograpic data, hint a central-western african origin for the MSY variation, and fit recent archaeological evidence about an early next generation sequencing analysis of the human Y chromosome provides new clues about ancient genetic events in Africa Andrea Massaia,1 Beniamino Trombetta,1 Giovanna Bellusci,2 Natalie M. Myres,3 Andrea Novelletto,2 Rosaria Scozzari,1 Fulvio Cruciani1 1Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy; 2Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy; 3AncestryDNA, Provo, UT, USA The male-specific portion of the human Y chromosome (MSY) has been intensively studied for phylogeographic purposes. However, the deepest lineages of its phylogeny remained largely unexplored, resulting in a biased distribution of known markers over the phylogenetic tree. We characterized by high-coverage next generation sequencing a set of deep rooting lineages, framed in a larger collection of worldwide Y chromosomes; we identified 2,386 SNPs, 80% of which novel. Evidence for some degree of purifying selection emerged in the form of an excess of private missense variants. The resulting MSY tree recapitulated the previously known topology but showed drastically different relative branch lengths, with remarkably older node ages. Our dating results, together with phylogeograpic data, hint a central-western african origin for the MSY variation, and fit recent archaeological evidence about an early exit of Homo sapiens out of the African continent. Our experimental design produced an unbiased resource of new MSY markers and novel insights on a period of human evolution previously considered poorly accessible with paternally-inherited markers.