An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa

Abstract

Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage nextgeneration sequencing, including 18 deep-rooting ones, and identified 2386 SNPs, 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 has survived in the phylogeny. Some degree of purifying selection emerged in the form of an excess of private missense variants. Our tree recapitulated the previously known topology, but the relative lengths of major branches were drastically modified and the associated node ages were remarkably older. We found significantly different branch lengths when comparing the rare deep-rooted A1b African lineage with the rest of the tree. Our dating results and phylogeography led to the following main conclusions: (1) Patrilineal lineages with ages approaching those of early AMH fossils survive today only in central-western Africa; (2) only a few evolutionarily successful MSY lineages survived between 160 and 115 kya; and (3) an early exit out of Africa (before 70 kya), which fits recent western Asian archaeological evidence, should be considered. Our experimental design produced an unbiased resource of new MSY markers informative for the initial formation of the anatomically modern human gene pool, i.e., a period of our evolution that had been previously considered to be poorly accessible with paternally inherited markers.

The study of human Y chromosome variation through ancient DNA

“…The extant variation in other continents is mainly restricted to three branches of the M168 clade: D, C and F (Hallast et al 2015; Karmin et al 2015; Poznik et al 2013, 2016; Scozzari et al 2014; Wei et al 2013). Genetic variation within each of these three clades coalesces to a single founding lineage within 40–60 KYA time depth, consistent with the Out of Africa (OOA) dispersal model (Stringer 2002).…”

Genetic Diversity on the Sex Chromosomes

“…2011; Barbieri et al. 2016), including ancient population structure (Scozzari et al. 2014) and recent population expansions (Hallast et al.…”

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

“…Previous studies have established a standard Y chromosome haplogroup nomenclature based on resequencing of limited tracts of the locus in small numbers of geographically diverse samples (The Y Chromosome Consortium 2002; Karafet et al 2008;van Oven et al 2013). As a result, the precise order and timing of the phylogenetic splits has only recently started to emerge from whole Y chromosome sequences (Francalacci et al 2013;Mendez et al 2013;Poznik et al 2013;Wei et al 2013;Lippold et al 2014;Scozzari et al 2014;Yan et al 2014;Hallast et al 2015). While the male to female effective population size ratio has been estimated as being below one throughout much of human evolutionary history (Lippold et al 2014), the factors affecting its dynamics are still poorly understood.…”