Abstract
Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.
Highlights
The male-specific region of the Y chromosome (MSY) has been widely exploited in studies of human evolution and population history (Jobling and Tyler-Smith 2003), but has suffered from ascertainment bias in the sequence variants studied. Phylogenies constructed from such variants over the last two decades (Hammer 1995; Underhill et al 2000; Y Chromosome Consortium 2002; Karafet et al 2008) have been useful in defining haplogroups whose distributions can be investigated in different populations, nodes could not be dated directly from sequence variation
Application of next-generation sequencing (NGS) to large segments of the MSY can provide unbiased ascertainment of single nucleotide polymorphisms (SNPs) and allows detailed phylogenies to be constructed in which branch-lengths are proportional to time, allowing direct assessment of the times-to-most-recent-common-ancestor (TMRCAs) of nodes
Elsewhere (Batini C, Hallast P, Zadik D, Maisano Delser P, Benazzo A, Ghirotto S, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Dupuy BM, Eriksen H, King TE, Lopez de Munain A, Lopez-Parra AM, Milasin J, Novelletto A, Pamjav H, Sajantila A, Tolun A, Winney B and Jobling MA, submitted.) we have described an NGS-based MSY phylogeny based on 5,996 SNPs ascertained in 334 human Y chromosomes comprising 17 population samples from Europe and the Near East, focused on illuminating the origins and histories of European patrilineages
Summary
The male-specific region of the Y chromosome (MSY) has been widely exploited in studies of human evolution and population history (Jobling and Tyler-Smith 2003), but has suffered from ascertainment bias in the sequence variants studied. Five NGS-based trees (1000 Genomes Project Consortium et al 2010; Francalacci et al 2013; Poznik et al 2013; Wei, Ayub, Chen, et al 2013; Scozzari et al 2014) have been described (table 1), providing insights into events in human evolution and population relationships from a patrilineal perspective. These trees vary greatly in their sample sizes (from 36 to 1,208 Y chromosomes), their number of population samples (from 1 to 9), and their representation of known lineages. In low-coverage approaches, imputation methods have been employed to infer the allelic states of missing genotypes based on the phylogeny itself, and singletons (variants present only once in the data set) that define the lengths of terminal branches have been poorly ascertained, with consequent likely underestimation of branch lengths (Francalacci et al 2013)
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