2014/12/02 by Pille Hallast, Chiara Batini, Daniel Zadik +26 · 4 citations
Biochemistry, Genetics and Molecular Biology · #Genetic diversity and population structure #Forensic and Genetic Research #Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities #Biology #Haplogroup #Phylogenetic tree #Clade #Genetics #Evolutionary biology #Single-nucleotide polymorphism #Mutation rate #Nonsynonymous substitution #Microsatellite #Most recent common ancestor #DNA sequencing #Haplotype #Gene #Genome #Allele #Genotype
paper · pdf · doi:10.1093/molbev/msu327
openalex publication_date 2014/12/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.