期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 32, 期 3, 页码 661-673出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msu327
关键词
Y-chromosome phylogeny; single nucleotide polymorphisms; targeted resequencing; Y-STRs; purifying selection
资金
- Wellcome Trust Senior Fellowship [087576]
- Leverhulme Trust [F/00 212/AM]
- College of Medicine, Biological Sciences & Psychology studentship from the University of Leicester
- Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (NWO)
- Finnish Foundations' Professor Pool (Paulo Foundation)
- Ministry of Science of Serbia [175075]
- grant PRIN [2012JA4BTY_003]
- Wellcome Trust [098051]
- KU Leuven BOF-Centre of Excellence Financing on Eco- and socio-evolutionary dynamics [PF/2010/07]
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 51x, 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.
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