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Mol Biol Evol. 2015 Mar;32(3):661-73. doi: 10.1093/molbev/msu327. Epub 2014 Dec 2.

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades.

Author information

1
Department of Genetics, University of Leicester, Leicester, United Kingdom.
2
Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain.
3
Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.
4
Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
5
Istituto Italiano di Antropologia, Rome, Italy Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
6
Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway.
7
Centre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland Utsjoki Health Care Centre, Utsjoki, Finland.
8
Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT.
9
Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium Department of Imaging & Pathology, Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium.
10
Department of Neurosciences, University of the Basque Country, San Sebastián, Spain.
11
National Center for Thalassemias, Athens, Greece.
12
School of Dental Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia.
13
Department of Biology, Tor Vergata University, Rome, Italy.
14
Network of Forensic Science Institutes, Institute of Forensic Medicine, Budapest, Hungary.
15
Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas.
16
Institute of Human Genetics, University of Freiburg, Freiburg, Germany.
17
Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey.
18
Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
19
Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium.
20
Department of Oncology, University of Oxford, Oxford, United Kingdom.
21
Department of Genetics, University of Leicester, Leicester, United Kingdom maj4@le.ac.uk.

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.

KEYWORDS:

Y-STRs; Y-chromosome phylogeny; purifying selection; single nucleotide polymorphisms; targeted resequencing

PMID:
25468874
PMCID:
PMC4327154
DOI:
10.1093/molbev/msu327
[Indexed for MEDLINE]
Free PMC Article

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