Статья

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Pille HallastDepartment of Genetics, University of Leicester, Leicester, United KingdomChiara BatiniDepartment of Genetics, University of Leicester, Leicester, United KingdomDaniel ZadikDepartment of Genetics, University of Leicester, Leicester, United KingdomPierpaolo Maisano DelserDepartment of Genetics, University of Leicester, Leicester, United KingdomJon H. WettonDepartment of Genetics, University of Leicester, Leicester, United KingdomEduardo Arroyo‐PardoLaboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, SpainGianpiero L. CavalleriMolecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, IrelandPeter de KnijffDepartment of Human Genetics, Leiden University Medical Centre, Leiden, The NetherlandsGiovanni Destro‐BisolIstituto Italiano di Antropologia, Rome, Italy Department of Environmental Biology, Sapienza University of Rome, Rome, ItalyB.M. DupuyDivision of Forensic Sciences, Norwegian Institute of Public Health, Oslo, NorwayHeidi EriksenCentre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland Utsjoki Health Care Centre, Utsjoki, FinlandLynn B. JordeDepartment of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UTTuri KingDepartment of Genetics, University of Leicester, Leicester, United KingdomMaarten LarmuseauLaboratory 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, BelgiumAdolfo López de MunaínDepartment of Neurosciences, University of the Basque Country, San Sebastián, SpainAna María López‐ParraLaboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, SpainAphrodite LoutradisNational Center for Thalassemias, Athens, GreeceJelena Milas̆inSchool of Dental Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, SerbiaAndrea NovellettoDepartment of Biology, Tor Vergata University, Rome, ItalyHorolma PamjavAntti SajantilaDepartment 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, TexasW. SchemppInstitute of Human Genetics, University of Freiburg, Freiburg, GermanyMary SearsDepartment of Genetics, University of Leicester, Leicester, United KingdomAslıhan TolunDepartment of Molecular Biology and Genetics, Boğaziçi University, Istanbul, TurkeyChirs Tyler-SmithWellcome Trust Sanger Institute, Hinxton, Cambridge, United KingdomAnneleen Van GeystelenLaboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, BelgiumScott WatkinsDepartment of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UTBruce WinneyDepartment of Oncology, University of Oxford, Oxford, United KingdomMark A. JoblingDepartment of Genetics, University of Leicester, Leicester, United Kingdom [email protected]

2014en

ABI

Аннотация

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.

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Идентификаторы

DOI: 10.1093/molbev/msu327

Цитирования и источники

Цитирований: 2Использованных источников: 0

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