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Title: The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades.
Authors: Hallast, Pille
Batini, Chiara
Zadik, Daniel
Maisano Delser, Pierpaolo Maisano
Wetton, Jon H.
Arroyo-Pardo, E.
Cavalleri, GL.
de Knijff, P.
Destro Bisol, G.
Dupuy, B. M.
Eriksen, H. A.
Jorde, L. B.
King, Turi E.
Larmuseau, M. H.
López de Munain, A.
López-Parra, A. M.
Loutradis, A.
Milasin, J.
Novelletto, A.
Pamjav, H.
Sajantila, A.
Schempp, W.
Sears, Matt
Tolun, A.
Tyler-Smith, C.
Van Geystelen, A.
Watkins, S.
Winney, B.
Jobling, Mark A.
First Published: 2-Dec-2014
Publisher: Oxford University Press (OUP)
Citation: Molecular Biology and Evolution, 2015, 32 (3), pp. 661-673
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.
DOI Link: 10.1093/molbev/msu327
ISSN: 0737-4038
eISSN: 1537-1719
Version: Publisher Version
Status: Peer-reviewed
Type: Journal Article
Rights: Copyright © The Authors 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Appears in Collections:Published Articles, Dept. of Genetics

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