A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei1,2,
- Qasim Ayub1,
- Yuan Chen1,
- Shane McCarthy1,
- Yiping Hou2,
- Ignazio Carbone3,
- Yali Xue1 and
- Chris Tyler-Smith1,4
- 1The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
- 2Department of Forensic Genetics, School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu, 610041 Sichuan, PR China;
- 3Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695-7244, USA
Abstract
We have identified variants present in high-coverage complete sequences of 36 diverse human Y chromosomes from Africa, Europe, South Asia, East Asia, and the Americas, representing eight major haplogroups. After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels. We constructed phylogenetic trees using these variants, or subsets of them, and recapitulated the known structure of the tree. Assuming a male mutation rate of 1 × 10−9 per base pair per year, the time depth of the tree (haplogroups A3-R) was ∼101,000–115,000 yr, and the lineages found outside Africa dated to 57,000–74,000 yr, both as expected. In addition, we dated a striking Paleolithic male lineage expansion to 41,000–52,000 yr ago and the node representing the major European Y lineage, R1b, to 4000–13,000 yr ago, supporting a Neolithic origin for these modern European Y chromosomes. In all, we provide a nearly 10-fold increase in the number of Y markers with phylogenetic information, and novel historical insights derived from placing them on a calibrated phylogenetic tree.
Footnotes
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↵4 Corresponding author
E-mail cts{at}sanger.ac.uk
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.143198.112.
Freely available online through the Genome Research Open Access option.
- Received May 16, 2012.
- Accepted October 2, 2012.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
