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A calibrated human Y-chromosomal phylogeny based on resequencing.

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.

SUBMITTER: Wei W

PROVIDER: S-EPMC3561879 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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A calibrated human Y-chromosomal phylogeny based on resequencing.

Wei Wei W Ayub Qasim Q Chen Yuan Y McCarthy Shane S Hou Yiping Y Carbone Ignazio I Xue Yali Y Tyler-Smith Chris C

Genome research 20121004 2

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 ...[more]

PMID: 23038768

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Dataset Information

A calibrated human Y-chromosomal phylogeny based on resequencing.

Publications

A calibrated human Y-chromosomal phylogeny based on resequencing.

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