title: 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.
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Qasim
authors.initials: Q
authors.lastname: Ayub
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Shane
authors.initials: S
authors.lastname: McCarthy
authors.forename: Yiping
authors.initials: Y
authors.lastname: Hou
authors.forename: Ignazio
authors.initials: I
authors.lastname: Carbone
authors.forename: Yali
authors.initials: Y
authors.lastname: Xue
authors.forename: Chris
authors.initials: C
authors.lastname: Tyler-Smith
mesh_terms: D041322:Chromosomes, Human, Y; D004641:Emigration and Immigration; D005006:Ethnicity / Q000235:genetics; D005828:Genetics, Population; D006239:Haplotypes; D006801:Humans; D008297:Male; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide