Type

Journal Article

Authors

Mark A Jobling
Bruce Winney
Scott Watkins
Anneleen Van Geystelen
Chris Tyler-Smith
Aslıhan Tolun
Matt Sears
Werner Schempp
Antti Sajantila
Horolma Pamjav
and 19 others

Subjects

Biochemistry

Topics
tandem repeats snps y chromosome single nucleotide polymorphisms next generation sequencing chromosome 13 tree confidence

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. (2014)

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.
Collections Ireland -> Royal College of Surgeons in Ireland -> PubMed

Full list of authors on original publication

Mark A Jobling, Bruce Winney, Scott Watkins, Anneleen Van Geystelen, Chris Tyler-Smith, Aslıhan Tolun, Matt Sears, Werner Schempp, Antti Sajantila, Horolma Pamjav and 19 others

Experts in our system