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

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Hallast, P., Batini, C., Zadik, D., Delser, P., M., Wetton, J., H., Arroyo-Pardo, E., Cavalleri, G., L., De Knijff, P., Bisol, G., D., Dupuy, B., M., Eriksen, H., A., Jorde, L., B., King, T., E., Larmuseau, M., H., De Munain, A., L., L??pez-Parra, A., M., Loutradis, A., Milasin, J., Novelletto, A., Pamjav, H., Sajantila, A., Schempp, W., Sears, M., Tolun, A., Tyler-Smith, C., Van Geystelen, A., Watkins, S., Winney, B., Jobling, M., A., & Ramachandran, S. Molecular Biology and Evolution, 32(3):661-673, 2014.

Paper abstract bibtex

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 analysing 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 non-synonymous variants in 15 MSY single-copy genes.

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 title = {The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades},
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 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 analysing 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 non-synonymous variants in 15 MSY single-copy genes.},
 bibtype = {article},
 author = {Hallast, Pille and Batini, Chiara and Zadik, Daniel and Delser, Pierpaolo Maisano and Wetton, Jon H. and Arroyo-Pardo, Eduardo and Cavalleri, Gianpiero L. and De Knijff, Peter and Bisol, Giovanni Destro and Dupuy, Berit Myhre and Eriksen, Heidi A. and Jorde, Lynn B. and King, Turi E. and Larmuseau, Maarten H. and De Munain, Adolfo L??pez and L??pez-Parra, Ana M. and Loutradis, Aphrodite and Milasin, Jelena and Novelletto, Andrea and Pamjav, Horolma and Sajantila, Antti and Schempp, Werner and Sears, Matt and Tolun, Aslihan and Tyler-Smith, Chris and Van Geystelen, Anneleen and Watkins, Scott and Winney, Bruce and Jobling, Mark A. and Ramachandran, Sohini},
 journal = {Molecular Biology and Evolution},
 number = {3}
}

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