TY  - JOUR
AU  - Hallast, Pille
AU  - Batini, Chiara
AU  - Zadik, Daniel
AU  - Delser, Pierpaolo Maisano
AU  - Wetton, Jon H.
AU  - Arroyo-Pardo, Eduardo
AU  - Cavalleri, Gianpiero L.
AU  - de Knijff, Peter
AU  - Bisol, Giovanni Destro
AU  - Dupuy, Berit Myhre
AU  - Eriksen, Heidi A.
AU  - Jorde, Lynn B.
AU  - King, Turi E.
AU  - Larmuseau, Maarten H.
AU  - Lopez de Munain, Adolfo
AU  - Lopez-Parra, Ana M.
AU  - Loutradis, Aphrodite
AU  - Milašin, Jelena
AU  - Novelletto, Andrea
AU  - Pamjav, Horolma
AU  - Sajantila, Antti
AU  - Schempp, Werner
AU  - Sears, Matt
AU  - Tolun, Aslihan
AU  - Tyler-Smith, Chris
AU  - Van Geystelen, Anneleen
AU  - Watkins, Scott
AU  - Winney, Bruce
AU  - Jobling, Mark A.
PY  - 2015
UR  - https://smile.stomf.bg.ac.rs/handle/123456789/1973
AB  - 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 51x, 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.
PB  - Oxford Univ Press, Oxford
T2  - Molecular Biology & Evolution
T1  - The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades
VL  - 32
IS  - 3
SP  - 661
EP  - 673
DO  - 10.1093/molbev/msu327
ER  - 

@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 Lopez de Munain, Adolfo and Lopez-Parra, Ana M. and Loutradis, Aphrodite and Milašin, 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.",
year = "2015",
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 51x, 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.",
publisher = "Oxford Univ Press, Oxford",
journal = "Molecular Biology & Evolution",
title = "The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades",
volume = "32",
number = "3",
pages = "661-673",
doi = "10.1093/molbev/msu327"
}

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., Lopez de Munain, A., Lopez-Parra, A. M., Loutradis, A., Milašin, 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.. (2015). The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades. in Molecular Biology & Evolution
Oxford Univ Press, Oxford., 32(3), 661-673.
https://doi.org/10.1093/molbev/msu327

Hallast P, Batini C, Zadik D, Delser PM, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Bisol GD, Dupuy BM, Eriksen HA, Jorde LB, King TE, Larmuseau MH, Lopez de Munain A, Lopez-Parra AM, Loutradis A, Milašin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Geystelen A, Watkins S, Winney B, Jobling MA. The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades. in Molecular Biology & Evolution. 2015;32(3):661-673.
doi:10.1093/molbev/msu327 .

Hallast, Pille, Batini, Chiara, Zadik, Daniel, Delser, Pierpaolo Maisano, Wetton, Jon H., Arroyo-Pardo, Eduardo, Cavalleri, Gianpiero L., de Knijff, Peter, Bisol, Giovanni Destro, Dupuy, Berit Myhre, Eriksen, Heidi A., Jorde, Lynn B., King, Turi E., Larmuseau, Maarten H., Lopez de Munain, Adolfo, Lopez-Parra, Ana M., Loutradis, Aphrodite, Milašin, Jelena, Novelletto, Andrea, Pamjav, Horolma, Sajantila, Antti, Schempp, Werner, Sears, Matt, Tolun, Aslihan, Tyler-Smith, Chris, Van Geystelen, Anneleen, Watkins, Scott, Winney, Bruce, Jobling, Mark A., "The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades" in Molecular Biology & Evolution, 32, no. 3 (2015):661-673,
https://doi.org/10.1093/molbev/msu327 . .