TY  - JOUR
AU  - Batini, Chiara
AU  - Hallast, Pille
AU  - Zadik, Daniel
AU  - Delser, Pierpaolo Maisano
AU  - Benazzo, Andrea
AU  - Ghirotto, Silvia
AU  - Arroyo-Pardo, Eduardo
AU  - Cavalleri, Gianpiero L.
AU  - de Knijff, Peter
AU  - Dupuy, Berit Myhre
AU  - Eriksen, Heidi A.
AU  - King, Turi E.
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  - Tolun, Aslihan
AU  - Winney, Bruce
AU  - Jobling, Mark A.
PY  - 2015
UR  - https://smile.stomf.bg.ac.rs/handle/123456789/1987
AB  - The proportion of Europeans descending from Neolithic farmers similar to 10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Ychromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting similar to 2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.
PB  - Nature Publishing Group, London
T2  - Nature Communications
T1  - Large-scale recent expansion of European patrilineages shown by population resequencing
VL  - 6
DO  - 10.1038/ncomms8152
ER  - 

@article{
author = "Batini, Chiara and Hallast, Pille and Zadik, Daniel and Delser, Pierpaolo Maisano and Benazzo, Andrea and Ghirotto, Silvia and Arroyo-Pardo, Eduardo and Cavalleri, Gianpiero L. and de Knijff, Peter and Dupuy, Berit Myhre and Eriksen, Heidi A. and King, Turi E. 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 Tolun, Aslihan and Winney, Bruce and Jobling, Mark A.",
year = "2015",
abstract = "The proportion of Europeans descending from Neolithic farmers similar to 10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Ychromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting similar to 2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.",
publisher = "Nature Publishing Group, London",
journal = "Nature Communications",
title = "Large-scale recent expansion of European patrilineages shown by population resequencing",
volume = "6",
doi = "10.1038/ncomms8152"
}

Batini, C., Hallast, P., Zadik, D., Delser, P. M., Benazzo, A., Ghirotto, S., Arroyo-Pardo, E., Cavalleri, G. L., de Knijff, P., Dupuy, B. M., Eriksen, H. A., King, T. E., Lopez de Munain, A., Lopez-Parra, A. M., Loutradis, A., Milašin, J., Novelletto, A., Pamjav, H., Sajantila, A., Tolun, A., Winney, B.,& Jobling, M. A.. (2015). Large-scale recent expansion of European patrilineages shown by population resequencing. in Nature Communications
Nature Publishing Group, London., 6.
https://doi.org/10.1038/ncomms8152

Batini C, Hallast P, Zadik D, Delser PM, Benazzo A, Ghirotto S, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Dupuy BM, Eriksen HA, King TE, Lopez de Munain A, Lopez-Parra AM, Loutradis A, Milašin J, Novelletto A, Pamjav H, Sajantila A, Tolun A, Winney B, Jobling MA. Large-scale recent expansion of European patrilineages shown by population resequencing. in Nature Communications. 2015;6.
doi:10.1038/ncomms8152 .

Batini, Chiara, Hallast, Pille, Zadik, Daniel, Delser, Pierpaolo Maisano, Benazzo, Andrea, Ghirotto, Silvia, Arroyo-Pardo, Eduardo, Cavalleri, Gianpiero L., de Knijff, Peter, Dupuy, Berit Myhre, Eriksen, Heidi A., King, Turi E., Lopez de Munain, Adolfo, Lopez-Parra, Ana M., Loutradis, Aphrodite, Milašin, Jelena, Novelletto, Andrea, Pamjav, Horolma, Sajantila, Antti, Tolun, Aslihan, Winney, Bruce, Jobling, Mark A., "Large-scale recent expansion of European patrilineages shown by population resequencing" in Nature Communications, 6 (2015),
https://doi.org/10.1038/ncomms8152 . .

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 . .