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Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences
Open accessAbstract
We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.
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TL;DR
The paper analyzes 1,244 worldwide Y chromosomes from the 1000 Genomes Project, cataloging >65,000 variants and building a calibrated Y-chromosome phylogeny. It finds repeated, extreme male-lineage expansions across all five continental superpopulations, often near times of known migrations or technological changes.
Key findings
- The dataset comprised 1,244 Y chromosomes from 26 populations, with >65,000 variants across six classes; the phylogeny used 60,555 biallelic SNVs from 10.3 Mb, and with a mutation rate of 0.76 × 10−9 per bp per year the tree TMRCA was ~190 ky, while non-African lineages had a TMRCA of ~76 ky.
- CNVs were the most functionally impactful class: 20 of 100 CNVs overlapped 27 protein-coding genes, and the Y-chromosome ratio of deletions to duplications overlapping protein-coding genes was 1.5, versus 0.84 on autosomes; 39% of CNVs had mutated multiple times, including one CNV with 154 inferred events.
- STRs were the most mutable class, with a median of 16 mutations per locus and an average mutation rate of 3.9 × 10−4 per generation; allele length explained more than half the variance in log mutation rate for uninterrupted STRs.
- The phylogeny showed bursts of extreme male expansion in each continental superpopulation, including Q1a-M3 in the Americas at ~15 kya, E1b-M180 in sub-Saharan Africa at ~5 kya, R1b-L11 in Western Europe at ~4.8–5.9 kya, eight South Asian expansions at ~4.0–7.3 kya, and one notable expansion each in East Asian O2b-M176 and O3-M122.
Methods
- Used Y-chromosome reads from 1,244 males in phase 3 of the 1000 Genomes Project, sampled from 26 populations, with median haploid coverage of 4.3×.
- Called SNVs, MNVs, indels, CNVs, and STRs using multiple haploid-tailored methods, including SAMtools, FreeBayes, Platypus, Cortex_var, GATK, GenomeSTRiP, cnvHitSeq, HipSTR, aCGH, and fibre-FISH validation.
- Constructed a maximum-likelihood phylogeny with RAxML8 from 60,555 biallelic SNVs, then modeled haplogroup expansions using a two-phase exponential growth model with coalescent simulations in ms.
Limitations
- The paper states that modest sequencing coverage caused data missingness: small CNVs and long STRs were largely undetected, and low-frequency variants, including SNVs, were under-represented.
- The paper notes that lymphoblastoid cell culture could generate false discoveries, though these were not shared and were minimized by focusing on higher-frequency internal-branch variation.
- The paper states that expansion inference assumes no population structure immediately downstream of the node under investigation, and that links between expansions and historical/archaeological events remain unproven and depend on calibration choice; the text also makes evident that the 26-population sample lacked New Guinea, so haplogroups M and S were absent.
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“We find that rapid expansions are not confined to unusual circumstances30,31.”
§ Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences > Discussion
What the sources say
- Not checked yetcites [30] Zerjal, T. et al. The genetic legacy of the Mongols. Am. J. Hum. Genet. 72, 717–721 (2003). source
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- Not checked yetcites [31] Balaresque, P. et al. Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations. Eur. J. Hum. Genet. 23, 1413–1422 (2015). source
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“the TMRCA of all non-African lineages (i.e., the TMRCA of haplogroups DE and CF) is ~76 ky”
§ Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences > Results > Phylogeny
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“Foremost, the abundance of extreme male-lineage expansions underscores differences between male and female demographic histories.”
§ Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences > Discussion
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“When calibrated with a mutation rate estimate of 0.76 × 10−9 mutations per base pair per year9, the time to the most recent common ancestor (TMRCA) of the tree is ~190 ky”
§ Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences > Results > Phylogeny
What the sources say
- Not checked yetcites [9] Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014). source
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“In South Asia, we detect eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93”
§ Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences > Results > Haplogroup Expansions
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In the citing paper
“This may match the conditions under which star-shaped ‘bursts’ appeared in the Y-chromosome genealogy of dominant clades among modern populations6.”
From Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck (2018) · cites this paper as [6]
In the citing paper
“The inferred bottleneck and associated star-like expansions on the phylogenetic tree were confined to male-inherited Y-chromosomes (Fig. 3) and were not apparent in female-inherited mitochondrial DNA.”
From Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck (2018) · cites this paper as Poznik et al. [6]
In the citing paper
“Therefore, our model reliably produces dynamics that strongly and plausibly replicate two features of the population genetics of the Y-chromosome in that period: the reduction in diversity, interpreted as a population bottleneck4, and the occurrence of star-shaped phylogenies6.”
From Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck (2018) · cites this paper as [6]
In the citing paper
“These results were further supported by a study on 26 human populations from the 1000 Genomes Project, which found evidence for a similar bottleneck of male effective population size2.”
From Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck (2024) · cites this paper as [2]
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationMEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular biology and evolution · doi:10.1093/molbev/mst197 · Cited by 41,174
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationThe variant call format and VCFtools
Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,450
Self-citationEvolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
ggplot2: Elegant Graphics for Data Analysis
Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447
A method and server for predicting damaging missense mutations.
Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010) · Nature Methods · doi:10.1038/nmeth0410-248 · Cited by 13,194
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,510
Kumar, P., Henikoff, S., & Ng, P. C. (2009) · Nature Protocols · doi:10.1038/nprot.2009.86 · Cited by 6,521
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
Haplotype-based variant detection from short-read sequencing
Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700
Self-citationGenerating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,389
Origins and functional impact of copy number variation in the human genome
The Wellcome Trust Case Control Consortium, Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T. D., Barnes, C., et al. (2010) · Nature · doi:10.1038/nature08516 · Cited by 1,970
Self-citationMassive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940
Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation
van Oven, M., & Kayser, M. (2009) · Human Mutation · doi:10.1002/humu.20921 · Cited by 1,810
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
McLaren, W. M., Yates, B., Ríos, D., Chen, Y., Flicek, P., & Cunningham, F. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq330 · Cited by 1,586
Self-citationPopulation genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550
Copy number variation in human health, disease, and evolution
Zhang, F., Gu, W., Hurles, M. E., & Lupski, J. R. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164217 · Cited by 1,207
Rimmer, A., Phan, H. T. T., Mathieson, I., Iqbal, Z., Twigg, S. R. F., Wilkie, A. O. M., McVean, G., & Lunter, G. A. (2014) · Nature Genetics · doi:10.1038/ng.3036 · Cited by 1,058
Genome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023
The human Y chromosome: an evolutionary marker comes of age
Jobling, M. A., & Tyler‐Smith, C. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1124 · Cited by 988
Self-citationAn early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802
De novo assembly and genotyping of variants using colored de Bruijn graphs
Iqbal, Z., Cáccamo, M., Turner, I., Flicek, P., & McVean, G. (2012) · Nature Genetics · doi:10.1038/ng.1028 · Cited by 656
Self-citationThe Genetic Legacy of the Mongols
Zerjal, T., Xue, Y., Bertorelle, G., Wells, R. S., Bao, W., Zhu, S., Qamar, R., Ayub, Q., Mohyuddin, A., Fu, S., et al. (2003) · The American Journal of Human Genetics · doi:10.1086/367774 · Cited by 563
Self-citationGenomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, M. C., Malaspinas, A.-S., et al. (2015) · Science · doi:10.1126/science.aab3884 · Cited by 540
Self-citationKloss‐Brandstätter, A., Pacher, D., Schönherr, S., Weißensteiner, H., Binna, R., Specht, G., & Kronenberg, F. (2010) · Human Mutation · doi:10.1002/humu.21382 · Cited by 510
A recent bottleneck of Y chromosome diversity coincides with a global change in culture
Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 485
Self-citationLarge multiallelic copy number variations in humans
Handsaker, R. E., Van Doren, V., Berman, J. R., Genovese, G., Kashin, S., Boettger, L. M., & McCarroll, S. A. (2015) · Nature Genetics · doi:10.1038/ng.3200 · Cited by 402
Self-citationJobling, M., Hollox, E., Hurles, M., Kivisild, T., & Tyler-Smith, C. (2013) · doi:10.1201/9781317952268 · Cited by 385
Self-citationOut of Africa and back again: nested cladistic analysis of human Y chromosome variation
Hammer, M. F., Karafet, T., Rasanayagam, A., Wood, E. T., Altheide, T. K., Jenkins, T., Griffiths, R., Templeton, A. R., & Zegura, S. L. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025939 · Cited by 361
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Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., et al. (2015) · Science · doi:10.1126/science.aab3761 · Cited by 345
Self-citationEuropean Societies in the Bronze Age
Harding, A. (2000) · Cambridge University Press eBooks · doi:10.1017/cbo9780511605901 · Cited by 345
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Groucutt, H. S., Petraglia, M. D., Bailey, G. N., Scerri, E. M. L., Parton, A., Clark‐Balzan, L., Jennings, R. P., Lewis, L., Blinkhorn, J., Drake, N., et al. (2015) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21455 · Cited by 334
Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females
Poznik, G. D., Henn, B. M., Yee, M.-C., Sliwerska, E., Euskirchen, G. M., Lin, A. A., Snyder, M., Quintana-Murci, L., Kidd, J. M., Underhill, P. A., et al. (2013) · Science · doi:10.1126/science.1237619 · Cited by 248
Self-citationXue, Y., Wang, Q., Long, Q., Ng, B. L., Swerdlow, H., Burton, J., Skuce, C. D., Taylor, R., Abdellah, Z., Zhao, Y., et al. (2009) · Current Biology · doi:10.1016/j.cub.2009.07.032 · Cited by 221
Self-citationCopy number variation and evolution in humans and chimpanzees
Perry, G. H., Yang, F., Marques-Bonet, T., Murphy, C., Fitzgerald, T., Lee, A. S., Hyland, C., Stone, A. C., Hurles, M. E., Tyler-Smith, C., et al. (2008) · Genome Research · doi:10.1101/gr.082016.108 · Cited by 202
Self-citationEuropean Societies in the Bronze Age. By Anthony F. Harding.
Wells, P. S. (2001) · American Journal of Archaeology · doi:10.2307/507281 · Cited by 162
A calibrated human Y-chromosomal phylogeny based on resequencingPreprint
Wei, W., Ayub, Q., Chen, Y., McCarthy, S., Hou, Y., Carbone, I., Xue, Y., & Tyler‐Smith, C. (2012) · Genome Research · doi:10.1101/gr.143198.112 · Cited by 150
Self-citationBringing together linguistic and genetic evidence to test the Bantu expansion
de Filippo, C., Bostoen, K. A. G., Stoneking, M., & Pakendorf, B. (2012) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.0318 · Cited by 148
Sparse representation and Bayesian detection of genome copy number alterations from microarray data
Piqué-Regi, R., Monso-Varona, J., Ortega, A., Seeger, R. C., Triche, T. J., & Asgharzadeh, S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm601 · Cited by 131
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Betzig, L. (2012) · Evolution and Human Behavior · doi:10.1016/j.evolhumbehav.2011.10.008 · Cited by 128
Carpenter, D., Dhar, S., Mitchell, L. M., Fu, B., Tyson, J., Shwan, N. A. A., Yang, F., Thomas, M. G., & Armour, J. A. L. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv098 · Cited by 128
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Willems, T., Gymrek, M., Poznik, G. D., Tyler‐Smith, C., The 1000 Genomes Project Chromosome Y Group, & Erlich, Y. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.04.001 · Cited by 105
Self-citationGribble, S. M., Wiseman, F. K., Clayton, S., Prigmore, E., Langley, E., Yang, F., Maguire, S., Fu, B., Rajan, D., Sheppard, O., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060482 · Cited by 102
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Helgason, A., Einarsson, A. W., Guðmundsdóttir, V. B., Sigurðsson, Á., Gunnarsdóttir, E. D., Jagadeesan, A., Ebenesersdóttir, S. S., Kong, A., & Stefánsson, K. (2015) · Nature Genetics · doi:10.1038/ng.3171 · Cited by 93
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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., et al. (2015) · Nature Communications · doi:10.1038/ncomms8152 · Cited by 91
Balaresque, P., Poulet, N., Cussat-Blanc, S., Gerard, P., Quintana-Murci, L., Heyer, E., & Jobling, M. A. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.285 · Cited by 89
Patton, L. L., & Bryant, E. (2004) · Routledge eBooks · doi:10.4324/9780203641880 · Cited by 79
Lohmueller, K. E., Bustamante, C. D., & Clark, A. G. (2009) · Genetics · doi:10.1534/genetics.108.099275 · Cited by 57
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Piqué-Regi, R., Cáceres, A., & González, J. R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-380 · Cited by 55
Balanovsky, O., Zhabagin, M., Agdzhoyan, A., Chukhryaeva, M., Zaporozhchenko, V., Utevska, O., Highnam, G., Sabitov, Z., Greenspan, E., Dibirova, K., et al. (2015) · PLOS ONE · doi:10.1371/journal.pone.0122968 · Cited by 40
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Self-citation
Research works printed but not linked: 1
- Verma, R.S. & Babu, A. Human Chromosomes: Principles & Techniques 2nd edn. (McGraw-Hill, 1995).
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Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., et al. (2023) · Nature · doi:10.1038/s41586-023-06457-y · Cited by 471
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The population history of northeastern Siberia since the Pleistocene
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Metadata
- Authors
- The 1000 Genomes Project Consortium, Poznik, G. D., Xue, Y., Mendez, F. L., Willems, T. F., Massaia, A., Wilson Sayres, M. A., Ayub, Q., McCarthy, S. A., Narechania, A., Kashin, S., Chen, Y., Banerjee, R., Rodriguez-Flores, J. L., Cerezo, M., Shao, H., Gymrek, M., Malhotra, A., Louzada, S., Desalle, R., Ritchie, G. R. S., Cerveira, E., Fitzgerald, T. W., Garrison, E., Marcketta, A., Mittelman, D., Romanovitch, M., Zhang, C., Zheng-Bradley, X., Abecasis, G. R., McCarroll, S. A., Flicek, P., Underhill, P. A., Coin, L., Zerbino, D. R., Yang, F., Lee, C., Clarke, L., Auton, A., Erlich, Y., Handsaker, R. E., Bustamante, C. D., & Tyler-Smith, C.
- Affiliations
- Stanford University (US)
- Wellcome Sanger Institute (GB)
- New York Genome Center (US)
- American Museum of Natural History (US)
- Broad Institute (US)
- The University of Queensland (AU)
- Harvard–MIT Division of Health Sciences and Technology (US)
- The Jackson Laboratory for Genomic Medicine (US)
- European Bioinformatics Institute (GB)
- Albert Einstein College of Medicine (US)
- Virginia Tech (US)
- University of Michigan (US)
- Harvard University (US)
- Ewha Womans University (KR)
- Corresponding author
- Bustamante, Carlos D
- ORCID
- Poznik, G David
- Xue, Yali
- Mendez, Fernando L
- Willems, Thomas F
- Wilson Sayres, Melissa A
- Ayub, Qasim
- McCarthy, Shane A
- Narechania, Apurva
- Kashin, Seva
- Chen, Yuan
- Banerjee, Ruby
- Shao, Haojing
- Gymrek, Melissa
- Malhotra, Ankit
- Louzada, Sandra
- Desalle, Rob
- Ritchie, Graham R S
- Cerveira, Eliza
- Fitzgerald, Tomas W
- Garrison, Erik
- Marcketta, Anthony
- Mittelman, David
- Zhang, Chengsheng
- Zheng-Bradley, Xiangqun
- Abecasis, Gonçalo R
- McCarroll, Steven A
- Flicek, Paul
- Underhill, Peter A
- Coin, Lachlan
- Zerbino, Daniel R
- Yang, Fengtang
- Lee, Charles
- Clarke, Laura
- Auton, Adam
- Erlich, Yaniv
- Handsaker, Robert E
- Bustamante, Carlos D
- Venue
- Nature Genetics
- Published
- 2016-04-25
- Volume
- 48
- Issue
- 6
- Pages
- 593-599
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4884158
- OpenAlex
- W2345012058
- Semantic Scholar
- 60b848357d9372347034887aea7e5f0ffc96328f
- Cited by
- 331
- References
- 58
- Citations by year
- 2026: 26 · 2025: 26 · 2024: 25 · 2023: 19 · 2022: 29 · 2021: 34 · 2020: 34 · 2019: 33 · 2018: 45 · 2017: 47 · 2016: 13
- FWCI
- 5.13
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Oxford University Research Archive (ORA) (University of Oxford) (submittedVersion, other-oa)
- Max Planck Digital Library (submittedVersion, other-oa)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Spiral (Imperial College London) (submittedVersion)
- Funders
- National Science Foundation (1201234, 1147470)
- Wellcome Trust (104947/Z/14/Z, 095908/Z/11/Z, 085532/Z/08/Z, 098051)
- European Molecular Biology Laboratory
- National Institutes of Health
- Center for Computational, Evolutionary and Human Genomics, Stanford University
- National Human Genome Research Institute (U41HG007497, R01HG003229)
- National Institute of General Medical Sciences (R01GM090087)
- U.S. National Library of Medicine (T15LM007033)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- Y chromosome, population growth, copy number variation, phylogenetic tree, historical migration, technological innovation, 1000 Genomes Project
- MeSH terms
- Demography, Haplotypes, Humans, Male, Mutation, Phylogeny, Polymorphism, Single Nucleotide, Chromosomes, Human, Y
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-12, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-12 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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