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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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In the paper
“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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In the paper
“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]
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Cited by
Insights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020
Self-citationThe formation of human populations in South and Central Asia
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The complete sequence of a human Y chromosome
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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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
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- CoChat. (2026). Citation check: Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. https://app.cochat.ai/papers/10.1038/ng.3559
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- 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., . . . Tyler-Smith, C. (2016). Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics. https://doi.org/10.1038/ng.3559
