The DOI matches its Crossref record; 58 of the 58 references it cites were found in a registry or an index; none of the 12 sources its claims cite is checked for support yet.
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.
Overview
CoChat Summary
Written by AI from the paper’s full text.
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.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
13 Own result · 11 Own method · 8 Own interpretation · 5 Check pending · 2 No full text of the sources · 1 Not checked yet
A check of a cited source is scheduled, or we don’t hold its full text yet; the claim is checked once it runs.
In the paper
“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
A check is scheduled.
- 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
A check is scheduled.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Not checked yet
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A check of a cited source is scheduled, or we don’t hold its full text yet; the claim is checked once it runs.
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
A check is scheduled.
plainstates a cause- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Not checked yet
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“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
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- The quote only partly states this claim. 1
- It may state two separate claims as one. 12
- Probably not a substantial claim. 13
Create a free account to see these claims.
Create a free account to see these assumptions.
13 more claims
Create a free account to see all 40 claims and to verify the 9 references still open.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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
Research works printed but not linked: 1
- Verma, R.S. & Babu, A. Human Chromosomes: Principles & Techniques 2nd edn. (McGraw-Hill, 1995).
Cited by
Items 201–300 of 337
Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment
Tseng, B., Hwa, H., Lin, C.-Y., Yu, Y., Linacre, A. M. T., & Jc, L. (2022) · Journal of Human Genetics · doi:10.1038/s10038-022-01033-0 · Cited by 7
Silcocks, M., & Dunstan, S. J. (2023) · Communications Biology · doi:10.1038/s42003-023-05388-8 · Cited by 7
Sequeira, J. J., Vinuthalakshmi, K., Das, R., van Driem, G. L., & Mustak, M. S. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2023.1303628 · Cited by 7
Ancestral inference from haplotypes and mutations
Griffiths, R., & Tavaré, S. (2018) · Theoretical Population Biology · doi:10.1016/j.tpb.2018.04.006 · Cited by 7
Y‑chromosomale STR-Analyse in der forensischen Praxis
Roewer, L., & Willuweit, S. (2018) · Rechtsmedizin · doi:10.1007/s00194-018-0229-7 · Cited by 7
Kampuansai, J., Kutanan, W., Dudás, E., Vágó-Zalán, A., Galambos, A., & Pamjav, H. (2020) · Molecular Genetics and Genomics · doi:10.1007/s00438-019-01644-x · Cited by 7
Singh, P. P., Vishwakarma, S., Sultana, G. N. N., Pilvar, A., Karmin, M., Rootsi, S., Villems, R., Metspalu, M., Behar, D. M., Kivisild, T., et al. (2020) · European Journal of Human Genetics · doi:10.1038/s41431-020-00745-1 · Cited by 7
Editorial: Forensic investigative genetic genealogy and fine-scale structure of human populations
Guanglin, H., Wei, L., & Mengge, W. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2022.1067865 · Cited by 7
Tariq, M. D., Ahmad, H., Hemphill, B. E., Farooq, U., & Schurr, T. G. (2022) · Scientific Reports · doi:10.1038/s41598-022-05076-3 · Cited by 6
Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis
Fan, H., Xu, Y., Zhao, Y., Feng, K., Hong, L., Zhao, Q., Lu, X., Shi, M., Li, H., Wang, L., et al. (2024) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2024.103029 · Cited by 6
A generalized structured coalescent for purifying selection without recombination
Strütt, S., Excoffier, L., & Peischl, S. (2025) · Genetics · doi:10.1093/genetics/iyaf013 · Cited by 6
Li, M., Zhang, H., Tao, R., Chen, A., Zhou, P., Yu, C., Bian, Y., Zhang, S., Chen, F., & Li, C. (2025) · BMC Genomics · doi:10.1186/s12864-025-11634-6 · Cited by 6
Postillone, M. B., & Pérez, S. I. (2017) · Human Biology · doi:10.13110/humanbiology.89.3.05 · Cited by 6
Y chromosome sequence and epigenomic reconstruction across human populations
Esteller-Cucala, P., Palmada‐Flores, M., Kuderna, L. F. K., Fontsere, C., Armero, A. S., Dabad, M., Torralvo, M., Faella, A., Ferrández-Peral, L., Llovera, L., et al. (2023) · Communications Biology · doi:10.1038/s42003-023-05004-9 · Cited by 6
Y chromosome variation and prostate cancer ancestral disparities
Soh, P. X. Y., Adams, A., Bornman, R. M. S., Jiang, J., Stricker, P. D., Mutambirwa, S. B. A., Jaratlerdsiri, W., & Hayes, V. M. (2025) · iScience · doi:10.1016/j.isci.2025.112437 · Cited by 6
Hernández, C. L., Dugoujon, J., Sánchez, L. J., Cuesta, P., Novelletto, A., & Calderón, R. (2019) · Annals of Human Biology · doi:10.1080/03014460.2019.1587507 · Cited by 6
Doniec, A., Januła, M., Grzmil, P., & Kupiec, T. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102751 · Cited by 6
A Role for Chromosomal Microarray Testing in the Workup of Male Infertility
McIntyre, K., Murphy, E., Mertens, L., Dubuc, A. M., Heim, R. A., & Mason‐Suares, H. (2020) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2020.06.009 · Cited by 6
Sun, J., Wei, L., Wang, L., Huang, Y., Yan, S. L., Cheng, H., Ong, R. T., Saw, W., Fan, Z., Deng, X., et al. (2020) · American Journal of Human Biology · doi:10.1002/ajhb.23486 · Cited by 6
Self-citationAncient DNAs and the Neolithic Chinese super-grandfather Y haplotypesPreprint
Zhang, Y., Lei, X., Chen, H., Zhou, H., & Huang, S. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/487918 · Cited by 6
Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goatsPreprint
Nijman, I. J., Rosen, B. D., Zheng, Z., Jiang, Y., Cumer, T., Daly, K. G., Bâlteanu, V. A., Berger, B., Blichfeldt, T., Boink, G., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.17.952051 · Cited by 6
He, G., Wang, Z., Jiang, Y., Yuan, H., Luo, L., Feng, Y., Bu, F., Cheng, J., Liu, C., Tang, R., et al. (2026) · Science Advances · doi:10.1126/sciadv.adu7935 · Cited by 5
Santo, L. N. D., Quilodrán, C. S., & Currat, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad252 · Cited by 5
Arciero, E., Almarri, M. A., Mezzavilla, M., Xue, Y., Hallast, P., Hammoud, C., Chen, Y., Skov, L., Kraaijenbrink, T., Ayub, Q., et al. (2025) · Current Biology · doi:10.1016/j.cub.2025.06.048 · Cited by 5
Self-citationDíaz-Castillo, C. (2018) · Evolutionary Biology · doi:10.1007/s11692-018-9454-y · Cited by 5
Betzig, L. L. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108131797.005 · Cited by 5
Diversity of Mexican Paternal Lineages Reflects Evidence of Migration and 500 Years of Admixture
Gómez, R., Schurr, T. G., & Meraz-Ríos, M. A. (2021) · Oxford University Press eBooks · doi:10.1093/oso/9780190945961.003.0012 · Cited by 5
Exact calculation of the joint allele frequency spectrum for isolation with migration modelsPreprint
Kern, A. D., & Hey, J. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/065003 · Cited by 5
Neolithic super-grandfather Y haplotypes, their related surnames, and autism spectrum disorderPreprint
He, P., Chen, N., Hu, Z., Zhu, Z., Xia, K., & Huang, S. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/077222 · Cited by 5
Estimation of population-specific values of theta for PowerPlex Y23 profiles
Buckleton, J., Hall, T. O., Bright, J., Yung, M. C., Goudet, J., Kruijver, M., & Weir, B. S. (2024) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2024.103175 · Cited by 4
Ravasini, F., Barbaro, C. C., Scheib, C. L., Tambets, K., Metspalu, M., Cruciani, F., Trombetta, B., & D’Atanasio, E. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf149 · Cited by 4
He, G., Liu, C., & Wang, M. (2025) · Forensic Science International · doi:10.1016/j.forsciint.2025.112370 · Cited by 4
Words for the Animal Elephant/Mammoth in Relation to the DNA Genealogy Data
Jandáček, P., & Perdih, A. (2017) · Advances in Anthropology · doi:10.4236/aa.2017.74014 · Cited by 4
Genetic Evaluation of Male Infertility
Fakhro, K. A., Robay, A., Rodríguez-Flores, J. L., & Crystal, R. G. (2020) · Springer eBooks · doi:10.1007/978-3-030-37972-8_6 · Cited by 4
High-Selectivity Single-Nucleotide Variant Capture Technology Based on the DNA Reaction Network
Tang, W., Zhang, Y., Wang, J., Zhao, Y., Xu, X., Liu, C., Liu, Y., & Zhang, X. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c05280 · Cited by 4
Poriswanish, N., Eales, J., Xu, X., Scannali, D., Neumann, R., Wetton, J. H., Tomaszewski, M., Jobling, M. A., & May, C. A. (2025) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2025.01.026 · Cited by 4
Kilin-Klyosov TMRCA Calculator for Time Spans up to Millions of Years
Klyosov, A. A., & Kilin, V. V. (2016) · Advances in Anthropology · doi:10.4236/aa.2016.63007 · Cited by 4
Xia, Z., Chen, H., Zhang, Y., & Huang, S. (2021) · Research Square · doi:10.21203/rs.3.rs-1087730/v1 · Cited by 4
Genome-wide genealogies reveal deep admixtures forming modern humansPreprint
Loya, H., Hinch, A. G., Palamara, P. F., Speidel, L., & Myers, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.17.719197 · Cited by 4
García‐Olivares, V., Muñoz‐Barrera, A., Rubio‐Rodríguez, L. A., Jáspez, D., Usera, A. D.-D., Íñigo-Campos, A., Veeramah, K. R., Alonso, S., Thomas, M., Lorenzo-Salazar, J. M., et al. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.09.012 · Cited by 3
Early male and female footprints of modern humans across Eurasia and Australasia.
Cabrera, V. M. (2024) · Medical Research Archives · doi:10.18103/mra.v12i8.5552 · Cited by 3
A history of male migration in and out of the Green Sahara
Xue, Y. (2018) · Genome biology · doi:10.1186/s13059-018-1410-8 · Cited by 3
Self-citationFollowing the evolution of Homo sapiens across Africa using a uniparental genetic guide
Cabrera, V. M. (2023) · Medical Research Archives · doi:10.18103/mra.v11i1.3460 · Cited by 3
Huang, S. (2026) · Communications in Information and Systems · doi:10.4310/cis.260612023234 · Cited by 3
Sapozhnikov, M., Medina-Paz, F., Castagnola, M. J., & Zapico, S. C. (2024) · Forensic Sciences · doi:10.3390/forensicsci4040043 · Cited by 3
Puurand, T., Möls, M., Kaplinski, L., Maal, K., Krjutškov, K., Salumets, A., Kivisild, T., & Remm, M. (2025) · Genome biology · doi:10.1186/s13059-025-03714-3 · Cited by 3
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCRPreprint
Puig, M., Lerga-Jaso, J., Giner-Delgado, C., Pacheco, S., Izquierdo, D., Delprat, A., Gayà‐Vidal, M., Regan, J. F., Karlin-Neumann, G. A., & Cáceres, M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/766915 · Cited by 3
A generalized structured coalescent for purifying selection without recombinationPreprint
Strütt, S., Excoffier, L., & Peischl, S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.11.598434 · Cited by 3
Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies
Bozlak, E., Pokharel, K., Weldenegodguad, M., Paasivaara, A., Stammler, F., Røed, K. H., Kantanen, J., & Wallner, B. (2024) · Ecology and Evolution · doi:10.1002/ece3.11573 · Cited by 2
Identification of common human TMEM173 genotypes associated with Alzheimer's disease
Usher, M. R., Aybar-Torres, A., & Jin, L. (2025) · Journal of Alzheimer s Disease · doi:10.1177/13872877251396973 · Cited by 2
Lu, Q., Cheng, H., Li, L., Yao, H., Ru, K., Wen, S., Shi, M., Zeng, Z., & Wei, L. (2020) · Annals of Human Biology · doi:10.1080/03014460.2020.1748226 · Cited by 2
Moderní chemická analýza v archeologii, I. díl
(2021) · doi:10.5507/prf.21.24459486 · Cited by 2
The Archaeogenetics of Southeast Asia
Soares, P. A., Mormina, M., Rito, T., & Richards, M. B. (2022) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780199355358.013.3 · Cited by 2
Zurel, H., Bhérer, C., Batten, R., MacMillan, M. E., Demiriz, S., Mirhendi, S., Gilbert, E. H., Cavalleri, G. L., Leach, R. A., Scott, R. E. M., et al. (2024) · European Journal of Human Genetics · doi:10.1038/s41431-024-01719-3 · Cited by 2
Carter, R., Lee, S., & Sanford, J. C. (2018) · Proceedings of the International Conference on Creationism/Proceedings of the ... International Conference on Creationism · doi:10.15385/jpicc.2018.8.1.15 · Cited by 2
Malyarchuk, B. А. (2019) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vj19.529 · Cited by 2
A single nucleotide substitution in the flanking region of DYS533 with low peak height
Watahiki, H., Fujii, K., Fukagawa, T., Mita, Y., Kitayama, T., & Mizuno, N. (2020) · Japanese Journal of Forensic Science and Technology · doi:10.3408/jafst.798 · Cited by 2
Ancient Y chromosomes confirm origin of modern human paternal lineages in Asia rather than AfricaPreprint
Chen, H., Zhang, Y., & Huang, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.10.986042 · Cited by 2
Lipp, H. (2025) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2025.1654703 · Cited by 1
Yang, T., Liu, Y., Zou, S., Li, X., Wang, Z., Luo, L., Tang, R., Liu, C., Hu, L., He, G., et al. (2025) · BMC Biology · doi:10.1186/s12915-025-02442-1 · Cited by 1
Human evolution, migration, and adaptation in the Last Glacial environments
Fu, Q. (2025) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/csb-2025-5524 · Cited by 1
Wang, M., Feng, Y., Luo, L., Wang, Z., Chen, J., Sun, Q., Huang, Y., Tang, R., Liu, C., & He, G. (2026) · International Journal of Legal Medicine · doi:10.1007/s00414-026-03798-x · Cited by 1
Malaria shaped human spatial organization for the past 74 thousand years
Colucci, M., Leonardi, M., Blinkhorn, J., Irish, S. R., Padilla‐Iglesias, C., Kaboth‐Bahr, S., Gosling, W. D., Snow, R. W., Manica, A., & Scerri, E. M. L. (2026) · Science Advances · doi:10.1126/sciadv.aea2316 · Cited by 1
Y chromosome and male fertility: The AZF genes and their deletion
Krausz, C. G., Abrardo, C., Vargha, J., Bonini, V., & Kopa, Z. (2026) · Annales d Endocrinologie · doi:10.1016/j.ando.2026.102555 · Cited by 1
Suzuki, Y., Owa, C., Kobayashi, H., Nakabayashi, R., McNulty, B., Violich, I., Paten, B., Miga, K. H., & Morishita, S. (2026) · Nature Communications · doi:10.1038/s41467-026-73461-x · Cited by 1
Human Genetics: Busy Subway Networks in Remote Oceania?
Bergström, A., & Tyler‐Smith, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.03.033 · Cited by 1
Self-citationPaleogenetic Studies of Migration Processes in Eurasia
Сергеевич, П. А., Trapezov, R. O., & Cherdantsev, S. V. (2022) · Archaeology Ethnology and Anthropology of Eurasia · doi:10.17746/1563-0110.2022.50.2.140-149 · Cited by 1
Song, M., Jiang, L., Lyu, Q., Ying, J., Wang, Z., Zhou, Y., Song, F., Luo, H., Song, X., & Ying, B. (2022) · Electrophoresis · doi:10.1002/elps.202200109 · Cited by 1
Parallels and promising directions in the study of genetic, cultural, and moral evolutionPreprint
Maddamsetti, R., & Bower‐Bir, J. S. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1810.00501 · Cited by 1
ybyra: Y-chromosome haplogroup calling using a tree-based scoring methodPreprint
Pinotti, T., McColl, H., Sikora, M., & Czech, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.20.689455 · Cited by 1
Revisiting the lineages of the Cohanim using data from next-generation sequencingPreprint
Lipson, J., Bohrer, S. G., Cohen-Weinstein, S., Cooper, L., Revivo, D., Staetsky, L., Maier, P. A., Runfeldt, G., & Skorecki, K. L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.08.692646 · Cited by 1
Genetic history of Rus’Preprint
Андреева, Т. В., Станиславовна, К. С., Malyarchuk, A. B., Gusev, F. E., Ustkachkintseva, T. V., Adrianova, I. Y., Доценко, Г. С., Дмитриевна, С. А., Kuznetsova, I. L., Dudko, N. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.30.695215 · Cited by 1
Bursts of male-lineage expansions
Jones, B. L. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.63
Ai, H., Ren, J., Ma, J., Zhang, Z., Li, W., Yang, B. J., & Huang, L. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/126060
Gimbutas’ Smile – An Archaeology Led, Archaeogenetic ModelPreprint
Kenyon, B. (2017) · Preprints.org · doi:10.20944/preprints201712.0137.v1
An Exploration of Irish Surname History through Patrilineal Genetics
Farmer, S. K. (2020) · Purdue e-Pubs (Purdue University System) · doi:10.25394/pgs.7438922.v1
Pillai, K. (2018) · MOspace Institutional Repository (University of Missouri) · doi:10.32469/10355/66120
The Parallel Lives of Human Y Chromosome Lineages Across the Strait of Gibraltar
García-Fernández, C., & Calafell, F. (2019) · Springer eBooks · doi:10.1007/978-3-030-30363-1_11
The Genetic Population Structure of Robinson Crusoe Island, Chile
Mountford, H. S., Villanueva, P., Fernández, M. A., Lilian Jara, S., Barbieri, Z. D., Carvajal‐Carmona, L. G., Cazier, J., & Newbury, D. F. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00669
La transition néolithique : la contribution de la génétique
Chiaroni, J., & Schmitt, A. (2020) · Corps · doi:10.3917/corp1.017.0143
Rondeau, R. (2021) · Summit (Simon Fraser University)
Calculating the divergence time by direct comparison between individuals and the out-groupPreprint
Sun, T., Liu, Q., Shang, M., & Wang, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.04.438302
Evolution and Sex Differences in Political Engagement
Geary, D. C. (2021) · Psychological Inquiry · doi:10.1080/1047840x.2021.1930766
Predicting gene regulatory changes across human evolution using ancient DNA
Colbran, L. L. (2020)
Nagy, P. L., Olasz, J., Neparáczki, E., Rouse, N. A., Kapuria, K., Cano, S., Chen, H., Cristofaro, J. D., Runfeldt, G., Ekomasova, N. V., et al. (2021) · European Journal of Human Genetics · doi:10.1038/s41431-020-00795-5
Self-citationFertility from the Dawn of Humanity Through the Nineteenth Century
Skirbekk, V. (2022) · Springer eBooks · doi:10.1007/978-3-030-91611-4_4
Pre-Islamic art of Afghanistan and Pakistan. A survey of research interest
Balcerowicz, P. (2018) · Art of the Orient · doi:10.15804/aoto201811
Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypesPreprint
Zhang, Y., Lei, X., Chen, H., Li, J., Hui, Z., & Huang, S. (2019) · doi:10.21203/rs.2.10181/v1
da Silva, T. F. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2022.tde-04052022-183443
Estudio de linajes autóctonos del cromosoma Y en poblaciones humanas del NOA y NEA
Sepúlveda, P. B. P. (2020) · El Servicio de Difusión de la Creación Intelectual (National University of La Plata) · doi:10.35537/10915/141508
The first out of Africa migrants
Herrera, R. J., & Garcia‐Bertrand, R. (2023) · Elsevier eBooks · doi:10.1016/b978-0-12-819086-9.00015-4
He, G., Huang, Y., Chen, J., Wang, Z., Li, X., Duan, S., Sun, Q., Yan, J., Liu, C., & Wang, M. (2023) · doi:10.22541/au.168933511.19000548/v1
HaploSight: An alternative approach for Y chromosomal haplogroup identificationPreprint
Laoprapaipan, L., Phusawang, K., Laorchairangsi, P., Kitnitchee, A., Wachirawanitchkit, H., Suwanparsert, B., & Promnun, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.13.584919
He, G., Wang, M., Miao, L., Chen, J., Zhao, J., Sun, Q., Duan, S., Wang, Z., Xu, X., Sun, Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22621162
Chen, H., Lü, Y., Lu, D., & Xu, S. (2021) · Figshare · doi:10.6084/m9.figshare.14189627
Chen, H., Lü, Y., Lu, D., & Xu, S. (2021) · Figshare · doi:10.6084/m9.figshare.14189615
Chen, H., Lü, Y., Lu, D., & Xu, S. (2021) · Figshare · doi:10.6084/m9.figshare.14189624
Chen, H., Lü, Y., Lu, D., & Xu, S. (2021) · Figshare · doi:10.6084/m9.figshare.14189630
Chen, H., Lu, Y., Lu, D., & Xu, S. (2021) · Figshare · doi:10.6084/m9.figshare.14189621
Natural Selection and Human Emotions
Betzig, L. L. (2024) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780197544754.013.52
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 ›
Are you an author, or do you see a problem with this page? Request a review
