Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants
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Exponential Growth Effects: Humans are an extraordinarily successful species, as measured by our large population size—approximately 7 billion—much of which can be put down to recent explosive growth. Leveraging human genomic data, Keinan and Clark (p. 740 ) examined the effects of population growth on our ability to detect rare genetic variants, those hypothesized to be most likely associated with disease. It appears that rapid recent growth increases the load of rare variants and is likely to play an important role in the individual genetic burden of complex disease risk.
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These genes were targeted by positive selection and did not merely experience a relaxation of constraint or accumulate rare variants as a result of human population size growth.
“Positively selected sites were detected in genes showing higher median γ values, suggesting that these genes were targeted by positive selection, and did not merely experience a relaxation of constraint or accumulated rare variants as a result of human population size growth47 (Fig. 4).”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [47]
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Cites
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336 · see citing works
Self-citationA map of human genome variation from population-scale sequencing.
The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877 · see citing works
THE ATHEROSCLEROSIS RISK IN COMMUNIT (ARIC) STUDY: DESIGN AND OBJECTIVES
THE ARIC INVESTIGATORS (1989) · American Journal of Epidemiology · doi:10.1093/oxfordjournals.aje.a115184 · Cited by 3,491 · see citing works
Sequence Variations in <i>PCSK9,</i> Low LDL, and Protection against Coronary Heart Disease
Cohen, J. C., Boerwinkle, E., Mosley, T. H., & Hobbs, H. H. (2006) · New England Journal of Medicine · doi:10.1056/nejmoa054013 · Cited by 3,181 · see citing works
(1989) · PubMed · Cited by 3,139 · see citing works
Integrating common and rare genetic variation in diverse human populations
The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026 · see citing works
Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397 · see citing works
Kingmán, J. F. C. (1982) · Stochastic Processes and their Applications · doi:10.1016/0304-4149(82)90011-4 · Cited by 2,123 · see citing works
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906 · see citing works
Personal genomes: The case of the missing heritability
Maher, B. (2008) · Nature · doi:10.1038/456018a · Cited by 1,737 · see citing works
Missing heritability and strategies for finding the underlying causes of complex disease
Eichler, E. E., Flint, J., Gibson, G. C., Kong, A., Leal, S. M., Moore, J. H., & Nadeau, J. H. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2809 · Cited by 1,671 · see citing works
Population Growth and Technological Change: One Million B.C. to 1990
Kremer, M. R. (1993) · The Quarterly Journal of Economics · doi:10.2307/2118405 · Cited by 1,595 · see citing works
Human genetic variation and its contribution to complex traits
Frazer, K. A., Murray, S. S., Schork, N. J., & Topol, E. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2554 · Cited by 1,073 · see citing works
Rate, molecular spectrum, and consequences of human mutation
Lynch, M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912629107 · Cited by 792 · see citing works
How Many People Can the Earth Support?
Cohen, J. E. (1998) · Bulletin of the American Academy of Arts and Sciences · doi:10.2307/3824523 · Cited by 698 · see citing works
Fisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 683 · see citing works
Siva, N. (2008) · Nature Biotechnology · doi:10.1038/nbt0308-256b · Cited by 629 · see citing works
Assessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628 · see citing works
Self-citationDemographic history and rare allele sharing among human populations
Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G., Clark, A. G., Yu, F., Gibbs, R. A., The 1000 Genomes Project, Bustamante, C. D., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019276108 · Cited by 625 · see citing works
Self-citationCalibrating a coalescent simulation of human genome sequence variation
Schaffner, S. F., Foo, C., Gabriel, S., Reich, D., Daly, M. J., & Altshuler, D. (2005) · Genome Research · doi:10.1101/gr.3709305 · Cited by 616 · see citing works
Coalescents With Multiple Collisions
Pitman, J. (1999) · The Annals of Probability · doi:10.1214/aop/1022874819 · Cited by 497 · see citing works
Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia
Johansen, C. T., Wang, J., Lanktree, M. B., Cao, H., McIntyre, A. D., Ban, M. R., Martins, R. A., Kennedy, B. A., Hassell, R. G., Visser, M. E., et al. (2010) · Nature Genetics · doi:10.1038/ng.628 · Cited by 437 · see citing works
The general coalescent with asynchronous mergers of ancestral lines
Sagitov, S. (1999) · Journal of Applied Probability · doi:10.1239/jap/1032374759 · Cited by 375 · see citing works
Keinan, A., Mullikin, J. C., Patterson, N., & Reich, D. (2007) · Nature Genetics · doi:10.1038/ng2116 · Cited by 272 · see citing works
Self-citationDeep resequencing reveals excess rare recent variants consistent with explosive population growth
Coventry, A., Bull–Otterson, L., Liu, X., Clark, A. G., Maxwell, T. J., Crosby, J. R., Hixson, J. E., Rea, T. J., Muzny, D. M., Lewis, L. R., et al. (2010) · Nature Communications · doi:10.1038/ncomms1130 · Cited by 221 · see citing works
Self-citationHigh-Resolution Detection of Identity by Descent in Unrelated Individuals
Browning, S. R., & Browning, B. L. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.02.021 · Cited by 214 · see citing works
Coalescents With Multiple Collisions
Pitman, J. (1999) · The Annals of Probability · doi:10.1214/aop/1022677552 · Cited by 210 · see citing works
Coalescents with Simultaneous Multiple Collisions
Schweinsberg, J. (2000) · Electronic Journal of Probability · doi:10.1214/ejp.v5-68 · Cited by 206 · see citing works
Glatt, C. E., DeYoung, J. A., Delgado, S., Service, S. K., Giacomini, K. M., Edwards, R. H., Risch, N., & Freimer, N. B. (2001) · Nature Genetics · doi:10.1038/86948 · Cited by 154 · see citing works
Roberts, L. J. (2011) · Science · doi:10.1126/science.333.6042.540 · Cited by 135 · see citing works
Albrechtsen, A., Korneliussen, T. S., Moltke, I., Hansen, T. V. O., Nielsen, F. C., & Nielsen, R. (2008) · Genetic Epidemiology · doi:10.1002/gepi.20378 · Cited by 104 · see citing works
Gene Genealogies Within a Fixed Pedigree, and the Robustness of Kingman’s Coalescent
Wakeley, J., King, L., Low, B. S., et al. (2012) · Genetics · doi:10.1534/genetics.111.135574 · Cited by 93 · see citing works
How many people have ever lived on earth?
Haub, C. (1995) · PubMed · Cited by 91 · see citing works
Gene Genealogies When the Sample Size Exceeds the Effective Size of the Population
Wakeley, J. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg024 · Cited by 62 · see citing works
Detailed Investigation of the Role of Common and Low-Frequency WFS1 Variants in Type 2 Diabetes Risk
Fawcett, K. A., Wheeler, E., Morris, A. P., Ricketts, S. L., Hallmans, G., Rolandsson, O., Daly, A., Wasson, J., Permutt, A., Hattersley, A. T., et al. (2009) · Diabetes · doi:10.2337/db09-0920 · Cited by 38 · see citing works
The promise and limitations of population exomics for human evolution studies
Tennessen, J. A., O’Connor, T. D., Bamshad, M. J., & Akey, J. M. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-127 · Cited by 21 · see citing works
Akey, J. M. (2011) · Genome biology · doi:10.1186/gb-2011-12-s1-i1 · Cited by 8 · see citing works
Akey, J. M. (2011) · Genome biology · doi:10.1186/1465-6906-12-s1-i1 · Cited by 1 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- [19]The ARIC Investigators Am. J. Epidemiol 1989 129 687 2646917
- [30]Haub C Popul. Today 1995 23 4 12288594
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An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711 · see citing works
A polygenic burden of rare disruptive mutations in schizophrenia
Purcell, S. M., Moran, J. L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P., O’Dushlaine, C., Chambert, K., Bergen, S. E., Kähler, A., et al. (2014) · Nature · doi:10.1038/nature12975 · Cited by 1,385 · see citing works
Searching for missing heritability: Designing rare variant association studies
Zuk, O., Schaffner, S. F., Samocha, K., Do, R., Hechter, E., Kathiresan, S., Daly, M. J., Neale, B. M., Sunyaev, S. R., & Lander, E. S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1322563111 · Cited by 635 · see citing works
Whole-genome sequencing of quartet families with autism spectrum disorder
Yuen, R. K. C., Thiruvahindrapuram, B., Merico, D., Walker, S., Tammimies, K., Hoang, N., Chrysler, C., Nalpathamkalam, T., Pellecchia, G., Liu, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3792 · Cited by 514 · see citing works
Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture
Browning, S. R., Browning, B. L., Zhou, Y., Tucci, S., & Akey, J. M. (2018) · Cell · doi:10.1016/j.cell.2018.02.031 · Cited by 381 · see citing works
The influence of evolutionary history on human health and disease
Benton, M. L., Abraham, A., LaBella, A. L., Abbot, P., Rokas, A., & Capra, J. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00305-9 · Cited by 291 · see citing works
The deleterious mutation load is insensitive to recent population history.
Simons, Y. B., Turchin, M. C., Pritchard, J. K., & Sella, G. (2014) · Nature Genetics · doi:10.1038/ng.2896 · Cited by 279 · see citing works
Ortega, V. E., & Meyers, D. A. (2014) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.10.040 · Cited by 237 · see citing works
Recovery of trait heritability from whole genome sequence data
Wainschtein, P., Jain, D., Zheng, Z., TOPMed Anthropometry Working Group, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Cupples, L. A., Shadyab, A. H., McKnight, B., Shoemaker, B. M., Mitchell, B. D., et al. (2019) · doi:10.1101/588020 · Cited by 515 · see citing works
Carmi, S., Hui, K. Y., Kochav, E., Liu, X., Xue, J., Grady, F., Guha, S., Upadhyay, K., Ben-Avraham, D., Mukherjee, S., et al. (2014) · Nature Communications · doi:10.1038/ncomms5835 · Cited by 188 · see citing works
Ancestry-specific recent effective population size in the Americas
Browning, S. R., Browning, B. L., Daviglus, M. L., Durazo-Arvizu, R. A., Schneiderman, N., Kaplan, R. C., & Laurie, C. C. (2018) · PLOS Genetics · doi:10.1371/journal.pgen.1007385 · Cited by 187 · see citing works
Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases
Hudson, G., Gomez-Duran, A., Wilson, I. J., & Chinnery, P. F. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004369 · Cited by 148 · see citing works
Whole‐exome sequencing in 20,197 persons for rare variants in Alzheimer's disease
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Slavney, A., Arbiza, L., Clark, A. G., & Keinan, A. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msv225 · Cited by 26 · see citing works
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Babb, P. L., Fernandez-Duque, E., & Schurr, T. G. (2015) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2015.05.006 · Cited by 16 · see citing works
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Azeez, B., Mossey, P., Tiffin, N., Adeyemo, W., Eshete, M., Chrispinanus, M., Audu, R., Chika, O., Pius, A., Mobolanle, O., et al. (2015) · Pan African Medical Journal · doi:10.11604/pamj.2015.21.229.7380 · Cited by 13 · see citing works
- Authors
- Keinan, A., & Clark, A. G.
- Affiliations
- Cornell University (US)
- Corresponding author
- Keinan, Alon
- Venue
- Science
- Published
- 2012-05-11
- Volume
- 336
- Issue
- 6082
- Pages
- 740-743
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3586590
- OpenAlex
- W2094608047
- Cited by
- 548
- References
- 39
- Citations by year
- 2026: 8 · 2025: 24 · 2024: 16 · 2023: 20 · 2022: 27 · 2021: 24 · 2020: 30 · 2019: 40 · 2018: 48 · 2017: 31 · 2016: 50 · 2015: 64 · 2014: 61 · 2013: 74 · 2012: 31
- FWCI
- 44.33
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (5p50gm065509-10)
- National Heart, Lung, and Blood Institute (HL102419, RC2HL102419)
- National Human Genome Research Institute (R01HG003229, U01HG005715)
- National Institute of General Medical Sciences (P50-GM065509, GM-065509)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- rare variants, site frequency spectrum, genetic load, population genetics, sample size effects, genetic burden, demographic history
- MeSH terms
- Gene Frequency, Genetics, Population, Haplotypes, Heterozygote, Humans, Models, Genetic, Mutation, Population Density, Population Growth, Genetic Variation, Genome, Human, Sequence Analysis, DNA, Sample Size, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, White People, Asian People, Genetic Association Studies
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