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The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation
Open accessAbstract
There has long been interest in understanding the genetic basis of human adaptation. To what extent are phenotypic differences among human populations driven by natural selection? With the recent arrival of large genome-wide data sets on human variation, there is now unprecedented opportunity for progress on this type of question. Several lines of evidence argue for an important role of positive selection in shaping human variation and differences among populations. These include studies of comparative morphology and physiology, as well as population genetic studies of candidate loci and genome-wide data. However, the data also suggest that it is unusual for strong selection to drive new mutations rapidly to fixation in particular populations (the 'hard sweep' model). We argue, instead, for alternatives to the hard sweep model: in particular, polygenic adaptation could allow rapid adaptation while not producing classical signatures of selective sweeps. We close by discussing some of the likely opportunities for progress in the field.
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“As previously noted (Hawks et al. 2007;Karasov et al. 2010;Pritchard et al. 2010), effective population size is one of the most important factors limiting the availability of adaptive mutations.”
From The timing of pigmentation lightening in Europeans (2013) · cites this paper as Pritchard et al. 2010
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“It is possible that a polygenic combination of “soft” sweeps in networks of genes (Cordaux and Batzer, 2009; Erwin and Davidson, 2009; Pritchard et al., 2010) rather than a positive selection at single loci may be one of the major mechanisms regulating the evolution of expression (Khaitovich et…”
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“…space – any signatures left from such selective episodes were not strong enough to alter the allele frequency spectra and extent of haplotype homozygosity of sialic acid biology genes within a single population or acrossmultiple populations to detectable levels (Bell 2010; Pritchard et al. 2010).”
BackgroundWeak Correlation between Nucleotide Variation and Recombination Rate across the House Mouse Genome
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“The soft sweeps or sets of partial sweeps that would emerge to underlie adaptation are notoriously hard to detect because of diminished signal of linked selection (Pritchard et al., 2010; Yeaman, 2015).”
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“Many phenotypic traits are also polygenic, meaning that they are affected by genetic variation at multiple sites and/or genes 12,13 .”
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit
Sheppard, E. C., Martin, C. A., Armstrong, C., González‐Quevedo, C., Illera, J. C., Suh, A., Spurgin, L. G., & Richardson, D. S. (2022) · Molecular Ecology · doi:10.1111/mec.16461 · Cited by 9
“Using genome- wide markers would allow for discovery of further loci but even traditional population- level based approaches may have limited power to detect small frequency shifts responsible for adaptation in polygenic traits (Pritchard et al., 2010).”
BackgroundMosaic patterns of selection in genomic regions associated with diverse human traits
Abraham, A., LaBella, A. L., Capra, J. A., & Rokas, A. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010494 · Cited by 12
Widespread gene flow following range expansion in Anna's Hummingbird
Adams, N., Bandivadekar, R. R., Battey, C. J., Clark, M. W., Epperly, K., Ruegg, K., Tell, L. A., & Bay, R. A. (2023) · Molecular Ecology · doi:10.1111/mec.16928 · Cited by 11
“Further, our low-coverage approach and moderate sample size may not have the power to detect multiple small shifts in allele frequencies across loci that could lead to adaptive evolution, a common issue with genome-wide scans for polygenic traits (Kemper et al., 2014; Pritchard et al., 2010).”
BackgroundGenetic and Phenotypic Consequences of Introgression Between Humans and Neanderthals
Wills, C. J. (2011) · Advances in genetics · doi:10.1016/b978-0-12-386481-9.00002-x · Cited by 11
Tollenaere, C., Jacquet, S., Ivanova, S., Loiseau, A., Duplantier, J., Streiff, R., & Brouat, C. (2012) · Molecular Ecology · doi:10.1111/mec.12115 · Cited by 12
“Polygenic adaptation may also occur more frequently than previously thought in human populations (Pritchard et al. 2010).”
BackgroundHernandez, M., & Perry, G. H. (2021) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21893 · Cited by 10
“Neither are signatures of polygenic adaptation, a process in which smaller frequency changes in aggregate across many alleles with individually-smaller effects on a phenotype can have large evolutionary effects for complex traits.(36) Despite these limitations, genome-wide scans conducted over the past two decades wit…”
BackgroundMunshi‐South, J., Zolnik, C. P., & Harris, S. E. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/025007 · Cited by 10
Pearless, S. M., & Freed, N. E. (2024) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2024.1335452 · Cited by 10
Chen, C., Moyzis, R. K., Lei, X., Chen, C., & Dong, Q. (2016) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780199357376.013.22 · Cited by 9
Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea
Lee, Y.-S., Shin, D., Won, K.-H., Kim, D. C., Lee, S. C., & Song, K. (2019) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.19.0026 · Cited by 9
“XP-EHH uses the haplotype homozygosity and XP-CLR uses the population differentiation between the two object and reference population [14,15].”
MethodThe resistome and genomic reconnaissance in the age of malaria elimination
Kümpornsin, K., Kochakarn, T., & Chookajorn, T. (2019) · Disease Models & Mechanisms · doi:10.1242/dmm.040717 · Cited by 9
“3) (Pritchard et al., 2010).”
Moggi‐Cecchi, J., & Stanyon, R. (2014) · Cataloghi e collezioni · doi:10.36253/978-88-6655-611-4 · Cited by 10
Evolution in small steps and giant leaps
Whiteman, N. K. (2022) · Evolution · doi:10.1111/evo.14432 · Cited by 10
Ghat: an R package for identifying adaptive polygenic traits
Mahmoud, M., Tost, M. L., Ha, N.-T., Simianer, H., & Beissinger, T. M. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac319 · Cited by 8
Zanetti, D., Carreras‐Torres, R., Esteban, E., Vía, M., & Moral, P. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134840 · Cited by 11
“Finally, much of human adaptation may proceed by either polygenic adaptation or soft sweeps that can be difficult to detect using standard methods [64].”
BackgroundZhang, M., Azad, P., & Woodruff, R. C. (2010) · Genetica · doi:10.1007/s10709-010-9535-z · Cited by 9
“…2001; Yedid and Bell 2002; Bull and Otto 2005; Rokyta et al. 2005; Houle and Kondrashov 2006; Barrett and Schluter 2007; Lynch 2007; Brookfield 2009; Stoltzfus and Yampolsky 2009; Woodruff and Zhang 2009; Azad et al. 2010; Lynch and Abegg 2010; Pritchard et al. 2010 and references therein).”
BackgroundDussex, N., Kutschera, V. E., Wiberg, R. A. W., Parker, D. J., Hunt, G. R., Gray, R. D., Rutherford, K., Abe, H., Fleischer, R. C., Ritchie, M. G., et al. (2020) · Molecular Ecology · doi:10.1111/mec.15775 · Cited by 10
“Conversely, for genes under positive selection and indicating an excess of non-synonymous fixed differences, this index will result in a value of NI 1 (Rand & Kann, 1996).”
BackgroundInfluentialUnderstanding Heritability: What it is and What it is Not
Johnson, W., Penke, L., & Spinath, F. M. (2011) · European Journal of Personality · doi:10.1002/per.835 · Cited by 10
A Population Genetic Signature of Polygenic Local AdaptationPreprint
Berg, J. J., & Coop, G. (2013) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/000026 · Cited by 9
Self-citationLiu, X., Loh, P., O’Connor, L. J., Gazal, S., Schoech, A. P., Maier, R. M., Patterson, N. J., & Price, A. L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/357483 · Cited by 8
Brand, C. M., White, F. J., Ting, N., & Webster, T. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.14.422788 · Cited by 9
“For these polygenic traits, shifts in the physical or social environment might result in allele frequency changes at many loci, of which, according to models, few to none of which would reach fixation (Pritchard et al. 2010).”
BackgroundPutilov, A. A., Dorokhov, V. B., & Poluektov, M. G. (2018) · Chronobiology International · doi:10.1080/07420528.2017.1417314 · Cited by 8
“The second approach was also previously widely applied in various studies on genetics of human adaptation (Coop et al. 2009; Fraser 2013; Hancock et al. 2011; Pritchard et al. 2010; Thompson et al. 2004).”
BackgroundSelection and adaptation in human migration
Bell, A. V. (2023) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.22003 · Cited by 12
“68 Despite the lack of evidence for thrifty genes, the case is instructive in clarifying the difficulty in gene studies of adaptation in migrating populations.”
de Jong, M. A., van Rensburg, A. J., Whiteford, S., Yung, C. J., Beaumont, M., Jiggins, C. D., & Bridle, J. R. (2023) · Molecular Ecology · doi:10.1111/mec.17138 · Cited by 8
Quantitative omnigenic model discovers interpretable genome-wide associations
Ružičková, N., Hledík, M., & Tkačik, G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2402340121 · Cited by 8
The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance
Brunharo, C. A. C. G., Short, A. W., Bobadilla, L. K., & Streisfeld, M. A. (2025) · Molecular Ecology · doi:10.1111/mec.17775 · Cited by 8
“Under a model where the genetic architecture of resistance includes a few, large-effect loci, the application of paraquat in agricultural fields is expected to result in signatures of a selective sweep surrounding the loci involved in resistance (Pritchard et al. 2010).”
Lexer, C., & Stölting, K. N. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04362.x · Cited by 8
Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome.
Garke, C., Ytournel, F., Sharifi, A. R., Pimentel, E. C. G., Ludwig, A., & Simianer, H. (2014) · Animal Genetics · doi:10.1111/age.12150 · Cited by 10
Amin, M. R., Hasan, M., Arnab, S. P., & DeGiorgio, M. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad216 · Cited by 9
“Displaying the feature maps in this fashion enables visualization of the characteristics of haplotype (Pritchard et al. 2010).”
Metadata
- Authors
- Pritchard, J. K., Pickrell, J. K., & Coop, G.
- Affiliations
- Howard Hughes Medical Institute (US)
- University of Chicago (US)
- University of California, Davis (US)
- Corresponding author
- Pritchard, Jonathan K.
- Venue
- Current Biology
- Publisher
- Elsevier BV
- Published
- 2010-02
- Volume
- 20
- Issue
- 4
- Pages
- R208-R215
- ISSN
- 0960-9822 (ISSN-L)
- PMC
- PMC2994553
- OpenAlex
- W2135370544
- Cited by
- 932
- References
- 80
- Citations by year
- 2026: 46 · 2025: 35 · 2024: 38 · 2023: 46 · 2022: 47 · 2021: 69 · 2020: 64 · 2019: 63 · 2018: 72 · 2017: 54 · 2016: 73 · 2015: 69 · 2014: 72 · 2013: 51 · 2012: 64
- FWCI
- 32.95
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Current Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health
- National Institute of Mental Health (R01MH084703)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- human adaptation, positive selection, hard sweeps, soft sweeps, polygenic adaptation, selective sweeps, human population variation, natural selection, candidate loci
- MeSH terms
- Adaptation, Biological, Genetics, Population, Humans, Selection, Genetic, Multifactorial Inheritance
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