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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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“Several recent studies also suggest that classic “hard” selective sweeps may be rare in Drosophila (Sella et al. 2009; Karasov et al. 2010) and humans (Pritchard et al. 2010; Hernandez et al. 2011), implying that models that better account for linkage between sites need to be explored.”
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“…across ecoregions significantly correlated with elevation, but also to interrogate for concerted shifts of allele frequencies on genes involved in particular biological functions as expected under a model of polygenic selection (Pritchard et al. 2010; Stephan 2016; Novembre and Barton 2018).”
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“, 2018), our observations indicate that signatures of selection for human-directed behavior in dogs are likely to be weak and prone to false positives (sensu lato Messer and Petrov, 2013; Pritchard et al., 2010).”
BackgroundEvolutionary Physiology and Genomics in the Highly Adaptable Killifish ( Fundulus heteroclitus )
Crawford, D. L., Schulte, P. M., Whitehead, A., & Oleksiak, M. F. (2020) · Comprehensive physiology · doi:10.1002/cphy.c190004 · Cited by 23
“That is, this high level of standing genetic variation occurs because with polygenic adaptation few alleles are swept to fixation during selection and thus, there is a great reduction in the rate or near elimination of purge genetic variation even under strong selection (153, 170, 209).”
InfluentialGenomic patterns of species diversity and divergence in Eucalyptus
Hudson, C. J., Freeman, J. S., Myburg, A. A., Potts, B. M., & Vaillancourt, R. E. (2015) · New Phytologist · doi:10.1111/nph.13316 · Cited by 20
Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex
Leigh, D. M., Lischer, H. E. L., Guillaume, F., Grossen, C., & Günther, T. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13442 · Cited by 21
“Polygenic architectures were chosen because they are more often the subjects of selection in natural scenarios and thus increased the biological realism of our simulations (Pritchard et al., 2010; Burke et al., 2010; Timpson et al., 2018; Barghi et al., 2020).”
BackgroundOjeda‐Granados, C., Abondio, P., Setti, A., Sarno, S., Gnecchi‐Ruscone, G. A., González-Orozco, E., Fanti, S. D., Jimenez-Kaufmann, A., Rangel‐Villalobos, H., Moreno‐Estrada, A., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab290 · Cited by 20
“Therefore, polygenic selective events are expected to have occurred more frequently than hard/soft selective sweeps (Pritchard et al. 2010; Hernandez et al. 2011).”
van der Zee, M. J., Whiting, J. R., Paris, J. R., Bassar, R. D., Travis, J., Weigel, D., Reznick, D. N., & Fraser, B. A. (2022) · Evolution Letters · doi:10.1002/evl3.272 · Cited by 24
Mafessoni, F., & Lachmann, M. (2015) · Genetics · doi:10.1534/genetics.115.178160 · Cited by 20
Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model
Lillie, M., Honaker, C. F., Siegel, P. B., & Carlborg, Ö. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400038 · Cited by 21
“3.52; Robinson et al. 2011; Thorvaldsdottir et al. 2013).”
InfluentialDoes Adaptive Protein Evolution Proceed by Large or Small Steps at the Amino Acid Level?
Bergman, J., & Eyre‐Walker, A. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz033 · Cited by 19
Selective Sweep at a QTL in a Randomly Fluctuating Environment
Chevin, L. (2019) · Genetics · doi:10.1534/genetics.119.302680 · Cited by 17
What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit?
Jakobson, C. M., & Jarosz, D. F. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-021920-102037 · Cited by 19
Archambeau, J., Garzón, M. B., Barraquand, F., de Miguel, M., Plomion, C., & González‐Martínez, S. C. (2022) · The American Naturalist · doi:10.1086/720619 · Cited by 20
“…al. (2015), who used nine nuSSRs as well as a subset of the same SNPs as in our study (1,745 SNPs) to infer population genetic structure in maritime pine (referred as the population demographic history) using the Bayesian approach available in Structure v. 2.3.3 (Pritchard et al. 2000; Table S3).”
MethodInfluentialGenomic evidence for fisheries-induced evolution in Eastern Baltic cod
Han, K. Y., Brennan, R. S., Monk, C. T., Jentoft, S., Helmerson, C., Dierking, J., Hüssy, K., Kokubun, É. E., Fuß, J., Krause‐Kyora, B., et al. (2025) · Science Advances · doi:10.1126/sciadv.adr9889 · Cited by 22
“…the relatively low sample size, dictated by the availability of extractable DNA traces attached to historical otoliths, and the polygenic genetic basis of life history traits such as growth ( 41 , 42 ), we did not identify any loci with sufficiently large effect size upon multiple error correction.”
Human cerebral evolution and the clinical syndrome of amyotrophic lateral sclerosis
Henderson, R. D., Garton, F. C., Kiernan, M. C., Turner, M. R., & Eisen, A. (2018) · Journal of Neurology Neurosurgery & Psychiatry · doi:10.1136/jnnp-2017-317245 · Cited by 20
Small, S. T., Costantini, C., Sagnon, N., Guelbeogo, M. W., Emrich, S., Kern, A. D., Fontaine, M. C., & Besansky, N. J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2219835120 · Cited by 19
“The recency and rapidity of local adaptation to a new habitat in K is difficult to reconcile with new mutation alone, because many traits involved in adaptation to local environments are expected to be highly polygenic (49) and it is unlikely that all alleles involved are newly mutated.”
BackgroundComplement polymorphisms: Geographical distribution and relevance to disease
Ermini, L., Wilson, I., Goodship, T., & Sheerin, N. (2011) · Immunobiology · doi:10.1016/j.imbio.2011.07.020 · Cited by 22
Seixas, S., Ivanova, N., Worman, Z., Rocha, J., & Victor, B. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032518 · Cited by 19
“Such a model of directional selection is based on the assumption that adaptation may exploit the standing genetic pool of a population in such a way that shifts of selective pressures favor previously neutral or weakly deleterious variants [49–53].”
BackgroundEvidence for Population-Specific Positive Selection on Immune Genes ofAnopheles gambiae
Crawford, J. E., Bischoff, E., Garnier, T., Gnémé, A., Eiglmeier, K., Holm, I., Riehle, M. M., Guelbeogo, M. W., Sagnon, N., Lazzaro, B. P., et al. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.004473 · Cited by 18
Yoder, J. B., & Tiffin, P. (2017) · Journal of Heredity · doi:10.1093/jhered/esx042 · Cited by 19
“Populations at nonequilibrium demographic conditions, experiencing more complex landscapes, experiencing weaker selection, or selection distributed across multiple loci (Kelly 2006; Pritchard et al. 2010; Savolainen et al. 2013; Anderson et al. 2014b), would all violate these assumptions and thereby both increase the…”
BackgroundA theory of oligogenic adaptation of a quantitative trait
Höllinger, I., Wölfl, B., & Hermisson, J. (2023) · Genetics · doi:10.1093/genetics/iyad139 · Cited by 16
“Pritchard and colleagues (Pritchard et al. 2010; Pritchard and Di Rienzo 2010) proposed the concept of “polygenic adaptation” as an alternative to the selective sweep model with the goal of characterizing—and, if possible, detecting—patterns of QT adaptation at the genomic level.”
The Effects of Microsatellite Selection on Linked Sequence Diversity
Haasl, R. J., Johnson, R., & Payseur, B. A. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu134 · Cited by 18
“Key words: microsatellites, natural selection, genomic scans for selection, mutation, short tandem repeats.”
BackgroundStudying the genetic basis of speciation in high gene flow marine invertebrates
Pogson, G. H. (2016) · Current Zoology · doi:10.1093/cz/zow093 · Cited by 18
“prediction that soft sweeps (Hermisson and Pennings 2005; Pritchard et al. 2010) could be more common than hard sweeps.”
BackgroundVy, H. M. T., Won, Y., & Kim, Y. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx207 · Cited by 17
Mason, N. A., & Unitt, P. (2017) · Journal of Avian Biology · doi:10.1111/jav.01507 · Cited by 18
The Genetics of Human Pigmentary Disorders
Rees, J. L. (2011) · Journal of Investigative Dermatology · doi:10.1038/skinbio.2011.5 · Cited by 18
“mental one in a way few could have hoped for even in the mid 1980s (Voight et al., 2006; Sabeti et al., 2007; Pickrell et al., 2009; Pritchard et al., 2010; Hancock et al., 2011).”
BackgroundFüller, J., Ferchaud, A., Laporte, M., Luyer, J. L., Davis, T. B., Côté, S. D., & Bernatchez, L. (2019) · Molecular Ecology · doi:10.1111/mec.15317 · Cited by 18
Stern, A. J., & Nielsen, R. (2019) · Wiley eBooks · doi:10.1002/9781119487845.ch14 · Cited by 18
Dominance shifts increase the likelihood of soft selective sweeps
Muralidhar, P., & Veller, C. (2022) · Evolution · doi:10.1111/evo.14459 · Cited by 16
Polygenic score accuracy in ancient samples: Quantifying the effects of allelic turnover
Carlson, M. O., Rice, D. P., Berg, J. J., & Steinrücken, M. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010170 · Cited by 17
“For example, detection imbalances have been observed in case-control GWA studies [34], and many polygenic traits are likely under some form of selection [35, 36].”
BackgroundAdaptive Fixation in Two-Locus Models of Stabilizing Selection and Genetic Drift
Wollstein, A., & Stephan, W. (2014) · Genetics · doi:10.1534/genetics.114.168567 · Cited by 17
Kakioka, R., Kokita, T., Kumada, H., Watanabe, K., & Okuda, N. (2015) · Molecular Ecology · doi:10.1111/mec.13309 · Cited by 17
“Polygenic inheritance could allow rapid adaptive shifts of traits by small changes of allele frequency that spread across many QTLs (Pritchard & Di Rienzo 2010; Pritchard et al. 2010).”
BackgroundInference of Evolutionary Forces Acting on Human Biological Pathways
Daub, J. T., Dupanloup, I., Robinson‐Rechavi, M., & Excoffier, L. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv083 · Cited by 17
“In the long run this would lead to an increase in the frequency of a suitable combination of alleles that control the favored phenotype (Pritchard et al. 2010).”
BackgroundImpact of polymorphic transposable elements on linkage disequilibrium along chromosomes
Choudhury, R. R., Rogivue, A., Gugerli, F., & Parisod, C. (2019) · Molecular Ecology · doi:10.1111/mec.15014 · Cited by 17
The Columbian Exchange as a source of adaptive introgression in human populations
Jordan, I. K. (2016) · Biology Direct · doi:10.1186/s13062-016-0121-x · Cited by 16
“, hard versus soft selective sweeps, the role of de novo versus standing genetic variation and the prevalence of polygenic selection [22, 31, 42].”
BackgroundEvolutionary genomics of gypsy moth populations sampled along a latitudinal gradient
Friedline, C. J., Faske, T. M., Lind, B. M., Hobson, E. M., Parry, D., Dyer, R. J., Johnson, D. M., Thompson, L. M., Grayson, K. L., & Eckert, A. J. (2019) · Molecular Ecology · doi:10.1111/mec.15069 · Cited by 17
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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