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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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“In recent decades, research bridging the fields of molecular population genetics and quantitative genetics (Barghi et al., 2020; Barton, 1999; Pritchard et al., 2010 ; Pritchard & Di Rienzo, 2010 ) has revealed that the genomic architecture of a trait is a core de - terminant of whether and how…”
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“Here, we introduce CNNs designed to directly use individual genotypes for the joint estimation of s and T , considering additive models for positive (Maynard Smith & Haigh, 1974; Pritchard et al., 2010; Stephan et al., 1992) and negative selection (Charlesworth et al., 1993).”
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“Our resultssupportthenotion that variants related to cognitive and psychiatric phenotypes have become more prevalent faster than other SNPs throughout e volution, possibly due to selection pressures (Pritchard et al. 2010; Karlsson et al. 2014; Simons et al. 2022).”
Adaptive Evolution FavoringKLK4Downregulation in East Asians
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Natural selection among Eurasians at genomic regions associated with HIV-1 control
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“Alternatively, local adaptation may also proceed through shifts in standing polymorphism at many loci (Pritchard et al., 2010; Hancock et al., 2010).”
BackgroundSigns of Selective Pressure on Genetic Variants Affecting Human Height
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“…acting on standing genetic variation present in the ancestral population or if very large effective population sizes characterize one or both diverging populations (Pritchard et al. 2010), the signature of divergence around loci under selection is expected to be minimal (Hermisson & Pennings 2005).”
BackgroundPiffer, D. (2023) · Qeios · doi:10.32388/hdjk5p · Cited by 4
Ata, N., Gündüz, Z., Kaşıkçı, D., Canatan, T., Cemal, İ., & Yılmaz, O. (2025) · Small Ruminant Research · doi:10.1016/j.smallrumres.2025.107521 · Cited by 4
McDonough, Y., Ruzicka, F., & Connallon, T. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2406335121 · Cited by 4
“X models, we focus on positively selected substitutions, which are expected to increase signals of adaptive substitution in population genomic data ( 58 , 59 ).”
Ribeiro, T. D. S., Lollar, M. J., Sprengelmeyer, Q. D., Huang, Y., Benson, D. M., Orr, M. S., Johnson, Z. C., Corbett-Detig, R. B., & Pool, J. E. (2025) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkaf051 · Cited by 3
“A number of important uncertainties persist regarding the genetic architectures of adaptive trait changes in nature, including the number and effect sizes of contributing variants, and their frequencies be - fore and after the action of positive selection (Pritchard et al .”
Gross, K., Yazdi, H. P., Schlager, E., Lilley, J., Romero‐Bravo, A., Runemark, A., Thompson, J. N., & Friberg, M. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2505119122 · Cited by 3
“1 B and SI Appendix , Table S6), cluster analysis in STRUCTURE (57) (Fig.”
Populations adapt to fluctuating selection using derived and ancestral allelic diversity
Lin, W.-H., Rocco, M. J., Bertozzi-Villa, A., & Kussell, E. L. (2015) · Evolution · doi:10.1111/evo.12665 · Cited by 5
“Population genetics data indicate that selective sweeps from standing variation make up a significant percentage of recent adaptations in flies and humans (Burke et al. 2010; Pritchard et al. 2010; Hernandez et al. 2011).”
BackgroundNaturally Available Genetic Adaptation in Common Bean and Its Response to Climate Change
Cortés, A. J., & Blair, M. W. (2018) · InTech eBooks · doi:10.5772/intechopen.72380 · Cited by 4
Barbhuiya, M. A., Uddin, A., & Chakraborty, S. (2018) · Mitochondrial DNA Part A · doi:10.1080/24701394.2018.1532414 · Cited by 4
“By the selection-mutation-drift model, CUB is defined by a balance among evolutionary forces, i.e., mutation pressure, genetic drift, and weak selection (Pritchard et al. 2010).”
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The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci
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Genome-wide analysis revisits incipient sympatric and allopatric speciation in a beetle
Hong, W., Li, K., Sharaf, K., Song, X., Pavlı́ček, T., Zhao, H., & Nevo, E. (2020) · Israel Journal of Ecology and Evolution · doi:10.1163/22244662-bja10018 · Cited by 4
Landscape genomic tests for associations between loci and environmental gradients
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“In theory, predictable patterns of clinal variation in allele frequencies can arise from divergent selection across environmental gradients [1], although demographic factors may complicate identification of adaptive changes [4,5].”
Polymorphism at genes involved in salt tolerance in Arabidopsis thaliana (Brassicaceae)
Puerma, E., & Aguadé, M. (2013) · American Journal of Botany · doi:10.3732/ajb.1200332 · Cited by 4
The genetics of host adaptation in the parasiticplant Striga hermonthica
Pescott, O. L. (2013) · Cited by 4
Foll, M., Gaggiotti, O. E., Daub, J. T., & Excoffier, L. (2014) · arXiv (Cornell University) · Cited by 4
Directional Selection and Adaptation
Racimo, F., Schraiber, J. G., Casey, F., & Huerta‐Sánchez, E. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-800049-6.00028-7 · Cited by 4
Ecological and association genetics in two Mediterranean pine species
Quilón, I. R. (2017) · UPM Digital Archive (Technical University of Madrid) · doi:10.20868/upm.thesis.47140 · Cited by 4
Richards, E. J., Poelstra, J. W., & Martin, C. H. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/217984 · Cited by 4
“…may have been adaptive and undergone soft selective sweeps, although the relative contributions of hard sweeps versus soft sweeps during adaptation and speciation is still the subject of much debate (Hermisson and Pennings 2005, 2017; Pritchard et al. 2010; Jensen 2014; Schrider et al. 2015).”
BackgroundLaval, G., Patin, É., Boutillier, P., & Quintana‐Murci, L. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.22.886234 · Cited by 4
Deep estimation of the intensity and timing of selection from ancient genomesPreprint
Laval, G., Patin, É., Quintana‐Murci, L., & Kerner, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.27.550703 · Cited by 4
How weedy Arabidopsis thaliana dominated the world: ancestral variation and polygenic adaptationPreprint
Lo, C., Chien, C., Lin, Y., Yeh, P.-M., & Lee, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.28.591542 · Cited by 5
Striking Departures from Polygenic Architecture in the Tails of Complex TraitsPreprint
Souaiaia, T., Wu, H. M., Ori, A. P. S., Choi, S. W., Hoggart, C., & O’Reilly, P. F. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.18.624155 · Cited by 4
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“…Hoban et al. 2016; Wadgymar et al. 2022), during which natural selection leads to locally adapted genotypes by acting on de-novo mutations or standing genetic variation (Ament-Velásquez et al. 2022; Matuszewski, Hermisson, and Kopp 2015; Pritchard, Pickrell, and Coop 2010; Teotónio et al. 2009).”
Deep learning insights into distinct patterns of polygenic adaptation across human populations
Tripathi, D., Bhattacharyya, C., & Basu, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1027 · Cited by 3
Arenas, S., & Cortés, A. J. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27020652 · Cited by 3
“The reduction in GW, TDM, and GY under drought, with increases in between-genotype variability, suggests that these traits depend more heavily on context-specific interactions and may be governed by many small-effect loci [8,49], consistent with their highly polygenic nature [18,50].”
Omics Technologies in Molecular Biology
Cortés, A. J. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27083349 · Cited by 3
“While these approaches have offered key regulatory understanding, they frequently fell short in explaining complex polygenic phenotypes due to the multi-layered [3] and sometimes epistatic [4] nature of biological regulation [5].”
Model Comparison of Heritability Enrichment Analysis in Livestock Population
Cai, X., Teng, J., Ren, D., Zhang, H., Li, J., & Zhang, Z. (2022) · Genes · doi:10.3390/genes13091644 · Cited by 3
“, the direction of selection) is the result of the many signals of positive and negative selection on trait-associated variants cancelling each other out [34].”
BackgroundA Completionist Approach to Discovering and Characterizing Bacterial Diversity
Cohan, F. M., & Kopac, S. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-28818-0.00009-4 · Cited by 3
DR5 is a restriction factor for human herpesviruses
Han, C., Gui, C., Su, B., Liu, N., Yan, H., & Lan, K. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2417372122 · Cited by 3
“This process promotes better adaptations and ultimately increases survival and reproduction rates ( 53 ).”
The State of Forest Genetic Diversity: Anthropogenic Impacts and Conservation Initiatives
Konrad, H., George, J., & Szukala, A. (2025) · Springer eBooks · doi:10.1007/978-3-031-82206-3_4 · Cited by 6
A Comprehensive Review of GWASs of Human Hair Traits
Needle, C. D., Brinks, A. L., Perez, O. D., Shapiro, J., Sicco, K. I. L., Tsirigos, A., & Petukhova, L. (2025) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2025.07.004 · Cited by 3
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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