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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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“For example, a modest shift in the allele frequencies toward alleles that favor lighter skin or less hair may thus ‘‘shift the balance’’ such that the appearance of many or most individuals in a population changes (Hernandez et al., 2011; Pritchard and Di Rienzo, 2010; Pritchard et al., 2010).”
BackgroundAdaptations to Climate-Mediated Selective Pressures in Sheep
Lv, F., Agha, S., Kantanen, J., Colli, L., Stucki, S., Kijas, J., Joost, S., Li, M.-H., & Ajmone‐Marsan, P. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu264 · Cited by 199
“It has been argued that selection on standing variation played an important role in the adaptive evolution of complex traits in humans [70–71]; therefore, the signals that we detected may help elucidate the genetic architecture of common phenotypes with complex patterns of inheritance.”
BackgroundPalla, L., & Dudbridge, F. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.06.005 · Cited by 187
“new mutations.(19) Methods for the estimation of the number of genes affecting a trait have been proposed since the early 20 century, including complex segregation analysis comparing single- and multi-locus models with or without polygenic background,(20) but only with the recent availability of dense genome-wide data…”
BackgroundThe population biology of fungal invasions
Gladieux, P., Feurtey, A., Hood, M. E., Snirc, A., Clavel, J., Dutech, C., Roy, M., & Giraud, T. (2014) · Molecular Ecology · doi:10.1111/mec.13028 · Cited by 192
“Second, adaptation may be faster if the mutational targets are larger than a single nucleotide (Pritchard et al. 2010).”
Evidence for Polygenic Adaptation to Pathogens in the Human Genome
Daub, J. T., Hofer, T., Cutivet, E., Dupanloup, I., Quintana‐Murci, L., Robinson‐Rechavi, M., & Excoffier, L. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst080 · Cited by 193
“that selection on complex phenotypes has been acting in more subtle ways, for instance by acting on many genes at a time and modifying allele frequencies only slightly (Hancock, Alkorta-Aranburu, et al. 2010; Hancock, Witonsky, et al. 2010; Pritchard et al. 2010).”
BackgroundResultInfluentialBenestan, L., Quinn, B. K., Maaroufi, H., Laporte, M., Clark, F. K., Greenwood, S. J., Rochette, R., & Bernatchez, L. (2016) · Molecular Ecology · doi:10.1111/mec.13811 · Cited by 188
“…(EA) analyses represent an alternative and/or complementary avenue to PD approaches that may allow detecting adaptive patterns missed by PD methods (Pritchard et al. 2010; Rellstab et al. 2015; Francois et al. 2016) insofar as the environmental variables investigated are relevant to genetic…”
BackgroundAltitude Adaptation: A Glimpse Through Various Lenses
Simonson, T. S. (2015) · High Altitude Medicine & Biology · doi:10.1089/ham.2015.0033 · Cited by 181
“…(ongoing) versus complete (fixed or nearly fixed) adaptive events (Nielsen et al., 2007), ‘‘hard’’ or ‘‘soft’’ sweeps, novel or standing (pre-existing) genetic variation (Pritchard et al., 2010), or long-range haplotype versus allele-frequency based tests of selection (Sabeti et al., 2007).”
Stanton‐Geddes, J., Paape, T. D., Epstein, B., Briskine, R. V., Yoder, J. B., Mudge, J., Bharti, A. K., Farmer, A. D., Zhou, P., Denny, R. L., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0065688 · Cited by 186
“The extensive LD among flowering time and trichome density candidate SNPs also suggests that selection may maintain functionally divergent alleles, that alleles are subject to local adaptation, or have experienced recent soft-sweeps [28].”
BackgroundGossmann, T. I., Keightley, P. D., & Eyre‐Walker, A. (2012) · Genome Biology and Evolution · doi:10.1093/gbe/evs027 · Cited by 178
“The correlation seems less consistent with a model in which adaptation comes from standing genetic variation (Pritchard et al. 2010; Pritchard and Rienzo 2010) for two reasons.”
BackgroundGenome-Wide Analysis of Cold Adaptation in Indigenous Siberian Populations
Cardona, A., Pagani, L., Antão, T., Lawson, D. J., Eichstaedt, C. A., Yngvadóttir, B., Shwe, M. T. T., Wee, J. T. S., Romero, I. G., Raj, S. M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098076 · Cited by 181
“This lack of significant enrichment could be explained by the fact that the selection tests we used are designed to detect hard sweeps at individual loci that may be generally rare while soft sweeps affecting large number of functionally related genes would require different approaches of detection [52].”
Evidence for recent, population-specific evolution of the human mutation rate
Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165
Human Immunology through the Lens of Evolutionary Genetics
Quintana‐Murci, L. (2019) · Cell · doi:10.1016/j.cell.2019.02.033 · Cited by 182
“A subtler mechanism of adaptation is polygenic adaptation, in which minor allele frequency changes at multiple loci contribute to the adaptive phenotype (Pritchard et al., 2010) (Figure 2A).”
The timing of pigmentation lightening in Europeans
Beleza, S., Santos, A. M., McEvoy, B., Alves, I., Martinho, C., Cameron, E., Shriver, M. D., Parra, E. J., & Rocha, J. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss207 · Cited by 156
“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.”
BackgroundGenomic Signature of Adaptation to Climate in Medicago truncatula
Yoder, J. B., Stanton‐Geddes, J., Zhou, P., Briskine, R. V., Young, N. D., & Tiffin, P. (2014) · Genetics · doi:10.1534/genetics.113.159319 · Cited by 173
Metspalu, M., Romero, I. G., Yunusbayev, B., Chaubey, G., Mallick, C. B., Hudjashov, G., Nelis, M., Mägi, R., Metspalu, E., Remm, M., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.11.010 · Cited by 170
Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster
Flatt, T. (2020) · Genetics · doi:10.1534/genetics.119.300160 · Cited by 174
A Genomic Map of the Effects of Linked Selection in Drosophila
Elyashiv, E., Sattath, S., Hu, T. T., Strutsovsky, A., McVicker, G., Andolfatto, P., Coop, G., & Sella, G. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006130 · Cited by 167
“[18] also led to too large a rate of deleterious mutation and work done since suggests that classic sweeps contribute little to the effects of linked selection on genetic variation [49,77,78].”
BackgroundSelf-citationSabbagh, A., Darlu, P., Crouau‐Roy, B., & Poloni, E. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018507 · Cited by 161
“This complex model of ‘multiallelic’ directional selection seems to better fit the patterns of NAT2 diversity observed in present-day populations than the standard ‘hard sweep’ model which assumes the rapid fixation of a single newly arisen advantageous mutation [10].”
BackgroundStanding genetic variation as the predominant source for adaptation of a songbird
Lai, Y.-T., Yeung, C. K. L., Omland, K. E., Pang, E.-L., Hao, Y., Liao, B., Cao, H.-F., Zhang, B.-W., Yeh, C., Hung, C., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1813597116 · Cited by 165
“The higher polymorphism levels of the other candidate SNPs suggest that they are probably under soft sweep or polygenic selection and thus unable to drive these advantageous genetic variants to fixation (40).”
The genomic signature of parallel adaptation from shared genetic variation
Roesti, M., Gavrilets, S., Hendry, A. P., Salzburger, W., & Berner, D. (2014) · Molecular Ecology · doi:10.1111/mec.12720 · Cited by 161
“This traditional theoretical scenario might not be adequate when adaptation occurs from standing (pre-existing) genetic variation rather than from novel mutations (Hermisson & Pennings 2005; Barrett & Schluter 2008; Pritchard et al. 2010).”
McManus, I. C., Davison, A., & Armour, J. A. L. (2013) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12102 · Cited by 159
Will human influences on evolutionary dynamics in the wild pervade the Anthropocene?
Pelletier, F., & Coltman, D. W. (2018) · BMC Biology · doi:10.1186/s12915-017-0476-1 · Cited by 166
Stephan, W. (2015) · Molecular Ecology · doi:10.1111/mec.13288 · Cited by 161
“Subtle to moderate allele frequency changes at many loci Several authors have argued verbally that adaptation in natural populations occurs not by sweeps alone, but involves subtle allele frequency shifts at many loci controlling polygenic traits (e.g. Pritchard et al. 2010).”
BackgroundGlémin, S., & Ronfort, J. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01778.x · Cited by 161
Lohmueller, K. E., Albrechtsen, A., Li, Y., Kim, S. Y., Korneliussen, T. S., Vinckenbosch, N., Tian, G., Huerta‐Sánchez, E., Feder, A. F., Grarup, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002326 · Cited by 155
Chen, J., Källman, T., Ma, X., Gyllenstrand, N., Zaina, G., Morgante, M., Bousquet, J., Eckert, A. J., Wegrzyn, J., Neale, D. B., et al. (2012) · Genetics · doi:10.1534/genetics.112.140749 · Cited by 153
“Or do they reflect the deployment in space of polymorphisms already segregating in the ancestral populations, i.e., through soft sweeps (Pritchard et al. 2010; Savolainen et al. 2011)?”
BackgroundExplaining additional genetic variation in complex traits
Robinson, M. R., Wray, N. R., & Visscher, P. M. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.02.003 · Cited by 152
Detecting positive selection in the genome
Booker, T. R., Jackson, B., & Keightley, P. D. (2017) · BMC Biology · doi:10.1186/s12915-017-0434-y · Cited by 151
“If polygenic traits are the target of selection, partial sweeps may be common, because selection can bring about rapid evolution by acting on standing variation at multiple loci, affecting levels of diversity at linked neutral sites [67, 71].”
BackgroundStölting, K. N., Nipper, R. W., Lindtke, D., Caseys, C., Waeber, S., Castiglione, S., & Lexer, C. (2012) · Molecular Ecology · doi:10.1111/mec.12011 · Cited by 147
Sheehan, M. J., & Nachman, M. W. (2014) · Nature Communications · doi:10.1038/ncomms5800 · Cited by 157
“Due to the complex genetic architecture of facial variation 32–34 we expect a modest signature of elevated diversity in genomic regions underlying identity signals as a whole 35,36 , though there may be stronger evidence for NFDS at a subset of loci.”
Polygenic adaptation: From sweeps to subtle frequency shifts
Höllinger, I., Pennings, P. S., & Hermisson, J. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008035 · Cited by 145
“The result also shows that the adaptive scenario does not depend directly on the number of loci in the genetic basis of the trait, but rather on their combined mutation rate (the mutational target size, sensu [11]).”
BackgroundSelection signatures in livestock genome: A review of concepts, approaches and applications
Saravanan, K. A., Panigrahi, M., Kumar, H., Bhushan, B., Dutt, T., & Mishra, B. P. (2020) · Livestock Science · doi:10.1016/j.livsci.2020.104257 · Cited by 163
Effects of Linked Selective Sweeps on Demographic Inference and Model Selection
Schrider, D. R., Shanku, A. G., & Kern, A. D. (2016) · Genetics · doi:10.1534/genetics.116.190223 · Cited by 148
“Polygenic selection, in which alleles at several different loci underlying a trait under selection will experience a change in frequency, is also thought to be widespread (Pritchard et al. 2010; Berg and Coop 2014).”
Background
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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