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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Effective population size is one of the most important factors limiting the availability of adaptive mutations.
“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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Brutsaert, T. D. (2007) · Respiratory Physiology & Neurobiology · doi:10.1016/j.resp.2007.03.004 · Cited by 65 · cited 1× · see citing works
“Compared to related lowland populations, these high-elevation populations show a suite of physiological adaptations to low oxygen [11].”
Ashworth, J. T., Allison, M. J., Gerszten, E., & Pezzia, A. (1976) · American Journal of Physical Anthropology · doi:10.1002/ajpa.1330450111 · Cited by 44 · see citing works
Mutation, selection and the future of human evolution
Reed, F. A., & Aquadro, C. F. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.07.005 · Cited by 33 · cited 1× · see citing works
“It has been proposed that recent population growth of humans could have supplied a greater input of new mutations [51,52]; additionally, even modest population growth can greatly increase fixation probabilities of favored alleles [53].”
Population Genomic Analysis of ALMS1 in Humans Reveals a Surprisingly Complex Evolutionary History
Scheinfeldt, L., Biswas, S., Madeoy, J. J., Connelly, C. F., Schadt, E. E., & Akey, J. M. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp045 · Cited by 30 · see citing works
Orr's Quantitative Trait Loci Sign Test Under Conditions of Trait Ascertainment
Anderson, E. C., & Slatkin, M. (2003) · Genetics · doi:10.1093/genetics/165.1.445 · Cited by 22 · see citing works
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
Boyle, E. A., Li, Y. I., & Pritchard, J. K. (2017) · Cell · doi:10.1016/j.cell.2017.05.038 · Cited by 2,851 · see citing works
Self-citationHarnessing genomics for delineating conservation units
Funk, W. C., McKay, J., Hohenlohe, P. A., & Allendorf, F. W. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2012.05.012 · Cited by 1,121 · see citing works
Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models
Frichot, É., Schoville, S. D., Bouchard, G., & François, O. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst063 · Cited by 815 · see citing works
“An alternative way to investigate signatures of local adaptation, especially when beneficial alleles have weak phenotypic effects, is by identifying polymorphisms that exhibit high correlation with environmental variables (Joost et al. 2007; Hancock et al. 2008; Coop et al. 2010; Poncet et al. 2010; Pritchard et al. 2…”
BackgroundTracing the peopling of the world through genomics
Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works
Self-citationDetecting Natural Selection in Genomic Data
Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694 · see citing works
THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER
Rockman, M. V. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01486.x · Cited by 661 · see citing works
“…and of the subsequent extensive local adaptation of human populations bear few of the hallmarks of selective sweeps (Hernandez et al. 2011), and fixed differences among human populations are exceptionally rare, despite sufficient time for new mutations to have fixed (Pritchard et al. 2010).”
BackgroundResultInfluentialRicherson, P., Baldini, R., Bell, A. V., Demps, K., Frost, K., Hillis, V., Mathew, S., Newton, E. K., Naar, N., Newson, L., et al. (2016) · Behavioral and Brain Sciences · doi:10.1017/s0140525x1400106x · Cited by 639 · see citing works
Deciphering the evolution of herbicide resistance in weeds
Délye, C., Jasieniuk, M., & Corre, V. L. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.06.001 · Cited by 651 · see citing works
Kiryluk, K., Li, Y., Scolari, F., Sanna‐Cherchi, S., Choi, M., Verbitsky, M., Fasel, D. A., Lata, S., Prakash, S., Shapiro, S. L., et al. (2014) · Nature Genetics · doi:10.1038/ng.3118 · Cited by 633 · see citing works
Robust Identification of Local Adaptation from Allele Frequencies
Günther, T., & Coop, G. (2013) · Genetics · doi:10.1534/genetics.113.152462 · Cited by 591 · see citing works
“Many available tests for selection are designed to detect rapid complete sweeps from new mutations; however, such events are likely just a small percentage of adaptive genetic change (Coop et al., 2009; Pritchard et al., 2010; Cao et al., 2011; Hernandez et al., 2011).”
BackgroundSelf-citationFumagalli, M., Sironi, M., Pozzoli, U., Ferrer-Admettla, A., Pattini, L., & Nielsen, R. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002355 · Cited by 600 · see citing works
“Additionally, it has been recently suggested that most selection in humans may not be caused by hard sweeps, but rather by selection acting on standing variation in many genes (‘soft sweeps’) [17,18].”
BackgroundHorton, M., Hancock, A. M., Huang, Y. S., Toomajian, C., Atwell, S., Auton, A., Muliyati, N. W., Platt, A., Sperone, F. G., Vilhjálmsson, B. J., et al. (2012) · Nature Genetics · doi:10.1038/ng.1042 · Cited by 550 · see citing works
“Because PHS, CLR and F ST analyses identify loci at different stages in the selection process or loci that are experiencing different modes of adaptatio”
BackgroundNatural selection and infectious disease in human populations
Karlsson, E. K., Kwiatkowski, D. P., & Sabeti, P. C. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3734 · Cited by 526 · see citing works
Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates
Gautier, M. (2015) · Genetics · doi:10.1534/genetics.115.181453 · Cited by 505 · see citing works
A method for genome-wide genealogy estimation for thousands of samples
Speidel, L., Forest, M., Shi, S., & Myers, S. R. (2019) · Nature Genetics · doi:10.1038/s41588-019-0484-x · Cited by 480 · see citing works
A population genetic signal of polygenic adaptation
Berg, J. J., & Coop, G. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004412 · Cited by 487 · see citing works
“Because this signal is so weak at the level of the individual locus, it may be impossible to identify against the genome-wide background without a very specific annotation of which sites are the target of selection on a given trait [15,16].”
Self-citationProgress and promise of genome-wide association studies for human complex trait genetics
Stranger, B. E., Stahl, E. A., & Raj, T. (2011) · Genetics · doi:10.1534/genetics.110.120907 · Cited by 567 · see citing works
“…positive selection described above, however, are based on detecting signals of selective sweeps at individual loci (Maynard Smith and Haigh 1974) and are not able to detect adaptive events that affected many alleles of small effect (Chevin et al. 2008; Hancock et al. 2010; Pritchard et al. 2010).”
BackgroundGenomic signatures of selection at linked sites: unifying the disparity among species
Cutter, A. D., & Payseur, B. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3425 · Cited by 465 · see citing works
Adaptation–not by sweeps alone
Pritchard, J. K., & Di Rienzo, A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2880 · Cited by 445 · see citing works
Self-citationLowry, D. B., Hoban, S., Kelley, J. L., Lotterhos, K. E., Reed, L. K., Antolin, M. F., & Storfer, A. T. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12635 · Cited by 451 · see citing works
“Adaptations can also occur through soft sweeps on standing genetic variation, can be highly polygenic and can occur without any adaptive alleles going to fixation (Pritchard et al. 2010).”
BackgroundClassic Selective Sweeps Were Rare in Recent Human Evolution
Hernandez, R. D., Kelley, J. L., Elyashiv, E., Melton, S., Auton, A., McVean, G., 1000 Genomes Project, Sella, G., & Przeworski, M. (2011) · Science · doi:10.1126/science.1198878 · Cited by 427 · see citing works
Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps
Garud, N. R., Messer, P. W., Buzbas, E. O., & Petrov, D. A. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005004 · Cited by 442 · see citing works
“melanogaster is indeed common and often driven by strong selection, it should be possible to detect genomic signatures of recent and strong adaptation [12,13,14].”
BackgroundEvolutionary genetics of plant adaptation
Anderson, J. T., Willis, J. H., & Mitchell‐Olds, T. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.04.001 · Cited by 438 · see citing works
Detection of human adaptation during the past 2000 years
Field, Y., Boyle, E. A., Telis, N., Gao, Z., Gaulton, K. J., Golan, D., Yengo, L., Rocheleau, G., Froguel, P., McCarthy, M. I., et al. (2016) · Science · doi:10.1126/science.aag0776 · Cited by 383 · see citing works
Self-citationRabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
Carneiro, M., Rubin, C.-J., Di Palma, F., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., et al. (2014) · Science · doi:10.1126/science.1253714 · Cited by 404 · see citing works
“However, allele frequency shifts were detected at many loci spread across the genome and the great majority of ‘domestic’ alleles were also found in wild rabbits, implying that directional selection events associated with rabbit domestication are consistent with polygenic and soft sweep modes of selection (18) that pr…”
BackgroundPolygenic adaptation: a unifying framework to understand positive selection
Barghi, N., Hermisson, J., & Schlötterer, C. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0250-z · Cited by 404 · see citing works
Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Pielberg, G., Sigurðsson, S., Fall, T., Seppälä, E. H., Hansen, M. S., Lawley, C., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002316 · Cited by 390 · see citing works
“However, less extreme selective episodes (soft sweeps), such as incomplete selective sweeps or selection on standing variation may also be common [46,47].”
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis
Diabetes Genetics Replication and Meta-analysis Consortium, Stahl, E. A., Myocardial Infarction Genetics Consortium, Wegmann, D., Trynka, G., Gutierrez-Achury, J., Do, R., Voight, B. F., Kraft, P., Chen, R., et al. (2012) · Nature Genetics · doi:10.1038/ng.2232 · Cited by 388 · see citing works
“…such as Bayesian and pathway-based GWAS 48,49 , estimating the accuracy of the risk prediction that is attainable with additional validated or unvalidated risk alleles 50,51 and developing and testing hypotheses for the polygenic adaptation 52,53 that has affected the risk of complex disease.”
BackgroundSignatures of negative selection in the genetic architecture of human complex traits
Zeng, J., de Vlaming, R., Wu, Y., Robinson, M. R., Lloyd-Jones, L. R., Yengo, L., Yap, C. X., Xue, A., Sidorenko, J., McRae, A. F., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0101-4 · Cited by 391 · see citing works
Going global by adapting local: A review of recent human adaptation
Fan, S., Hansen, M. E. B., Lo, Y., & Tishkoff, S. A. (2016) · Science · doi:10.1126/science.aaf5098 · Cited by 378 · see citing works
On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure
Ferrer-Admetlla, A., Liang, M., Korneliussen, T. S., & Nielsen, R. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu077 · Cited by 362 · see citing works
“Thus, the hard sweep model may not be entirely appropriate for describing the process of adaptation in recent human history (Pritchard et al. 2010).”
BackgroundEvolutionary conflicts between viruses and restriction factors shape immunity
Duggal, N. K., & Emerman, M. (2012) · Nature reviews. Immunology · doi:10.1038/nri3295 · Cited by 362 · see citing works
“For example, simian foamy viruses (SFVs) are considered to be non-pathogenic in their natural hosts 72, 73 .”
BackgroundFariello, M. I., Boitard, S., Naya, H., SanCristobal, M., & Servin, B. (2013) · Genetics · doi:10.1534/genetics.112.147231 · Cited by 343 · see citing works
“In many real situations, selection will rather act effectively on multi-locus haplotypes (Pritchard et al., 2010), due for instance to recurrent mutations affecting the same gene, or to polygenic selection.”
BackgroundEvidence of widespread selection on standing variation in Europe at height-associated SNPs
Turchin, M. C., Chiang, C. W., Palmer, C. D., Sankararaman, S., Reich, D., Genetic Investigation of ANthropometric Traits (GIANT) Consortium, & Hirschhorn, J. N. (2012) · Nature Genetics · doi:10.1038/ng.2368 · Cited by 329 · see citing works
On the accumulation of deleterious mutations during range expansions
Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013) · Molecular Ecology · doi:10.1111/mec.12524 · Cited by 304 · see citing works
“Evolution during range expansions is often viewed as a process in which species evolve adaptively as they encounter new environments (Barrett & Schluter 2008; Pritchard et al. 2010).”
Using genomics to characterize evolutionary potential for conservation of wild populations
Harrisson, K. A., Pavlova, A., Telonis‐Scott, M., & Sunnucks, P. (2014) · Evolutionary Applications · doi:10.1111/eva.12149 · Cited by 318 · see citing works
“Polygenic models of adaptation have been under-represented in population genetics, a field that has tended to favour classical sweep models focussing on shifts towards fixation of beneficial alleles at one or a few loci (Pritchard et al. 2010).”
BackgroundInfluentialPurfield, D. C., McParland, S., Wall, E., & Berry, D. P. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176780 · Cited by 309 · see citing works
Adaptations to Climate-Mediated Selective Pressures in Humans
Hancock, A. M., Witonsky, D., Alkorta‐Aranburu, G., Beall, C. M., Gebremedhin, A., Sukernik, R. I., Utermann, G., Pritchard, J. K., Coop, G., & Rienzo, A. D. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001375 · Cited by 299 · see citing works
Self-citationGenetic redundancy fuels polygenic adaptation in Drosophila
Barghi, N., Tobler, R., Nolte, V., Jakšić, A. M., Mallard, F., Otte, K. A., Dolezal, M., Taus, T., Kofler, R., & Schlötterer, C. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000128 · Cited by 293 · see citing works
“However, such simple traits are the exception rather than the rule, and most traits are polygenic, with many contributing loci [10,11].”
Deschamps, M., Laval, G., Fagny, M., Itan, Y., Abel, L., Casanova, J.-L., Patin, E., & Quintana-Murci, L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.014 · Cited by 257 · see citing works
“We simulated neutrally evolving regions and positive selection assuming the hard sweep model.(60) Specifically, a single new advantageous mutation with”
Biological invasions, climate change and genomics
Chown, S. L., Hodgins, K. A., Griffin, P. C., Oakeshott, J. G., Byrne, M. M., & Hoffmann, A. A. (2014) · Evolutionary Applications · doi:10.1111/eva.12234 · Cited by 284 · see citing works
“For example, detecting small effect loci underlying polygenic traits has been a major challenge regardless of the method applied (Pritchard et al. 2010; Le Corre and Kremer 2012).”
BackgroundWhat is the evidence for heterozygote advantage selection?
Hedrick, P. W. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2012.08.012 · Cited by 283 · see citing works
Ecker, J. R., Bickmore, W. A., Barroso, I., Pritchard, J. K., Gilad, Y., & Segal, E. (2012) · Nature · doi:10.1038/489052a · Cited by 278 · see citing works
Self-citationToward a new history and geography of human genes informed by ancient DNA
Pickrell, J. K., & Reich, D. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.07.007 · Cited by 271 · see citing works
Self-citationThinking About the Evolution of Complex Traits in the Era of Genome-Wide Association Studies
Sella, G., & Barton, N. (2019) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022316 · Cited by 263 · see citing works
“These considerations, bolstered by the aforementioned evidence, have largely shifted the search for the genetic basis of human adaptation toward polygenic adaptation (134, 135).”
BackgroundThe Neutral Theory in Light of Natural Selection
Kern, A. D., & Hahn, M. W. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy092 · Cited by 263 · see citing works
“…theme in population genetics, there is good theoretical reason to believe that phenotypes that are highly polygenic (i.e., that result from genetic contributions at many loci) might not be associated with fixation of advantageous alleles at all (Pritchard et al. 2010; Jain and Stephan 2017).”
BackgroundFunctional Genetic Variants Revealed by Massively Parallel Precise Genome Editing
Sharon, E., Chen, S.-A. A., Khosla, N. M., Smith, J. D., Pritchard, J. K., & Fraser, H. B. (2018) · Cell · doi:10.1016/j.cell.2018.08.057 · Cited by 225 · see citing works
“Although each of these large-effect variants represents a fascinating example, these outliers may not be very informative for understanding the evolutionary process more generally, which is thought to be dominated by variants of much smaller effect (Pritchard et al., 2010).”
BackgroundSelf-citationHuman adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency
Hancock, A. M., Witonsky, D., Ehler, E., Alkorta‐Aranburu, G., Beall, C. M., Gebremedhin, A., Sukernik, R. I., Utermann, G., Pritchard, J. K., Coop, G., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914625107 · Cited by 255 · see citing works
“Whereas approaches that detect selection under a hard sweep model aim to identify loci that drove a new allele quickly to high frequency in the population (11), our approach is well suited to detect small shifts in the frequencies of beneficial alleles that have a broad geographic distribution [see Hancock et al.”
BackgroundMethodSelf-citationHermisson, J., & Pennings, P. S. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12808 · Cited by 256 · see citing works
“Currently, the corresponding patterns of polygenic adaptation (Pritchard et al., 2010) that can be distributed across many loci remain largely unexplored (see Berg and Coop, 2014, for the case without epistasis).”
BackgroundGenetic signatures of high-altitude adaptation in Tibetans
Yang, J., Jin, Z., Chen, J., Huang, X., Li, X., Liang, Y., Mao, J.-Y., Chen, X., Zheng, Z., Bakshi, A., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617042114 · Cited by 250 · see citing works
“It is noteworthy that there are surprisingly few loci that have been identified given the large sample size of this study, consistent with a model of polygenic adaptation (38).”
ResultSork, V. L., Davis, F. W., Westfall, R. D., Flint, A. L., Ikegami, M., WANG, H., & Grivet, D. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04726.x · Cited by 247 · see citing works
“They could have been shaped by selection on genes that are linked to the markers due to genetic hitchhiking (Barton 2000) or selective sweeps associated with polygenic traits (Pritchard et al. 2010).”
BackgroundGene expression drives local adaptation in humans
Fraser, H. B. (2013) · Genome Research · doi:10.1101/gr.152710.112 · Cited by 247 · see citing works
“(Hancock et al. 2010, 2011; Pritchard et al. 2010).”
BackgroundControlling false discoveries in genome scans for selection
François, O., Martins, H., Caye, K., & Schoville, S. D. (2015) · Molecular Ecology · doi:10.1111/mec.13513 · Cited by 246 · see citing works
“Many studies have proposed that EA methods improve the ability to detect adaptation from standing variation (Pritchard et al. 2010).”
BackgroundGenes, Culture, and Agriculture
O’Brien, M. J., & Laland, K. N. (2012) · Current Anthropology · doi:10.1086/666585 · Cited by 243 · see citing works
“Computer simulations coupled with approximate Bayesian computation (ABC; Bertorelle, Benazzo, and Mona 2010) techniques represent one of the most promising approaches for combining multiple sources of information and test scenarios, that is, hypotheses (Fagundes et al. 2007; Ray et al. 2009).”
MethodHuman brain evolution: transcripts, metabolites and their regulators
Somel, M., Liu, X., & Khaitovich, P. (2013) · Nature reviews. Neuroscience · doi:10.1038/nrn3372 · Cited by 243 · see citing works
Population genetic differentiation of height and body mass index across Europe
Robinson, M. R., Hemani, G., Medina‐Gómez, C., Mezzavilla, M., Esko, T., Shakhbazov, K., Powell, J. E., Vinkhuyzen, A. A. E., Berndt, S. I., Gustafsson, S., et al. (2015) · Nature Genetics · doi:10.1038/ng.3401 · Cited by 225 · see citing works
Hohenlohe, P. A., Phillips, P. C., & Cresko, W. A. (2010) · International Journal of Plant Sciences · doi:10.1086/656306 · Cited by 220 · see citing works
Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa
Ranciaro, A., Campbell, M. C., Hirbo, J. B., Ko, W., Froment, A., Anagnostou, P., Kotze, M. J., Ibrahim, M. E., Nyambo, T., Omar, S. A., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.02.009 · Cited by 220 · see citing works
The polymorphic prelude to Bateson–Dobzhansky–Muller incompatibilities
Cutter, A. D. (2012) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.11.004 · Cited by 220 · see citing works
Adaptive evolution: evaluating empirical support for theoretical predictions
Olson-Manning, C. F., Wagner, M. R., & Mitchell‐Olds, T. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3322 · Cited by 210 · see citing works
Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana
Expósito‐Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H. A., & Weigel, D. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0423-0 · Cited by 203 · see citing works
Chen, D. T., Jiang, X., Akula, N., Shugart, Y. Y., Wendland, J. R., Steele, C. J. M., Kassem, L., Park, J.-H., Chatterjee, N., Jamain, S., et al. (2011) · Molecular Psychiatry · doi:10.1038/mp.2011.157 · Cited by 208 · see citing works
What can patterns of differentiation across plant genomes tell us about adaptation and speciation?
Strasburg, J. L., Sherman, N. A., Wright, K. M., Moyle, L. C., Willis, J. H., & Rieseberg, L. H. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2011.0199 · Cited by 206 · see citing works
Jones, C. M., Liyanapathirana, M., Agossa, F. R., Weetman, D., Ranson, H., Donnelly, M. J., & Wilding, C. S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201475109 · Cited by 206 · see citing works
“Indeed, the rapid rise in frequency of such a beneficial mutation has produced an associated reduction in haplotype diversity at linked loci through a recent positive “hard sweep” (16); EHH analysis demonstrated that, compared with the marked LD associated with 1575Y (EHH = 1; Fig.”
BackgroundHuman pigmentation genes under environmental selection
Sturm, R. A., & Duffy, D. L. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-248 · Cited by 203 · see citing works
“The pigmentation gene set has responded in different ways at different periods of our history [137], with light skin developing in parallel in Europe and Asia by at least two mechanisms.”
BackgroundRecent natural selection causes adaptive evolution of an avian polygenic trait
Bosse, M., Spurgin, L. G., Laine, V. N., Cole, E. F., Firth, J. A., Gienapp, P., Gosler, A., McMahon, K., Poissant, J., Verhagen, I., et al. (2017) · Science · doi:10.1126/science.aal3298 · Cited by 199 · see citing works
Parallel adaptation: one or many waves of advance of an advantageous allele?
Ralph, P., & Coop, G. (2010) · Genetics · doi:10.1534/genetics.110.119594 · Cited by 165 · see citing works
Self-citationThe Human Condition—A Molecular Approach
Pääbo, S. (2014) · Cell · doi:10.1016/j.cell.2013.12.036 · Cited by 197 · see citing works
“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 193 · see citing works
“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 185 · see citing works
“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 185 · see citing works
“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 178 · see citing works
“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 184 · see citing works
“…(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 179 · see citing works
“…(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 181 · see citing works
“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 180 · see citing works
“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 177 · see citing works
“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 · see citing works
Human Immunology through the Lens of Evolutionary Genetics
Quintana‐Murci, L. (2019) · Cell · doi:10.1016/j.cell.2019.02.033 · Cited by 171 · see citing works
“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 · see citing works
“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 · see citing works
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 165 · see citing works
Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster
Flatt, T. (2020) · Genetics · doi:10.1534/genetics.119.300160 · Cited by 165 · see citing works
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 158 · see citing works
“[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 · see citing works
“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 158 · see citing works
“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 157 · see citing works
“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 157 · see citing works
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 153 · see citing works
Stephan, W. (2015) · Molecular Ecology · doi:10.1111/mec.13288 · Cited by 156 · see citing works
“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 156 · see citing works
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 149 · see citing works
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 · see citing works
“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 147 · see citing works
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 143 · see citing works
“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 · see citing works
Sheehan, M. J., & Nachman, M. W. (2014) · Nature Communications · doi:10.1038/ncomms5800 · Cited by 145 · see citing works
“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 146 · see citing works
“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 150 · see citing works
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 141 · see citing works
“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
- 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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