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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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Cites
Introduction to Quantitative Genetics.
Edwards, A. W. F., & Falconer, D. S. (1982) · Biometrics · doi:10.2307/2529912 · Cited by 21,447
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
XV.—The Correlation between Relatives on the Supposition of Mendelian Inheritance.
Fisher, R. A. (1919) · Transactions of the Royal Society of Edinburgh · doi:10.1017/s0080456800012163 · Cited by 4,387
The hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (1974) · Genetical Research · doi:10.1017/s0016672300014634 · Cited by 3,415 · cited 1×
“The standard approaches to detecting selection in population genetic data have been strongly shaped by the classical hitch-hiking model explored in detail by Maynard Smith and Haigh [40].”
A Map of Recent Positive Selection in the Human Genome
Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,925 · cited 1×
“These include signals of partial sweeps [20], reduced diversity at putatively neutral sites [28,29] and an excess of SNPs with extreme population differentiation (high FST) within genes (Figure 1A) [30].”
Self-citationThe hitch-hiking effect of a favourable gene
Smith, J. M., & Haigh, J. (2007) · Genetics Research · doi:10.1017/s0016672308009579 · Cited by 2,675
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131
Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation
Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A. M., Ramachandran, S., Cann, H. M., Barsh, G. S., Feldman, M. W., Cavalli-Sforza, L. L., et al. (2008) · Science · doi:10.1126/science.1153717 · Cited by 1,915
The effect of deleterious mutations on neutral molecular variation.
Charlesworth, B., Morgan, M. T., & Charlesworth, D. (1993) · Genetics · doi:10.1093/genetics/134.4.1289 · Cited by 1,814 · cited 2×
“Taken together, these observations are most easily explained by either widespread positive selection, or possibly by background selection against mildly deleterious alleles [29,32].”
Effective population size and patterns of molecular evolution and variation
Charlesworth, B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2526 · Cited by 1,743
Flagged first, then by citations
Cited by
Sorted by citations
Items 101–200 of 928
Widespread Signals of Convergent Adaptation to High Altitude in Asia and America
Foll, M., Gaggiotti, O. E., Daub, J. T., Vatsiou, A. I., & Excoffier, L. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.09.002 · Cited by 153
MECHANISMS IN ENDOCRINOLOGY: Genetics of FSH action: a 2014-and-beyond view
Simoni, M., & Casarini, L. (2013) · European Journal of Endocrinology · doi:10.1530/eje-13-0624 · Cited by 145
Ravinet, M., Westram, A. M., Johannesson, K., Butlin, R. K., André, C., & Panova, M. (2015) · Molecular Ecology · doi:10.1111/mec.13332 · Cited by 141
“However, if the parallel phenotypic traits involved in ecotype formation have a polygenic basis, selection would be difficult to detect using an outlier analysis (Chevin & Hospital 2008; Pritchard et al. 2010).”
MethodHeritability and the evolution of cognitive traits: Table 1
Croston, R., Branch, C. L., Kozlovsky, D. Y., Dukas, R., & Витальевич, П. В. (2015) · Behavioral Ecology · doi:10.1093/beheco/arv088 · Cited by 148
“Many cognitive traits are quantitative in nature, and thus should be expected to evolve as a result of selection on many small effect variants through polygenic adaptation (e.g., Pritchard and Di Rienzo 2010; Pritchard et al. 2010).”
BackgroundOn the unfounded enthusiasm for soft selective sweeps
Jensen, J. D. (2014) · Nature Communications · doi:10.1038/ncomms6281 · Cited by 140
Population genetic tools for dissecting innate immunity in humans
Quintana‐Murci, L., & Clark, A. G. (2013) · Nature reviews. Immunology · doi:10.1038/nri3421 · Cited by 160
Li, J., Li, H., Jakobsson, M., Li, S., Sjödin, P., & Lascoux, M. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05308.x · Cited by 143
“There are good reasons to believe that soft selection may be more important than hard sweeps also in natural populations (Colosimo et al. 2004, 2005; Pritchard et al. 2010).”
BackgroundAdaptations to new environments in humans: the role of subtle allele frequency shifts
Hancock, A. M., Alkorta‐Aranburu, G., Witonsky, D., & Rienzo, A. D. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2010.0032 · Cited by 142
“In fact, selection models of quantitative traits predict that when a selection pressure changes, small allele frequency shifts will occur at many loci until the population reaches a new phenotypic optimum (Falconer & MacKay 1996; Pritchard et al. 2010).”
BackgroundPopulation Genetics in the Human Microbiome
Garud, N. R., & Pollard, K. S. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.10.010 · Cited by 142
A golden age for evolutionary genetics? Genomic studies of adaptation in natural populations
Nadeau, N. J., & Jiggins, C. D. (2010) · Trends in Genetics · doi:10.1016/j.tig.2010.08.004 · Cited by 147
Harnessing Crop Wild Diversity for Climate Change Adaptation
Cortés, A. J., & López-Hernández, F. (2021) · Genes · doi:10.3390/genes12050783 · Cited by 145
On the Evolutionary Origins of Obesity: A New Hypothesis
Sellayah, D., Cagampang, F. R. A., & Cox, R. (2014) · Endocrinology · doi:10.1210/en.2013-2103 · Cited by 155
Catchen, J., Bassham, S., Wilson, T., Currey, M. C., O'Brien, C., Yeates-Burghart, Q. S. L., & Cresko, W. A. (2013) · Molecular Ecology · doi:10.1111/mec.12330 · Cited by 138
“selection that is distinct from the background level of divergence caused by neutral processes such as genetic drift (Lewontin & Krakauer 1973; Maynard Smith & Haigh 1974; Baer 1999; Beaumont & Balding 2004; Storz 2005; Stinchcombe & Hoekstra 2008; Akey 2009; Nosil et al. 2009; Pritchard et al. 2010; Renaut et al. 201…”
BackgroundEstimating the genome-wide contribution of selection to temporal allele frequency change
Buffalo, V., & Coop, G. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1919039117 · Cited by 116
Self-citationSelection for complex traits leaves little or no classic signatures of selection
Kemper, K. E., Saxton, S. J., Bolormaa, S., Hayes, B. J., & Goddard, M. E. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-246 · Cited by 134
“Certainly the evidence and persuasiveness of authors advocating adaptation via standing polymorphisms is increasing [5-7] and the influential paradigm of ‘hard sweep’ selection signatures is beginning to lose favour as the primary mechanism of adaptation [1].”
BackgroundGenetic ancestry effects on the response to viral infection are pervasive but cell type specific
Randolph, H. E., Mu, Z., Fiege, J. K., Thielen, B. K., Grenier, J., Cobb, M., Hussin, J., Barreiro, L. B., Langlois, R. A., & Barreiro, L. B. (2021) · Science · doi:10.1126/science.abg0928 · Cited by 133
Laporte, M., Pavey, S. A., Rougeux, C., Pierron, F., Lauzent, M., Budzinski, H., Labadie, P., Geneste, E., Couture, P., Baudrimont, M., et al. (2015) · Molecular Ecology · doi:10.1111/mec.13466 · Cited by 130
“Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection will cause subtle allelic changes among covarying loci more than pronounced changes at few loci of large effects (McKay & Latta 2002; Pritchard et al. 2010; Le Corre & Kremer 2012; Messer & Petrov 2013; Bourret et…”
BackgroundMethodInfluentialTowards the identification of the loci of adaptive evolution
Pardo‐Díaz, C., Salazar, C. A., & Jiggins, C. D. (2014) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12324 · Cited by 141
Signatures of selection in sheep bred for resistance or susceptibility to gastrointestinal nematodes
McRae, K. M., McEwan, J. C., Dodds, K. G., & Gemmell, N. J. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-637 · Cited by 134
“Selection under a polygenic adaptation model would result in modest allele frequency changes across the genome, which may be undetectable using current methods for detecting selection [29].”
MethodRecent demography drives changes in linked selection across the maize genome
Beissinger, T. M., Wang, L., Crosby, K., Durvasula, A., Hufford, M. B., & Ross‐Ibarra, J. (2016) · Nature Plants · doi:10.1038/nplants.2016.84 · Cited by 124
“[58] Jonathan K Pritchard, Joseph K Pickrell, and Graham Coop.”
BackgroundResultParchman, T. L., Gompert, Z., Braun, M. J., Brumfield, R. T., McDonald, D. B., Uy, J. A. C., Zhang, G., Jarvis, E. D., Schlinger, B. A., & Buerkle, C. A. (2013) · Molecular Ecology · doi:10.1111/mec.12201 · Cited by 129
Selection and Adaptation in the Human Genome
Fu, W., & Akey, J. M. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153509 · Cited by 129
“, selection on standing variation (63, 123) (Figure 2b) or selection acting simultaneously on multiple independent loci (Figure 2c).”
BackgroundMunshi‐South, J., Zolnik, C. P., & Harris, S. E. (2016) · Evolutionary Applications · doi:10.1111/eva.12357 · Cited by 129
“…experiments (Teot onio et al. 2009; Burke et al. 2010), ancestral variation in model organisms (Rockman 2008; Scarcelli and Kover 2009), humans (Pritchard et al. 2010), artificial selection in crops (Gibson and Dworkin 2004), viral pathogens (Pennings 2012), and invasive species (Prentis et…”
BackgroundSelective trade-offs maintain alleles underpinning complex trait variation in plants
Troth, A., Puzey, J. R., Kim, R. S., Willis, J. H., & Kelly, J. K. (2018) · Science · doi:10.1126/science.aat5760 · Cited by 118
Local Adaptation in the Flowering-Time Gene Network of Balsam Poplar, Populus balsamifera L.
Keller, S. R., Levsen, N. D., Olson, M. S., & Tiffin, P. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss121 · Cited by 124
“Species-wide samples will not show standard signatures of selective sweeps when selection acts locally, especially for genes that contribute to variation in polygenic traits (Kelly 2006; Pritchard and Di Rienzo 2010; Pritchard et al. 2010).”
BackgroundGenetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations
Desai, M. M., Walczak, A. M., & Fisher, D. S. (2012) · Genetics · doi:10.1534/genetics.112.147157 · Cited by 115
Threespine Stickleback: A Model System For Evolutionary Genomics
Reid, K., Bell, M. A., & Veeramah, K. R. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-111720-081402 · Cited by 120
Bellucci, E., Bitocchi, E., Ferrarini, A., Benazzo, A., Biagetti, E., Klie, S., Minio, A., Rau, D., Rodriguez, M., Panziera, A., et al. (2014) · The Plant Cell · doi:10.1105/tpc.114.124040 · Cited by 120
Detecting Polygenic Adaptation in Admixture Graphs
Racimo, F., Berg, J. J., & Pickrell, J. K. (2018) · Genetics · doi:10.1534/genetics.117.300489 · Cited by 118
“This process is called polygenic adaptation and may underlie major evolutionary processes in recent human history [10, 11, 12, 13].”
BackgroundSelf-citationGenomics of Parallel Ecological Speciation in Lake Victoria Cichlids
Meier, J. I., Marques, D. A., Wagner, C. E., Excoffier, L., & D, O. S. C. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy051 · Cited by 112
Polygenic adaptation after a sudden change in environment
Hayward, L. K., & Sella, G. (2022) · eLife · doi:10.7554/elife.66697 · Cited by 115
“These considerations refocused the quest for the genetic basis of human adaptation on polygenic adaptation (Pritchard et al., 2010; Pritchard and Di Rienzo, 2010).”
BackgroundThe population genomics of plant adaptation
Siol, M., Wright, S., & Barrett, S. C. H. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03401.x · Cited by 123
“…originate from standing genetic variation that has been present in a population for some time before the new selective episode that assembles the adaptation being considered (this is referred to as a soft selective sweep; Orr & Betancourt, 2001; Hermisson & Pennings, 2005; Pritchard et al., 2010).”
BackgroundIdentification of selection signatures in livestock species
Gouveia, J. J. D. S., da Silva, M. V. G. B., Paiva, S. R., & de Oliveira, S. M. P. (2014) · Genetics and Molecular Biology · doi:10.1590/s1415-47572014000300004 · Cited by 123
“…genetic variation, it causes a “soft sweep” in which the footprint left by selection tends to be less pronounced and the frequency of the selected allele at the beginning of the selected phase is the crucial factor influencing the selective sweep (Przeworski et al., 2005; Pritchard et al., 2010).”
BackgroundRecent human adaptation: genomic approaches, interpretation and insights
Scheinfeldt, L., & Tishkoff, S. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3604 · Cited by 118
The genomics of local adaptation in trees: are we out of the woods yet?
Lind, B. M., Menon, M., Bolte, C. E., Faske, T. M., & Eckert, A. J. (2018) · Tree Genetics & Genomes · doi:10.1007/s11295-017-1224-y · Cited by 124
The omnigenic model and polygenic prediction of complex traits
Mathieson, I. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.07.003 · Cited by 116
“It is often assumed that the response to selection on highly polygenic traits is driven by small but correlated shifts in the frequencies of associated variants.(23) This can be detected by looking for shifts in allele frequency that are systematically correlated with the allelic effect sizes.”
BackgroundInvoking adaptation to decipher the genetic legacy of past climate change
de Lafontaine, G., Napier, J. D., Petit, R. J., & Hu, F. S. (2018) · Ecology · doi:10.1002/ecy.2382 · Cited by 116
Population Genomics of Herbicide Resistance: Adaptation via Evolutionary Rescue
Kreiner, J. M., Stinchcombe, J. R., & Wright, S. (2017) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042817-040038 · Cited by 109
Cortés, A. J., & Blair, M. W. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.00128 · Cited by 109
“Moreover, the origin of habitatassociated variants from novel or standing genetic variation leads to distinctively different patterns of genomic divergence (Hermisson and Pennings, 2005; Barrett and Schluter, 2008; Pritchard et al., 2010).”
BackgroundHuman Disease Variation in the Light of Population Genomics
Prohaska, A., Racimo, F., Schork, A. J., Sikora, M., Stern, A. J., Ilardo, M. A., Allentoft, M. E., Folkersen, L., Buil, A., Moreno-Mayar, J. V., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.052 · Cited by 110
“Polygenic adaptation has been suggested to be the reason why population geneticists have found relatively few highly differentiated alleles across human populations (Pritchard et al., 2010).”
BackgroundDetection of selective sweeps in structured populations: a comparison of recent methods
Vatsiou, A. I., Bazin, E., & Gaggiotti, O. E. (2016) · Molecular Ecology · doi:10.1111/mec.13360 · Cited by 111
Sattath, S., Elyashiv, E., Kolodny, O., Rinott, Y., & Sella, G. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001302 · Cited by 109
“Other modes of adaptation, such as polygenic selection, may also contribute differentially to the two inference methodologies [38].”
BackgroundCommon Risk Alleles for Inflammatory Diseases Are Targets of Recent Positive Selection
Raj, T., Kuchroo, M. R., Replogle, J. M., Raychaudhuri, S., Stranger, B. E., & Jager, P. L. D. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.03.001 · Cited by 110
“Many of the GWAS SNPs are probably evolving under such sweeps.(10,35) The iHS statistic uses the lengths of the haplotypes surrounding each core SNP to identify SNPs for which alleles have rapidly risen in frequency.”
MethodJosephs, E. B., Stinchcombe, J. R., & Wright, S. (2017) · New Phytologist · doi:10.1111/nph.14410 · Cited by 117
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers
Perry, G. H., Foll, M., Grenier, J.-C., Patin, E., Nédélec, Y., Pacis, A., Barakatt, M., Gravel, S., Zhou, X., Nsobya, S. L., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402875111 · Cited by 105
“We note that we use polygenic to reference multiple regions of the genome generally (30) rather than necessarily implicate the involvement of any gene coding changes in the phenotype.”
MethodInterpreting polygenic scores, polygenic adaptation, and human phenotypic differences
Rosenberg, N. A., Edge, M. D., Pritchard, J. K., & Feldman, M. W. (2019) · Evolution, Medicine, and Public Health · doi:10.1093/emph/eoy036 · Cited by 105
Self-citationMallard, F., Nolte, V., Tobler, R., Kapun, M., & Schlötterer, C. (2018) · Genome biology · doi:10.1186/s13059-018-1503-4 · Cited by 103
Randhawa, I. A. S., Khatkar, M. S., Thomson, P. C., & Raadsma, H. W. (2014) · BMC Genetics · doi:10.1186/1471-2156-15-34 · Cited by 105
“…in silico analysis of genetic polymorphism data have provided insights to many questions about the origin of species [2], evolution [3], co-evolution and selection [4], domestication [5], genetic control of adaptation and diseases [6-8], and genetic diversity [9,10] for a wide range of species.”
Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin
Brauer, C. J., Hammer, M. P., & Beheregaray, L. B. (2016) · Molecular Ecology · doi:10.1111/mec.13830 · Cited by 101
“Here, we expect a relatively low average and broad distribution of FST values for polygenic ‘soft’ selective sweeps because in this scenario adaptation is expected to proceed without major changes in allele frequency (Pritchard et al. 2010).”
BackgroundResultInfluentialShi, H., Burch, K. S., Johnson, R., Freund, M. K., Kichaev, G., Mancuso, N., Manuel, A. M., Dong, N., & Paşaniuc, B. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.04.012 · Cited by 92
Understanding rare and common diseases in the context of human evolution
Quintana‐Murci, L. (2016) · Genome biology · doi:10.1186/s13059-016-1093-y · Cited by 103
“signals probably result from background selection [74, 93, 123, 124].”
BackgroundImaGene: a convolutional neural network to quantify natural selection from genomic data
Torada, L., Lorenzon, L., Beddis, A., Işıldak, U., Pattini, L., Mathieson, S., & Fumagalli, M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-2927-x · Cited by 107
“However, most adaptive processes happened via weak-to-moderate selection from standing variation [12].”
BackgroundBarquera, R., Collen, E., Di, D., Bühler, S., Teixeira, J. C., Llamas, B., Nunes, J. M., & Sanchez‐Mazas, A. (2020) · HLA · doi:10.1111/tan.13956 · Cited by 98
Quantifying the Variation in the Effective Population Size Within a Genome
Gossmann, T. I., Woolfit, M., & Eyre‐Walker, A. (2011) · Genetics · doi:10.1534/genetics.111.132654 · Cited by 99
“Advantageous mutations can also arise from standing genetic variation (Pritchard and Rienzo 2010; Pritchard et al. 2010).”
BackgroundDetecting signatures of positive selection in non-model species using genomic data
Weigand, H., & Leese, F. (2018) · Zoological Journal of the Linnean Society · doi:10.1093/zoolinnean/zly007 · Cited by 110
Antagonistic Pleiotropy in Human Disease
Byars, S., & Voskarides, K. (2019) · Journal of Molecular Evolution · doi:10.1007/s00239-019-09923-2 · Cited by 96
Utility of pooled sequencing for association mapping in nonmodel organisms
Micheletti, S. J., & Narum, S. R. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12784 · Cited by 98
Completely phased genome sequencing through chromosome sorting
Yang, H., Chen, X., & Wong, W. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1016725108 · Cited by 95
Bourgeois, Y., & Warren, B. H. (2021) · Molecular Ecology · doi:10.1111/mec.15989 · Cited by 103
“Association methods may help to target variants undergoing soft sweeps, weak selection or those involved in polygenic control of traits (Pritchard et al., 2010).”
MethodPopulation genomics of human adaptation
Lachance, J., & Tishkoff, S. A. (2013) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-110512-135833 · Cited by 95
“P A A uthor M anuscript genetic theory suggests that soft sweeps may be widespread, especially for genes with large mutational target sizes, and present methods have low power to detect adaptation from standing variation (Pritchard et al 2010).”
BackgroundOlson, M. S., Levsen, N. D., Soolanayakanahally, R. Y., Guy, R. D., Schroeder, W. R., Keller, S. R., & Tiffin, P. (2012) · Molecular Ecology · doi:10.1111/mec.12067 · Cited by 98
“These patterns are consistent with expectations from a recent hard sweep in the far northern populations (Pritchard et al. 2010), but also may have been generated via allele surfing along the front of the expanding range (Klopfstein et al. 2006).”
BackgroundThe genomic basis of adaptation in plants
Flood, P. J., & Hancock, A. M. (2017) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2017.02.003 · Cited by 96
Travisano, M., & Shaw, R. G. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01802.x · Cited by 96
“The more assiduous are efforts to unravel the complexity, the more idiosyncratic is the detail that emerges (Martin and Willis 2010), as has been demonstrated in human studies (Pritchard and Di Rienzo 2010; Pritchard et al. 2010).”
BackgroundFariello, M. I., Boitard, S., Mercier, S., Robelin, D., Faraut, T., Arnould, C., Recoquillay, J., Bouchez, O., Salin, G., Déhais, P., et al. (2017) · Molecular Ecology · doi:10.1111/mec.14141 · Cited by 105
“Markers in the neighbourhood of the selection target might thus also show departures from the patterns expected under the null hypothesis of neutral evolution (Pritchard, Pickrell, & Coop, 2010).”
BackgroundGlobal genetic differentiation of complex traits shaped by natural selection in humans
Guo, J., Wu, Y., Zhu, Z., Zheng, Z., Trzaskowski, M., Zeng, J., Robinson, M. R., Visscher, P. M., & Yang, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04191-y · Cited by 91
Schrider, D. R., Mendes, F. K., Hahn, M. W., & Kern, A. D. (2015) · Genetics · doi:10.1534/genetics.115.174912 · Cited by 93
“A third scenario of positive selection that has garnered a great deal of attention over the past 2 decades is that of “ partial ” or “ incomplete ” sweeps, where a sweeping allele has not reached fi xation (Hudson et al. 1994; Voight et al. 2006; Pritchard et al. 2010).”
BackgroundWhole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes
Udpa, N., Ronen, R., Zhou, D., Liang, J., Stobdan, T., Appenzeller, O., Yin, Y., Du, Y., Guo, L., Cao, R., et al. (2014) · Genome biology · doi:10.1186/gb-2014-15-2-r36 · Cited by 96
“Such intermediate frequencies in lowlander controls are consistent with selection acting on standing variation, rather than a de novo mutation [35].”
Polimanti, R. A., & Gelernter, J. E. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006618 · Cited by 98
Mojica, J. P., Lee, Y. W., Willis, J. H., & Kelly, J. K. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05662.x · Cited by 90
“Counter to initial expectations, hard sweeps wherein a novel mutation is immediately favoured and spreads to fixation, for example (Coop et al. 2009; Pritchard et al. 2010; Simonson et al. 2010), seem to be relatively infrequent.”
Understanding and predicting complex traits: knowledge from cattle
Kemper, K. E., & Goddard, M. E. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds332 · Cited by 93
“GWAS data can be used to identify biological pathways responsible for genetic variation or selection response (1,31,38).”
MethodInterspecific introgression mediates adaptation to whole genome duplication
Marburger, S., Monnahan, P. J., Seear, P. J., Martin, S. H., Koch, J., Paajanen, P., Bohutínská, M., Higgins, J. D., Schmickl, R., & Yant, L. J. (2019) · Nature Communications · doi:10.1038/s41467-019-13159-5 · Cited by 83
Zhang, Y., Wang, Y., Li, Y., Wu, J., Wang, X., Bian, C., Tian, Y., Sun, G., Han, R., Liu, X., et al. (2020) · Heredity · doi:10.1038/s41437-020-00365-x · Cited by 90
“12 34 56 78 90 () ;,: 12 34 56 78 90 (); ,: produced (Pritchard et al. 2010).”
The paradox of adaptive trait clines with nonclinal patterns in the underlying genes
Lotterhos, K. E. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2220313120 · Cited by 90
“Much of the existing literature on polygenic adaptation has focused on whether subtle allele frequency changes along environmental gradients result in detectable clines, which is a concept that falls under the GEA paradigm (16, 51).”
Jeong, C., Witonsky, D., Basnyat, B., Neupane, M., Beall, C. M., Childs, G. H., Craig, S. R., Novembre, J., & Rienzo, A. D. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007650 · Cited by 88
“However, genome-wide association studies have revealed that most 43 phenotypic variation in humans is highly polygenic; in other words, it is due to the combined effects of a 44 large number of alleles with small effects [10-12].”
BackgroundContinent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe
Salmón, P., Jacobs, A., Ahrén, D., Biard, C., Dingemanse, N. J., Dominoni, D. M., Helm, B., Lundberg, M., Señar, J. C., Sprau, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23027-w · Cited by 90
From R.A. Fisher’s 1918 Paper to GWAS a Century Later
Visscher, P. M., & Goddard, M. E. (2019) · Genetics · doi:10.1534/genetics.118.301594 · Cited by 79
Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds
Boitard, S., Boussaha, M., Capitan, A., Rocha, D., & Servin, B. (2016) · Genetics · doi:10.1534/genetics.115.181594 · Cited by 90
“Indeed, recent intensive selection in modern livestock breeds has mainly targeted polygenic traits such as milk or meat production, which is much more likely to produce soft- and incomplete-sweep patterns than hard-sweep patterns (Pritchard et al. 2010; Hernandez et al. 2011).”
BackgroundHill, E. W., Gu, J., McGivney, B. A., & MacHugh, D. E. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2010.02104.x · Cited by 84
Detecting adaptive evolution based on association with ecological gradients: Orientation matters!
Frichot, É., Schoville, S. D., de Villemereuil, P., Gaggiotti, O. E., & François, O. (2015) · Heredity · doi:10.1038/hdy.2015.7 · Cited by 82
“See Figure 1 for a representation of our simulation framework.”
BackgroundInfluentialMcGivney, B. A., Han, H., Corduff, L. R., Katz, L. M., Tozaki, T., MacHugh, D. E., & Hill, E. W. (2020) · Scientific Reports · doi:10.1038/s41598-019-57389-5 · Cited by 90
The evolution of skin pigmentation-associated variation in West Eurasia
Ju, D., & Mathieson, I. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2009227118 · Cited by 84
“Therefore, while the existence of selective sweeps at a handful of skin pigmentation loci is well established, the evidence for polygenic selection—a coordinated shift in allele frequencies across many trait-associated variants (11)—is less clear.”
BackgroundCarneiro, M., Albert, F. W., Melo‐Ferreira, J., Galtier, N., Gayral, P., Blanco, J., Villafuerte, R., Nachman, M. W., & Ferrand, N. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss025 · Cited by 89
“In fact, empirical data in several systems suggest that modes of selection based on preexisting variation or polygenic selection may be more predominant than previously thought (Barrett and Schluter 2008; Coop et al. 2009; Hancock et al. 2010; Pritchard et al. 2010; Hernandez et al. 2011).”
BackgroundLimited Evidence for Classic Selective Sweeps in African Populations
Granka, J. M., Henn, B. M., Gignoux, C. R., Kidd, J. M., Bustamante, C. D., & Feldman, M. W. (2012) · Genetics · doi:10.1534/genetics.112.144071 · Cited by 81
“…based on standing genetic variation, also have the potential to uncover signals of positive selection (Coop et al., 2010; Hancock et al., 2010a,b; Pritchard et al., 2010; Pritchard and Di Rienzo, 2010; Fumagalli et al., 2011; Hancock et al., 2011; Hernandez et al., 2011; Tennessen and Akey,…”
BackgroundInfluentialNatural Selection in the Great Apes
Cagan, A., Theunert, C., Laayouni, H., Santpere, G., Pybus, M., Casals, F., Prüfer, K., Navarro, A., Marquès‐Bonet, T., Bertranpetit, J., et al. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw215 · Cited by 85
“Understanding the adaptive genetic changes that led to the emergence of modern humans continues to be a major focus of modern genomics (Pritchard et al. 2010; Enard et al. 2014).”
BackgroundTelomere Length and the Cancer–Atherosclerosis Trade-Off
Stone, R. C., Horvath, K., Kark, J. D., Susser, E., Tishkoff, S. A., & Aviv, A. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006144 · Cited by 83
“Complex traits that are influenced by multiple genetic loci may be targets of polygenic adaptation [64,65], i.”
BackgroundHeer, K., Behringer, D., Piermattei, A., Bässler, C., Brandl, R., Fady, B., Jehl, H., Liepelt, S., Lorch, S., Piotti, A., et al. (2018) · Molecular Ecology · doi:10.1111/mec.14538 · Cited by 82
The application gap: Genomics for biodiversity and ecosystem service management
Heuertz, M., Carvalho, S. B., Galindo, J., Rinkevich, B., Robakowski, P., Aavik, T., Altınok, İ., Barth, J. M. I., Cotrim, H. C., Goessen, R., et al. (2023) · Biological Conservation · doi:10.1016/j.biocon.2022.109883 · Cited by 89
Patterns of Neutral Diversity Under General Models of Selective Sweeps
Coop, G., & Ralph, P. L. (2012) · Genetics · doi:10.1534/genetics.112.141861 · Cited by 78
“However, it seems likely that such full sweeps constitute only a small proportion of the selected loci whose frequency changes in response to adaptation (see Pritchard et al. 2010, for a recent discussion).”
BackgroundSelf-citationColonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E. P., Xue, Y., & Tyler‐Smith, C. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r88 · Cited by 87
“Genetic influences on fitness are typically small, and many variants usually affect the same trait, so adaptation is generally the result of small changes in frequency of multiple alleles: a ‘soft sweep’ [2].”
BackgroundTowards evolutionary predictions: Current promises and challenges
Wortel, M. T., Agashe, D., Bailey, S. F., Bank, C., Bisschop, K., Blankers, T., Cairns, J., Colizzi, E. S., Cusseddu, D., Desai, M. M., et al. (2022) · Evolutionary Applications · doi:10.1111/eva.13513 · Cited by 80
RADseq approaches and applications for forest tree genetics
Parchman, T. L., Jahner, J. P., Uckele, K. A., Galland, L. M., & Eckert, A. J. (2018) · Tree Genetics & Genomes · doi:10.1007/s11295-018-1251-3 · Cited by 82
“…of adaptation relative to the size and complexity of genomes (reviewed by Lind et al. 2018 for trees), the evolutionary processes affecting genetic architectures (e.g., hard versus soft sweeps; Pritchard et al. 2010), and research goals (e.g., partial discovery versus complete description).”
BackgroundAdaptations to local environments in modern human populations
Jeong, C., & Di Rienzo, A. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.06.011 · Cited by 80
Genome Resequencing Reveals Rapid, Repeated Evolution in the Colorado Potato Beetle
Pélissié, B., Chen, Y. H., Cohen, Z., Crossley, M. S., Hawthorne, D. J., Izzo, V. M., & Schoville, S. D. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac016 · Cited by 86
“2019), whereas repeated selection by insecticides on standing genetic variation likely results in polygenic trait architecture (multiple genes contributing to resistance phenotypes), which we assess based on the number of selected genes and pathways, as well as the size of selective sweeps (Pritchard et al. 2010).”
Molecular hyperdiversity and evolution in very large populations
Cutter, A. D., Jovelin, R., & Dey, A. (2013) · Molecular Ecology · doi:10.1111/mec.12281 · Cited by 76
“sweeps involving polygenic selection on traits (Pritchard et al. 2010)? Our expectations also depend on”
BackgroundInfluentialThe Effect of Neutral Recombination Variation on Genome Scans for Selection
Lotterhos, K. E. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400088 · Cited by 82
Palamara, P. F., Terhorst, J., Song, Y. S., & Price, A. L. (2018) · Nature Genetics · doi:10.1038/s41588-018-0177-x · Cited by 75
Hsieh, P., Veeramah, K. R., Lachance, J., Tishkoff, S. A., Wall, J. D., Hammer, M. F., & Gutenkunst, R. N. (2016) · Genome Research · doi:10.1101/gr.192971.115 · Cited by 77
“3B,C), a pattern expected under an incomplete selective sweep (Voight et al. 2006; Pickrell et al. 2009; Pritchard et al. 2010).”
InfluentialFagny, M., Patin, É., Enard, D., Barreiro, L. B., Quintana‐Murci, L., & Laval, G. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu118 · Cited by 83
“However, others have suggested that these enrichment signals might actually result, at least in part, from the action of background selection (Coop et al. 2009; Pritchard et al. 2010; Hernandez et al. 2011).”
BackgroundMethodResultInfluentialTorre, A. R. D. L., Wilhite, B., & Neale, D. B. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz220 · Cited by 79
Crossley, M. S., Chen, Y. H., Groves, R. L., & Schoville, S. D. (2017) · Molecular Ecology · doi:10.1111/mec.14339 · Cited by 71
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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