The DOI matches its Crossref record; 80 of the 80 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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 301–400 of 928
Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning
Xue, A. T., Schrider, D. R., Kern, A. D., della Torre, A., Kern, A. D., Caputo, B., Kabula, B. I., White, B. J., Godfray, H. C. J., Edi, C., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa259 · Cited by 48
“However, it is important to consider that our partial sweep calls could be 561 capturing more complex selective dynamics at play, for example polygenic and quantitative 562 trait adaptation [35,36], balancing selection [37], and introgression of beneficial alleles.”
BackgroundJunge, C., Vøllestad, L. A., Barson, N. J., Haugen, T. O., Otero, J., Sætre, G., Leder, E. H., & Primmer, C. R. (2011) · Heredity · doi:10.1038/hdy.2010.160 · Cited by 48
Parallel Adaptive Divergence among Geographically Diverse Human Populations
Tennessen, J. A., & Akey, J. M. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002127 · Cited by 49
“The extent to which the same genes underlie repeated adaptive events is unclear, but a growing number of observations suggest that parallel evolution at the molecular level may be quite prevalent [19–21], and from first principles it seems especially likely when selection acts on the same standing genetic variation in…”
BackgroundResultInfluentialEarly modern human dispersal from Africa: genomic evidence for multiple waves of migration
Tassi, F., Ghirotto, S., Mezzavilla, M., Vilaça, S. T., De Santi, L., & Barbujani, G. (2015) · Investigative Genetics · doi:10.1186/s13323-015-0030-2 · Cited by 41
“If we also consider that genomic regions with large allele frequency differences are not generally associated with high levels of LD, in contrast with what would be expected after a selective sweep [77, 79], it seems fair to conclude that the main allele frequency shifts occurred in a rather remote past and are unlike…”
ResultWhich Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding?
Moyerbrailean, G. A., Kalita, C. A., Harvey, C. T., Wen, X., Luca, F., & Piqué-Regi, R. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005875 · Cited by 45
“Similar challenges also arise when exploring the evolutionary functional significance of non-coding variants, for example through analysis of differences in genotype distribution across populations [4, 5].”
BackgroundHuman adaptation and population differentiation in the light of ancient genomes
Key, F. M., Fu, Q., Romagné, F., Lachmann, M., & Andrés, A. M. (2016) · Nature Communications · doi:10.1038/ncomms10775 · Cited by 45
Evidence that the rate of strong selective sweeps increases with population size in the great apes
Nam, K., Munch, K., Mailund, T., Nater, A., Greminger, M. P., Krützen, M., Marquès‐Bonet, T., & Schierup, M. H. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1605660114 · Cited by 48
“In humans, such alternative modes of selection may play a significant role in recent adaptation (2, 34).”
BackgroundThe landscape of expression and alternative splicing variation across human traits
García-Pérez, R., Ramírez, J. M., Ripoll-Cladellas, A., Chazarra-Gil, R., Oliveros, W., Soldatkina, O., Bosio, M., Rognon, P. J., Capella-Gutiérrez, S., Calvo, M., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100244 · Cited by 44
“Further analyses might be needed to address whether these differences arose as a product of positive selection simultaneously targeting ribosomal protein genes.(113) Importantly, a recent publication reported expression—rather than splicing—differences in ribosomal proteins between populations using single-cell data,(…”
BackgroundFornarino, S., Laval, G., Barreiro, L. B., Manry, J., Vasseur, E., & Quintana‐Murci, L. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr137 · Cited by 51
“This picture would then be consistent with a model of adaptation that occurs with modest advantageous changes, simultaneously across many loci (Pritchard and Di Rienzo 2010; Pritchard et al. 2010).”
Clo, J., Gay, L., & Ronfort, J. (2019) · Evolution; international journal of organic evolution · doi:10.1111/evo.13789 · Cited by 36
“Standing genetic variation is known to play a key role in adaptation processes, at least in the short-term response to selection (Orr and Betancourt 2001; Hermisson and Pennings 2005; Barrett and Schluter 2008; Pritchard et al. 2010; Glémin and Ronfort 2013).”
BackgroundGarud, N. R., & Rosenberg, N. A. (2015) · Theoretical Population Biology · doi:10.1016/j.tpb.2015.04.001 · Cited by 46
“Soft sweeps can provide an effective mechanism for natural selection and might explain a sizeable fraction of selective events in many systems (Orr and Betancourt, 2001; Innan and Kim, 2004; Pritchard et al., 2010;Messer and Petrov, 2013).”
InfluentialThe Reproductive Ecology of Industrial Societies, Part II
Stulp, G., Sear, R., Schaffnit, S. B., Mills, M. C., & Barrett, L. (2016) · Human Nature · doi:10.1007/s12110-016-9272-9 · Cited by 53
Goubert, C., Henri, H., Minard, G., Moro, C. V., Mavingui, P., Vieira, C. P., & Boulesteix, M. (2017) · Molecular Ecology · doi:10.1111/mec.14184 · Cited by 46
“The strength of such signals can be influenced by the origin of the adaptive mutation, e.g., if it arises de novo or if it spreads from the standing genetic variation (Pritchard et al. 2010; Messer & Petrov 2013).”
BackgroundCortés, A. J., Skeen, P., Blair, M. W., & Chacón-Sánchez, M. I. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01816 · Cited by 46
Bergey, C. M., Lopez, M., Harrison, G. F., Patin, É., Cohen, J. A., Quintana‐Murci, L., Barreiro, L. B., & Perry, G. H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1812135115 · Cited by 49
Signatures of natural selection between life cycle stages separated by metamorphosis in European eel
Pujolar, J., Jacobsen, M., Bekkevold, D., Lobón-Cerviá, J., Jónsson, B., Bernatchez, L., & Hansen, M. M. (2015) · BMC Genomics · doi:10.1186/s12864-015-1754-3 · Cited by 20
“Both scenarios lead to shifts in allele frequencies rather than fixation, thus tend to be more difficult to detect than hard sweeps using standard tests of selection [23, 45, 46].”
BackgroundGenomic Data Reveal a Complex Making of Humans
Alves, I., Hanulová, A. Š., Foll, M., & Excoffier, L. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002837 · Cited by 49
“While most people assumed that the out-of-Africa expansion had been characterized by a series of adaptations to new environments [4–6] leading to recurrent selective sweeps [7], our genome actually contains little trace of recent complete sweeps [2,3,8] and the genetic differentiation of human population has been very…”
BackgroundInfluentialManunza, A., Cardoso, T. F., Noce, A., Martínez, A. M., Pons, A., Asensio, L. A. B., Landi, V., Sánchez, A., Jordana, J., Bermejo, J. V. D., et al. (2016) · Scientific Reports · doi:10.1038/srep27296 · Cited by 45
“The classical phenotypic classification of ovine Spanish breeds proposed by Antonio Sánchez-Belda highlights the existence of four main lineages16: (1) Churro (Churra and Latxa breeds, that have a coarse wool), (2) Merino (not represented in our dataset), (3) Medium Fine Wool (Segureña, Gallega, Ripollesa, Rasa Aragon…”
BackgroundThe genomic basis of adaptation to high‐altitude habitats in the eastern honey bee ( Apis cerana )
Montero‐Mendieta, S., Tan, K., Christmas, M. J., Olsson, A., Vilà, C., Wållberg, A., & Webster, M. T. (2018) · Molecular Ecology · doi:10.1111/mec.14986 · Cited by 46
Genetic variations associated with six-white-point coat pigmentation in Diannan small-ear pigs
Lü, M., Han, X.-M., Ma, Y., Irwin, D. M., Gao, Y., Deng, J.-K., Adeola, A. C., Xie, H., & Zhang, Y. (2016) · Scientific Reports · doi:10.1038/srep27534 · Cited by 43
Avila, L. M., Cerrudo, D., Swanton, C. J., & LUKENS, L. N. (2016) · Journal of Experimental Botany · doi:10.1093/jxb/erv554 · Cited by 45
Polygenic Adaptation has Impacted Multiple Anthropometric TraitsPreprint
Berg, J. J., Zhang, X., & Coop, G. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/167551 · Cited by 46
Self-citationOutlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird
Tigano, A., Shultz, A. J., Edwards, S. V., Robertson, G. J., & Friesen, V. L. (2017) · Ecology and Evolution · doi:10.1002/ece3.2819 · Cited by 43
Genetic surfing in human populations: from genes to genomes
Peischl, S., Dupanloup, I., Bosshard, L., & Excoffier, L. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.08.003 · Cited by 43
Sweeney, T., Hanrahan, J. P., Ryan, M. T., & Good, B. (2016) · Parasite Immunology · doi:10.1111/pim.12347 · Cited by 43
Novel candidate genes underlying extreme trophic specialization in Caribbean pupfishes
McGirr, J. A., & Martin, C. H. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw286 · Cited by 38
“…as ours (Dittmar et al. 2016), and the relative importance McGirr and Martin . doi:10.1093/molbev/msw286 MBE of hard sweeps versus soft sweeps during adaptation is a subject of much debate (Hermisson and Pennings 2005; Pritchard et al. 2010; Jensen 2014; Garud et al. 2015; Schrider et al. 2015).”
BackgroundInfluentialThe Reproductive Ecology of Industrial Societies, Part I
Stulp, G., Sear, R., & Barrett, L. (2016) · Human Nature · doi:10.1007/s12110-016-9269-4 · Cited by 45
“…pregnancies from previous relationships, and that previously married and unmarried men are less likely to be included in demographic samples, leading to sex differences in the number of reported children (Rendall et al. 1999; Stulp, Kuijper, et al. 2012; see Stulp et al. 2016 for more examples).”
BackgroundBrennan, R. S., deMayo, J. A., Dam, H. G., Finiguerra, M. B., Baumann, H., Buffalo, V., & Pespeni, M. H. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2201521119 · Cited by 45
“This is further complicated when adaptation proceeds from standing genetic variation on polygenic traits, which can lead to diffuse and subtle signals of selection that can be difficult to distinguish from drift (Kemper et al., 2014; Pritchard et al., 2010).”
BackgroundResultInfluentialDecker, J. E., Vasco, D. A., McKay, S., McClure, M. C., Rolf, M. M., Kim, J., Northcutt, S. L., Bauck, S. W., Woodward, B. W., Schnabel, R. D., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-606 · Cited by 46
“However, recently, there has been a call to employ polygenic models to simultaneously identify loci responding to selection but that do not fit the typical “hard sweep” paradigm [17,18].”
BackgroundLu, M., Loopstra, C. A., & Krutovsky, K. V. (2019) · Ecology and Evolution · doi:10.1002/ece3.5225 · Cited by 41
Wu, W., Clark, E., Stoddard, G. J., Watkins, W. S., Esplin, M. S., Manuck, T. A., Xing, J., Varner, M. W., & Jorde, L. B. (2013) · BMC Genetics · doi:10.1186/1471-2156-14-30 · Cited by 41
“However, there is no strong evidence of natural selection near rs1800795 [56-58].”
BackgroundOleksyk, T. K., Nelson, G. W., An, P., Kopp, J. B., & Winkler, C. A. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011474 · Cited by 41
“Under neutral conditions, FST is determined by genetic drift affecting all loci across the genome in a similar way, but selection can cause differences between populations in the locus and the surrounding genomic region [1,18,19,38].”
BackgroundAdmixture has obscured signals of historical hard sweeps in humans
Souilmi, Y., Tobler, R., Johar, A., Williams, M., Grey, S. T., Schmidt, J. M., Teixeira, J. C., Rohrlach, A. B., Tuke, J., Johnson, O. L., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01914-9 · Cited by 40
“…modes of selection—for example, ‘soft sweeps’ (where the beneficial allele sits on multiple genetic backgrounds) 7,8 or polygenic selection (subtle frequency shifts across numerous loci with small fitness effects) 9,10 —though the evidence for these processes has also been challenged 5,11–13 .”
Genetic Architecture of Parallel Pelvic Reduction in Ninespine Sticklebacks
Shikano, T., Laine, V. N., Herczeg, G., Vilkki, J., & Merilä, J. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007237 · Cited by 41
Stölting, K. N., Paris, M., Meier, C., Heinze, B., Castiglione, S., Bartha, D., & Lexer, C. (2015) · New Phytologist · doi:10.1111/nph.13392 · Cited by 40
“…Sanger sequencing; # out, number of SNP loci with outlier status. ht tp :// do c. re ro .c h perennial plant species are sufficiently large to give rise to new genetic variants that make an important contribution to the genetic variation used by spatially varying selection (Pritchard et al., 2010).”
BackgroundInfluentialRecent Selection Changes in Human Genes under Long-Term Balancing Selection
de Filippo, C., Key, F. M., Ghirotto, S., Benazzo, A., Meneu, J. R., Weihmann, A., Program, N. C. S., Parra, G., Green, E. D., & Andrés, A. M. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw023 · Cited by 38
“2014), mostly due to our low effective population size (Lynch 2010, 2011), it is likely that these novel adaptations are largely mediated by selection on previously existing variation (Pritchard et al. 2010; Messer and Petrov 2013).”
BackgroundHsieh, P., Hallmark, B., Watkins, J. C., Karafet, T. M., Osipova, L. P., Gutenkunst, R. N., & Hammer, M. F. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx226 · Cited by 39
Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome
Booker, T. R., & Keightley, P. D. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy188 · Cited by 44
“40 may cause small shifts in allele frequency at numerous loci without necessarily resulting in 947 fixations [67, 68].”
BackgroundRapid repeatable phenotypic and genomic adaptation following multiple introductions
van Boheemen, L. A., & Hodgins, K. A. (2020) · Molecular Ecology · doi:10.1111/mec.15429 · Cited by 41
The genomics of rapid climatic adaptation and parallel evolution in North American house mice
Ferris, K. G., Chavez, A. S., Suzuki, T. A., Beckman, E. J., Phifer‐Rixey, M., Bi, K., & Nachman, M. W. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009495 · Cited by 45
“Additionally, there are probably genes that have responded to selection through modest changes in allele frequency [42] and these may not be detected by LFMM.”
BackgroundInfluentialSmadja, C. M., Loire, É., Caminade, P., Thoma, M., Latour, Y., Roux, C., Thoß, M., Penn, D. J., Ganem, G., & Boursot, P. (2015) · Molecular Ecology · doi:10.1111/mec.13301 · Cited by 39
“Soft selective sweeps and polygenic adaptation (Przeworski et al. 2005; Pritchard et al. 2010) would be difficult to detect using an approach like ours, despite being also consistent with a reinforcement process (Hopkins et al. 2012).”
MethodRecent Advances in Understanding the Role of Nutrition in Human Genome Evolution
Ye, K., & Gu, Z. (2011) · Advances in Nutrition · doi:10.3945/an.111.001024 · Cited by 40
“Positive selection alone has a wide range of modes, leaving distinct signatures along the selected genomic region (36).”
BackgroundTeaching evolution and the nature of science
Futuyma, D. J. (2011) · Cambridge University Press eBooks · doi:10.1017/cbo9780511980381.023 · Cited by 39
Living in an adaptive world: Genomic dissection of the genus Homo and its immune response
Quach, H., & Quintana‐Murci, L. (2017) · The Journal of Experimental Medicine · doi:10.1084/jem.20161942 · Cited by 42
“Conversely, positive selection acts upon advantageous mutations after different evolutionary trends (Pritchard et al., 2010).”
BackgroundSazzini, M., Abondio, P., Sarno, S., Gnecchi‐Ruscone, G. A., Ragno, M., Giuliani, C., Fanti, S. D., Ojeda‐Granados, C., Boattini, A., Marquis, J., et al. (2020) · BMC Biology · doi:10.1186/s12915-020-00778-4 · Cited by 40
“Combinations of favorable variants in multiple adaptive haplotypes at moderate frequency, rather than remarkable increase in frequency of a single haplotype (as supposed under the hard sweep model), represent the main genomic footprint of polygenic adaptation [37, 38].”
BackgroundTrans-population Analysis of Genetic Mechanisms of Ethnic Disparities in Neuroblastoma Survival
Gamazon, E. R., Pinto, N. R., Konkashbaev, A. I., Im, H. K., Diskin, S. J., London, W. B., Maris, J. M., Dolan, M. E., Cox, N. J., & Cohn, S. L. (2012) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djs503 · Cited by 39
Otte, K. A., Nolte, V., Mallard, F., & Schlötterer, C. (2021) · Genome biology · doi:10.1186/s13059-021-02425-9 · Cited by 40
Evidence for Selection on Gene Expression in Cultivated Rice (Oryza sativa)
House, M., Griswold, C. K., & LUKENS, L. N. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu110 · Cited by 37
“Soft sweeps of these selected genes may not greatly distort expected patterns of nucleotide variation (Pritchard et al. 2010).”
BackgroundHebert, F. O., Renaut, S., & Bernatchez, L. (2013) · Molecular Ecology · doi:10.1111/mec.12447 · Cited by 38
“…differentiation and that might be directly or indirectly selected, selection acting on standing genetic variation and on polygenic phenotypes could also be responsible for soft or incomplete sweeps that remain undetected (Pritchard & Di Rienzo 2010; Pritchard et al. 2010; Le Corre & Kremer 2012).”
BackgroundFast and robust detection of ancestral selective sweeps
Cheng, X., Xu, C., & DeGiorgio, M. (2017) · Molecular Ecology · doi:10.1111/mec.14416 · Cited by 40
Spinassé, L. B., Santos, A. R., Suffys, P. N., Muxfeldt, E. S., & Salles, G. F. (2014) · Pharmacogenomics · doi:10.2217/pgs.13.202 · Cited by 38
Chen, M., Sidore, C., Akiyama, M., Ishigaki, K., Kamatani, Y., Schlessinger, D., Cucca, F., Okada, Y., & Chiang, C. W. K. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.05.014 · Cited by 32
“Since each genetic locus contributes a small effect to complex traits, polygenic adaptation is expected to be different from the classic selective sweep, where a beneficial allele is driven to near-fixation in a population because of strong positive selection.(1) In polygenic adaptation, only a subtle but coordinated…”
BackgroundCheeseman, I. H., McDew‐White, M., Phyo, A. P., Sriprawat, K., Nosten, F. H., & Anderson, T. J. C. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu397 · Cited by 37
“…may not generalize well to other settings where selection is more ancient, weaker or from standing variation (Hermisson and Pennings 2005; Pennings and Hermisson 2006; Pritchard et al. 2010) or where there is a more substantial level of background noise generated by divergence between pools.”
BackgroundMethodInfluentialScreen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon
Vasemägi, A., Nilsson, J. Å., McGinnity, P., Cross, T. F., O'Reilly, P. T., Glebe, B. D., Peng, B., Berg, P. R., & Primmer, C. R. (2012) · Comparative and Functional Genomics · doi:10.1155/2012/628204 · Cited by 37
“In conclusion, our results together with other recent studies [1, 11, 80, 81] illustrate the significance of standing genetic variation during the early stages of adaptation in leading to rapid evolutionary responses to novel environments.”
Introgression of a Block of Genome Under Infinitesimal Selection
Sachdeva, H., & Barton, N. (2018) · Genetics · doi:10.1534/genetics.118.301018 · Cited by 37
Mayol, M., Riba, M., Cavers, S., Grivet, D., Vincenot, L., Cattonaro, F., Vendramin, G. G., & González‐Martínez, S. C. (2019) · Evolutionary Applications · doi:10.1111/eva.12838 · Cited by 37
“It is thus possible that the higher overall nucleotide diversity and Fu & Li's D* values reflect slight changes of allele frequency but at many genes at the same time, which is difficult to identify with conventional single‐locus approaches (Pritchard et al., 2010).”
BackgroundThe impact of genetic adaptation on chimpanzee subspecies differentiation
Schmidt, J. M., de Manuel, M., Marquès‐Bonet, T., Castellano, S., & Andrés, A. M. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008485 · Cited by 35
“This would suggest that adaptation from standing genetic variation is important throughout primate evolution, not just in recent human evolution [69].”
BackgroundDistinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies
Barghi, N., & Schlötterer, C. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa073 · Cited by 39
Sunde, J., Yıldırım, Y., Tibblin, P., Bekkevold, D., Skov, C., Nordahl, O., Larsson, P., & Forsman, A. (2021) · Molecular Ecology · doi:10.1111/mec.16315 · Cited by 37
“The selection pressure on each locus will therefore not be that pronounced, and the adaptive responses associated with such traits commonly manifest as smaller allele frequency shifts at many (hundreds to thousands) loci (Pritchard & Di Rienzo, 2010; Pritchard et al., 2010).”
BackgroundPolymorphism, Divergence, and the Role of Recombination in Saccharomyces cerevisiae Genome Evolution
Cutter, A. D., & Moses, A. M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq356 · Cited by 36
“With the emerging acknowledgement of the importance of selective sweeps deriving from standing genetic variation (Pritchard et al. 2010), more sophisticated treatment is needed to infer the relative roles of these two forms of selection.”
BackgroundSurvey of Global Genetic Diversity Within theDrosophilaImmune System
Early, A. M., Arguello, J. R., Cardoso-Moreira, M., Gottipati, S., Grenier, J. K., & Clark, A. G. (2016) · Genetics · doi:10.1534/genetics.116.195016 · Cited by 32
Harder, A. M., Willoughby, J. R., Ardren, W. R., & Christie, M. R. (2019) · Molecular Ecology · doi:10.1111/mec.15334 · Cited by 36
Epstein, B., Burghardt, L. T., Heath, K. D., Grillo, M. A., Kostanecki, A., Hämälä, T., Young, N. D., & Tiffin, P. (2022) · Molecular Ecology · doi:10.1111/mec.16602 · Cited by 37
“Although population genomic analyses can be powerful for identifying evidence of strong selection acting on genes that have a major phenotypic effect, their power to detect evidence of selection acting on phenotypes with a polygenic basis is limited (Chevin & Hospital, 2008; Pritchard et al., 2010).”
BackgroundMedina‐Gómez, C., Chesi, A., Heppe, D. H. M., Zemel, B. S., Yin, J.-L., Kalkwarf, H. J., Albert Hofman, D., Lappe, J. M., Kelly, A. T., Kayser, M., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv170 · Cited by 34
Kim, E.-S., Ros‐Freixedes, R., Pena, R. N., Baas, T. J., Estany, J., & Rothschild, M. F. (2015) · Journal of Animal Science · doi:10.2527/jas.2015-8879 · Cited by 35
“Standard meth ods for detecting selective sweeps would have little power in the case of polygenic traits, even with strong selection for a trait because the response to selection would be generated by modest allele frequency shifts at many loci that are already polymorphic (Pritchard et al., 2010).”
Ecological population genomics in the marine environment
Crawford, D. L., & Oleksiak, M. F. (2016) · Briefings in Functional Genomics · doi:10.1093/bfgp/elw008 · Cited by 35
Statistical questions in experimental evolution
Desai, M. M. (2013) · Journal of Statistical Mechanics Theory and Experiment · doi:10.1088/1742-5468/2013/01/p01003 · Cited by 34
“Recent work in population genetics is now suggesting that these interference phenomena are important far more broadly than just microbial evolution experiments, and may be generally important in interpreting patterns of molecular evolution [103]–[106].”
Cryptic Genetic Variation in Evolutionary Developmental Genetics
Paaby, A. B., & Gibson, G. C. (2016) · Biology · doi:10.3390/biology5020028 · Cited by 38
“In humans, shifts in allele frequencies are often “soft”, implicating high polygenicity and small effect sizes in the underlying trait architecture [40,41].”
BackgroundA Simple Test Identifies Selection on Complex Traits
Beissinger, T., Kruppa, J., Cavero, D., Ha, N.-T., Erbe, M., & Simianer, H. (2018) · Genetics · doi:10.1534/genetics.118.300857 · Cited by 32
“Conversely, population-genetic studies aiming to scan for selection have been most successful at identifying hard sweeps, where a new mutation of large effect rapidly rises to fixation as a result of selection (Pritchard et al. 2010).”
BackgroundVRK2, a Candidate Gene for Psychiatric and Neurological Disorders
Li, M., & Yue, W. (2018) · Complex Psychiatry · doi:10.1159/000493941 · Cited by 37
The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area
Tilot, A. K., Khramtsova, E. A., Liang, D., Grasby, K. L., Jahanshad, N., Painter, J. N., Colodro‐Conde, L., Bralten, J., Hibar, D. P., Lind, P. A., et al. (2020) · Cerebral Cortex · doi:10.1093/cercor/bhaa327 · Cited by 32
Molecular Adaptation during a Rapid Adaptive Radiation
Kapralov, M. V., Votintseva, A. A., & Filatov, D. A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst013 · Cited by 34
“…view of the cost of positive selection is now considered too extreme (Turner and Williamson 1968; Nunney 2003), as much of adaptation can occur via soft or polygenic selection (Pritchard et al. 2010) that does not require elimination of all individuals that do not possess the advantageous allele.”
BackgroundSignatures of Selection in Nelore Cattle Revealed by Whole-Genome Sequencing Data
Maiorano, A. M., Cardoso, D. F., Carvalheiro, R., Júnior, G. A. F., de Albuquerque, L. G., & de Oliveira, H. N. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110304 · Cited by 33
Neethiraj, R., Hornett, E. A., Hill, J. A., & Wheat, C. W. (2017) · Molecular Ecology · doi:10.1111/mec.14205 · Cited by 32
“Messer & Petrov 2013), adaptive footprints may be weak and on the order of bp in length (Pritchard et al. 2010).”
BackgroundGutiérrez‐Gil, B., Esteban‐Blanco, C., Wiener, P., Chitneedi, P., Suárez‐Vega, A., & Arranz, J. J. (2017) · Genetics Selection Evolution · doi:10.1186/s12711-017-0354-x · Cited by 35
Gene Expression Modularity Reveals Footprints of Polygenic Adaptation in Theobroma cacao
Hämälä, T., Guiltinan, M. J., Marden, J. H., Maximova, S. N., dePamphilis, C. W., & Tiffin, P. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz206 · Cited by 37
Genetic Adaptation in New York City Rats
Harpak, A., Garud, N. R., Rosenberg, N. A., Petrov, D. A., Combs, M. A., Pennings, P. S., & Munshi‐South, J. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa247 · Cited by 36
“241 Other modes of adaptation, such as polygenic adaptation [73, 74, 75, 76], may be common 242 in NYC rats, but entirely missed in this study.”
BackgroundEvolutionary genetics of skin pigmentation in African populations
Feng, Y., McQuillan, M. A., & Tishkoff, S. A. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab007 · Cited by 34
Parvizi, E., Dhami, M. K., Yan, J., & McGaughran, A. (2022) · Molecular Ecology · doi:10.1111/mec.16740 · Cited by 32
“For instance, during rapid fixation of de novo mutations, variation at linked sites will be purged (Pritchard et al., 2010) and only a few master regulatory genes will be differentially expressed in invasive populations (Pélissié et al., 2022).”
BackgroundCombining Genotype, Phenotype, and Environment to Infer Potential Candidate Genes
Talbot, B., Chen, T.-W., Zimmerman, S. J., Joost, S., Eckert, A. J., Crow, T. M., Semizer-Cuming, D., Seshadri, C., & Manel, S. (2016) · Journal of Heredity · doi:10.1093/jhered/esw077 · Cited by 34
“Therefore, interest in genome scans, the survey of genetic variability across whole genomes or across a large number of loci from distinct environments (Luikart et al. 2003; Pritchard et al. 2010) is growing (Haasl and Payseur 2016; Jensen et al.”
Origin, fate, and architecture of ecologically relevant genetic variation
Colautti, R. I., Lee, C., & Mitchell‐Olds, T. (2012) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2012.01.016 · Cited by 36
Eckert, A. J., Bower, A. D., Jermstad, K. D., Wegrzyn, J., Knaus, B. J., Syring, J. V., & Neale, D. B. (2013) · Molecular Ecology · doi:10.1111/mec.12514 · Cited by 30
“Some of this disconnect is also probably related to the type of selection for which we are searching for within conifer genomes (e.g. hard vs. soft sweeps, polygenic adaptation, local adaptation, see Pritchard et al. 2010).”
BackgroundCentennial perspective on human adaptability
Leonard, W. R. (2018) · American Journal of Physical Anthropology · doi:10.1002/ajpa.23401 · Cited by 34
Bresadola, L., Caseys, C., Castiglione, S., Buerkle, C. A., Wegmann, D., & Lexer, C. (2019) · New Phytologist · doi:10.1111/nph.15930 · Cited by 31
“93 Recent results from Genome-Wide Association Studies (GWASs) in trees, humans, 94 and other species suggest that the architecture of adaptive traits is often polygenic, that is, 95 they are not determined by a few genes of large effect, but rather by many loci with small 96 effect (Pritchard et al., 2010; Rockman, 2…”
BackgroundDerbyshire, M. C. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00644 · Cited by 33
Campbell, M. C., & Ranciaro, A. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab027 · Cited by 32
Sikkink, K. L., Ituarte, C. M., Reynolds, R. M., Cresko, W. A., & Phillips, P. C. (2014) · Genomics · doi:10.1016/j.ygeno.2014.09.014 · Cited by 33
“For example, most experimental evolution studies in microbes are initiated using a single clonal individual, whereas most plant and animal populations harbor substantial levels of standing genetic variation, which undoubtedly plays an important role in the response to selection [4,5].”
BackgroundComeault, A. A., de Carvalho, C. F., Dennis, S. R., Soria‐Carrasco, V., & Nosil, P. (2016) · Evolution · doi:10.1111/evo.12931 · Cited by 33
“For example, when adaptation is the result of many loci, each having small effects on phenotypic variation, the genetic response to selection is expected to result in minor and even transient shifts in allele frequencies across loci (Pritchard et al. 2010; Berg and Coop 2014; Yeaman 2015).”
BackgroundGholami, M., Reimer, C., Erbe, M., Preisinger, R., Weigend, A., Weigend, S., Servin, B., & Simianer, H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0130497 · Cited by 31
“A complete hard sweep is expected to be large [44], while a soft sweep is more likely to have smaller size [45].”
BackgroundEnvironmental Adaptation Contributes to Gene Polymorphism across the Arabidopsis thaliana Genome
Lee, C., & Mitchell‐Olds, T. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss174 · Cited by 31
“However, several recent discussions emphasize the importance of polygenic adaptation, where evolution of a quantitative trait occurs by small changes in allele frequency at many loci (Pritchard et al. 2010; Rockman 2012).”
BackgroundHollowell, A. C., Regus, J. U., Turissini, D. A., Gano‐Cohen, K. A., Bantay, R., Bernardo, A., Moore, D., Pham, J. K., & Sachs, J. L. (2016) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.0496 · Cited by 31
“Selective sweeps are predicted to result in reduced genetic diversity in the genome region where they occur [70,71].”
BackgroundFine-scale genetic structure due to adaptive divergence among microhabitats
Wagner, D. N., Baris, T. Z., Dayan, D. I., Du, X., Oleksiak, M. F., & Crawford, D. L. (2017) · Heredity · doi:10.1038/hdy.2017.6 · Cited by 29
“This reliance is tempered if adaptation does not depend on one allele completely replacing another (Otto and Whitlock, 1997) but instead requires small allele frequency changes at many loci (Turelli and Barton, 2004; Przeworski et al., 2005; Pritchard et al., 2010).”
BackgroundThe demographic and adaptive history of central African hunter-gatherers and farmers
Patin, É., & Quintana‐Murci, L. (2018) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2018.07.008 · Cited by 37
Human adaptation over the past 40,000 years
Mathieson, I. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.06.003 · Cited by 32
“This observation, coupled with the relatively limited number of selective sweeps, suggested that polygenic adaptation might be an important force in human evolution (42).”
BackgroundThe role played by natural selection on Mendelian traits in humans
Quintana‐Murci, L., & Barreiro, L. B. (2010) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2010.05856.x · Cited by 32
Zhen, Y., Huber, C. D., Davies, R. W., & Lohmueller, K. E. (2020) · Genome Research · doi:10.1101/gr.256636.119 · Cited by 32
Adaptive evolution of loci covarying with the human African Pygmy phenotype
Mendizabal, I., Marigorta, U. M., Lao, Ó., & Comas, D. (2012) · Human Genetics · doi:10.1007/s00439-012-1157-3 · Cited by 32
“d Haplotype plots for region 12 (marked with red arrows) in Mbuti, Biaka, Yoruba and French from HGDP Selection Browser (Coop et al. 2009; Pickrell et al. 2009; Pritchard et al. 2010).”
BackgroundLeón, R. G., Dunne, J. C., & Gould, F. L. (2020) · Pest Management Science · doi:10.1002/ps.5988 · Cited by 29
Lea, A. J., García, A. R., Arevalo, J. M. G., Ayroles, J. F., Buetow, K. H., Cole, S. W., Rodríguez, D. E., Cayuba, M. G., Highland, H. M., Hooper, P. L., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207544120 · Cited by 29
“Recent theoretical and empirical work (32, 33, 63) suggests that most adaptive traits are shaped by simultaneous selection on numerous genetic variants, rather than strong selection at a single locus.”
InfluentialAfrica: the next frontier for human disease gene discovery?
Ramsay, M., Tiemessen, C. T., Choudhury, A., & Soodyall, H. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr401 · Cited by 30
“It is more likely that selection acts on many loci simultaneously to effect genetic adaptation through a process of modulating allele frequencies of existing genetic variants (58).”
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review