The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

Pritchard, Jonathan K.; Pickrell, Joseph K.; Coop, Graham

doi:10.1016/j.cub.2009.11.055

Cited by 887 publications

(964 citation statements)

References 77 publications

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“…Indeed soft sweeps (Innan and Kim 2004;Hermisson and Pennings 2005;Pennings and Hermisson 2006;Garud et al 2015) and partial sweeps Sabeti et al 2002;Voight et al 2006), may be widespread, and differ in their effects on linked polymorphism (Orr and Betancourt 2001;Meiklejohn et al 2004;Przeworski et al 2005;Teshima et al 2006;Schrider et al 2015;Vy and Kim 2015). 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). Such polygenic adaptation is known to leave its own unique signature on patterns of population genetic variation (Berg and Coop 2014).…”

Section: Discussionmentioning

confidence: 99%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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The availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies, they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of data sets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models-often severely. We find that selection can lead to incorrect inferences of population size changes when none have occurred. Moreover, we show that linked selection can lead to incorrect demographic model selection, when multiple demographic scenarios are compared. We argue that natural populations may experience the amount of recent positive selection required to skew inferences. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.KEYWORDS population genetics; positive selection; demographic inference T HE widespread availability of population genomic data has spurred a new generation of studies aimed at understanding the histories of natural populations from a host of model and nonmodel organisms alike. In particular, genomescale variation data allows for inference of demographic factors such as population size changes, the timing and ordering of population splits, migration rates between populations, and the founding of admixed populations (Pool et al. 2010;Pickrell and Pritchard 2012;Sousa and Hey 2013). Such efforts can refine our picture of demographic events inferred from the archaeological record (e.g., Fagundes et al. 2007;Goebel et al. 2008), or reveal such events in species where no archaeological data are available, and can aid conservation efforts by complementing census data (e.g., Hájková et al. 2007;Garrick et al. 2015).Population genomic data sets are well suited for this task simply because demographic changes leave their mark on patterns of genetic variation. Recent population growth, for example, will result in an excess of rare variation compared to equilibrium expectations (Fu 1997), while population contraction will result in an excess of intermediate frequency alleles (Maruyama and Fuerst 198...

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Section: Discussionmentioning

confidence: 99%

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

2016

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“…In general, thick‐billed murres seem to be able to cope with a variety of environmental conditions (McFarlane Tranquilla et al., 2015). The ability to adjust to a variable environment could be enabled by phenotypic plasticity, high levels of standing genetic variation, or both (Crispo, 2008; Pritchard, Pickrell, & Coop, 2010). We did observe high levels of standing genetic variation (although we do not know whether this variation has adaptive value), but levels of phenotypic plasticity are virtually unknown in this species.…”

Section: Discussionmentioning

confidence: 99%

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Tigano

Shultz

Edwards

et al. 2017

Ecology and Evolution

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Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick‐billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick‐billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome‐wide markers mapped to a newly assembled thick‐billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non‐breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

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“…In evolutionary genetic studies of natural selection, two major outcomes of natural selection are now distinguished, hard sweeps and soft sweeps [22]. Hard sweeps are the outcome of a single instance of an advantageous mutation arising and spreading through a population.…”

Section: Models Of Adaptive Evolution: Hard and Soft Sweepsmentioning

confidence: 99%

Human population structure and the adaptive response to pathogen-induced selection pressures

Novembre

Han

2012

Phil. Trans. R. Soc. B

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The past few years of research in human evolutionary genetics have provided novel insights and questions regarding how human adaptations to recent selective pressures have taken place. Here, we review the advances most relevant to understanding human evolution in response to pathogen-induced selective pressures. Key insights come from theoretical models of adaptive evolution, particularly those that consider spatially structured populations, and from empirical population genomic studies of adaptive evolution in humans. We also review the CCR5-D32 HIV resistance allele as a case study of pathogen resistance in humans. Taken together, the results make clear that the human response to pathogen-induced selection pressures depends on a complex interplay between the age of the pathogen, the genetic basis of potential resistance phenotypes, and how population structure impacts the adaptive process in humans.

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The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

Cited by 887 publications

References 77 publications

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Human population structure and the adaptive response to pathogen-induced selection pressures

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