Genetic hitchhiking in spatially extended populations

Barton, Nicholas H.; Etheridge, Alison; Kelleher, Jerome; Véber, Amandine

doi:10.1016/j.tpb.2012.12.001

Cited by 54 publications

(105 citation statements)

References 43 publications

(63 reference statements)

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“…Inclusion of these complications in methods for estimating selection parameters is a challenging problem. However, we note that the spread to a high frequency of a favorable mutation in a population spread over a two-dimensional environment is much slower than in a panmictic population, which implies that there is more opportunity for recombination to dilute the effects of SSWs than with panmixia (47). This process would thus cause our γ estimates to be smaller than the true values, and the p estimates to be larger.…”

Section: Discussionmentioning

confidence: 82%

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Campos

Zhao

Charlesworth

2017

Proc. Natl. Acad. Sci. U.S.A.

118

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We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (π S ) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (K A ). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on π S and found that these could account for only part of the observed correlation between π S and K A . We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high K A . Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored. background selection | selective sweeps | sequence diversity | gene conversion | Drosophila melanogaster

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Section: Discussionmentioning

confidence: 82%

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Campos

Zhao

Charlesworth

2017

Proc. Natl. Acad. Sci. U.S.A.

118

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“…We expect our approach to be useful also for investigating genetic consequences of range expansions and genetic hitchhiking on spatial selective sweeps with long-distance dispersal (50)(51)(52)(53). A generalization of the analysis of the phenomenon of "allele surfing," which has been mainly analyzed assuming shortrange migration so far (54)(55)(56), could be used to clarify the conditions under which long-distance dispersal increases or decreases genetic diversity-both effects have been seen in simulations (57)(58)(59).…”

Section: Discussionmentioning

confidence: 98%

Acceleration of evolutionary spread by long-range dispersal

Hallatschek

Fisher

2014

Proc. Natl. Acad. Sci. U.S.A.

126

173

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The spreading of evolutionary novelties across populations is the central element of adaptation. Unless populations are well mixed (like bacteria in a shaken test tube), the spreading dynamics depend not only on fitness differences but also on the dispersal behavior of the species. Spreading at a constant speed is generally predicted when dispersal is sufficiently short ranged, specifically when the dispersal kernel falls off exponentially or faster. However, the case of long-range dispersal is unresolved: Although it is clear that even rare long-range jumps can lead to a drastic speedup-as air-trafficmediated epidemics show-it has been difficult to quantify the ensuing stochastic dynamical process. However, such knowledge is indispensable for a predictive understanding of many spreading processes in natural populations. We present a simple iterative scaling approximation supported by simulations and rigorous bounds that accurately predicts evolutionary spread, which is determined by a trade-off between frequency and potential effectiveness of long-distance jumps. In contrast to the exponential laws predicted by deterministic "mean-field" approximations, we show that the asymptotic spatial growth is according to either a power law or a stretched exponential, depending on the tails of the dispersal kernel. More importantly, we provide a full time-dependent description of the convergence to the asymptotic behavior, which can be anomalously slow and is relevant even for long times. Our results also apply to spreading dynamics on networks with a spectrum of long-range links under certain conditions on the probabilities of long-distance travel: These are relevant for the spread of epidemics.long-range dispersal | selective sweeps | epidemics | range expansions | species invasions H umans have developed convenient transport mechanisms for nearly any spatial scale relevant to the globe. We walk to the grocery store, bike to school, drive between cities, or take an airplane to cross continents. Such efficient transport across many scales has changed the way we and organisms traveling with us are distributed across the globe (1-5). This has severe consequences for the spread of epidemics: Nowadays, human infectious diseases rarely remain confined to small spatial regions, but instead spread rapidly across countries and continents by travel of infected individuals (6).Besides hitchhiking with humans or other animals, small living things such as seeds, microbes, or algae are easily caught by wind or sea currents, resulting in passive transport over large spatial scales (7-16). Effective long-distance dispersal is also widespread in the animal kingdom, occurring when individuals primarily disperse locally but occasionally move over long distances. And such animals, too, can transport smaller organisms.These active and passive mechanisms of long-range dispersal are generally expected to accelerate the growth of fitter mutants in spatially extended populations. However, how can one estimate the resulting speedup and the assoc...

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“…This quantity has not been worked out for a model with simultaneous local sweeps, but will be somewhat analogous to the “spatial Λ-Fleming–Viot” models of Barton et al (2013b), in which local sweeps occur independently across the range. Lineages that are closely linked to the sweeping allele (~ v / χ Morgans) will be moved towards the center of the sweep (a displacement O ( χ )), and pairs of lineages caught up in the same sweep could be forced to coalesce (see Barton et al, 2013a, for work on geographic hitchhiking). In this case lineages and alleles are literally hitchhiking across space.…”

Section: Discussionmentioning

confidence: 99%

The Role of Standing Variation in Geographic Convergent Adaptation

Ralph

Coop²

2015

The American Naturalist

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The extent to which populations experiencing shared selective pressures adapt through a shared genetic response is relevant to many questions in evolutionary biology. In a number of well studied traits and species, it appears that convergent evolution within species is common. In this paper, we explore how standing, genetic variation contributes to convergent genetic responses in a geographically spread population, extending our previous work on the topic. Geographically limited dispersal slows the spread of each selected allele, hence allowing other alleles – newly arisen mutants or present as standing variation – to spread before any one comes to dominate the population. When such alleles meet, their progress is substantially slowed – if the alleles are selectively equivalent, they mix slowly, dividing the species range into a random tessellation, which can be well understood by analogy to a Poisson process model of crystallization. In this framework, we derive the geographic scale over which a typical allele is expected to dominate, the time it takes the species to adapt as a whole, and the proportion of adaptive alleles that arise from standing variation. Finally, we explore how negative pleiotropic effects of alleles before an environment change can bias the subset of alleles that contribute to the species’ adaptive response. We apply the results to the many geographically localized G6PD deficiency alleles thought to confer resistance to malaria, where the large mutational target size makes it a likely candidate for adaptation from standing variation, despite the selective cost of G6PD deficiency alleles in the absence of malaria. We find the numbers and geographic spread of these alleles matches our predictions reasonably well, consistent with the view that they arose from a combination of standing variation and new mutations since the advent of malaria. Our results suggest that much of adaptation may be geographically local even when selection pressures are homogeneous. Therefore, we argue that caution must be exercised when arguing that strongly geographically restricted alleles are necessarily the outcome of local adaptation. We close by discussing the implications of these results for ideas of species coherence and the nature of divergence between species.

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Genetic hitchhiking in spatially extended populations

Cited by 54 publications

References 43 publications

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Acceleration of evolutionary spread by long-range dispersal

The Role of Standing Variation in Geographic Convergent Adaptation

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