The effects of epistasis and linkage on the invasion of locally beneficial mutations and the evolution of genomic islands

Pontz, Martin; Bürger, Reinhard

doi:10.1016/j.tpb.2022.01.004

Cited by 6 publications

(7 citation statements)

References 24 publications

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“…Perhaps the most significant result of our analysis is that the strength of selection for dominance and epistasis modifiers is relatively stronger than that for recombination modifiers. This is in contrast to situations where locally adapted alleles are not yet established, linkage between the modifier and existing adaptation loci is important [ 27 ]. We further found that modifiers of dominance spread fastest when they are unlinked to the locus they modify, but are linked to another locus that also contributes to local adaptation.…”

Section: Discussionmentioning

confidence: 99%

“…For example, when there is dispersal between demes facing different environmental conditions, migration-selection balance can lead to the long-term maintenance of heterozygotes and result in selection for dominance modifiers [ 37 ]. Understanding selection on modifiers of epistasis is complex, depending on the sign of linkage disequilibrium between deleterious alleles being purged or beneficial alleles being favored with the mutant modifier alleles, as well as on the dominance interactions at each locus [ 27 , 39 ]. We do know, however, that in general an epistatic modifier affecting the total fitness load of a structured population is expected to be strongly selected relative to modifiers affecting only specific loci [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

“…How these "genomic islands" of differentiation and isolation originate and are maintained is intriguing. One possibility is that selection causes a build up of linked alleles that contribute to local adaptation, either by favoring mutations, such as chromosomal inversions, that eliminate recombination between pre-existing locally-adapted alleles [18][19][20], or by favoring mutations that just happen to be linked to locally-adapted alleles when they appear during ongoing local adaptation [21][22][23][24][25][26][27]. Another possibility is that genomic islands of differentiation and isolation are created by genetic drift and the accumulation of mutations in genome locations of reduced recombination rates under allopatry, in a manner similar to how Dobzhansky-Muller incompatibilities arise and are maintained [28,29].…”

Section: Introductionmentioning

confidence: 99%

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Selection on modifiers of genetic architecture under migration load

Proulx

Teotónio

2022

PLoS Genet

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Gene flow between populations adapting to differing local environmental conditions might be costly because individuals can disperse to habitats where their survival is low or because they can reproduce with locally maladapted individuals. The amount by which the mean relative population fitness is kept below one creates an opportunity for modifiers of the genetic architecture to spread due to selection. Prior work that separately considered modifiers changing dispersal, recombination rates, or altering dominance or epistasis, has typically focused on the direction of selection rather than its absolute magnitude. We here develop methods to determine the strength of selection on modifiers of the genetic architecture, including modifiers of the dispersal rate, in populations that have previously evolved local adaptation. We consider scenarios with up to five loci contributing to local adaptation and derive a new model for the deterministic spread of modifiers. We find that selection for modifiers of epistasis and dominance is stronger than selection for decreased recombination, and that selection for partial reductions in recombination are extremely weak, regardless of the number of loci contributing to local adaptation. The spread of modifiers that reduce dispersal depends on the number of loci, epistasis and extent of local adaptation in the ancestral population. We identify a novel effect, that modifiers of dominance are more strongly selected when they are unlinked to the locus that they modify. These findings help explain population differentiation and reproductive isolation and provide a benchmark to compare selection on modifiers under finite population sizes and demographic stochasticity.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Selection on modifiers of genetic architecture under migration load

Proulx

Teotónio

2022

PLoS Genet

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“…The effects of multilocus (non-epistatic) selection have been studied extensively in the context of populations along a geographic cline. Theory demonstrates that closely linked locally selected alleles can strongly reshape their expected frequencies across geographic clines (e.g., [11][12][13]), and fixation probabilities in a continent-island model (e.g., [14][15][16][17]). More generally, linkage among selected alleles can generate dynamics in clines that include combinations of loci involved in complex selection (e.g., [18]).…”

Section: Introductionmentioning

confidence: 99%

Inferring multi-locus selection in admixed populations

Ayala,

Genetti,

Corbett-Detig

2023

PLoS Genet

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Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive genetic variation. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as linkage among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster and Passer italiae, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.

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“…The effects of multilocus selection have been studied extensively in the context of populations along a geographic cline. Theory demonstrates that closely linked locally selected alleles can strongly reshape their expected frequencies across geographic clines (e.g., [11][12][13]), and fixation probabilities in a continent-island model (e.g., [14][15][16][17]). More generally, linkage among selected alleles can generate complex dynamics in clines that include combinations of loci involved in complex selection (e.g., [18]).…”

Section: Introductionmentioning

confidence: 99%

Inferring multi-locus selection in admixed populations

Ayala

Corbett-Detig

2023

Preprint

View full text Add to dashboard Cite

Admixture, the exchange of genetic information between distinct source populations, is thought to be a major source of adaptive novelty. Unlike mutation events, which periodically generate single alleles, admixture can introduce many selected alleles simultaneously. As such, the effects of linkage between selected alleles may be especially pronounced in admixed populations. However, existing tools for identifying selected mutations within admixed populations only account for selection at a single site, overlooking phenomena such as interference among proximal selected alleles. Here, we develop and extensively validate a method for identifying and quantifying the individual effects of multiple linked selected sites on a chromosome in admixed populations. Our approach numerically calculates the expected local ancestry landscape in an admixed population for a given multi-locus selection model, and then maximizes the likelihood of the model. After applying this method to admixed populations of Drosophila melanogaster, we found that the impacts between linked sites may be an important contributor to natural selection in admixed populations. Furthermore, for the situations we considered, the selection coefficients and number of selected sites are overestimated in analyses that do not consider the effects of linkage among selected sites. Our results imply that linkage among selected sites may be an important evolutionary force in admixed populations. This tool provides a powerful generalized method to investigate these crucial phenomena in diverse populations.

show abstract

The effects of epistasis and linkage on the invasion of locally beneficial mutations and the evolution of genomic islands

Cited by 6 publications

References 24 publications

Selection on modifiers of genetic architecture under migration load

Selection on modifiers of genetic architecture under migration load

Inferring multi-locus selection in admixed populations

Inferring multi-locus selection in admixed populations

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