The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations

Aeschbacher, Simon; Bürger, Reinhard

doi:10.1534/genetics.114.163477

Cited by 56 publications

(92 citation statements)

References 125 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Moreover, Yeaman () employed a semiheuristic approximation to the EP (Yeaman & Otto ) that has not been formally tested in the case of multiple linked loci under selection. Here, we first verify this approximation by comparison with an alternative, more formally derived one (Aeschbacher & Bürger ). Second, we extend the work of Yeaman () to quantify more comprehensively the potential importance of increased EP at linked mutations as an explanation for the evolution of genomic islands.…”

Section: Introductionmentioning

confidence: 82%

The evolution of genomic islands by increased establishment probability of linked alleles

2016

Self Cite

View full text Add to dashboard Cite

Genomic islands are clusters of loci with elevated divergence that are commonly found in population genomic studies of local adaptation and speciation. One explanation for their evolution is that linkage between selected alleles confers a benefit, which increases the establishment probability of new mutations that are linked to existing locally adapted polymorphisms. Previous theory suggested there is only limited potential for the evolution of islands via this mechanism, but involved some simplifying assumptions that may limit the accuracy of this inference. Here, we extend previous analytical approaches to study the effect of linkage on the establishment probability of new mutations and identify parameter regimes that are most likely to lead to evolution of islands via this mechanism. We show how the interplay between migration and selection affects the establishment probability of linked vs. unlinked alleles, the expected maximum size of genomic islands, and the expected time required for their evolution. Our results agree with previous studies, suggesting that this mechanism alone is unlikely to be a general explanation for the evolution of genomic islands. However, this mechanism could occur more readily if there were other pre-adaptations to reduce local rates of recombination or increase the local density of mutational targets within the region of the island. We also show that island formation via erosion following secondary contact is much more rapid than island formation from de novo mutations, suggesting that this mechanism may be more likely.

show abstract

Section: Introductionmentioning

confidence: 82%

The evolution of genomic islands by increased establishment probability of linked alleles

2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…Our model currently does not account for the clustering of locally adaptive mutations arising in tight linkage to previously established MSPs and the synergistic sheltering effect among MSPs that protects them from being swamped by gene flow (20,50). If accounted for, this clustering would lead to an even more pronounced uptick of between-population diversity in regions of low recombination.…”

Section: Discussionmentioning

confidence: 99%

“…At a focal neutral site, the baseline migration rate m is reduced to an effective migration rate me (19,20). This reduction in effective gene flow increases with the strength of selection at the MSPs and decreases with their recombinational distance from the focal neutral site (Fig.…”

Section: Significancementioning

confidence: 99%

Population-genomic inference of the strength and timing of selection against gene flow

Aeschbacher

Selby

Willis

et al. 2017

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

Self Cite

123

128

View full text Add to dashboard Cite

The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations. Our theory shows that the selection density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationship. We then develop a procedure for parameter estimation that accounts for the confounding effect of background selection. Applying this method to two datasets from Mimulus guttatus, we infer a strong signal of adaptive divergence in the face of gene flow between populations growing on and off phytotoxic serpentine soils. However, the genome-wide intensity of this selection is not exceptional compared with what M. guttatus populations may typically experience when adapting to local conditions. We also find that selection against genomewide introgression from the selfing sister species M. nasutus has acted to maintain a barrier between these two species over at least the last 250 ky. Our study provides a theoretical framework for linking genome-wide patterns of divergence and recombination with the underlying evolutionary mechanisms that drive this differentiation.speciation with gene flow | local adaptation | recombination | divergence | Mimulus E stimating the timing and strength of divergent selection is fundamental to understanding the evolution and persistence of organismal diversity (1-3). Genes underlying local adaptation and speciation act as barriers to gene flow, such that genetic divergence around these loci is higher compared with the rest of the genome. However, a framework that explicitly links observable patterns of DNA polymorphism with the underlying evolutionary mechanisms and allows for robust parameter inference has so far been missing (4).One way of studying adaptive genomic divergence in the face of gene flow is to apply methods for demographic inference to scenarios of speciation (e.g., refs. 5 and 6). This approach allows dating population splits and inferring the presence or absence of gene flow, yet generally does not explicitly account for natural selection (but see ref. 7). Another approach is to scan genomes for loci that are statistical outliers of divergence among populations. These scans are used to identify candidate loci underlying speciation or local adaptation (e.g., refs. 8 and 9) and include the search for so-called genomic islands of divergence (e.g., ref. 10) (i.e., extended genomic regions of elevated divergence). Methods of this type can be confounded by other modes of selection, as well as demography, and will always propose a biased subset of candidate loci (11,12).A third approach is to test for a negative correlation between abso...

show abstract

“…Eq. (24) in Aeschbacher and Bürger (2014). Hence, linkage to more than one selected site may magnify barriers to gene flow substantially.…”

Section: Discussionmentioning

confidence: 99%

The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci

Akerman

Bürger

2014

Theoretical Population Biology

Self Cite

View full text Add to dashboard Cite

For a subdivided population the consequences of dominance and gene flow for the maintenance of multilocus polymorphism, local adaptation, and differentiation are investigated. The dispersing population inhabits two demes in which selection acts in opposite direction. Fitness is determined additively by two linked diallelic loci with arbitrary intermediate dominance (no over- or underdominance). For weak as well as strong migration, the equilibrium structure is derived. As a special case, a continuous-time continent–island model (CI model) is analyzed, with one-way migration from the continent to the island. For this CI model, the equilibrium and stability configuration is obtained explicitly for weak migration, for strong migration, for independent loci, and for complete linkage. For independent loci, the possible bifurcation patterns are derived as functions of the migration rate. These patterns depend strongly on the degree of dominance. The effects of dominance, linkage, and migration on the amount of linkage disequilibrium (LD) and the degree of local adaptation are explored. Explicit formulas are obtained for D (=x1x4−x2x3) and r2 (the squared correlation in allelic state). They demonstrate that dominant island alleles increase D and decrease r2. Local adaptation is elevated by dominance of the locally adaptive alleles. The effective migration rate at a linked neutral locus is calculated. If advantageous alleles are dominant, it is decreased only slightly below the actual migration rate. For a quantitative trait that is determined by two additive loci, the influence of dominance on measures of differentiation is studied. Explicit expressions for QST and two types of FST at equilibrium are deduced and their relation is discussed.

show abstract

The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations

Cited by 56 publications

References 125 publications

The evolution of genomic islands by increased establishment probability of linked alleles

The evolution of genomic islands by increased establishment probability of linked alleles

Population-genomic inference of the strength and timing of selection against gene flow

The consequences of dominance and gene flow for local adaptation and differentiation at two linked loci

Contact Info

Product

Resources

About