Unpacking Conditional Neutrality: Genomic Signatures of Selection on Conditionally Beneficial and Conditionally Deleterious Mutations

Mee, Jonathan A.; Yeaman, Sam

doi:10.1086/702314

Cited by 34 publications

(48 citation statements)

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“…These genes, however, did not show any enrichment along genetic-tradeoff QTL, and significant increases in LD. Some of the factors that may contribute to this observation, are that some of these expression interactions are neutral/nearly-neutral, or they involve adaptive mutations of small effect size (Yeaman 2015;Hoban, et al 2016;Forester, et al 2018;Mee and Yeaman 2019).…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Genetic variation linked to expression and fitness GxE interactions can exhibit: (a) genetic tradeoffs, where the derived genotype is advantageous in one environment but deleterious in the other; and (b) conditional neutrality where the derived genotype is advantageous (conditionally advantageous) or deleterious (conditionally deleterious) in one environment and neutral in the other (Anderson, et al 2011;Mee and Yeaman 2019). Despite the presence of fitness GxE interactions, instances of conditionally deleterious or more correctly non-locally maladaptive mutations, do not represent instances of 'adaptation' (Mee and Yeaman 2019). To identity candidate genetic variation underlying local adaptation at the single nucleotide level, the two of the main approaches used are: (a) identifying single nucleotide polymorphism (SNP) that show significantly higher allele frequency differentiation between populations than expected under neutral models of evolution (Beaumont and Balding 2004;Foll, et al 2014;de Villemereuil and Gaggiotti 2015) and (b) identifying alleles showing significant associations to environment while accounting for population/geographic structure (Lasky, et al 2012;Zhou and Stephens 2012;Gunther and Coop 2013;Luu, et al 2017;Caye, et al 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Nonetheless, the enrichment of fitness associations along GxE genes was not significant despite being higher than E genes. This discordance could be the result of differences in purifying selection between E and GxE genes leading to an enrichment of slightly deleterious climate-associated SNPs in the latter set (Mee and Yeaman 2019).…”

Section: Introductionmentioning

confidence: 99%

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Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

Price¹,

Mullen²,

Lin³

et al. 2020

Preprint

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Understanding how genomic and expression variation is linked to adaptation of plants to local environments is fundamental to the fields of evolutionary biology and species conservation. Using locally adapted Arabidopsis thaliana Italy and Sweden populations, we examine how variation in gene expression under control and cold acclimation conditions, is linked to allele frequency differentiation (AFD); linkage disequilibrium (LD); selective constraint at nonsynonymous sites; and genetic-tradeoff quantitative trait loci (GT-QTL). Our results indicate that contrary to genes showing a main effect in environment (E), expression genotype by environment interactions (GxE) show significantly higher AFD along cis-regulatory and nonsynonymous sites than the neutral expectation; and interestingly, highly differentiated GxE genes show higher expression and inter-species selective constraint than the rest of the genes. When examining the association between genomic signatures of selection along GxE/E genes and GT-QTL, we find that GxE genes showing a high AFD and LD, display a significant and much higher enrichment along GT-QTL than the genome-wide/E set of genes. Nonetheless, E genes show a higher enrichment than the genome-wide control. In summary, our results suggest, that these highly expressed and selectively constrained GxE genes, may have been part of a cold-responsive regulon of E genes that experienced recent selection when migrating to new environments. Candidate GxE genes underlying GT-QTL reveal interesting biological processes that may underlie local adaptation to temperature, including flowering time, light-dependent cold acclimation, freezing tolerance, and response to hypoxia. Finally, we find no evidence linking lower expression of the CBF-dependent freezing tolerance pathway to genetic-tradeoffs and adaptation to warmer climates.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

Price¹,

Mullen²,

Lin³

et al. 2020

Preprint

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“…In contrast, however, strains of Anabaena with a history of salt stress had reduced competitive ability in the no-salt assay environment. Such a pattern is an indication of conditionally deleterious mutations [49], i.e. mutations that are neutral in the local environment and deleterious in an alternative environment.…”

Section: Discussionmentioning

confidence: 99%

Adaptation and competition in deteriorating environments

Limberger

Fussmann

2019

Preprint

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16Evolution might mitigate negative effects of environmental change on diversity by rescuing 17 populations from extinction. However, biotic interactions could affect adaptation to abiotic 18 change, and conversely, adaptation to an abiotic stressor could influence biotic interactions. 19We used experimental evolution of microalgae to investigate reciprocal effects of competition 20 and adaptation to salt stress. We found that evolutionary history influenced competitive 21 interactions and community properties. In high-salt environments, communities assembled 22 from lines with a history of salt stress declined more slowly in diversity than communities 23 assembled from lines without prior exposure to salt. We also found that a history of salt stress 24 can lead to reduced competitive ability in the ancestral environment. While competition had 25 no effect on adaptation to salt, we found that competition can hinder evolutionary rescue by 26 preventing that adaptation translates into population persistence. Collectively, our results 27 highlight the importance of considering evolutionary rescue in a community context. 28

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Global adaptation complicates the interpretation of genome scans for local adaptation

2021

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Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species-wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome-wide distribution of FST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward-in-time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate FST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to FST. However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of FST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.

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Unpacking Conditional Neutrality: Genomic Signatures of Selection on Conditionally Beneficial and Conditionally Deleterious Mutations

Cited by 34 publications

References 34 publications

Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

Linking genomic signatures of selection to expression variation and direct evidence of local adaptation

Adaptation and competition in deteriorating environments

Global adaptation complicates the interpretation of genome scans for local adaptation

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