Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses

Hughes, Kimberly A.; Leips, Jeff

doi:10.1111/nyas.13256

Cited by 49 publications

(51 citation statements)

References 215 publications

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“…show signatures of balancing selection (Turelli & Barton, ). While abundant trade‐off has been identified in yeast GEI studies, only a few loci have a large effect with characteristics of antagonistic pleiotropy (Hughes & Leips, ; Qian, Ma, Xiao, Wang, & Zhang, ; Smith & Kruglyak, ; Yadav et al, ). We would like to state that these are deductions since it is not possible to accurately estimate the evolutionary importance of effect size of an allele based on phenotypic measurements in a laboratory condition.…”

Section: Gene–environment Interactionsmentioning

confidence: 99%

Gene–gene and gene–environment interactions in complex traits in yeast

Yadav

Sinha

2018

Yeast

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One of the fundamental questions in biology is how the genotype regulates the phenotype. An increasing number of studies indicate that, in most cases, the effect of a genetic locus on the phenotype is context-dependent, i.e. it is influenced by the genetic background and the environment in which the phenotype is measured. Still, the majority of the studies, in both model organisms and humans, that map the genetic regulation of phenotypic variation in complex traits primarily identify additive loci with independent effects. This does not reflect an absence of the contribution of genetic interactions to phenotypic variation, but instead is a consequence of the technical limitations in mapping gene-gene interactions (GGI) and gene-environment interactions (GEI). Yeast, with its detailed molecular understanding, diverse population genomics and ease of genetic manipulation, is a unique and powerful resource to study the contributions of GGI and GEI in the regulation of phenotypic variation. Here we review studies in yeast that have identified GGI and GEI that regulate phenotypic variation, and discuss the contribution of these findings in explaining missing heritability of complex traits, and how observations from these GGI and GEI studies enhance our understanding of the mechanisms underlying genetic robustness and adaptability that shape the architecture of the genotype-phenotype map.

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Section: Gene–environment Interactionsmentioning

confidence: 99%

Gene–gene and gene–environment interactions in complex traits in yeast

Yadav

Sinha

2018

Yeast

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“…Antagonistic pleiotropy between environments likely involves complex allocation trade-offs that emerge due to compromises between growth and stress regulation [57,58]. Juvenile sea bream are subject to different sources of stress, ranging from highly unstable conditions in brackish lagoons to frequent starvation in the marine environment [26].…”

Section: Discussionmentioning

confidence: 99%

Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream

Rey

Darnaude

Ferraton

et al. 2020

Genes

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Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition; these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.

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“…Although genomic approaches have been less successful at determining the specific genes affecting highly polygenic traits, these methods still can elucidate trait genetic architecture, such as the number of quantitative-trait loci (QTL) or causal variants, trait heritabilities, and genetic covariances among traits [11][12][13]. Summaries of trait genetic architecture can help explain patterns and dynamics of evolutionary change (e.g., [12,14,15]). Nonetheless, most empirical work on the genetics of adaptation comes from a modest number of model systems, and even in these systems the genetic basis of the full suite of traits selected during a bout of adaptation is rarely analyzed.…”

Section: Introductionmentioning

confidence: 99%

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

Rêgo

Chaturvedi

Springer

et al. 2020

Genes

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Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for two host-specific performance traits (weight and development time), which had low to modest heritabilities. We found less evidence of parallelism in genotype-phenotype associations across these lines than in allele frequency changes during the experiments. Differential gene expression caused by differences in recent evolutionary history exceeded that caused by immediate rearing host. Together, the three genomic datasets suggest that genes affecting traits other than weight and development time are likely to be the main causes of parallel evolution and that detoxification genes (especially cytochrome P450s and beta-glucosidase) could be especially important for colonization of lentil by C. maculatus.

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Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses

Cited by 49 publications

References 215 publications

Gene–gene and gene–environment interactions in complex traits in yeast

Gene–gene and gene–environment interactions in complex traits in yeast

Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant

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