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

Abstract

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.

Investigating Genetic Diversity and Genomic Signatures of Hatchery-Induced Evolution in Gilthead Seabream (Sparus aurata) Populations

“…Nevertheless, given the polygenic nature of most traits, the typical small effective population size of cultured populations, and the early stage of domestication for aquaculture species, the identification of single loci with large effects is most often observed [19,20]. Growing attention is thus being paid to methods of detecting polygenic selection and of identifying intermediate and smaller effect variants or rare alleles in order to prioritize genomic regions for the next phase of breeding programs and to identify the genetic architecture that shapes the desired phenotypes in important aquaculture species [21][22][23][24][25].…”

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

“…Compared with our database, finding out growth-related functional annotation and molecular mechanisms are both shared in the GH/IGF axis and its downstream signaling pathways. However, these studies have focused on gene function and its integrated signal pathways; by contrast, transcripts identified using a transcriptome profile may influence target traits through various genes [ 84 , 85 , 86 ].…”

Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation

“…Additionally, stochastic neutral processes might change the genomic background of selection, which would be particularly problematic for polygenic adaptation. In polygenic traits, the effect size of individual loci is small, such that the genetic architecture of adaptation becomes less stable in the presence of high gene flow and drift (Babin et al, 2017; Bernatchez, 2016; Rey et al, 2020; Yeaman, 2015; Yeaman & Otto, 2011; Yeaman & Whitlock, 2011). Small effect loci and unstable genetic architectures are therefore less likely to yield replicable results in outlier locus analyses.…”

“…Rey et al (2020) showed that body shape, growth, and condition factor exhibit habitat divergence in juvenile sea bream despite panmixia in the larval pool. In both Moody et al (2015) and Rey et al (2020), the phenotypes considered appeared to have a (partial) heritable genetic basis, but are likely to have appreciable environmental components as well.…”

“…Our study was not equipped to directly address the role of genetic carry‐over effect across ontogeny in B. cocosensis because the year‐round recruitment in this species makes it challenging to track discrete cohorts through time. However, extending such considerations to genetic variation might provide novel insights into ontogenetic shifts in selection and constraints to adaptation in marine environments (Marshall & Morgan, 2011; Rey et al, 2020). Certainly, sampling multiple ecological dimensions provides greater resolution on when and where selective processes operate, and hence their relevant scale, in marine metapopulations.…”