Environmental selection on transcriptome‐derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

Abstract

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5-12 °C) and two salinity clines (5-35‰). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic-North Sea transition area, North Sea/British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea/North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

Signatures of selection in mammalian clock genes with coding trinucleotide repeats: Implications for studying the genomics of high‐pace adaptation

“…The candidate gene approach has been used empirically to identify patterns of adaptive genetic variation and disentangle such patterns from neutral genetic population structure (DeFaveri, Jonsson, & Merilä, 2013; Hemmer‐Hansen, Nielsen, Frydenberg, & Loeschke, 2007; Limborg et al., 2012; O'Malley et al., 2010). Candidate genes are selected based on known physiological functions perceived to be of relevance to the study species.…”

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

“…In fact, genetic diversity estimated using the fraction of loci at P 95 almost doubled (H E : 0.184) approaching to previous results (Vilas et al., 2015). Anyway, our data suggest that genetic diversity of turbot features in the lower range of values reported for other marine fish studied with SNP panels, such as European sea bass Dicentrarchus labrax (from 0.233 in the Atlantic Ocean to 0.290 in the West Mediterranean Sea; Souche et al., 2015), Atlantic herring ( Clupea harengus ; 0.270–0.310 along the Atlantic Ocean and the Baltic Sea; Limborg et al., 2012), and Asian sea bass ( Lates calcarifer ; 0.292–0.411; Wang, Wan, Lim, & Yue, 2015). …”

Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments

“…2010), but recent studies have demonstrated the importance of studying genomewide variation for improving estimates of fine‐scale population structure (Sanford and Kelly 2011; Limborg et al. 2012; Milano et al. 2014).…”