Population genomics of marine fishes: identifying adaptive variation in space and time

Abstract

Studies of adaptive evolution have experienced a recent revival in population genetics of natural populations and there is currently much focus on identifying genomic signatures of selection in space and time. Insights into local adaptation, adaptive response to global change and evolutionary consequences of selective harvesting can be generated through population genomics studies, allowing the separation of the effects invoked by neutral processes (drift-migration) from those due to selection. Such knowledge is important not only for improving our basic understanding of natural as well as human-induced evolutionary processes, but also for predicting future trajectories of biodiversity and for setting conservation priorities. Marine fishes possess a number of features rendering them well suited for providing general insights into adaptive genomic evolution in natural populations. These include well-described population structures, substantial and rapidly developing genomic resources and abundant archived samples enabling temporal studies. Furthermore, superior possibilities for conducting large-scale experiments under controlled conditions, due to the economic resources provided by the large and growing aquaculture industry, hold great promise for utilizing recent technological developments. Here, we review achievements in marine fish genomics to date and highlight potential avenues for future research, which will provide both general insights into evolution in high gene flow species, as well as specific knowledge which can lead to improved management of marine organisms.

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

“…However, various factors can bring about genetic differentiation, such as habitat shifts (ecotones) and oceanic currents (Blanco‐Gonzalez, Knutsen, & Jorde, 2016; Galarza et al., 2009; Nielsen, Nielsen, Meldrup, & Hansen, 2004; Vera et al., 2016a), and natural selection in response to environmental variation (Milano et al., 2014; Vandamme et al., 2014; Vilas, Bouza, Vera, Millán, & Martínez, 2010; Vilas et al., 2015). Distinguishing between neutral and adaptive genetic variation has become a central issue in evolutionary biology, allowing for understanding of population structure in both historical/demographic and adaptive terms (Bernatchez, 2016; Nielsen, Hemmer‐Hansen, Larsen, & Bekkevold, 2009), thereby providing essential information for the conservation and management of wild populations. Genetic diversity in the wild represents, in turn, the raw material for the foundation of aquaculture broodstock and consequently, a reference to identify selection signatures for targeted traits in farmed populations through genome scanning (Liu et al., 2017).…”

Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic

“…Recent advances in the field of population genetics and genomics have made it possible to avail of methodologies designed to investigate both neutral and adaptive variation in a common framework (Bonin et al, 2006;Bouck and Vision, 2007;Nielsen et al, 2009b;Seeb et al, 2011) allowing a more thorough understanding of the mechanisms driving demographic and ecological divergence. Fish, in particular, are having a crucial role in advancing the field of marine population genomics (Nielsen et al, 2009a); this is largely due to their diversity, their ecological and life-history variation, and the considerable economic importance of many wide-ranging species, which provide countless opportunities for the assessment of demographic and adaptive responses to environmental changes over large scales. In fact, several recent studies of marine fish populations have provided indication of adaptive genetic divergence (Hemmer-Hansen et al, 2007;Larmuseau et al, 2009), often coupled with low or absent divergence at neutral markers (Gaggiotti et al, 2009;Nielsen et al, 2009b).…”

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

“…Population structure is typically assessed by estimating divergence in the allele frequencies at neutral marker loci, whereas coding gene regions are usually not used for testing demographic independence or for estimating migration rates because selection biases parameter estimation (for example, Whitlock and McCauley, 1999). However, in some cases, such as mixed stock analysis in harvested species, gene loci influenced by selection can be valuable as population markers on ecological time scales where isolated populations have not yet diverged at neutral loci (O'Malley et al, 2007;Westgaard and Fevolden, 2007;Hauser and Carvalho, 2008;Nielsen et al, 2007Nielsen et al, , 2009a. Moreover, coding loci will help in identifying locally adapted populations (Hemmer-Hansen et al, 2007;Andersen et al, 2009;Gebremedhin et al, 2009;Nielsen et al, 2009a;Á rnason et al, 2009).…”