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

Abstract

Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

“…While sea cucumbers are not presently farmed in Canada, there is an interest in the development of aquaculture programmes for P. californicus in British Columbia (DFO, ). Improved knowledge about local adaptation has important implications for effectively managing breeding programmes and informing the foundation of aquaculture broodstock (Do Prado et al, ). Further insight into the extent to which populations are locally adapted to environmental conditions will be important for ensuring that potentially maladapted genotypes are not introduced into wild populations (Conover, ).…”

Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

“…The populations module was finally used to obtain the initial SNP dataset, which included only loci with a minimum depth of 10 reads (-m 10), genotyped in at least 70% of total individuals and genotyped in no less than 60% of the individuals in at least seven populations (-r 0.60, -p 7). Finally, SNPs were filtered by MAF (Minimum Allele Frequency of the less frequent allele, > 0.05) and by intrapopulation fixation index F IS [52] (loci with F IS ≥ 0.50 and ≤ −0.50 were discarded to minimize the presence of null alleles in the former and of paralog sequences in the latter [23]). Additionally, RAD-tags with more than three SNPs were removed.…”

“…Genome-wide SNP population screening allows assessing genetic diversity, demographic and population structure, adaptive variation and the genetic architecture associated with traits of interest [21]. Neutral and adaptive genetic variation accounts for the demographic history and adaptive evolution of populations [22,23]. Adaptive genetic markers allow to identification of populations that experience different environmental conditions, such as temperature or salinity [24].…”

“…The use of both types of markers may improve conservation and management strategies for species [25,26]. Moreover, wild populations adapted to different environmental conditions could be useful as founders for aquaculture broodstock [23]. Adaptive genes under divergent selection display higher differentiation than the neutral background of genomes [25].…”

Water quality and nitrogen budget in turbot Scophthalmus maximus culture system supplemented with lactic acid bacteria

“…Turbot, Scophthalmus maximus , naturally distributed along the east coast of Atlantic, is treated as a high‐valued flatfish and widely cultured around the world (Nielsen, Nielsen, Meldrup, & Hansen, ; Prado et al, ). Scophthalmus maximus has become one of the dominant mariculture species in industrial fish farming in north China since it was introduced in 1992 (Lei, ), reached an annual production of 42,000 tons in 2016 (Wang, ).…”