Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Abstract

Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish

“…The strong signal of population structure is surprising given the early life history of cunner, but the findings closely resemble those obtained with other labrids. Geographically and genetically distinct populations have previously been identified in Goldsinny wrasse ( Ctenolabrus rupestris ), a closely related species found along the Atlantic coastlines of Europe and North Africa, as well as the Sea of Marmara, the Black Sea and parts of the Mediterranean Sea (Jansson et al, 2020). Furthermore, work on corkwing wrasse ( Symphodus melops ) has identified a major genetic break between Scandinavia and more southern populations (Knutsen et al, 2013) despite a seemingly continuous marine environment.…”

Whole genome sequencing reveals fine-scale climate associated adaptive divergence near the range limits of a temperate reef fish

“…The strong signal of population structure is surprising given the early life history of cunner, but the findings closely resemble those of other Labridae. Geographically and genetically distinct populations have previously been identified in Goldsinny wrasse (Ctenolabrus rupestris), a closely related Labridae species found along the Atlantic coastlines of Europe and North Africa, as well as the Sea of Marmarra, the Black Sea and parts of the Mediterranean Sea (Jansson et al 2020). Furthermore, work on corkwing wrasse (Symphodus melops) has identified a major genetic break between Scandinavia and more southern populations (Knutsen et al 2013) despite a seemingly continuous marine environment.…”

Geographic variation in gene flow from a genetically distinct migratory ecotype drives population genetic structure of coastal Atlantic cod (Gadus morhua L.)

“…Consequently, genetic methods involving a handful of random and typically selectively neutral genetic markers, such as microsatellites, often struggle to resolve population structure (Jorde, Synnes, et al, 2018 ; Ryman et al, 2006 ). However, the proliferation of genomic methods and their application is now revealing previously hidden levels of genetic and genomic diversity among marine fish populations, including examples as diverse as Ballan wrasse ( Labrus bergylta ) (Jansson et al, 2020 ), Atlantic cod ( Gadus morhua ) (Kirubakaran et al, 2016 ; Sodeland et al, 2016 ), European sprat ( Sprattus sprattus ) (Quintela et al, 2020 ), and Atlantic herring ( Clupea harengus ) (Han et al, 2020 ; Martinez Barrio et al, 2016 ). Therefore, genomics, or the application of carefully selected panels of informative markers that have been mined from the genome, now provide unprecedented opportunities to study the evolutionary relationships among marine fish populations, and unravel their underlying causative mechanisms.…”