Genetic population structure in Greenland halibut (Reinhardtius hippoglossoides) and its relevance to fishery management

Abstract

Exploited marine resources can be managed more effectively when accurate information on geographic population structure is available. Genetic markers offer a powerful tool for fisheries management, because they reveal biologically sound management units. Single nucleotide polymorphisms (SNPs) markers derived from restriction-site associated DNA sequencing (RAD-seq) were developed and used to investigate the stock structure of Greenland halibut (Reinhardtius hippoglossoides). A total of 96 SNPs were analyzed from 384 individuals and eight locations across the Atlantic. Our results suggest a subdivision of Greenland halibut into two populations, an eastern Atlantic population and a western Atlantic population, with a proposed border across the Denmark Strait. In general, Greenland halibut display weak but significant population structure (overall F ST = 0.003; p < 0.001), which can be explained by connectivity among populations owing to the migratory behavior or egg and larval drift. Résumé :Les ressources marines exploitées peuvent être gérées plus efficacement quand de l'information exacte sur la structure géographique de leurs populations est disponible. Les marqueurs génétiques constituent un puissant outil pour la gestion des pêches parce qu'ils font ressortir des unités de gestion cohérentes sur le plan biologique. Des marqueurs de polymorphismes mononucléo-tidiques (SNPs) dérivés du séquençage d'ADN associé à un site de restriction (RAD-seq) ont été développés et utilisés pour étudier la structure des stocks de flétan noir (Reinhardtius hippoglossoides). Un total de 96 SNP ont été analysés de 384 individus et huit emplacements dans l'Atlantique. Nos résultats semblent indiquer le regroupement des flétans noirs en deux populations, une de l'est de l'Atlantique et l'autre de l'ouest de l'Atlantique, la frontière proposée entre les deux traversant le détroit du Danemark. En général, les flétans noirs présentent une structure de populations faible mais significative (F ST global = 0,003; p < 0,001) qui peut s'expliquer par la connectivité des populations découlant du comportement migratoire ou de la dérive des oeufs et des larves. [Traduit par la Rédaction]

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

“…The advent of high-throughput sequencing methods has significantly increased the amount of data and the resolution of genetic insight for fisheries management in other species (Hauser & Carvalho, 2008;Kumar & Kocour, 2017;Riginos, Crandall, Liggins, Bongaerts, & Treml, 2016;Valenzuela-Quiñonez, 2016). Many studies have attempted to identify neutral and adaptive genetic variation (e.g., Gagnaire et al, 2015;Nielsen, Hemmer-Hansen, Foged Larsen, & Bekkevold, 2009;Ovenden et al, 2015;Valenzuela-Quiñonez, 2016), which has improved the delineation of populations and fish stocks in both migratory species such as Greenland halibut Reinhardtius hippoglossoides (Walbaum, 1792) (Westgaard et al, 2017) and European hake Merluccius merluccius (Linnaeus, 1758) (Milano et al, 2014), and sedentary species such as bluespotted Cornetfish Fistularia commersonii Rüppell, 1838 (Bernardi, Azzurro, Golani, & Miller, 2016). Typically, neutral genetic variation reflects stochastic genetic drift and the degree of gene flow among populations, whereas adaptive variation suggests selective differences among populations (Funk, McKay, Hohenlohe, & Allendorf, 2012).…”

A cost‐and‐time effective procedure to develop SNP markers for multiple species: A support for community genetics

“…Westgaard et al. () used RAD‐Seq on DNA pools and Stacks software to isolate 200 SNP markers, but did not run further in silico filtering. Ninety‐six SNPs were actually polymorphic and at HWE after MassARRAY genotyping, corresponding to a 50% genotyping success.…”

“…Whether developed from HTS to build high-density arrays (e.g., -Rampant et al, 2016), or for more classical amplificationbased genotyping (e.g., Westgaard et al, 2017), potential SNP markers are first detected from the assembly of sequencing reads, which is performed by means of increasingly argued and documented decision steps (Mastretta-Yanes et al, 2015;Shafer et al, 2017). However, to date, precise strategies that favour the successful amplification by PCR are case-dependent and without an existing, standardized framework.…”

“…Thrasher, Butcher, Campagna, Webster, and Lovette () used ddRAD to perform relatedness analyses based on 150–600 optimized SNP markers. Other authors characterized small sets of SNP markers to be genotyped through a classical, affordable technology compared to GBS for large numbers of samples (e.g., Ackerman & Campbell, ; Westgaard et al., ). Mixing and sequencing DNA of individuals from a SNP discovery set is technically close to Pool‐Seq, and represents a valuable way to access molecular resources.…”

“…Thrasher, Butcher, Campagna, Webster, and Lovette (2018) used ddRAD to perform relatedness analyses based on 150-600 optimized SNP markers. Other authors characterized small sets of SNP markers to be genotyped through a classical, affordable technology compared to GBS for large numbers of samples (e.g., Ackerman & Campbell, 2012;Westgaard et al, 2017).…”