Genome-wide SNP based population structure in European hake reveals the need for harmonizing biological and management units

Abstract

Despite its economic importance, the population structure of the European hake, Merluccius merluccius, is unresolved, and the species is assessed based on two stocks (northern and southern) separated by the Capbreton Canyon. In order to shed light into the European hake population structure, we used Restriction-site-Associated DNA sequencing (RAD-seq) to discover and genotype thousands of genome-wide single nucleotide polymorphisms in more than a hundred samples. Our population genetic inferences confirm differentiation of Mediterranean and northeast Atlantic locations and reveal management relevant information within the latter. First, hake in the Norwegian Sea is genetically different from that of the rest of the locations under study and, second, samples from the eastern Bay of Biscay and the northwestern Iberian Peninsula are not genetically different. These results imply that samples from the northern stock belong to different genetic populations, and that samples belonging to locations included in the northern and southern stocks are part of a single genetically homogeneous population. Although the definition of the boundary between the northern and southern stocks and the potential need for additional stocks still requires further analyses, the mismatch between biological and management units should already be considered in further assessments of European hake.

EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries

“…Such fine-scale Atlantic ultrastructures are at odds with the third view of a quasi-panmictic scenario in the whole Atlantic metapopulation. This latter is supported by the higher divergence of samples from the range edges (the North Sea and the Canary Islands) upon a latitudinal IBD model, as depicted with random microsatellites [ 22 , 57 ], with a wide genomic SNPs coverage using RADseq [ 23 ] and with EST-microsatellites (this study). A similar conflicting scenario exists for the Mediterranean hake.…”

“…The European hake Merluccius merluccius is a paradigmatic demersal fish from the NE Atlantic on which large discrepancy has been reported regarding the microstructure depicted with SNPs from ESTs (e.g., k = 4 gene pools, [ 21 ]) and the highly connective unstructured Atlantic metapopulation (except the restricted gene flow with the North Sea) as depicted with both microsatellites [ 22 ] and SNPs [ 23 ]. A similar divergent insight can be found on the Mediterranean hake, where a multi-stock scenario ( k = 3) was proposed on a few outlier SNPs [ 24 ] as opposed to the single Mediterranean metapopulation suggested in previous studies with several marker types [ 22 , 25 ].…”

Evidence of stock connectivity, hybridization and misidentification in white anglerfish support the need of a genetics-informed fisheries management framework

“…Within the Northeast Atlantic, the white anglerfish is managed as three stocks: the Northern Shelf stock (Skagerrak, Kattegat, North Sea, West of Scotland and Rockall), the Northern stock (Celtic Seas and Northern Bay of Biscay) and the Southern Stock (Atlantic and Iberian waters) (ICES, 2019a; ICES, 2019b); yet, the few studies assessing the population structure, based on otolith shape analysis (Cañás et al, 2012), tagging surveys (Laurenson et al, 2005; Landa et al, 2008) and molecular markers, including allozymes (Crozier, 1987), mitochondrial DNA (Charrier et al, 2006) and microsatellites (Blanco et al, 2008), did not find differences between stocks. However, this needs to be confirmed with the analysis of a large number of genomic markers, which has been effective in resolving the population structure of marine fish when other markers failed (Rodríguez-Ezpeleta et al, 2016; Leone et al, 2019; Rodríguez-Ezpeleta et al, 2019). The white anglerfish coexists with its sympatric sister species, the black bellied anglerfish ( Lophius budegassa ), which has a more southern distribution (Relini, 1999; Ungaro et al, 2002).…”

“…Landa, Quincoces, Duarte, Fariña, & Dupouy, 2008;Laurenson, Johnson, & Priede, 2005) and molecular markers, including allozymes (Crozier, 1987), mitochondrial DNA (Charrier et al, 2006) and microsatellites (Blanco, Borrell, Cagigas, Vázquez, & Prado, 2008), did not find differences between stocks. However, this needs to be confirmed with the analysis of a large number of genomic markers, which has been effective in resolving the population structure of marine fish when other markers failed (Leone, Álvarez, García, Saborido-Rey, & Rodriguez-Ezpeleta, 2019;Rodríguez-Ezpeleta et al, 2016;Rodríguez-Ezpeleta et al, 2019). The white anglerfish coexists with its sympatric sister species, the black bellied anglerfish (Lophius budegassa), which has a more southern distribution (Relini, 1999;Ungaro et al, 2002).…”

Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol

“…Development of high-throughput sequencing and reduced representation approaches, such as restriction-site–associated DNA sequencing (RAD-seq), have dramatically reduced the cost of generating vast amounts of sequencing data. RAD-seq (Baird et al ., 2008) and its many variants, including but not limited to: ddRADseq (Peterson et al ., 2012), quaddRAD-seq (Franchini et al ., 2017) and adapterama (Glenn et al ., 2019; Bayona-Vásquez et al ., 2019) have been used in studies of phylogenetics (Massatti et al ., 2016; Lecaudey et al ., 2018; Near et al ., 2018), phylogeography (Jeffries et al ., 2016), association mapping (Nadeau et al ., 2014), introgression (Hohenlohe et al ., 2013), population structure and genetic diversity (Rodríguez-Ezpeleta et al ., 2016; Leone et al ., 2019; Gao et al ., 2017; Martin Cerezo et al ., 2020).…”