Abstract
Challenging long‐held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north‐east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.
Highlights
In marine fisheries, stocks or management units are often defined by national borders or economic zones that do not always reflect the true biological or genetic units (Kerr et al, 2016; Reiss, Hoarau, Dickey-Collas, & Wolff, 2009; Saha et al, 2015)
The initial scan for outlier detection performed across all of the 23 linkage groups (LGs) in all of the samples (8,174 SNPs) revealed that LG1, LG2, LG7 and LG12 contained relatively large genomic regions deviating from neutrality, as indicated by a large number of SNPs scoring a high probability for being under positive selection (Figure 2 and Figures S1a,b and S2)
The discriminant analysis of principal components (DAPC) outcome for the sets A and B of neutral markers (Figure 4a-b: including the White Sea; Figure S5a,b) agreed with STRUCTURE, with samples from different countries clustering separately while a gradient of genetic similarity was revealed from north to south in Norwegian coastal cod
Summary
Stocks or management units are often defined by national borders or economic zones that do not always reflect the true biological or genetic units (Kerr et al, 2016; Reiss, Hoarau, Dickey-Collas, & Wolff, 2009; Saha et al, 2015). The genomic resources available for Atlantic cod have rapidly expanded in recent years, for example, by the development of genome assemblies (Star et al, 2011; Tørresen et al, 2017) and a SNP array (Berg et al, 2016) These tools have permitted, for example, distinguishing between migratory and nonmigratory ecotypes throughout the species range (Barney, Munkholm, Walt, & Palumbi, 2017; Berg et al, 2017; Berg et al, 2016; Bradbury et al, 2013; Kirubakaran et al, 2016). Individuals displaying a call rate below 0.9 were excluded from analyses as were nonpolymorphic SNPs or SNP with a call rate
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