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Abstract: A large majority of Atlantic cod (Gadus morhua) found all year round in outer parts of fjords and along outer coastal areas in general in northern Norway have a genetic signature at the pantophysin (Pan I) locus that distinguish them from Norwegian coastal cod (NCC) found further inside fjords in the same areas. The identity of these fish has been controversial and to examine if they represent a distinct coastal cod group, or are identical to the migratory North East Arctic cod (NEAC) of the Barents Sea, a comparison was conducted at 10 microsatellite loci for 15 samples comprising each of the three groups inner coastal NCC, outer coastal cod and NEAC. Spatial analysis of molecular variance revealed that the outer coastal samples cannot be discriminated from NEAC by means of microsatellite markers, supporting the similarity of the two groups at the Pan I locus. This implies that a portion of the otherwise migratory NEAC, at least in its premature stage, remains in coastal areas in close contact with the genetically quite distinct NCC group. Both the coalescent-based simulation approach and the lnRH test for selective sweeps proved two of the microsatellite loci, GMO 34 and GMO 132 to be non-neutral. Notwithstanding, these two loci, together with the acknowledged non-neutral Pan I locus, which displayed profound linkage disequilibrium to GMO 34 within NEAC, are as yet the only nuclear markers which unambiguously discriminate between NEAC and NCC. Although the relative contribution of restricted gene flow versus selection as a causative agent for the divergence between NEAC and NCC has not been assessed, we believe the magnitude of differentiation at the three loci provides rational for maintaining NEAC and NCC as separate management units. [Copyright &y& Elsevier]

Five Atlantic cod ( Gadus morhua L.) microsatellites ( Gmo8, Gmo19, Gmo35, Gmo37 and Tch11) were selected for parentage assignment. All markers were co-amplified using dye-labelled primers and sized by automated sample processing in a 3130 xl Genetic Analyser. The genotyping of samples was reproducible and alleles from all loci could be genotyped confidently (precision and accuracy above 99.7 and 99.1% respectively). The number of alleles, observed allelic and genotypic frequencies were calculated. A population database was established for fish originating from randomly selected wild-caught Norwegian coastal- and North-East Arctic cod. Combined paternity exclusion and the probability of match were 99.97 and 1.5 × 10−9 respectively. The multiplex assay system was used successfully for parental assignment of 2336 juveniles from different mass spawning breeding tanks. Of all offspring, 91.2% were assigned to a single parental pair. In total, 523 different matings were recorded, and 69 of 70 dams and all of the 30 sires contributed to the offspring. [ABSTRACT FROM AUTHOR]

To obtain knowledge of feeding habits and prey consumption of grey seals, data were sampled in selected areas along the Norwegian coast. Prey were recovered from 182 grey seal gastrointestinal tracts and 199 faecal samples, collected during1999–2010 in Finnmark, Nordland and Rogaland counties. The most important prey were saithe Pollachius virens, cod Gadus morhua and wolffish Anarchichus spp. Wolffish was mainly eaten by seals ≥ five years old. Otherwise, the data did not suggest important temporal or spatial variations between the main prey items in the grey seal diet. However, capelin Mallotus villosus was eaten during spring in Finnmark suggesting that seasonally abundant pelagic fish species could be regionally important. Total annual grey seal consumption of various species was estimated using bio-energetic modelling. The input variables were seal numbers, energy demands, diet composition in terms of biomass and energy densities of prey species. Assuming the observed grey seals diet composition in the sampling areas were representative for the diet along the Norwegian coast, the mean total annual consumption by 3850 grey seals was estimated to be 8084 tons in Norwegian waters; saithe (3059 tons), cod (2598 tons) and wolffish (1364 tons) were consumed in highest quantities. [ABSTRACT FROM AUTHOR]

Identifying how physical and biotic factors shape genetic connectivity among populations in time and space is essential to our understanding of the evolutionary trajectory as well as the management of marine species. Atlantic cod is a widespread and commercially important marine species displaying several ecotypes with different life history strategies. Using three sets of SNPs: neutral, informative, and genome‐inversion linked, we studied population genetic structure of ~2500 coastal Atlantic cod (CC) from 40 locations along Norway's 2500 km coastline, including nine fjords. We observed: (1) a genetic cline, suggesting a mechanism of isolation by distance, characterized by a declining FST between CC and North East Arctic Cod (NEAC—genetically distinct migratory ecotype) with increasing latitude, (2) that in the north, samples of CC from outer‐fjord areas were genetically more similar to NEAC than were samples of CC from their corresponding inner‐fjord areas, (3) greater population genetic differentiation among CC sampled from outer‐fjord areas along the coast, than among CC sampled from their corresponding inner‐fjord areas, (4) genetic differentiation among samples of CC from both within and among fjords. Collectively, these results permit us to draw two main conclusions. First, that differences in the relative presence of the genetically highly distinct, migratory ecotype NEAC, declining from north to south and from outer to inner fjord, plays the major role in driving population genetic structure of the Norwegian CC. Second, that there is limited connectivity between CC from different fjords. These results suggest that the current management units implemented for this species in Norway should be divided into smaller entities. Furthermore, the situation where introgression from one ecotype drives population genetic structure of another, as is the case here, may exist in other species and geographical regions, thus creating additional challenges for sustainable fisheries management. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate. Results: We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P < 0.0001. Dataset 2: global FST = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north. Conclusion: We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision. [ABSTRACT FROM AUTHOR]