Farming of Atlantic cod Gadus morhua in the vicinity of major spawning sites for Norwegian coastal cod populations - is it hazardous?

Waters along and adjacent to the coast of northern Norway are unique in housing two major populations of Atlantic cod with very di erent life histories. The Northeast Arctic cod (NEAC) has its nursery and feeding grounds in the Barents Sea but migrates to the coast of northern Norway to spawn. Norwegian coastal cod (NCC) is more stationary, spawns mainly at local sites in individual ords but to some degree also overlap with the spawning sites of NEAC (Fig.1). These distinctive patterns in life history are re ected in a clear-cut genetic divergence between the two populations. Various molecular genetic markers (scnDNA, microsatellites and SNPs) have displayed genetic di erences between NEAC and NCC which are remarkable for marine sh with a comparable gene ow potential (cf. Sarvas and Fevolden 2005, Wennevik et al. 2008, and Westgaard and Fevolden 2008 for recent updates)

A mitogenomic approach to the taxonomy of pollocks: Theragra chalcogramma and T. finnmarchica represent one single species

<p>Abstract</p> <p>Background</p> <p>The walleye pollock (<it>Theragra chalcogramma</it>) and Norwegian pollock (<it>T. finnmarchica</it>) are confined to the North Pacific and North Atlantic Oceans, respectively, and considered as distinct species within the family Gadidae. We have determined the complete mtDNA nucleotide sequence of two specimens of Norwegian pollock and compared the sequences to that of 10 specimens of walleye pollock representing stocks from the Sea of Japan and the Bering Sea, 2 specimens of Atlantic cod (<it>Gadus morhua</it>), and 2 specimens of haddock (<it>Melanogrammus aeglefinus</it>).</p> <p>Results</p> <p>A total number of 204 variable positions were identified among the 12 pollock specimens, but no specific substitution pattern could be identified between the walleye and Norwegian pollocks. Phylogenetic analysis using 16.500 homologous mtDNA nucleotide positions clearly identify the Norwegian pollock within the walleye pollock species cluster. Furthermore, the Norwegian pollock sequences were most similar to mitochondrial genotypes present in walleye pollock specimens from the Sea of Japan, an observation supported both by neighbor-joining, maximum parsimony, and maximum likelihood analyses.</p> <p>Conclusion</p> <p>We infer that walleye pollock and Norwegian pollock represent one single species and that Norwegian pollock has been recently introduced from the Pacific to the Atlantic Oceans.</p

Speciation reversal in European whitefish (Coregonus lavaretus (L.)) caused by competitor invasion

Invasion of exotic species has caused the loss of biodiversity and imparts evolutionary and ecological changes in the introduced systems. In northern Fennoscandia, European whitefish (Coregonus lavaretus (L.)) is a highly polymorphic species displaying adaptive radiations into partially reproductively isolated and thus genetically differentiated sympatric morphs utilizing the planktivorous and benthivorous food niche in many lakes. In 1993, Lake Skrukkebukta was invaded by vendace (Coregonus albula (L.)) which is a zooplanktivorous specialist. The vendace displaced the densely rakered whitefish from its preferred pelagic niche to the benthic habitat harbouring the large sparsely rakered whitefish. In this study, we investigate the potential influence of the vendace invasion on the breakdown of reproductive isolation between the two whitefish morphs. We inferred the genotypic and phenotypic differentiation between the two morphs collected at the arrival (1993) and 15 years after (2008) the vendace invasion using 16 microsatellite loci and gill raker numbers, the most distinctive adaptive phenotypic trait between them. The comparison of gill raker number distributions revealed two modes growing closer over 15 years following the invasion. Bayesian analyses of genotypes revealed that the two genetically distinct whitefish morphs that existed in 1993 had collapsed into a single population in 2008. The decline in association between the gill raker numbers and admixture values over 15 years corroborates the findings from the Bayesian analysis. Our study thus suggests an apparent decrease of reproductive isolation in a morph-pair of European whitefish within 15 years (. 3 generations) following the invasion of a superior trophic competitor (vendace) in a subarctic lake, reflecting a situation of ‘‘speciation in reverse’’

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

<p>Abstract</p> <p>Background</p> <p>The Atlantic cod (<it>Gadus morhua</it>) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection.</p> <p>Results</p> <p>A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. <it>F</it>_{<it>ST </it>}values were highly variable, with the majority of SNPs displaying very little differentiation while others had <it>F</it>_{<it>ST </it>}values as high as 0.83. The <it>F</it>_{<it>ST </it>}values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus.</p> <p>Conclusion</p> <p>The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.</p

Extreme male-skewed sex ratios on spaning grounds for Atlantic cod Gadus morhua with typical coastal cod signatures of the Pan I (pantophysin) locus

Large offshore and small inshore populations of Atlantic cod Gadus morhua L. display differences in migratory patterns and settling regimes, but little is known about possible differences in spawning behaviour. Cod presumably of the Norwegian coastal cod type were therefore sampled during 7 spawning seasons (2002-2013) in Malangen, northern Norway. A spawning site in neighbouring Balsfjord was sampled during 5 consecutive spawning seasons (2002-2006). Length, weight, sex and maturity stage were recorded for each individual fish (n = 995). To verify their population assignment, frequencies of the 2 different Pan I (pantophysin) alleles were measured in 6 sampling years in Malangen and 3 in Balsfjord (n = 728). During all survey years there was an extreme skewed sex ratio at the spawning sites. In 6 of 7 seasons in Malangen, 8–9 of 10 fish were males, and in Balsfjord 9 of 10 fish were males on average, indicating some form of lekking behaviour among the spawning fish. Average size of the fish varied among years and also between sexes in individual years, although not consistently. The smallest proportion of mature fish was seen in Malangen in the year with the earliest sampling date (23 February). This was also the sample with the least skewed sex ratio (6.5 of 10 fish were males). The frequency of the Pan IA allele of the Malangen cod was highly stable among years at close to 90%, showing that this spawning ground is exclusively used by coastal cod. In Balsfjord, frequencies of the Pan IA allele were lower (67-78%). This fjord is suggested to be more penetrable for the migratory NE Arctic cod with their high frequencies of the Pan IB allele, making it a less exclusively coastal cod residence. In both fjords, length of mature males but not females varied among the Pan I genotypes

Fra lokale ideer til nasjonale løsninger? InnoMed sin rolle for innovasjoner i helse- og omsorgssektoren

Denne rapporten er en evaluering av InnoMed - Nasjonalt kompetansenettverk for behovsdrevet innovasjon i helsesektoren. InnoMed har til formål å bidra til kvalitet og effektivitet i helsesektoren gjennom utvikling av løsninger forankret i nasjonale behov og som kan ha internasjonale markedsmuligheter. Formålet med evalueringen har vært å undersøke i hvilken utstrekning InnoMeds innovasjoner blir bredt implementert i helse- og omsorgssektoren, hvordan veien fra ideer blir fanget opp til de blir implementert fungerer, og hensiktsmessigheten i hvordan InnoMed er regulert og finansiert

Settling-depth vs. genotype and size vs. genotype correlations at the Pan I locus in 0-group Atlantic cod Gadus morhua

We sampled 0-group juvenile Atlantic cod Gadus morhua L. within fjords and offshore in northern Norway from 1994 to 2008 using different gears for the 3 sampling depths: shore seine (0−3 m), pelagic trawl (various depths), and bottom trawl (>80 m). Frequencies of alleles at the Pan I locus (4218 fish analysed) showed highly significant differences among samples collected in the different habitats. The Pan IA allele showed a mean frequency of ~80% in the shore seine samples, 12% in the bottom trawl samples, and between 5 and 57% in the pelagic samples. These differences are thought to reflect the co-occurrence of different populations of cod in the area with different settling regimes. Shallow-water settlers are thought to represent the stationary Norwegian coastal cod (NCC), the deep-water settlers represent the migratory Arcto-Norwegian cod (ANC), and the non-settled individuals represent a variable mixture of the 2 populations. For designated samples, we analyzed 16 microsatellites (non-neutral and neutral) that supported a genetic divergence between shallow-water and deep-water settlers. Correlations between length and Pan I genotypes within selected samples showed that the Pan IBB homozygotes (typical of ANC) were significantly longer than the Pan IAA homozygotes (typical of NCC). This could reflect differences in spawning time and growth conditions between ANC and NCC, just as well as one genotype being superior to the others in terms of growth performance. Finally, we argue that the Pan I difference between 0-group NCC and ANC is not caused by contemporary selection but reflects adaptation on an ecological post-glacial time scale

Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome

Abstract Background Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. Results The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. Conclusions We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits.</p

Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome

Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits

Population structure of the deep-sea shrimp (

In order to elucidate the population structure of the deep-sea shrimp (Pandalus borealis) in the NE Atlantic, 32 subsamples and 3865 individuals were analysed for allozymic variation. They were caught at various locations in the Barents Sea, in waters off Svalbard, Jan Mayen and Iceland, and in fjords along the Norwegian coast. Only three enzymes (malate dehydrogenase, phosphoglucomutase and glucosephosphate isomerase) of the 22 initially tested showed a combination of gel images that could be interpreted with confidence and allozymic variation. The locus coding for malate dehydrogenase was by far the most polymorphic. Samples caught within the Barents Sea and in the Svalbard area showed no significant heterogeneity in allele frequencies, supporting earlier suggestions of only one population of P. borealis in the Barents Sea. Genetic differentiation was found, however, between Norwegian fjords and the Barents Sea, and among fjords