Development of tri- and tetranucleotide repeat microsatellite loci in Atlantic cod (Gadus morhua)

The pantophysin gene and its relationship with survival in early life stages of Atlantic cod

Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.

Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline

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.

Genetic variation and local differences in Pacific cod Gadus macrocephalus around Japan

The population structure of the Pacific cod Gadus macrocephalus was examined using 15 microsatellite loci and mitochondrial DNA (ND2 region). In total, 274 individuals were sampled from 16 locations around Japan to estimate the level of genetic differentiation and effective population size (N_e ). Pairwise F_ST , analysis of molecular variance and Bayesian clustering analysis suggested the presence of two genetically distinct groups in waters around Japan, with a higher N_e value in the eastern group than in the western group. A possible factor that restricts gene flow between groups may be related to the water temperature differences in the south-western part of the Sea of Japan, where the Tsushima Warm Current flows around the area inhabited by the western group, which may limit migration between the west and east.

Differential Survival among Batches of Atlantic Cod (Gadus morhua L.) from Fertilisation through to Post-Metamorphosis

Aquaculture production of cod has decreased from over 20,000 tonnes in 2009 to less than 2,000 tonnes in 2014 and the industry faces many challenges, one of which is high and unpredictably variable mortality rates in the early life stages. Hence, full-cycle farming with hatchery produced juveniles is still considered unprofitable compared to fisheries and on-growing of wild cod. In the present study, potential batch differences in progeny survival of wild-caught, hatchery-spawned Faroe Bank cod (Gadus morhua L.) were investigated at two defined periods during early life history; i) the embryo stage (60 day degrees post fertilisation) and ii) the fry stage (110 days post hatch), post metamorphosis. The fry stage experiment was conducted in three replicates (N = 300 per replicate), and a panel of three polymorphic microsatellite markers was used for parental analysis. Mean survival rate at the embryo stage was 69% (± 20% SD). Survival was positively associated with egg diameter (P < 0.01), explaining 90% of the variation in egg survival rates. The data were too scarce to conclude either way concerning a possible correlation between survival rates between the two periods (P < 0.10). Offspring from three batches (from a total of eight) dominated in the fry stage, contributing over 90% of the progeny, and results were consistent over all three replicate tanks. The skewed batch representation observed may be of relevance to the effective management of selective breeding programmes for cod.

Restricted Gene Flow for Gadus macrocephalus from Yellow Sea Based on Microsatellite Markers: Geographic Block of Tsushima Current

The Pacific cod Gadus macrocephalus is a demersal, economically important fish in the family Gadidae. Population genetic differentiation of Pacific cod was examined across its northwestern Pacific range by screening variation of eight microsatellite loci in the present study. All four populations exhibited high genetic diversity. Pairwise fixation index (Fst) suggested a moderate to high level of genetic differentiation among populations. Population of the Yellow Sea (YS) showed higher genetic difference compared to the other three populations based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE, which implied restricted gene flow among them. Wilcoxon signed rank tests suggested no significant heterozygosity excess and no recent genetic bottleneck events were detected. Microsatellite DNA is an effective molecular marker for detecting the phylogeographic pattern of Pacific cod, and these Pacific cod populations should be three management units.

Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration

Background

In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species.

Results

Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2–5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours.

Conclusions

Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.

Electronic supplementary material

The online version of this article (doi:10.1186/s13104-016-1878-9) contains supplementary material, which is available to authorized users.

Applying population genetics for authentication of marine fish: the case of saithe (Pollachius virens)

The number of fishery products with a quite detailed description of the origin is increasing. This trend is driven by the interest of consumers and the fight against illegal unregulated and unreported fisheries. Unfortunately, there is a lack of methods to prove this information experimentally besides the document-based traceability assessments. For marine fish population genetics is a promising strategy, but research is concentrated only on a few species. Saithe is a commercially important fish species, despite the fact that genetic knowledge is scarce regarding the specification of populations. For a comparative study cost- and time-effective strategies were tested: We found RAPD-PCR to be a useful method for low-budget research or prestudies. Adoption of microsatellites from closely related species turned out to be possible with limited success quota. Our results suggest a clustered structure of populations within the Northeast Atlantic, probably overlapping in the northern North Sea.

A quick, least-invasive, inexpensive and reliable method for sampling Gadus morhua postlarvae for genetic analysis

The present study describes the successful design and testing of a quick, least-invasive, reliable and inexpensive sampling procedure for Atlantic cod Gadus morhua. This protocol can be easily applied to postlarval fish following a simple three-step procedure, without availing of commercial DNA extraction kits, while ensuring survival of sampled individuals.

Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof-of-concept study for the identification of escapees

This study presents a molecular genetic characterization of Atlantic cod reared in commercial marine farms. Samples consisted of approximately 47 fish collected from nine cages located on four farms throughout Norway. In addition, 28 farmed escapees were recaptured in the sea (443 fish in total). Nine microsatellite loci and the Pan I gene were analysed, revealing a total of 181 alleles. Each sample contained 43–63% of total allelic variation. Comparing variation with published data for wild cod indicates that lower genetic variation exists within single cages than in wild populations. Significant linkage disequilibrium was observed amongst pairs of loci in all samples, suggesting a low number of contributing parental fish. Global F_ST was 0.049, and the highest pairwise F_ST value (pooled loci) was 0.085. For single loci, the Pan I gene was the most diagnostic, displaying a global F_ST of 0.203. Simulations amongst the samples collected on farms revealed an overall correct self-assignment percentage of 75%, demonstrating a high probability of identifying individuals to their farm of origin. Identification of the 28 escapees revealed a single cage as the most likely source of origin for half of the escapees, whilst the remaining fish were assigned to a mixture of samples, suggesting more than one source of escapees.

Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence of fisheries-induced selection?

The intense fishing mortality imposed on Atlantic cod in Icelandic waters during recent decades has resulted in marked changes in stock abundance, as well as in age and size composition. Using a molecular marker known to be under selection (Pan I) along with a suite of six neutral microsatellite loci, we analysed an archived data set and revealed evidence of distinct temporal changes in the frequencies of genotypes at the Pan I locus among spawning Icelandic cod, collected between 1948 and 2002, a period characterized by high fishing pressure. Concurrently, temporal stability in the composition of the microsatellite loci was established within the same data set. The frequency of the Pan I^BB genotype decreased over a period of six decades, concomitant with considerable spatial and technical changes in fishing effort that resulted in the disappearance of older individuals from the fishable stock. Consequently, these changes have likely led to a change in the genotype frequencies at this locus in the spawning stock of Icelandic cod. The study highlights the value of molecular genetic approaches that combine functional and neutral markers examined in the same set of individuals for investigations of the selective effects of harvesting and reiterates the need for an evolutionary dimension to fisheries management.

Are low but statistically significant levels of genetic differentiation in marine fishes 'biologically meaningful'? A case study of coastal Atlantic cod

A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10-year period with an extensive capture-mark-recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average F(ST)  = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10-year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (N(e) ) of the two coastal cod populations to 198 and 542 and found a N(e) /N (spawner) ratio of 0.14.

Genetic, maternal, and environmental variance components for body weight and length of Atlantic cod at 2 points in life

Variance components were estimated for 2 body size traits of Atlantic cod at 2 time points. Wild-caught founders from 3 regions off eastern North America were spawned and their progeny were reared at 2 locations in 2 consecutive years. Full-sib families (n = 148) were kept separate until individuals achieved a size large enough to be tagged. At that time (220 d of age), BW and length of 47,637 offspring from 90 sires and 89 dams were recorded. The juveniles were then transferred to sea cages at 3 sites, where they grew further for more than a year. A second set of measurements was collected on 11,839 fish (634 d of age). Dispersion parameters were estimated using REML in bivariate analyses. Models included fixed degree-days (covariate), year × location subclasses, and genetic groups composed of connected families within region of origin. Random factors were animal (additive genetic effects), considering known relationships among the fish; dam (maternal effects); and family (effects common to full-sibs). At tagging, heritability estimates were small to moderate (0.15 and 0.24 for BW and length, respectively; SE = 0.14), similar to or somewhat larger than the proportions of variation ascribed to dams and families (11 to 16%). Later, heritability estimates were greater (0.27 ± 0.08 and 0.31 ± 0.09 for BW and length, respectively), whereas dam and family variance proportions were very small (3 to 4%). Omitting maternal or family components substantially increased the values obtained for heritability at both time points. At the later point, failure to account for maternal effects inflated heritability estimates by about 24% for both traits; ignoring family effects had double the impact. These effects persisted even though endogenous feeding lasts only a couple of weeks in this species and the fish had been pooled since tagging. Discarding data from parents that were completely confounded with their mates decreased heritability estimates slightly (by 0.04, for both traits) at the second point, with no loss of precision despite 15% fewer records and 34% fewer parents; the improved design seemed to have more fully disentangled the additive genetic effects. Estimates of genetic correlations between traits and between time points were very large (>0.89). The results imply that genetic variation exists for body size of cod at both stages. Poor data structure and inadequate models can potentially lead to overstatement of heritability, and thus also of the predicted selection response.

Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord

The interplay between structural connectivity (i.e. habitat continuity) and functional connectivity (i.e. dispersal probability) in marine fishes was examined in a coastal fjord (Holyrood Pond, Newfoundland, Canada) that is completely isolated from the North Atlantic Ocean for most of the year. Genetic differentiation was described in three species (rainbow smelt Osmerus mordax, white hake Urophycis tenuis and Atlantic cod Gadus morhua) with contrasting life histories using seven to 10 microsatellite loci and a protein-coding locus, PanI (G. morhua). Analysis of microsatellite differentiation indicated clear genetic differences between the fjord and coastal regions; however, the magnitude of difference was no more elevated than adjacent bays and was not enhanced by the fjord's isolation. Osmerus mordax was characterized by the highest structure overall with moderate differentiation between the fjord and St Mary's Bay (F(ST)c.0.047). In contrast, U. tenuis and G. morhua displayed weak differentiation (F(ST) < 0.01). Nonetheless, these populations did demonstrate high rates (< 75%) of Bayesian self-assignment. Furthermore, elevated differentiation was observed at the PanI locus in G. morhua between the fjord and other coastal locations. Interestingly, locus-specific genetic differentiation and expected heterozygosity were negatively associated in O. mordax, in contrast to the positive associations observed in U. tenuis and G. morhua. Gene flow in these species is apparently unencumbered by limited structural connectivity, yet the observed differentiation suggests that population structuring exists over small scales despite high dispersal potential.

A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua)

A first genetic linkage map of the Atlantic cod (Gadus morhua) was produced, based on segregation data from 12 full-sib families of Norwegian origin. The map contained 174 single nucleotide polymorphism markers and 33 microsatellites, distributed on 25 linkage groups and had a length of 1225 cM. A significant difference in recombination rates between sexes was found, the average ratio of female:male recombination rates being 1.78 +/- 1.62 (SD).

Connectivité entre les populations du fjord du Saguenay et celles du golfe du Saint-Laurent

L’analyse des marqueurs microsatellites et d’allozymes chez différentes espèces de poissons de fond (morue, flétan du Groenland et sébaste) et de crustacés (crabe des neiges et crevette nordique) montre que les organismes du Saguenay et du Saint-Laurent appartiennent aux mêmes populations. La seule différenciation génétique est observée au locus Pan I chez la morue. Cette différenciation pourrait toutefois être causée par la sélection, qui agirait dans le fjord du Saguenay, plutôt que par l’isolement génétique de la population. Les données complémentaires disponibles pour les poissons de fond (composition élémentaire des otolithes, morphométrie et faune parasitaire) montrent que les individus capturés dans le Saguenay diffèrent de ceux du Saint-Laurent. Ces différences suggèrent que les individus du Saguenay et du Saint-Laurent passent la majeure partie de leur cycle vital dans des environnements différents. Considérant la très faible survie larvaire observée dans le fjord, cette revue suggère que les populations de poissons de fond du Saguenay constituent des populations puits, dont le recrutement dépend de l’apport de juvéniles depuis le Saint-Laurent. Une fois les individus installés dans le Saguenay, ils y passent la majorité de leur vie. Même si nous ne possédons pas de données complémentaires pour les crustacés, il est possible que le même mécanisme opère chez ces espèces.

Large-scale sequence analyses of Atlantic cod

The Atlantic cod (Gadus morhua) is a key species in the North Atlantic ecosystem and commercial fisheries, with increasing aquacultural production in several countries. A Norwegian effort to sequence the complete 0.9Gbp genome by the 454 pyrosequencing technology has been initiated and is in progress. Here we review recent progress in large-scale sequence analyses of the nuclear genome, the mitochondrial genome and genome-wide microRNA identification in the Atlantic cod. The nuclear genome will be de novo sequenced with 25 times oversampling. A total of 120 mitochondrial genomes, sampled from several locations in the North Atlantic, are being completely sequenced by Sanger technology in a high-throughput pipeline. These sequences will be included in a new database for maternal marker reference of Atlantic cod diversity. High-throughput 454 sequencing, as well as Evolutionary Image Array (EvoArray) informatics, is used to investigate the complete set of expressed microRNAs and corresponding mRNA targets in various developmental stages and tissues. Information about microRNA profiles will be essential in the understanding of transcriptome complexity and regulation. Finally, developments and perspectives of Atlantic cod aquaculture are discussed in the light of next-generation high-throughput sequence technologies.

Characterization of 155 EST-derived microsatellites from Atlantic cod (Gadus morhua) and validation for linkage mapping

Microsatellite markers for Atlantic cod (Gadus morhua) were identified from a collection of 30 630 expressed sequence tags. Primers were designed for 395 microsatellites and 155 were successfully amplified. Allele number varied from 1 to 26 (average 6.34). Average observed and expected heterozygosities were 0.50 and 0.54, respectively. A subset of 105 microsatellites tested for Mendelian segregation showed no significant distortion of segregation when correcting for multiple tests. Null alleles were detected at four loci. Significant blastx matches were found for 23 loci. These microsatellites will be used to create a linkage map to enhance genetic selection in commercial cod breeding.

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

BACKGROUND

The Atlantic cod (Gadus morhua) 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.

RESULTS

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. FST values were highly variable, with the majority of SNPs displaying very little differentiation while others had FST values as high as 0.83. The FST 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.

CONCLUSION

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.

Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms

Microsatellites have gained wide application for elucidating population structure in nonmodel organisms. Since they are generally noncoding, neutrality is assumed but rarely tested. In Atlantic cod (Gadus morhua L.), microsatellite studies have revealed highly heterogeneous estimates of genetic differentiation among loci. In particular one locus, Gmo 132, has demonstrated elevated genetic differentiation. We investigated possible hitch-hiking selection at this and other microsatellite loci in Atlantic cod. We employed 11 loci for analysing samples from the Baltic Sea, North Sea, Barents Sea and Newfoundland covering a large part of the species' distributional range. The 'classical' Lewontin-Krakauer test for selection based on variance in estimates of F(ST) and (standardized genetic differentiation) revealed only one significant pairwise test (North Sea-Barents Sea), and the source of the elevated variance could not be ascribed exclusively to Gmo 132. In contrast, different variants of the recently developed ln Rtheta test for selective sweeps at microsatellite loci revealed a high number of significant outcomes of pair-wise tests for Gmo 132. Further, the presence of selection was indicated in at least one other locus. The results suggest that many previous estimates of genetic differentiation in cod based on microsatellites are inflated, and in some cases relationships among populations are obscured by one or more loci being the subject to hitch-hiking selection. Likewise, temporal estimates of effective population sizes in Atlantic cod may be flawed. We recommend, generally, to use a higher number of microsatellite loci to elucidate population structure in marine fishes and other nonmodel species to allow for identification of outlier loci that are subject to selection.

Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua)

DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin (Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size (Ne) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and Ne's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of Ne showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by Ne's exceeding thousand. Recent fishery-induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of Ne << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low Ne/N ratios. Our data suggest that very small Ne's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.

Transport of North Sea cod larvae into the Skagerrak coastal populations

The Atlantic cod (Gadus morhua) is economically one of the world's most important marine species--a species presently suffering from heavy overexploitation throughout its range of distribution. Although not fully understood, the Atlantic cod is believed to be structured into populations in a rather complex manner, whereby both highly migratory and more confined ocean-spawning stocks coexist with stationary coastal populations. Owing to the complex population structure, little is presently known about how overexploitation of offshore stocks may affect other segments of the species. Here, we use microsatellite DNA analyses of coastal and offshore cod in combination with oceanographic modelling to investigate the population structure of Atlantic cod in the North Sea-Skagerrak area and evaluate the potential for larval transport into coastal populations. Our results suggest an extensive but temporally variable drift of offshore cod larvae into coastal populations. In a year (2001) with high inflow of North Sea waters into the Skagerrak we find that juvenile cod caught along the Skagerrak coast are predominantly of North Sea origin, whereas in a year (2000) with low inflow juveniles appear to be of local origin. These findings indicate that offshore cod may influence coastal cod populations over large distances.

Evidence of a hybrid-zone in Atlantic cod (Gadus morhua) in the Baltic and the Danish Belt Sea revealed by individual admixture analysis

The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.

Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod

Compared with many terrestrial and freshwater environments, dispersal and interbreeding is generally much less restricted in the marine environment. We studied the tendency for a marine species, the Atlantic cod, to be sub-structured into genetically differentiated populations on a fine geographical scale. We selected a coastal area free of any obvious physical barriers and restricted sampling to a 300-km region, well within the dispersal ability of this species. Screening 10 polymorphic microsatellite loci in 6 samples we detected a weak, but consistent, differentiation at all 10 loci. The average FST over loci was small (0.0023) but highly significant statistically, demonstrating that genetically differentiated populations can arise and persist in the absence of physical barriers or great distance. We found no geographical pattern in the genetic differentiation and there was no apparent trend of isolation by distance along the coastline. These findings lend support to the notion that low levels of differentiation are due to passive transport of eggs or larvae by the ocean currents rather than to adult dispersal, the latter being strongly dependent on distance.

Male reproductive competition in spawning aggregations of cod (Gadus morhua, L.)

Reproductive competition may lead to a large skew in reproductive success among individuals. Very few studies have analysed the paternity contribution of individual males in spawning aggregations of fish species with huge census population sizes. We quantified the variance in male reproductive success in spawning aggregations of cod under experimental conditions over an entire spawning season. Male reproductive success was estimated by microsatellite-based parentage analysis of offspring produced in six separate groups of spawning cod. In total, 1340 offspring and 102 spawnings distributed across a spawning season were analysed. Our results show that multiple males contributed sperm to most spawnings but that paternity frequencies were highly skewed among males, with larger males on average siring higher proportions of offspring. It was further indicated that male reproductive success was dependent on the magnitude of the size difference between a female and a male. We discuss our results in relation to the cod mating system. Finally, we suggest that the highly skewed distribution of paternity success observed in cod may be a factor contributing to the low effective population size/census population size ratios observed in many marine organisms.