Offshore Cod Research Articles

Examining fish movement in terms of advection or diffusion: a case study of northeastern Atlantic cod

Advection (directional movement) and diffusion (dispersed movement) were applied for the first time to describe movement patterns in Atlantic cod in the North Sea and Baltic Sea between 1955 and 2020. The advection-diffusion approach provided more detailed estimates of movement that corresponded to previously observed patterns using different analytical techniques. Spatial patterns were evident with greater movement distances in cod from the North Sea and eastern Baltic Sea compared to the western Baltic and Kattegat-Skagerrak. Furthermore, comparative case studies on different ecotypes in the western and eastern Baltic suggested that inshore cod were more resident compared to offshore cod. This preliminary study highlights the usefulness of the advection-diffusion method to describe movements in fish populations, and can be further expanded by incorporating information on environment and mortality and providing information to spatially explicit population models.

Possible adverse impact of contaminants on Atlantic cod population dynamics in coastal ecosystems.

While many in-laboratory ecotoxicological studies have shown the adverse impact of pollutants to the fitness of an individual, direct evidence from the field on the population dynamics of wildlife animals has been lacking. Here, we provide empirical support for a negative effect of pollution on Atlantic cod (Gadus morhua) population dynamics in coastal waters of Norway by combining unique time series of juvenile cod abundance, body size, environmental concentration of toxic contaminants and a spatially structured population dynamics model. The study shows that mercury concentration might have decreased the reproductive potential of cod in the region despite the general decline in the environmental concentration of mercury, cadmium and hexachlorobenzene since the implementation of national environmental laws. However, some cod populations appeared to be more resistant to mercury pollution than others, and the strength and shape of mercury effect on cod reproductive potential was fjord-specific. Additionally, cod growth rate changed at scales smaller than fjords with a gradient related to the exposure to the open ocean and offshore cod. These spatial differences in life-history traits emphasize the importance of local adaptation in shaping the dynamics of local wildlife populations. Finally, this study highlights the possibility to mitigate pollution effects on natural populations by reducing the overall pollution level, but also reveals that pollution reduction alone is not enough to rebuild local cod populations. Cod population recovery probably requires complementary efforts on fishing regulation and habitat restoration.

Otolith chemistry and redistributions of Northern cod: evidence of Smith Sound – Bonavista Corridor connectivity

Stable oxygen isotope assays of otoliths (δ18Ooto) from migrant Atlantic cod (Gadus morhua Linnaeus, 1758) that overwintered in Smith Sound, Newfoundland, during 1995–2006 differed from those of nonmigrating summer residents and cod from Placentia Bay and Halibut Channel but did not differ from those of cod from the adjacent offshore Bonavista Corridor in summer. All fish sampled were of the 1990 year class (founder of the Smith Sound aggregation) at ages 8–10 years. Hence, overwintering Smith Sound and summering Bonavista Corridor cod likely experienced similar temperatures and salinities in each year of life, representing different migration stages of an intermixed group. Moreover, predictions of δ18Ooto from near-bottom ocean temperatures and salinities differed between inshore and offshore sites and, in general, matched observed signatures of inshore and offshore cod. The Bonavista Corridor cod, however, were an exception, having δ18Ooto signatures suggestive of inshore exposure. Our findings provide direct evidence of metapopulation structure in the Northern cod and are consistent with offshore rebuilding having been spurred by dispersal of cod from inshore Smith Sound.

Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak coast

Abstract Dramatic and persistent reductions in Atlantic cod (Gadus morhua) are common in many coastal areas. While offshore cod stocks still were abundant and productive, the Swedish west coast showed signs of diminishing adult cod abundance at the beginning of the 1980s, where the local cod component was considered to be extirpated. To survey the present cod spawning activity and stock composition, we initiated egg trawling over two consecutive years (203 hauls in total) in combination with population genetic analyses (425 individually genotyped eggs). Here, we provide evidence of cod spawning at the Swedish Skagerrak coast, suggesting recolonization or that local cod has recovered from a nearly depleted state. Early stage eggs were found inside fjords too far to have been transported by oceanic drift from offshore spawning areas. The cod eggs were genetically similar in early to late life-stages and cluster mainly with the local adult cod, indicating that eggs and adults belong to the same genetic unit. The cod eggs were genetically differentiated from adult North Sea cod, and, to a lesser degree, also from the Kattegat and Öresund cod, i.e. indicating a possible recovery of local coastal stock. The patterns of the genetic structure in the inshore areas are, however, difficult to fully disentangle, as Atlantic cod in the North Sea-Skagerrak area seem to be a mixture of co-existing forms: local cod completing their entire life cycle in fjords and sheltered areas, and oceanic populations showing homing behaviours. The egg abundances are considerably lower compared with what is found in similar studies along the Norwegian Skagerrak coast. Nevertheless, the discovery of locally spawning cod along the Swedish west coast—although at low biomasses—is an encouraging finding that highlights the needs for endurance in protective measures and of detailed surveys to secure intraspecific biodiversity and ecosystem services.

Genomic tools for management and conservation of Atlantic cod in a coastal marine protected area

Marine protected areas (MPAs) can serve as effective tools for the management and conservation of exploited marine species. The Gilbert Bay MPA in coastal Labrador was created to protect a genetically distinct population of Atlantic cod (Gadus morhua); however, decreases in abundance continue to occur potentially due to exploitation outside the MPA. We developed a single-nucleotide polymorphism (SNP) panel to identify Gilbert Bay cod in areas outside MPA boundaries where mixing with offshore cod occurs. In total, 361 individuals from Gilbert Bay, surrounding areas, and offshore were genotyped for 10 913 SNPs. Using FSTrankings and guided regularized random forest, we selected 23 SNPs that together generate 100% accuracy in individual assignment and accurately estimate the proportion of Gilbert Bay cod in fishery samples from sites outside MPA boundaries: on average, fishery samples included 17.3% Gilbert Bay cod. Estimates of effective population size for the Gilbert Bay population ranged from 655 to 1114. Our findings demonstrate the power of using genomic approaches for management of an exploited marine species and enhancing the design of MPAs.

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic.

Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11ksingle nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.

Learning from ‘apparent consensus’ in TAC disputes: Exploring knowledge overlaps in LEK and genetic categorization of Atlantic cod

The rapid development of genetic science has improved the methods for fisheries stock assessments with increasing implications for management. One key accomplishment has been the identification of different sub-populations of Atlantic cod. Recognizing that local coastal fishers in the North Atlantic have often held a local knowledge about local cod populations, this study examines the extent to which genetic analysis corroborates this local knowledge and vice versa. In Nuuk, capital of Greenland situated by the Nuuk fiord system, local fishers say that they and generations before them have been observing both inshore and offshore cod in the Nuuk fiord system. Fisher interviews were conducted in order to understand the construction as well as the content of this specific local ecological knowledge. Furthermore, fishers were invited to assign cod from their catches into categories based on their knowledge of inshore and offshore cod. These cod were subsequently analyzed and assigned to population using genetic methodologies. The comparison between visual and genetic assignment was not able to confirm any convincing consensus between fishers' understanding of offshore and inshore cod and the corresponding genetic categories. However, an examination of existing inshore and off-shore catch surveys confirmed the relevance of the morphological characteristics (liver condition and shape) of ecologically defined inshore and off-shore cod that provided the basis for fishers' categorizations. This opens a discussion of the fishers' way of knowing about inshore and offshore cod respectively and if and how the content of their knowledge could be made relevant in relation to scientific advice procedures.

Dynamics of the sea ice edge in Davis Strait

Sea ice concentration derived from satellite data were used to quantify sea ice characteristics in the Baffin Bay–Davis Strait–Labrador Sea area. The ice edge in Davis Strait extends from Disko Bay in West Greenland 2500 km south to Newfoundland. The mean intercept at the West Greenland coast between 1979 and 2002 was located at 66.9°N, assuming the ice edge was 85% ice concentration. The shallow banks of West Greenland (> 200 m) had, on average, an ice extent covering 30 to 100% of the bank area during March for the 24 year time series. This extent varied in concentration between 39 and 100%. However, intermediate ice concentrations (39–85% ice concentration) covered on average 25% of the banks. The Davis Strait ice edge showed considerable interannual variation correlated with the winter index of the North Atlantic Oscillation and the Arctic Oscillation. No temporal trend in ice extent could be detected over the 24 years. In addition to the ice production on the banks of West Greenland, sea ice produced further north in Baffin Bay was advected to the banks as shown by satellite tracked drifting buoys. Both the local sea ice production and the advected sea ice contributed significantly to sea temperatures and salinities measured during summer on the banks. No correlation between sea ice concentration and plankton abundance could be detected but the recruitment of the offshore cod ( Gadus morhua) component in South Greenland was negatively correlated to the amount of sea ice in Baffin Bay.

Genotyping of pantophysin I (Pan I) of Atlantic cod (Gadus morhua L.) by allele‐specific PCR

AbstractThe two main allelic variants of the Atlantic cod (Gadus morhua L.) pantophysin I (Pan I) locus have different frequencies within different cod stocks. The Dra I polymorphism which distinguishes the two alleles can thus be used for discrimination of coastal and offshore cod populations. We present a new method for Pan I genotyping using fluorescent allele‐specific duplex polymerase chain reaction (PCR). This method is more rapid, reliable and cost‐effective than the previously published method and it is not affected by DNA source and quality. This improvement is important for studies demanding high throughput and accuracy of Pan I genotyping

Multiple stock structure of Atlantic cod (Gadus morhua) off Newfoundland and Labrador determined from genetic variation

We examined variation at seven microsatellite loci (Gmo3, Gmo8, Gmo19, Gmo34, Gmo35, Gmo36, and Gmo37) and PanI in some 5230 Atlantic cod (Gadus morhua) from 19 inshore and offshore locations around Newfoundland and Labrador. The mean F ST estimate over all loci was 0.0080. Overall, the cod populations surveyed conformed to an isolation-by-distance structure, cod from more distant locations tending to be more genetically distinct. Among offshore sites, the Flemish Cap population (NAFO Division 3M) was the most distinctive, and among inshore sites, the Gilbert Bay population in southern Labrador (2J) was the most distinctive. In NAFO Divisions 3KL, no significant genetic differentiation was observed among inshore northern cod sampled in four bays (Notre Dame, Bonavista, Trinity, and Conception) along the northeast coast of Newfoundland, and the data do not support the hypothesis of separate “bay stocks”. Annual variation within sampling sites was as large, on average, as the differentiation among sampling sites. The inshore northern cod were distinct from the population in Gilbert Bay and from most offshore northern cod populations. On average, over all populations, regional differences in allele frequencies were seven times larger than annual variation. The offshore samples were more heterogeneous, and there may be at least three distinct offshore spawning populations of northern cod. In Subdivision 3Ps, no consistent differentiation was observed among sampling sites, two in inshore bays (Placentia, Fortune), and two offshore (Burgeo Bank, Halibut Channel). The southern Grand Bank (Divisions 3NO) may have a separate spawning population from those in other offshore sites, but additional sampling is required to confirm population distinctiveness.

Offshore spawning and year-class strength of northern cod (2J3KL) during the fishing moratorium, 1994-1996

Two new surveys have been conducted in recent years to assess the status of the northern cod (Gadus morhua) stock (2J3KL). An offshore acoustic survey in spring sampled concentrations of spawning adults and estimated potential fecundity. A pelagic juvenile fish survey carried out in late summer measured cod year-class strength prior to settlement. Spawning biomass of offshore cod decreased from 11 700 t in 1994 to 2000 t in 1995 to 900 t in 1996 with a corresponding decrease in eggs spawned. This decline was mirrored in the distribution and abundance of pelagic juvenile cod. Natural mortality estimated between the egg and pelagic juvenile stages increased from –0.068·day–1 in 1994 to –0.084·day–1 in 1995 to –0.112·day–1 in 1996. The decline in year-class strength of cod appeared to result primarily from a reduction in the number of offshore spawners compounded by an increase in natural mortality during the egg and larval stages. The decline in spawners occurred 2 years after the implementation of a fishing moratorium and cannot be linked to fishing. The rapid decline in abundance of adult fish combined with increased natural mortality during the egg and larval drift is consistent with depensation.

Bay‐scale population structure in coastal Atlantic cod in Labrador and Newfoundland, Canada

Polymorphisms at five microsatellite DNA loci provide evidence that Atlantic cod Gadus morhua inhabiting Gilbert Bay, Labrador are genetically distinguishable from offshore cod on the north‐east Newfoundland shelf and from inshore cod in Trinity Bay, Newfoundland. Antifreeze activity in the blood suggests that Gilbert Bay cod overwinter within the Bay. Gilbert Bay cod are also smaller (weight and length) for their age and consequently less fecund for their age, than cod elsewhere within the northern cod complex. The productivity and recruitment potential of coastal cod off Labrador may thus be much lower than that of offshore northern cod or of inshore cod farther south, implying that a more conservative management strategy may be required for cod from coastal Labrador than traditionally practised for northern cod inhabiting less harsh environments. Relatively high FST and RST measures of population structure suggest that important barriers to gene flow exist among five components that include two inshore (Gilbert and Trinity Bay) and three offshore cod aggregations on the north‐east Newfoundland Shelf and the Grand Bank. DA and DSW estimates of genetic distance that involve Gilbert Bay cod are approximately three‐ and 10–fold larger, respectively, than estimates not involving Gilbert Bay cod. The differences between inshore cod from Gilbert Bay and Trinity Bay raise the possibility that other genetically distinguishable coastal populations may exist, or may have existed prior to the northern cod fishery collapse. Harvesting strategies for northern cod should recognize the existence of genetic diversity between inshore and offshore components as well as among coastal components.

Genetic differentiation between inshore and offshore Atlantic cod (<I>Gadus morhua</I>) off Newfoundland: a test and evidence of temporal stability

Les differences genetiques entre la morue franche (Gadus morhua) hivernant dans les eaux cotieres de la baie Trinite, a Terre-Neuve, et celles hivernant dans les eaux du large dans la region du Grand Banc (Ruzzante et al. 1996; J. Can. Sci. Halieut. Aquat. 53: 634-645) sont demeurees stables entre 1992 et 1995. Les morues capturees dans les eaux cotieres en 1995 dans la baie Trinite (N = 150) se distinguaient encore sur le plan genetique (a l'aide de (δμ 2 ) et de D sw ) des morues du large (N = 140) capturees entre 1992 et 1994, et ne se distinguaient pas genetiquement des morues des eaux cotieres (N = 123) egalement prelevees entre 1992 et 1994. Des morues maintenues en captivite (N = 30), capturees dans les eaux cotieres en 1992 et elevees dans des parcs de filets jusqu'en 1995, provenaient tres vraisemblablement d'une population qui hiverne dans les eaux cotieres; elles etaient genetiquement differentes des morues du large, et ne se distinguaient pas des morues sauvages des eaux cotieres presentant une forte activite antigel, et des morues capturees dans une eau relativement froide (environ 0,2° C) en decembre 1995. Les morues gardees en captivite etaient genetiquement differentes d'autres morues capturees dans une eau relativement chaude (environ 3,3° C), mais ne se differenciaient pas des morues presentant une faible activite antigel. Malgre des indications d'une faible heterogeneite genetique sur l'ensemble des morues sauvages capturees dans les eaux cotieres en 1995, qui n'etait pas associee avec l'activite antigel ni avec la temperature de l'eau, l'ampleur des differences genetiques entre les morues des eaux cotieres et du large est demeuree identique pendant la periode 1992-1995.

Genetic differentiation between inshore and offshore Atlantic cod (Gadus morhua) off Newfoundland: microsatellite DNA variation and antifreeze level

Microsatellite DNA provided evidence that Atlantic cod overwintering in inshore Newfoundland are genetically distinguishable from cod overwintering offshore. We compared variation in five loci in samples from inshore locations around Trinity Bay, Newfoundland, and from an offshore region on the northern Grand Bank (North Cape). Cod collected inshore were divided into two groups on the basis of antifreeze level in blood: those with high antifreeze levels presumed to have overwintered in cold ( 2°C) waters. Fish overwintering inshore differed from offshore fish in allele sharing and in (δμ) 2 distances, while fish with low antifreeze levels did not. Subpopulation structure ( Rst) was detected when offshore cod were compared with inshore cod with high levels of antifreeze but not when compared with those with low levels of antifreeze. These results suggest that cod overwintering inshore are genetically distinct from offshore cod. Inshore and offshore cod from the areas studied remain genetically distinct despite the fact that individuals from the two populations intermingle inshore during the summer and fall feeding migration. Thus, we found evidence of population structure at a finer geographical scale than has been shown to date for this species.

Genetic differentiation between inshore and offshore Atlantic cod (<I>Gadus morhua</I>) off Newfoundland: microsatellite DNA variation and antifreeze level

Microsatellite DNA provided evidence that Atlantic cod overwintering in inshore Newfoundland are genetically distinguishable from cod overwintering offshore. We compared variation in five loci in samples from inshore locations around Trinity Bay, Newfoundland, and from an offshore region on the northern Grand Bank (North Cape). Cod collected inshore were divided into two groups on the basis of antifreeze level in blood: those with high antifreeze levels presumed to have overwintered in cold ( 2°C) waters. Fish overwintering inshore differed from offshore fish in allele sharing and in (δμ) 2 distances, while fish with low antifreeze levels did not. Subpopulation structure ( Rst) was detected when offshore cod were compared with inshore cod with high levels of antifreeze but not when compared with those with low levels of antifreeze. These results suggest that cod overwintering inshore are genetically distinct from offshore cod. Inshore and offshore cod from the areas studied remain genetically distinct despite the fact that individuals from the two populations intermingle inshore during the summer and fall feeding migration. Thus, we found evidence of population structure at a finer geographical scale than has been shown to date for this species.

Mitochondrial DNA sequence variation and genetic stock structure of Atlantic cod (Gadus morhua) from bay and offshore locations on the Newfoundland continental shelf.

Bay cod, Atlantic cod (Gadus morhua) that over-winter in the deep-water bays of north-eastern Newfoundland, have historically been regarded as distinct in migration and spawning behaviour from offshore (Grand Bank) cod stocks. To investigate their genetic relationships, we determined the DNA sequence of a 307-base-pair portion of the mitochondrial cytochrome b gene for 236 adult cod taken from the waters off north-eastern Newfoundland, including fish found over-wintering and spawning in Trinity Bay. Although 17 genotypes were found, a single common genotype occurs at a frequency of greater than 80% in all samples, and no alternative genotype occurs at a frequency of greater than 3%. Genotype proportions did not differ significantly among samples. Measures of genetic subdivision among sampling locations are nil. Cod over-wintering in Trinity Bay are not genetically distinct from offshore cod. In combination with tagging and physiological studies, these data suggest that there is sufficient movement of cod between bay and offshore locations to prevent the development or maintenance of independent inshore stocks. Adult cod that over-winter in Trinity Bay appear to represent an assemblage of temporarily nonmigratory fish that have become physiologically acclimated to cold-water inshore environments. The pattern of genetic variation in northern cod suggests a recent population structure characterized by extensive movement of contemporary individuals superimposed on an older structure characterized by a bottleneck in the population size of cod in the north-western Atlantic.

The interaction between offshore cod trawlers and harp Phoca groenlandica and hooded Cystophora cristata seals off Newfoundland, Canada

The direct interaction between the seals and the trawl or dragger fishery results in seals being trapped in trawler nets and either drowned, released, or killed. A study undertaken between 17 and 27 February 1992 showed that more seals interacted with the net whilst fishing for Atlantic cod Gadus morhua in 450 fathoms of water (10–60 seals) than when fishing for witch Glyptocephalus cynoglossus in over 750 fathoms of water (0–6 seals). Seals were captured only whilst fishing for Atlantic cod (eight harp seals and two hooded seals). Harp seals Phoca groenlandica (33.2±21.8) were more plentiful around the trawler than hooded seals (0.8±0.4) and adult male harp seals were most common (73%). The impact of the seals on the caught fish was negligible with less than 0.002% of the catch being taken by the seals. All observations (n=32) of seals eating Atlantic cod showed that they swallowed them head first and whole. The number of seals captured can be reduced by altering setting methods, and the provision of a runway for the seals over the work deck to the side of the trawler would obviate the need to kill them. We hypothesize that the apparent increase in harp sea/trawler interactions is the result of smaller catches of cod, with consequential decrease in spillage from the nets requiring the seals to enter the nets to obtain cod. This results in increased by-catch of seals.

Post-Mortem Glycolytic and Associated Changes in the Muscle of Trap- and Trawl-Caught Cod

Glycolytic activity in the muscle of heavily-feeding trap-caught cod (Gadus morhua) during the struggle involved in catching, and the subsequent post-mortem changes during holding in ice and at ambient temperatures were investigated. Struggling of the fish in the trap and during boating was sufficient to cause a partial depletion of the muscle energy reserves, as indicated by lactate production and nucleotide dephosphorylation and deamination. One cod from the trap, boated and killed without apparent struggling, had a high initial glycogen content of 550 mg/100 g. During subsequent storage of the brailed fish in air or ice the glycolytic processes, including nucleotide degradation, continued, although during the early post-mortem period the rate of lactate production greatly exceeded that of glycogen depletion. Little change in concentration of the metabolites occurred on freezing and storage at −26 °C for 4–6 weeks. In contrast, trawled offshore cod and haddock, regardless of ante-mortem treatment, contained little or no glycogen; almost complete dephosphorylation and deamination of the nucleotide compounds had occurred during the struggle involved in catching. Therefore, at the time of boating, the energy reserves in the trawled fish have been exhausted or nearly so.