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 F _ST and R _ST 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. D _A and D _SW 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.     

Nine new polymorphic microsatellite loci for the amplification of archived otolith DNA of Atlantic cod,Gadus morhua L.

Nine out of 22 microsatellite primers tested were successfully amplified on three samples of cod Gadus morhua L. (two contemporary and one archived otolith samples). All loci were polymorphic (5–23 alleles/locus). The average observed heterozygosity across loci and samples was 0.625, ranging from 0.294 to 0.895 at each locus. All loci were under Hardy–Weinberg equilibrium, except PGmo56 that showed significant excess of heterozygotes in all studied samples. The isolated loci were suitable for degraded DNA and therefore useful for conducting a long‐term temporal study with DNA obtained from archived otoliths of cod.     

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).     

A reappraisal of activity metabolism in Atlantic cod (Gadus morhua)

Atlantic cod ( Gadus morhua ) were forced to swim in a swim tunnel respirometer until fatigued; oxygen consumption rate (O₂) was measured during swimming at incremental speeds until the fish was exhausted and during recovery from exhaustion. Maximal oxygen consumption (O_2max) occurred during maximal activity as has been found for other fish species, but at odds with the current paradigm for Atlantic cod. Earlier experiments had drawn the conclusion that O_2max in Atlantic cod occurs during recovery from exhaustive exercise. We found no support for this paradigm in our experiments and we propose that the respiratory physiology of Atlantic cod is not unlike that of other fishes.     

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.     

Microsatellite variation in cod Gadus morhua throughout its geographic range

Previous genetic studies using neutral markers such as allozymes, mtDNA and minisatellite loci have demonstrated varying amounts of population structure in cod Gadus morhua throughout the Atlantic. Microsatellite loci, which are potentially the most informative of presently available neutral genetic markers, have been applied extensively within western and eastern Atlantic areas but not on a range-wide basis. In the present study, six microsatellite DNA loci were used to screen cod samples from nine locations throughout the geographic range from the Scotian Shelf in the West Atlantic to the Barents and Baltic Seas in the east. Overall F _ST value was 0·03 ( P = < 0·001) across all samples. Statistically significant population differences over all loci combined were evident between more geographically distant samples, using either heterogeneity tests or F _ST analysis, with at least one locus showing significant differences between all samples (prior to Bonferroni correction). A significant correlation was observed between genetic and geographical distance, suggesting a higher level of historical and contemporary gene flow between adjacent populations than more distant populations. Samples from either end of the geographic range (Scotian Shelf and Baltic Sea) were particularly distinct when analysed using the STRUCTURE programme and also showed a high level of self-assignment when individuals of either the Scotian Shelf or Baltic Sea were tested against the entire data set. The present microsatellite study demonstrates a high level of geographic population structure between the western Atlantic, middle and eastern Atlantic and Baltic Sea, and thus, the findings should be useful in devising overall management and conservation strategies for the species.     

Potential fitness benefits from mate selection in the Atlantic cod (Gadus morhua)

Little evidence of benefits from female mate choice has been found when males provide no parental care or resources. Yet, good genes models of sexual selection suggest that elaborated male sexual characters are reliable signals of mate quality and that the offspring of males with elaborate sexual ornaments will perform better than those of males with less elaborate ornaments. We used cod (Gadus morhua L.), an externally fertilizing species where males provide nothing but sperm, to examine the potential of optimal mate selection with respect to offspring survival. By applying in vitro fertilizations, we crossed eight females with nine males in all possible combinations and reared each of the 72 sib groups. We found that offspring survival was dependent on which female was mated with which male and that optimal mate selection has the potential to increase mean offspring survival from 31.9 to 55.6% (a 74% increase). However, the size of the male sexual ornaments and sperm quality (i.e. sperm velocity and sperm density) could not predict offspring survival. Thus, even if there may be large fitness benefits of mate selection, we might not yet have identified the male characteristics generating high offspring survival.     

Isolation by distance in the Atlantic cod, Gadus morhua, at large and small geographic scales

Genetic isolation by distance (IBD) has rarely been described in marine species with high potential for dispersal at both the larval and adult life-history stages. Here, we report significant relationships between inferred levels of gene flow and geographic distance in the Atlantic cod, Gadus morhua, at 10 nuclear restriction-fragment-length-polymorphism (RFLP) loci at small regional scales in the western north Atlantic region (< 1,600 km) that mirror those previously detected over its entire geographic range (up to 7,300 km). Highly significant allele frequency differences were observed among eight northwestern Atlantic populations, although the mean FST for all 10 loci was only 0.014. Despite this weak population structuring, the distance separating populations explained between 54% and 62% of the variation in gene flow depending on whether nine or 10 loci were used to estimate Nm. Across the species' entire geographic range, highly significant differences were observed among six regional populations at nine of the 10 loci (mean FST = 0.068) and seven loci exhibited significant negative relationships between gene flow and distance. At this large geographic scale, natural selection acting in the vicinity of one RFLP locus (GM798) had a significant effect on the correlation between gene flow and distance, and eliminating it from the analysis caused the coefficient of determination to increase from 17% to 62%. The role of vicariance was assessed by sequentially removing populations from the analysis and was found to play a minor role in contributing to the relationship between gene flow and distance at either geographic scale. The correlation between gene flow and distance detected in G. morhua at small and large spatial scales suggests that dispersal distances and effective population sizes are much smaller than predicted for the species and that the recent age of populations, rather than extensive gene flow, may be responsible for its weak population structure. Our results suggest that interpreting limited genetic differences among populations as reflecting high levels of ongoing gene flow should be made with caution.     

Genetic variation and population structure of cod, Gadus morhua L., in some fjords in northern Norway

Biochemical genetic polymorphism in cod from several fjords in Troms, northern Norway was analysed. Gene frequencies at several polymorphic loci ( Hb, Pgi, Ldh, Pgm, Gpd and Idh ) are given. Significant variation was found both within and between fjords, and even between samples from the same locality sampled in different years, indicating a mosaic structure of the cod population in the area studied. The results of the haemoglobin variation are compared to similar results obtained more than 20 years ago in the same and adjacent areas. The biochemical genetic variation is discussed in relation to stability of gene frequencies, isolation mechanisms and migration patterns.     

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 ( N _e ) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and N _e '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 N _e showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by N _e '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 N _e  << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species' biology and extremely low N _e / N ratios. Our data suggest that very small N _e '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.     

Plasticity in activity and latency to explore differs between juvenile Atlantic cod Gadus morhua across a temperature gradient

In the current study activity and latency to explore, as well as the correlation of these traits, were examined in individually marked juvenile Gadus morhua at 7, 10 and 13° C. It was concluded that individual rank order of both traits was maintained across temperature but that the level of change differed between individuals.     

Comparing microsatellite variation in north-east Atlantic cod (Gadus morhua L.) to genetic structuring as revealed by the pantophysin (Pan I) locus

Variation at seven microsatellite loci was compared with variation observed at Pan I, a single copy nuclear DNA gene coding for pantophysin, in 14 samples of Atlantic cod ( Gadus morhua ) stretching from Spitsbergen to the North Sea. Population structuring indicated by the two types of markers was concordant and in agreement with the traditional grouping of cod in the study area into three main populations: north-east Arctic cod (NEAC), Norwegian coastal cod (NCC) and North Sea cod (NSC). Microsatellites, however, revealed genetic heterogeneity not only within NCC, as did Pan I, but also within NEAC and NSC, which appeared to be homogenous when analysed for Pan I. Moreover, microsatellites displayed lower levels of differentiation than Pan I between NEAC and two other groups. Differences in the magnitude of differentiation for the two types of markers may be attributable to higher levels of polymorphism and alleged selective neutrality of microsatellites. Isolation by distance was clearly apparent for microsatellites but was less evident for Pan I, indicating that environmentally induced selection appears to shape the patterns of genetic differentiation for this marker. Even though the population structure of north-east Atlantic cod, as revealed by microsatellites and Pan I, appears to be maintained largely by restricted gene flow, selection acting on a recent historical time scale probably contributes to the observed geographic pattern of Pan I frequencies.     

Effects of freezing on length and mass measurements of Atlantic cod Gadus morhua in the Baltic Sea

An aggregated sample of 925 Atlantic cod Gadus morhua collected by four countries in different regions of the Baltic Sea during different seasons were measured (total length, L_T = 161–890 mm and weighed (mass, M = 45–6900 g) both before freezing and after defrosting. The cod were found to decrease significantly in both L_T and M following death and frozen storage. There was an average (±SD) change in L_T of −2.91% (±0.05%) following freezing, independent of starting L_T. Total M changed by −2.65% (±0.14%), independent of starting mass. Shrinkage of L_T and M did not differ significantly between 1 and 4 months frozen storage, though L_T shrinkage was significantly greater after 1 or 4 months in the freezer compared with after 5 days. There was significant variation in L_T and M shrinkage between regions of capture. A significant negative relationship between condition of cod and L_T or M change was also observed. Equations to back-calculate fresh L_T and M from thawed L_T, M and standard length (L_S), gutted L_T, gutted L_S and gutted M are provided.     

Size‐dependent social attraction and repulsion explains the decision of Atlantic cod Gadus morhua to enter baited pots

The present study tested whether the presence of already retained fishes inside baited fish pots acted as a social attraction and affected the entrance probability of Atlantic cod Gadus morhua in a fjord in northern Norway. Video analysis revealed that the probability of an entrance initially increased with the presence of low numbers of fishes inside the pot, but subsequently decreased at a critical number of caught fishes. The critical number was dependent on the size of the G. morhua attempting to enter. This demonstrates that social attraction and repulsion play a role in G. morhua pot fishing and has important implications for the capture efficiency of fisheries executed with pots.     

Winter feeding ecology of cod (Gadus morhua) in a fjord of southern Norway

We investigated the winter feeding ecology of cod ( Gadus morhua ) in the Risørfjord and Flødevigen areas on the Skagerrak coast, southern Norway. Diets from the ice-covered Risørfjord were compared with diets from the more coastal Flødevigen area. In the Risørfjord area the diet featured numerically both decapods (56.0%) and fish (27.8%), but fish dominated by mass (75.1%). The most numerous dietary items from the Flødevigen area were decapods (48.1%) and isopods (30.6%), although fish still made up the bulk of the diet's mass (52.6%). Diets at Flødevigen shifted from winter to spring, as polychaetes became important numerically (67.8%) and also contributed substantially by weight (53.6%). Since cod feed opportunistically, differences between areas and seasons probably reflected differences in prey diversity and abundance. Prey size variability increased with increasing predator length, but maximum prey size relative to predator length was constant at about 9%. Prey fish increased in both length and numbers with the length of cod, particularly in the Risørfjord area, where fish were more important in the diet than at Flødevigen. However, the majority of fish consumed in both areas were small gobiids. Based on growth patterns observed in otoliths, with opaque zones (indicating faster growth) formed during winter, the quality and quantity of the winter diet may determine annual growth rates of cod on the Skagerrak coast. Fish and decapods constituted important, high energy food sources, and there was little indication that cod were food limited during winter in this area.     

The distribution of Cryptocotyle spp. metacercariae in the skin of caged Atlantic cod (Gadus morhua)

In caged Atlantic cod (>40cm), Cryptocotyle spp. metacereariae were concentrated on the dorsal surface, but relatively scarce on the fins. Behaviour and mechanical forces probably affect this distribution.     

Genetic differentiation among Atlantic cod in south and south-east Icelandic waters: synaptophysin (Syp I) and haemoglobin (HbI) variation

Significant differences were found at the synaptophysin ( Syp I) locus between two groups of Icelandic cod Gadus morhua ; Loftstaõahraun (spawning ground), Reykjanesgrunn and Eyrabakkabugur (feeding grounds) on the one hand and Kantur (spawning ground) and Austfjarõadjúp (feeding ground) on the other. There was also a considerable genetic heterogeneity within the former group. The results indicate that the cod in south and south-east Icelandic waters do not belong to one panmictic population.     

Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994

We report on evidence of long term stability inthe geographic pattern of geneticdifferentiation among cod (Gadus morhua)collected from 5 spawning banks offNewfoundland and Labrador over a periodspanning three decades (1964–1994) and 2orders of magnitude of population sizevariation. Six microsatellite DNA lociamplified from archived otoliths (1964 and1978) and contemporary (1990s) tissue samplesrevealed fidelity to natal spawning banks overthis period. A two level (spawning bank anddecade) hierarchical and multilocus AMOVAindicated that 1.55% of the total variation inallele frequencies could be attributed(P = 0.036) to spatial structure while novariance component could be attributed totemporal changes. A finer scale analysis amongcod from just 3 of these spawning banksreveals, however, evidence consistent with somepost-collapse mixing between cod from twobanks. In the context of fisheries managementand conservation, the survival of the spatialpattern of genetic differentiation during thepopulation collapse suggests that if recoveryeventually occurs it will likely be throughpopulation re-growth in situ rather thanby migratory influx.     

Allometric growth in juvenile cod (Gadus morhua) and possible effects on cannibalism

Cod juveniles of about 20 mm had the lowest potential predator: prey length ratio based on mouth gape of the predator and the body height of the prey. This implies that the cannibalistic potential is maximized in this size range.