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 northeastern 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 northeastern 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 demography of a haemoglobin polymorphism in the Atlantic cod, Gadus morhua L.

Genetic stability was investigated at a polymorphic haemoglobin gene-locus in 13 124 Atlantic cod, Gadus morhua L. A total of 30 year-classes, sampled over 18 years, were variously sampled in 33 named localities. Regional populations showed distinctive allele frequencies, and each major cod fishery showed some degree of genetic imbalance, which was expressed as excessive numbers of homozygotes. This imbalance occurred seasonally in a proportion of the population samples in each of the major cod fisheries. The findings are attributable to migrations of distinctive genetic populations.     

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.     

Antimicrobial activity in serum of Atlantic cod Gadus morhua L.: comparison between cultured and wild fish

The present investigation determined the antibacterial activities in the sera of both cultured and wild Atlantic cod Gadus morhua . Serum samples from both groups of fish were quantified for total protein, and their effects against fish pathogens Listonella anguillarum , Aeromonas salmonicida and Yersinia ruckeri were determined using co-incubation assay. Total serum protein concentrations were not significantly different between farmed and wild Atlantic cod. Sera of cultured Atlantic cod significantly decreased growth of L. anguillarum by at least two-log₁₀ reductions in bacterial count, while those of the wild Atlantic cod were able to inhibit the growth of all three fish bacterial pathogens. The present study showed that sera from wild fish possess broader antibacterial activities than cultured Atlantic cod and that these could provide an explanation for the differences regarding their immunity to bacterial infections as well as their health status.     

Absence of restriction site variation in the mitochondrial ND5 and ND6 genes of Atlantic salmon amplified by the polymerase chain reaction

There was no restriction site variation in Atlantic salmon mitochondrial DNA in an amplified DNA segment beginning in the ND5 gene and terminating in the ND6 gene, although seven haplotypes were observed when the complete molecule was restricted.     

A retrospective approach to fractionize variation in body mass of Atlantic cod Gadus morhua

Eggs of a single spawning batch from wild-caught Norwegian Atlantic cod Gadus morhua were hatched and first fed on either natural zooplankton or enriched rotifers Brachionus plicatilis during the larval period. Juvenile G. morhua (initial mass 14·2 g) from the two first-feeding groups were then reared for 3 months under a variety of temperature (10 and 14° C) and salinity (15 and 32) combinations. All fish were individually tagged and microsatellite markers were used in a multiplex to trace the pedigree of all fish and body mass variation analysed according to different environmental and genetic sources. After the termination of the laboratory trial, the fish were transferred to land-based tanks and later to sea pens and reared at ambient conditions for 26 months until they were harvested in March 2009. Growth gain from the larval and juvenile periods was persistent during the 26 months of sea pen ongrowing. The final mass of the zooplankton group was 12% higher compared to the B. plicatilis group. Similarly, rearing under a temperature of 14° C and salinity of 15 during the initial 3 month period during the early juvenile stage resulted in 7-13% larger size at harvesting compared to the other three temperature and salinity combinations. The study indicates that the first-feeding method and temperature and salinity manipulation explain nearly 90% of the body mass variation explained by the model. The genetic effect (measured as body mass variation within the families studied) only accounted for c. 2% during the initial rearing period, whereas it has a large effect on growth variation (30%) during the long-term rearing at ambient conditions. Sex proportion and final maturation did not differ between family groups, and no interaction between sex and family group was seen.     

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.     

Gastric emptying in cod, Gadus morhua L.: emptying and retention of indigestible solids

Particles 2 mm or smaller may be passed relatively easily through the pylorus of the cod, Gadus morhua L., but, under some conditions, 5 mm particles are held in the stomach for prolonged periods. The emptying of indigestible particles appears to be impaired by the consumption of additional meals, and prolonged retention of these particles may occur in fish fed multiple meals. The findings agree in general with those reported for mammals and the results are discussed in relation to mechanisms thought to control gastric motor activity patterns.     

Lethal oxygen levels at different temperatures and the preferred temperature during hypoxia of the Atlantic cod, Gadus morhua L.

The behavioural thermoregulation of Atlantic cod Gadus morhua L. was investigated in a shuttlebox at normoxia and at three levels of hypoxia: 30, 20 and 15% oxygen saturation.
The preferred temperatures at normoxia, 30, 20 and 15% oxygen saturation were 13·9, 13·1. 10·0 and 8·8° C, respectively.
A decrease in metabolism and an increased blood oxygen affinity are among the physiological advantages of selecting a lower temperature during hypoxia. Furthermore the chances of surviving low oxygen saturations are better at low temperatures.
In natural environments, this behaviour may result in habitat shifts of fish living in heterothermal environments with changing oxygen saturations, especially in coastal areas with eutrophication, as for example the Baltic Sea.     

Choosing where to feed: the influence of competition on feeding behaviour of cod, Gadus morhua L.

Groups of cod, Gadus morhua L, presented with two feeding patches with a food abundance ratio of 2:1, distributed themselves between the patches in a ratio of 2.5:1. This is slightly higher than the 2:1 ratio predicted by the ideal free distribution theory. Large differences were observed in competitive ability between individual fish. A strong correlation was found between feeding success of individuals and time spent in a feeding patch. The more successful competitors caught about 2.5 times as many food items in the rich patch as in the poor patch. The less successful competitors caught an equal amount of food in both patches. All competitors, however, spent significantly more time in the rich patch. These results suggest that hunting success is the most important factor in assessing patch quality. However, it is not the only parameter which cod use in deciding where to feed.     

Genetic and environmental components of phenotypic variation in body shape among populations of Atlantic cod (Gadus morhua L.)

A common-garden experiment was conducted on larvae to test for genetic differences in body shape among populations of Atlantic cod ( Gadus morhua ). Offspring from four north-west Atlantic regions were reared from hatching to postmetamorphosis at two temperatures (7 ± 1 °C and 11 ± 1 °C) and two food levels (1500 and 4500 prey L⁻¹). Body shape differed between populations and treatments. Population differences were greatest between south-west Scotian Shelf cod and those further north; the former were characterized by a deeper body, larger head, and longer caudal peduncle than cod from the other populations. Significant differences were also observed between two putative populations on the south-west Scotian Shelf, suggesting genetic divergence between spawning aggregations at small spatial scales (< 100 km). Temperature and food supply also influenced body shape, with the effect of the former being more pronounced. Individuals reared at the higher temperature or food level had a deeper body and a larger head than those reared at the lower temperature or food supply. Phenotypic responses to changes in the rearing environment also differed among populations, indicating genetic differences in phenotypic plasticity. Differences between populations in morphology and in phenotypic plasticity suggest genetic divergence at both large (> 1000 km) and small (< 100 km) spatial scales. The genetic differences at large spatial scales counteracted the expected effects of temperature differences in the wild, suggesting countergradient variation in morphology among these populations.  © 2006 Her Majesty the Queen in Right of Canada. Journal compilation © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 351–365.     

Structural studies of the O-antigenic oligosaccharide from Vibrio salmonicida strain C2 isolated from Atlantic cod, Gadus morhua L

We report the chemical structure of the oligosaccharide part of Vibrio salmonicida lipopolysaccharide serotype C2, isolated from Atlantic cod (Gadus morhua L.). The structure was established by NMR spectroscopy and mass spectrometry. It is concluded that the oligosaccharide has the following structure in which L-alpha-D-Hepp is L-glycero-alpha-D-manno-heptopyranose, D-alpha-D-Hepp is D-glycero-alpha-D-manno-heptopyranose, alpha-NonA is 5-acetamidino-7-acetamido-3,5,7,9-tetradeoxy-L-glycero-alpha-D-galacto-nonulosonic acid, and PEA is phosphoethanolamine. [chemical structure: see text]     

Time of start of spawning in Atlantic cod (Gadus morhua) females in relation to vitellogenic oocyte diameter, temperature, fish length and condition

Spawning time of female Atlantic cod ( Gadus morhua L.) can be predicted to within 3 days using vitellogenic oocyte diameters measured over the last month before spawning. Simulations show that a l°C drop in temperature during vitellogenesis delays spawning by about 8–10 days. Similar results were obtained with fish on low ration for 4–8 months before spawning. Moderately fed females held over two to four consecutive spawning seasons demonstrated a significant delay (⋍3–40 days) in the date of first spawning as the fish grew older and more fecund. Forecasting studies on spawning migrating Arcto-Norwegian cod gave no evidence of a significant effect of fish length on the time of spawning. Warmer water temperature during vitellogenesis for the larger fish appears to compensate for the negative effect of fecundity On spawning time.     

Mitochondrial DNA in the Atlantic cod, Gadus morhua: lack of genetic divergence between eastern and western populations

Mitochondrial DNA variation was examined in two populations of Atlantic cod from the North Sea and the Grand Banks of Newfoundland. Eight restriction enzymes revealed no major genetic difference between these eastern and western populations. These results are discussed in relation to earlier electrophoretic studies on this species.     

Mitochondrial DNA variation in Atlantic capelin, Mallotus villosus: a comparison of restriction and sequence analyses

Divergence estimates were calculated using restriction analysis and cytochrome-b sequences for capelin Mallotus villosus mitochondrial genomes sampled from Newfoundland and Norwegian populations. On average, pairwise divergence values based on cytochrome-b sequences were 2.7 times greater than those based on restriction data. Since the rate of evolution in the cytochrome-b gene is low, it appears that restriction analysis underestimated divergence values, possibly due to limited sensitivity of this method when variable nucleotide positions are not randomly distributed. Mitochondrial genotypes were not shared among the two populations.     

Buoyancy variations in eggs of Atlantic cod (Gadus morhua L.) in relation to chorion thickness and egg size: theory and observations

Egg specific gravity is a function of egg volume, chorion volume, perivitelline space (PVS) and the specific gravity of chorion and ovoplasm. Experimental studies on cod ( Gadus morhua L.), a marine multiple batch spawner, showed that approx. forty per cent of the chorion volume is incorporated between batches and that the chorionic material has a mean specific gravity of 1·20 (range: 1·14–1·35). The chorion volume and specific gravity are low at the end of the spawning period in extremely fecund fish. Specific gravity of ovoplasm was observed to be 1·017 in marine eggs and calculated to be about 1·008 in brackish water eggs. Inherent variation in PVS is found to have little influence on egg specific gravity. With the other variables constant, egg specific gravity is inversely related to egg volume supported by studies on single batches of eggs. Measurements on every batch of eggs reveal that the production of large eggs (>1·3 mm) gives low density eggs initially and high density eggs towards the end of spawning, while the production of small eggs (<1·3mm) gives moderate specific gravity. These observations are discussed in relation to vertical distribution of the eggs and reproductive success of recruit and repeat spawners. There are indications that repeat spawners produce larger eggs.     

Detection of pathogenic Entamoeba histolytica DNA in liver abscess fluid by polymerase chain reaction.

, , and 1992. Detection of pathogenic Entamoeba histolytica DNA in liver abscess fluid by polymerase chain reaction. International Journal for Parasitology 22: 1193–1196. A sensitive method for detection of pathogenic Entamoeba histolytica DNA in drained fluids from liver abscess patients, using the polymerase chain reaction (PCR), has been developed. The PCR employs oligonucleotide primers specific for the gene encoding the 30 kDa molecule of pathogenic E. histolytica. Liver abscess fluids (19 samples), from 14 patients with a presumptive amebic liver abscess, were examined microscopically and by the PCR method. Only two of the 19 samples were positive microscopically, whereas all 19 samples tested positive by PCR. This technique can be used to confirm the diagnosis of amebic liver abscess.     

Microparticles from condensed DNA formed in the process of polymerase chain reaction

DNA microparticle formation in the course of a polymerase chain reaction (PCR) is reported. PCR with gene-specific and partially complementary primers and yeast genomic DNA as a template was shown to yield spherical DNA-composed microparticles as well as their aggregates and conglomerates, along with routine linear DNA. Microparticles were formed at late PCR stages and could be easily identified by the reaction with fluorescently labeled oligonucleotide primers or by staining of the PCR mixture with fluorescent dyes (acridine orange, propidium iodide or DAPI). According to the data of epifluorescent and electron microscopy, the microparticle size varied from 500 nm to 3–4 μm and the particles were multimeric star-shaped spheres or aggregates formed by several fused microspheres. Some properties of the microspheres were studied. It was found that the Mg⁺² cations comprising the PCR buffer played a key role in the formation of microparticles and the stabilization of their structures.     

Variation in coding exons of two electrophoretic alleles at the pigtail macaque carbonic anhydrase I locus as determined by direct,double-stranded sequencing of polymerase chain reaction (PCR) products

Two, electrophoretically distinct, forms of carbonic anhydrase I (CA Ia and CA Ib) are found at high polymorphic frequencies in red cells of natural populations of pigtail macaques,Macaca nemestrina, from southeast Asia. By use of the polymerase chain reaction, exons of the CA I gene were amplified from homozygous (a/a, b/b) and heterozygous (a/b) animals. Direct sequencing of the amplified DNA from four animals revealed differences between the a and the b electrophoretic alleles ranging from three to six nucleotides, and from one to three differences within each allele. These results indicate a greater genetic variability at the CA I locus in this macaque species than previously realized. We thank the personnel of the University of Washington, Regional Primate Research Center, Seattle, for sending us blood and tissue samples from pigtail macaques (supported by NIH Grant RR 00166). Our work was supported by NIH Grant GM 24681.     

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.