On genetic differentiation of the Pacific cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> tilesius, 1810 (Gadiformes: Gadidae)

The variability of the Gmo3, Gmo34, Gmo35, and Pgmo32 DNA microsatellite loci in Pacific cod Gadus macrocephalus samples from different areas of the North Pacific was analyzed. The data obtained show that Pacific cod from the southern Kuril Islands significantly differs from the populations of the Bering Sea, the Sea of Okhotsk, and the coastal waters of Canada (the microsatellite loci Gmo3 and Pgmo32 bear the highest differentiating capacity). Despite the significant geographical remoteness of these areas from one another, the above three Pacific cod populations exhibit a high degree of similarity (I = 0.997–0.999).     

Variability of microsatellite loci of Greenland cod <Emphasis Type="Italic">Gadus ogac</Emphasis> Richardson 1836: Comparison with other species of <Emphasis Type="Italic">Gadus</Emphasis> genus (Gadidae)

Comparative analysis of variability of seven microsatellite loci—Gmo3, Gmo-G12, Gmo-G18, Gmo19, Gmo34, Gmo35 and Pgmo32—was performed for the Greenland cod Gadus ogac, Pacific cod G. macrocephalus, Atlantic cod G. morhua, and White Sea cod G. morhua marisalbi. High genetic identity was observed between the Greenland cod and Pacific cod (I = 0.9520). Pair analysis of genetic differentiation was performed on the studied microsatellite loci according to θ (analogue of F _ST). The Greenland cod differed significantly from the Pacific, Atlantic, and the White Sea cod; however, the differentiation level varied. The lowest value was observed for the pair Greenland cod-Pacific cod (0.123), and the highest levels were registered for the pairs Greenland cod-Atlantic cod (0.605) and Greenland cod-White Sea cod (0.535).     

Formation of genetic diversity in populations of pacific cod (Gadus macrocephalus Tilesius) (Gadidae)

The variability of the Gmo3, Gmo34, Gmo35, Pgmo32, Gmo19 microsatellite DNA loci was examined in the population samples of Pacific cod from different parts of the North Pacific Ocean. The statistical tests showed that the differentiation of the population was the result of different levels of reproductive autonomy of the individual Pacific cod populations, formed in the Pleistocene-Holocene period with the specific features of transgressions and regressions of the World Ocean, and supported by the existing system of currents and the features of the migratory behavior of cod in North Pacific.     

Preliminary data on the variability of three microsatellite loci in Pacific <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> and Atlantic <Emphasis Type="Italic">G. morhua</Emphasis> cod (Gadidae)

Variability of microsatellite DNA loci Gmo3, Gmo34, and Gmo35 is studied in samples of Pacific cod Gadus macrocephalus and Atlantic cod G. morhua. The results show high values of identity of the samples within the North Pacific basin (0.9766–0.9924) and within the Northeast Atlantic basin (0.9580). Based on the pairwise assessment of genetic differentiation, the F _ST values are significantly different in all variants between the samples of Pacific and Atlantic cod (F _ST = 0.5235–0.6719, p < 0.001). Within the basins, the significant differences in the frequencies of main alleles are revealed in the loci Gmo3 and Gmo34 for the samples from the Pacific and Atlantic oceans, respectively.     

Data on variation of microsatellite loci in Kildin cod <Emphasis Type="Italic">Gadus morhua kildinensis</Emphasis> (Gadidae)

Variation of microsatellite loci Gmo8, Gmo-G12, Gmo-G18, Gmo19, PGmo32, Gmo34, and Gmo35 is investigated in Kildin cod Gadus morhua kildinensis. The investigated loci are characterized by a low level of variation: five loci are represented by two-allele systems and three loci are monomorphic. Mean value of heterozygosity calculated by all investigated loci is lower in Kildin cod than in Atlantic Gadus morhua—0.2854 vs. 0.5667.     

Seasonal distribution and migrations of Pacific cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> (Gadidae) in the northwestern part of the Sea of Japan and adjacent water areas

On the basis of materials collected in 32 expeditions in the northwestern part of the Sea of Japan from 1984 to 2009, seasonal and interannual dynamics of biomass of Pacific cod Gadus macrocephalus stock was analyzed. Seasonal variation of spatial and bathymetric distributions of this species is considered. The conclusion of the existence of seasonal migrations of cod along the continental coast is substantiated.     

Simultaneous Analysis of Six Microsatellite Markers in Atlantic Cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>): A Novel Multiplex Assay System for Use in Selective Breeding Studies

A novel hexaplex assay system including Gmo8, Gmo19, Gmo35, Gmo37, Tch11, and Tch12 microsatellites from Atlantic cod, consisting of trinucleotide or tetranucleotide repeat units, is introduced. All 6 loci were coamplified in a single reaction employing dye-labeled primers. Alleles from these loci were sized using an internal standard by automated sample processing in an ABI 310 Genetic Analyser. Amplified alleles in profiles containing selected microsatellites were typed clearly, providing easily interpretable results. Sequencing data indicated that alleles at all loci consisted of simple repeat units. This may help minimize the likelihood of stuttering upon polymerase chain reaction amplification. The results suggest that the presented hexaplex assay system may be a useful tool in a selective breeding program in which genetic identification will allow different genotypes to be reared together from fertilization. This should have a great impact as it will make selective breeding more efficient.     

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.     

A mitogenomic approach to the taxonomy of pollocks: <Emphasis Type="Italic">Theragra chalcogramma</Emphasis> and <Emphasis Type="Italic">T. finnmarchica</Emphasis> represent one single species

Background  

The walleye pollock (Theragra chalcogramma) and Norwegian pollock (T. finnmarchica) are confined to the North Pacific and North Atlantic Oceans, respectively, and considered as distinct species within the family Gadidae. We have determined the complete mtDNA nucleotide sequence of two specimens of Norwegian pollock and compared the sequences to that of 10 specimens of walleye pollock representing stocks from the Sea of Japan and the Bering Sea, 2 specimens of Atlantic cod (Gadus morhua), and 2 specimens of haddock (Melanogrammus aeglefinus).     

Multiple ice‐age refugia in Pacific cod,Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (F_ST = 0.028, r² = 0.33) and mtDNA (F_ST = 0.027, r² = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.     

Population Structure of Pacific Cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> in the Southern Part of the Range Based on the Microsatellite Analyses

The population structure of Pacific cod Gadus macrocephalus in the southern part of the range and adjacent regions is studied on the basis of the results of microsatellite analyses. Collected data indicate heterogeneity of this species population within the studied area. According to the obtained F_ST values, Pacific cod from the waters of the Republic of Korea (Yellow Sea side) and northwestern part of the Sea of Okhotsk significantly differ from all other studied regions (Table 4). Significant differentiation was also revealed between samples from the waters of the Tatar Strait and all other regions except for South Kurils Pacific cod (both Sea of Okhotsk and Pacific Ocean sides). These two latter sample collections were similar to each other as well. A low level of differentiation was also shown for the Peter the Great Bay and the East Sea/Sea of Japan waters of the Republic of Korea.     

EVOLUTION OF ATLANTIC AND PACIFIC COD: LOSS OF GENETIC VARIATION AND GENE EXPRESSION IN PACIFIC COD

An allozyme investigation of 41 protein-coding loci in two morphologically similar fishes, Atlantic and Pacific cod, indicates that Pacific cod experienced a severe population bottleneck that led to the loss of gene diversity and gene expression. Pacific cod possesses a significantly lesser amount of gene diversity (H = 0.032) than Atlantic cod (H = 0.125) and lacks gene expression for Me-3. Allele-frequency distributions differ between species as predicted by neutral theory: Atlantic cod has a U-shaped distribution, which is expected for populations in drift-mutation equilibrium, whereas Pacific cod has a J-shaped distribution with an excess of low-frequency alleles. This excess may be explained by the appearance of new alleles through mutation which have not yet reached intermediate frequencies through drift. The population bottleneck in Pacific cod was most likely associated with founder populations that dispersed into the Pacific Ocean after the Bering Strait opened. Under the molecular-clock hypothesis a Nei genetic distance of 0.415 (based on 41 loci) suggests that Pacific cod dispersed into the Pacific Ocean soon after the Bering Strait opened in the mid-Pliocene, 3.0 to 3.5 million years ago.     

Under-ice distribution of polar cod <Emphasis Type="Italic">Boreogadus saida</Emphasis> in the central Arctic Ocean and their association with sea-ice habitat properties

In the Arctic Ocean, sea-ice habitats are undergoing rapid environmental change. Polar cod (Boreogadus saida) is the most abundant fish known to reside under the pack-ice. The under-ice distribution, association with sea-ice habitat properties and origins of polar cod in the central Arctic Ocean, however, are largely unknown. During the RV Polarstern expedition ARK XXVII/3 in the Eurasian Basin in 2012, we used for the first time in Arctic waters a Surface and Under Ice Trawl with an integrated bio-environmental sensor array. Polar cod was ubiquitous throughout the Eurasian Basin with a median abundance of 5000 ind. km^?2. The under-ice population consisted of young specimens with a total length between 52 and 140 mm, dominated by 1-year-old fish. Higher fish abundance was associated with thicker ice, higher ice coverage and lower surface salinity, or with higher densities of the ice-amphipod Apherusa glacialis. The fish were in good condition and well fed according to various indices. Back-tracking of the sea-ice indicated that sea-ice sampled in the Amundsen Basin originated from the Laptev Sea coast, while sea-ice sampled in the Nansen Basin originated from the Kara Sea. Assuming that fish were following the ice drift, this suggests that under-ice polar cod distribution in the Eurasian Basin is dependent on the coastal populations where the sea-ice originates. The omnipresence of polar cod in the Eurasian Basin, in a good body condition, suggests that the central Arctic under-ice habitats may constitute a favourable environment for this species survival, a potential vector of genetic exchange and a recruitment source for coastal populations around the Arctic Ocean.     

Distribution and diet of 0-group cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>) and haddock (<Emphasis Type="Italic">Melanogrammus aeglefinus</Emphasis>) in the Barents Sea in relation to food availability and temperature

Distribution of 0-group cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) in August–September 2005 and 2006 was mainly restricted to the Atlantic waters of the western and central areas of the Barents Sea. The main distribution of 0-group fish overlapped largely with areas of high biomass (>7 gm⁻² dry weight) of zooplankton. The copepod Calanus finmarchicus and krill Thysanoessa inermis, which are dominant zooplankton species in both Atlantic and boreal waters of the Barents Sea, were the main prey of 0-group cod and haddock. The main distribution, feeding areas and prey of 0-group cod and haddock overlapped, implying that competition for food may occur between the two species. However, though their diet coincided to a certain degree, haddock seems to prefer smaller and less mobile prey, such as Limacina and appendicularians. As 0-group fish increased in size, there seems to be a shift in diet, from small copepods and towards larger prey such as krill and fish. Overall, a largely pelagic feeding behaviour of 0-group cod and haddock was evident from this study.     

Genetic divergence at the synaptophysin (Syp I) locus among Norwegian coastal and north-east Arctic populations of Atlantic cod

Several nuclear RFLP loci have been discovered recently that exhibit extensive allele frequency variation among Norwegian coastal and north-east Arctic populations of Atlantic cod Gadus morhua. One of these polymorphisms was detected by hybridizing an anonymous cDNA clone (GM798) against genomic DNA digested with the restriction enzyme DraI. This cDNA clone has now been sequenced and identified as synaptophysin (Syp I), an integral synaptic vesicle membrane protein. Primers were constructed that amplify an intron of the Syp I gene that is polymorphic for the DraI site, thus making it possible to use a PCR-based assay to score the polymorphism. A total of 965 individuals sampled from the Barents Sea, coastal areas and fjords in northern Norway have been analysed for this polymorphism. The results confirm that highly significant differences exist between NE Arctic and coastal cod at the Syp I locus. A cluster analysis revealed a deep split between coastal and Arctic populations and hierarchical F-statistics indicated that about 40% of the total variation was attributable to differences between Arctic and coastal groups. The temporal stability of allele frequencies was assessed by comparing Syp I allele frequencies among samples of juveniles (0 group) captured at specific locations in fjords in consecutive years and among samples of adults and juveniles collected from the same fjord. Samples of juveniles collected in 1994 and 1995 in Malangen were genetically indistinguishable whereas juveniles sampled from Dønnesfjord and Ullsfjorden over the same 2-year period exhibited significant differences. Adults and 0-group individuals collected from the same fjord were found to be genetically indistinguishable in Malangen, but not in Balsfjorden. In addition to detecting large differences among Arctic and coastal groups, the Syp I locus suggests that genetic heterogeneity exists among resident populations of cod in different fjords and that gene flow among populations throughout northern Norway may be considerably lower than previously believed.     

Brief morphological characteristics of cod <Emphasis Type="Italic">Gadus macrocephalus</Emphasis> (Gadidae) from coastal waters of the Komandor Islands

The results of the studies on morpho-biological characteristics of Pacific cod Gadus macrocephalus of Bering Island coastal waters (Komandor Islands) are presented. As assessed by several morphometric indices, the studied cod differs from the cod of the Bering Sea.     

Genetic divergence in nuclear genomes between populations of <Emphasis Type="Italic">Fagus crenata</Emphasis> along the Japan Sea and Pacific sides of Japan

Genetic diversity and structure in Fagus crenata were studied by analyzing 14 nuclear microsatellite loci in 23 populations distributed throughout the species’ range. Although population differentiation was very low (F _ST = 0.027; R _ST = 0.041), both neighbor-joining tree and Bayesian clustering analyses provided clear evidence of genetic divergence between populations along the Japan Sea (Japan Sea lineage) and Pacific (Pacific lineage) sides of Japan, indicating that physical barriers to migration and gene flow, notably the mountain ranges separating the populations along the Japan Sea and Pacific sides, have promoted genetic divergence between these populations. The two lineages of the nuclear genome are generally consistent with those of the chloroplast genome detected in a previous study, with several discrepancies between the two genomes. Within-population genetic diversity was generally very high (average H _E = 0.839), but decreased in a clinal fashion from southwest to northeast, largely among populations of the Japan Sea lineage. This geographical gradient may have resulted from the late-glacial and postglacial recolonization to the northeast, which led to a loss of within-population genetic diversity due to cumulative founder effects.     

Population variation in thermal growth responses of juvenile Atlantic cod (<Emphasis Type="Italic">Gadus morhua</Emphasis> L.)

Controlled environment experiments were carried out to investigate thermal influences and population differences on growth of wild-caught juvenile Atlantic cod Gadus morhua L. from two regions of differing thermal regime off Scotland; the Clyde Sea on the west coast and St Andrews Bay on the east coast. Cod from the Clyde demonstrated significantly higher growth rates than cod from St Andrews. In both populations the growth rate was greater at 12°C than at 8°C. These population and temperature effects act to reinforce one another and it could therefore be predicted that the growth differences between the two areas in the wild should be even more pronounced. The results are consistent with the suggestion that cod may be locally adapted to their thermal environment.     

Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across,but not within,basins of the Indo‐Pacific based on mitochondrial DNA

Genetic stock structure is atypical in tuna species, with most species demonstrating geographically‐broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo‐Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D‐loop) gene region. One hundred and thirty‐nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ?_ST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo‐Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.     

Feeding habits of harp seals (Phoca groenlandica) during early summer and autumn in the northern Barents Sea

The feeding habits of harp seals (Phoca groenlandica) in the Barents Sea were examined in studies conducted during June 1991, September 1990 and 1991, and October 1992. Analyses of stomach and intestinal contents were carried out and concurrent estimates of prey abundance were made using trawl gear. Harp seals appeared to feed at low intensity in the pack ice belt during the first half of June. There was little potential prey in the water column, but prawns (Pandalus borealis), capelin (Mallotus villosus) and polar cod (Boreogadus saida) were abundant close to the bottom. In September, the seals sampled in the northern pack ice areas of the Barents Sea fed on the pelagic amphipod Parathemisto libellula, krill (Thysanoessa spp.), prawns and, to a lesser extent, on fish species such as polar cod, sculpins (Cottidae) and snailfish (Liparidae). Trawling revealed that large quantities of Parathemisto libellala were present in the upper layers of the water column. Fish, mainly capelin and polar cod, were less abundant and occurred in deeper waters. In mid-October, the diet of seals in the northern Barents Sea consisted mainly of amphipods (Parathemisto sp.). Later in October, when increasing pack ice cover forced the harp seals to move south, the diet seemed to change from amphipods to fish prey, predominantly capelin and polar cod.