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193 results for “Cod”
Data for paper: The making of a genetic cline: introgression of oceanic genes into coastal cod populations in the North East Atlantic
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Data: Effects of seismic airgun playbacks on swimming patterns and behavioural states of Atlantic cod in a net pen
<p>Data abstract:</p> <p>We tracked individual fish using acoustic telemetry and exposed them to sound. Here, we provide (1) the raw acoustic tag detections, (2) the filtered/processed tag detections which served as an input for YAPS (Yet Another Positioning Solver), (3) the positions of the hydrophones (acoustic tag receivers), and (4) the positions of the fish (output of YAPS) and other relevant covariates (sun elevation, tide and treatment period).</p> <p> </p> <p>Paper abstract:</p> <p>Anthropogenic sound can affect fish behaviour and physiology which may affect their well-being. However, it remains a major challenge to translate such effects to consequences for fitness at an individual and population level. For this, energy budget models have been developed, but suitable data to parametrize these models are lacking. A first step towards such parametrization concerns the objective quantification of behavioural states at high resolution. We experimentally exposed individual Atlantic cod (<em>Gadus morhua</em>) in a net pen to the playback of seismic airgun sounds. We demonstrated that individual cod in the net pen did not change their swimming patterns immediately at the onset of the sound exposure. However, several individuals changed their time expenditure in three different behavioural states during the 1 h exposure. This may be suitable input for energy budget models that allow predictions about fitness consequences of acoustic disturbance.</p> <p> </p> <p>Paper reference:</p> <p>Hubert, J., Campbell, J. A., Slabbekoorn, H. (2020). Effects of seismic airgun playbacks on swimming patterns and behavioural states of Atlantic cod in a net pen. <em>Mar. Pollut. Bull.</em> <strong>160</strong>, 111680. DOI:10.1016/j.marpolbul.2020.111680</p>
The Pantophysin gene and its relationship with survival in Atlantic cod
Distinction between highly migratory Northeast Arctic cod and stationary Norwegian Coastal cod represents an important management issue. They overlap on the same spawning grounds where they are harvested, but display highly different abundences. This necessitates alternative management strategies. The bi-allelic genetic marker, pantophysin (Pan I), has been widely used as a diagnostic marker to discriminate between these two stocks. However, it has been proposed that this locus, or another gene(s) on chromosome 1 where it is located, may be under strong divergent selection between these two stocks. In order to address this, we compared relative survival rates between different Pan I genotypes in common garden pedigree-controlled experiments conducted in a temperature-controlled laboratory facility, and mesocosms. We found no evidence of departure from the expected 1:2:1 mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12 °C temperature regimes in the laboratory experiment weakly favoured the Pan IAA genotype thereafter. No difference was observed between genotype survival in the mesocosm experiments. These results demonstrate that there are no clear advantages of certain Pan I genotypes under the experimental conditions observed.
Data from: Seasonal dynamics of spatial distribution and overlap between Northeast Arctic cod (Gadus morhua) and capelin (Mallotus villosus) in the Barents Sea
The trophic link between cod (Gadus sp.) and capelin (Mallotus sp.) is important in many panarctic ecosystems. Since the early 2000s, the Northeast Arctic cod stock (G. morhua) in the Barents Sea has increased greatly, and the sea has been exceptionally warm. Such changes have potentially large effects on species distributions and overlap, which in turn could affect the strength of species interactions. Due to its high latitude location, the Barents Sea has strong seasonal variation in physical conditions and interactions. To study drivers of variation in cod-capelin overlap, we use data from two annual surveys run in winter and in autumn of 2004-2015. We first model winter and autumn spatial distributions of mature and immature cod and capelin. We then calculate overlap from model predictions on a grid with similar spatial resolution as the survey data. Our approach allowed us to interpret changes in overlap as species-specific effects of stock size and temperature, while accounting for sampling variation due to sampling time and depth. We found that during winter both species expanded their distribution in response to increased stock sizes, but how strongly and where the expansion occurred varied. The effect of temperature on distributions varied in space, and differed for cod and capelin and for different components of the two species. The results for autumn were clearer and more consistent. Both species expanded their distribution areas as their stock sizes increased. A positive effect of temperature was found in the north-eastern Barents Sea, where temperatures were lowest at the start of the study. Overlap increased and shifted north-eastwards during the study period and remained high despite a decline in the capelin stock. The increased overlap during autumn could mainly be attributed to the shift in cod distribution with increased cod stock biomass.
Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration
Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species. Results: Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2–5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours. Conclusions: Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.
Data from: Behavioural responses of Atlantic cod to sea temperature changes
Understanding responses of marine species to temperature variability is essential to predict impacts of future climate change in the oceans. Most ectotherms are expected to adjust their behavior to avoid extreme temperatures and minimize acute changes in body temperature. However, measuring such behavioral plasticity in the wild is challenging. Combining 4 years of telemetry-derived behavioral data on juvenile and adult (30–80 cm) Atlantic cod (Gadus morhua), and in situ ocean temperature measurements, we found a significant effect of sea temperature on cod depth use and activity level in coastal Skagerrak. During summer, cod were found in deeper waters when sea surface temperature increased. Further, this effect of temperature was stronger on larger cod. Diel vertical migration, which consists in a nighttime rise to shallow feeding habitats, was stronger among smaller cod. As surface temperature increased beyond ~15°C, their vertical migration was limited to deeper waters. In addition to larger diel vertical migrations, smaller cod were more active and travelled larger distances compared to larger specimens. Cold temperatures during winter tended, however, to reduce the magnitude of diel vertical migrations, as well as the activity level and distance moved by those smaller individuals. Our findings suggest that future and ongoing rises in sea surface temperature may increasingly deprive cod in this region from shallow feeding areas during summer, which may be detrimental for local populations of the species.
Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
Data from: Chromosomal inversions in the Atlantic cod genome: implications for management of Canada's Northern cod stock
Following stock collapse and over twenty years of moratoria, the state of Canada's Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative of a panmictic population. Several outlier SNPs were found to be associated with ecologically relevant physical characteristics (visual pigments, fin development, response to hypoxia, and various metabolic processes), which may be indicative of different ecological niches.
Data from: Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua
Accurate prediction of species distribution shifts in the face of climate change requires a sound understanding of population diversity and local adaptations. Previous modeling has suggested that global warming will lead to increased abundance of Atlantic cod (Gadus morhua) in the ocean around Greenland, but the dynamics of earlier abundance fluctuations are not well understood. We applied a retrospective spatiotemporal population genomics approach to examine the temporal stability of cod population structure in this region and to search for signatures of divergent selection over a 78-year period spanning major demographic changes. Analyzing >900 gene-associated single nucleotide polymorphisms in 847 individuals, we identified four genetically distinct groups that exhibited varying spatial distributions with considerable overlap and mixture. The genetic composition had remained stable over decades at some spawning grounds, whereas complete population replacement was evident at others. Observations of elevated differentiation in certain genomic regions are consistent with adaptive divergence between the groups, indicating that they may respond differently to environmental variation. Significantly increased temporal changes at a subset of loci also suggest that adaptation may be ongoing. These findings illustrate the power of spatiotemporal population genomics for revealing biocomplexity in both space and time and for informing future fisheries management and conservation efforts.
Data from: Can we rely on selected genetic markers for population identification? evidence from coastal Atlantic cod
The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high‐graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom‐settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high‐graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.
litico_2_sin_cod
Source: Objaverse 1.0 / Sketchfab
Litico 2 Sin Cod
Source: Objaverse 1.0 / Sketchfab
Data from: Do genetic ecotypes drive physiological responses to a changing world? Indications that coastal Atlantic cod are better adapted to ocean stressors
<p>Genotypic information for 48 Atlantic cod (<i>Gadus morhua</i>) used in study by Perry <i>et al</i>.: Do genetic ecotypes drive physiological responses to a changing world? Indications that coastal Atlantic cod are better adapted to ocean stressors.</p><p>Genotypes provided in the GenePop format, with the 3776 SNP loci used detailed in Henriksson <i>et al</i>. (<i>in prep</i>). For further information, please contact Simon Henriksson (simon.henriksson@gu.se). </p><p> </p>
Resource-driven colonization by cod in a high Arctic food web
Climate change is commonly associated with many species redistributions and the influence of other factors may be marginalized, especially in the rapidly warming Arctic. The Barents Sea, a high latitude large marine ecosystem in the Northeast Atlantic has experienced above average temperatures since the mid 2000's with divergent bottom temperature trends at sub-regional scales. Concurrently, the Barents Sea stock of Atlantic cod Gadus morhua, one of the most important commercial fish stocks in the world, increased following a large reduction in fishing pressure and expanded north of 80°N. We examined the influence of food availability and temperature on cod expansion using a comprehensive data set on cod stomach fullness stratified by sub-regions characterized by divergent temperature trends. We then tested whether food availability, as indexed by cod stomach fullness, played a role in cod expansion in sub-regions that were warming, cooling or showed no trend. The greatest increase in cod occupancy occurred in three northern sub-regions with contrasting temperature trends. Cod apparently benefited from initial high food availability in these regions that previously had few large-bodied fish predators. The stomach fullness in the northern sub-regions declined rapidly after a few years of high cod abundance, suggesting that the arrival of cod caused a top down effect on the prey base. Prolonged cod residency in the northern Barents Sea is, therefore, not a certainty.
Low-coverage whole-genome sequencing reveals molecular markers for spawning season and sex identification in Gulf of Maine Atlantic cod (Gadus morhua, Linnaeus 1758)
<p class="CxSpFirst">Atlantic cod (<i>Gadus morhua</i>,<i> </i>Linnaeus 1758) in the western Gulf of Maine are managed as a single stock despite several lines of evidence supporting two spawning groups (spring and winter) that overlap spatially, while exhibiting seasonal spawning isolation. Low-coverage whole genome sequencing was used to evaluate the genomic population structure of Atlantic cod spawning groups in the western Gulf of Maine and Georges Bank using 222 individuals collected over multiple years. Results indicated low total genomic differentiation, while also showing strong differentiation between spring and winter spawning groups at specific regions of the genome. Guided regularized random forest and ranked <i>F</i><sub>ST</sub> methods were used to select panels of single nucleotide polymorphisms (SNPs) that could reliably distinguish spring and winter-spawning Atlantic cod (88.5% assignment rate), as well as males and females (95.0% assignment rate) collected in the western Gulf of Maine. These SNP panels represent a valuable tool for fisheries research and management of Atlantic cod in the western Gulf of Maine that will aid investigations of stock production and support accuracy of future assessments.</p>
Distribution. Temperate to subarctic waters of the N Atlantic including S Davis Strait, Gulf of Saint Lawrence, Barents Sea, and North Sea, S to Cape Cod (USA) in the E and the coasts of N France in the W. Extralimital sightings in the Baltic Sea, Bay of Biscay, and Iberian Peninsula. in Delphinidae
Distribution. Temperate to subarctic waters of the N Atlantic including S Davis Strait, Gulf of Saint Lawrence, Barents Sea, and North Sea, S to Cape Cod (USA) in the E and the coasts of N France in the W. Extralimital sightings in the Baltic Sea, Bay of Biscay, and Iberian Peninsula.
Distribution. NE USA,in coastal S Maine, coastal and Merrimack River valley region of S New Hampshire, SE New York, W Massachusetts (including parts of Cape Cod), W & E (E of the Connecticut River) Connecticut, and Rhode Island. in Leporidae
Distribution. NE USA,in coastal S Maine, coastal and Merrimack River valley region of S New Hampshire, SE New York, W Massachusetts (including parts of Cape Cod), W & E (E of the Connecticut River) Connecticut, and Rhode Island.
Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change
<p>Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species' range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species' range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST =0.025 – 0.042) and relatively small (Ne = 433-1777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.</p>
FIGURE 4 in A new genus and species of the cod fish family Moridae (Order Gadiiformes) from southwestern Taiwan
FIGURE 4. Paratype of Pterophycis spatium sp. nov., ASIZP 58039, 210+ mm SL. A. lateral view (reversed). B. Ventral view of anterior body.
FIGURE 3 in A new genus and species of the cod fish family Moridae (Order Gadiiformes) from southwestern Taiwan
FIGURE 3. Pterophycis spatium sp. nov., holotype, NMMB-P22891, 243 mm SL. A. Lateral view. B. Ventral view of head. C. Lateral view of head.
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