Cod Populations Research Articles

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.

Loss of genetic diversity in Atlantic cod

Evolutionary Biology The collapse of the Northern cod population was one of the largest crashes of any marine vertebrate in the 20th century. Despite fishing bans, the species has yet to recover to historical levels. Kess et al. reconstructed these trends over the last century to illustrate how chromosomal structural diversity can mediate genetic, phenotypic, and demographic variation and how overfishing may have led to a loss of genetic diversity in Northern cod. They warn that removal of genomic diversity through overfishing may also reduce the buffering effect provided by phenotypic diversity in these populations, which increases the possibility of future collapse and alters the overall ecological function and composition of the Northwest Atlantic. Sci. Adv. 10.1126/sciadv.aav2461 (2019).

Comments on Local cod (Gadus morhua) revealed by egg surveys and population genetic analysis after longstanding depletion on the Swedish Skagerrak Coast by Svedäng et al.

Abstract Svedäng et al. (2018) concluded that “the occurrence of locally spawned cod eggs suggests that spawning on the Swedish Skagerrak coast takes place, which belong to either a coastal subpopulation that is a remnant stock of a once much larger cod population, or a newly formed subpopulation that is now successfully inhabiting the coastal ecosystems along the Swedish Skagerrak coast”. However, after carefully reviewing the results and the data presented by the authors, we were no longer convinced that the information presented provided enough evidence for a local, distinct, coastal cod population in the Swedish Skagerrak. Thus, we requested the original genotype data, which the authors kindly provided to us. This allowed us to explore the substructure of these samples further using STRUCTURE 2.3.2. Re-analysis of the data consistently rejects the existence of an independent coastal Swedish stock in contrast with Svedäng et al. (2018) conclusions. We acknowledge the observation of cod spawning in the area but, based on re-analysis of the original genetic data of Svedäng et al. (2018), we currently lack the scientific basis to assume the existence of established local stocks, and even less the demographic expansion of an older, relict population in the area.

Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank.

Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.

Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua)

BackgroundThe population of Atlantic cod (Gadus morhua), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world’s largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or “fjord” cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway.ResultsOur analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are “Carbohydrates”; “Amino Acids and Derivatives”; “Protein Metabolism”; “Cofactors, Vitamins, Prosthetic, Groups, and Pigments”; and “DNA Metabolism,” which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category “Protein Metabolism” is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol.ConclusionWe present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus (Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes.

Impacts of the Changing Ocean-Sea Ice System on the Key Forage Fish Arctic Cod (Boreogadus Saida) and Subsistence Fisheries in the Western Canadian Arctic—Evaluating Linked Climate, Ecosystem and Economic (CEE) Models

This study synthesizes results from observations, laboratory experiments and models to showcase how the integration of scientific methods and indigenous knowledge can improve our understanding of (a) past and projected changes in environmental conditions and marine species; (b) their effects on social and ecological systems in the respective communities; and (c) support management and planning tools for climate change adaptation and mitigation. The study links climate-ecosystem-economic (CEE) models and discusses uncertainties within those tools. The example focuses on the key forage species in the Inuvialuit Settlement Region (Western Canadian Arctic), i.e., Arctic cod (Boreogadus saida). Arctic cod can be trophically linked to sea-ice algae and pelagic primary producers and are key vectors for energy transfers from plankton to higher trophic levels (e.g., ringed seals, beluga), which are harvested by Inuit peoples. Fundamental changes in ice and ocean conditions in the region affect the marine ecosystem and fish habitat. Model simulations suggest increasing trends in oceanic phytoplankton and sea-ice algae with high interannual variability. The latter might be linked to interannual variations in Arctic cod abundance and mask trends in observations. CEE simulations incorporating physiological temperature limits data for the distribution of Arctic cod, result in an estimated 17% decrease in Arctic cod populations by the end of the century (high emission scenario), but suggest increases in abundance for other Arctic and sub-Arctic species. The Arctic cod decrease is largely caused by increased temperatures and constraints in northward migration, and could directly impact key subsistence species. Responses to acidification are still highly uncertain, but sensitivity simulations suggests an additional 1% decrease in Arctic cod populations due to pH impacts on growth and survival. Uncertainties remain with respect to detailed future changes, but general results are likely correct and in line with results from other approaches. To reduce uncertainties, higher resolution models with improved parameterizations and better understanding of the species' physiological limits are required. Arctic communities should be directly involved, receive tools and training to conduct local, unified research and food chain monitoring while decisions regarding commercial fisheries will need to be precautionary and adaptive in light of the existing uncertainties.

New data on Lake Mogilnoe (Kildin Island, Barents Sea): the results of the 2018 expeditions

Lake Mogilnoe (Kildin Island, the Barents Sea) is a meromictic lake located in the high latitudes of the Arctic. It was formed by separation from the Barents Sea and retained an underground connection with it through a rocky barrier. The first researchers of the lake mentioned the upper fresh-water layer, the middle salty layer, lower anaerobic layer containing hydrogen sulfide, and noted the existence of a layer with rose water in the redoxcline. Observations carried out during the 20th century pointed to a gradual change in the vertical structure of the lake: mineralization increase of the surface layer and the rise of the hydrogen sulfide distribution boundary. In the past 10 years, there have been signals about acceleration of these changes. This is a big concern about an isolated population of Kildin cod (G. morhua kildinensis) listed in the Red Book of the Russian Federation, an endemic to this lake subspecies of Atlantic cod. In July, August and October 2018, three expeditions were organized to Lake Mogilnoe to study the current hydrological state of the lake, seasonal variability of hydrological characteristics, and outline possible causes of the registered changes and the threat to the Kildin cod population.

Assessing a Threatened Fish Species under Budgetary Constraints: Evaluating the Use of Existing Monitoring Data

AbstractBecause of the high costs of collecting field data, many species recovery and management plans do not include a monitoring feedback component to measure the success of interventions and refine management strategies. Here, we demonstrate how leveraging existing monitoring data can provide broad‐scale, cost‐effective information about a threatened fish species, the Murray Cod Maccullochella peelii, which is of cultural and recreational importance in Australia. We applied a Bayesian hierarchical model of abundance to Murray Cod catch data collected as part of broad‐scale, general condition monitoring in the Murray–Darling Basin. The model uses replicated sampling at spatially independent sites to disentangle the confounding effects of detection probability and abundance on catch data. We demonstrate the reliability of the analysis for determining trends in abundance with a simulation study, and we show that basinwide abundance of Murray Cod declined by over 50% between 2010 and 2013. We found that detection probability of Murray Cod can vary substantially across space and through time, suggesting that accounting for variable detection will be important in any future evaluation of Murray Cod populations. This study highlights variable detection as an issue in monitoring regimes and demonstrates a method for the cost‐effective use of existing monitoring data to evaluate species abundance trends.

Ecological-economic sustainability of the Baltic cod fisheries under ocean warming and acidification

Human-induced climate change such as ocean warming and acidification, threatens marine ecosystems and associated fisheries. In the Western Baltic cod stock socio-ecological links are particularly important, with many relying on cod for their livelihoods. A series of recent experiments revealed that cod populations are negatively affected by climate change, but an ecological-economic assessment of the combined effects, and advice on optimal adaptive management are still missing. For Western Baltic cod, the increase in larval mortality due to ocean acidification has experimentally been quantified. Time-series analysis allows calculating the temperature effect on recruitment. Here, we include both processes in a stock-recruitment relationship, which is part of an ecological-economic optimization model. The goal was to quantify the effects of climate change on the triple bottom line (ecological, economic, social) of the Western Baltic cod fishery. Ocean warming has an overall negative effect on cod recruitment in the Baltic. Optimal management would react by lowering fishing mortality with increasing temperature, to create a buffer against climate change impacts. The negative effects cannot be fully compensated, but even at 3 °C warming above the 2014 level, a reduced but viable fishery would be possible. However, when accounting for combined effects of ocean warming and acidification, even optimal fisheries management cannot adapt to changes beyond a warming of +1.5° above the current level. Our results highlight the need for multi-factorial climate change research, in order to provide the best available, most realistic, and precautionary advice for conservation of exploited species as well as their connected socio-economic systems.

Disentangling structural genomic and behavioural barriers in a sea of connectivity

Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.

A simulation framework for evaluating multi-stage sampling designs in populations with spatially structured traits.

Selecting an appropriate and efficient sampling strategy in biological surveys is a major concern in ecological research, particularly when the population abundance and individual traits of the sampled population are highly structured over space. Multi-stage sampling designs typically present sampling sites as primary units. However, to collect trait data, such as age or maturity, only a sub-sample of individuals collected in the sampling site is retained. Therefore, not only the sampling design, but also the sub-sampling strategy can have a major impact on important population estimates, commonly used as reference points for management and conservation. We developed a simulation framework to evaluate sub-sampling strategies from multi-stage biological surveys. Specifically, we compare quantitatively precision and bias of the population estimates obtained using two common but contrasting sub-sampling strategies: the random and the stratified designs. The sub-sampling strategy evaluation was applied to age data collection of a virtual fish population that has the same statistical and biological characteristics of the Eastern Bering Sea population of Pacific cod. The simulation scheme allowed us to incorporate contributions of several sources of error and to analyze the sensitivity of the different strategies in the population estimates. We found that, on average across all scenarios tested, the main differences between sub-sampling designs arise from the inability of the stratified design to reproduce spatial patterns of the individual traits. However, differences between the sub-sampling strategies in other population estimates may be small, particularly when large sub-sample sizes are used. On isolated scenarios (representative of specific environmental or demographic conditions), the random sub-sampling provided better precision in all population estimates analyzed. The sensitivity analysis revealed the important contribution of spatial autocorrelation in the error of population trait estimates, regardless of the sub-sampling design. This framework will be a useful tool for monitoring and assessment of natural populations with spatially structured traits in multi-stage sampling designs.

Formation of the Population Structure of the Atlantic Cod Gadus morhua Linnaeus, 1758 in the Quaternary Period

This paper presents a comparative analysis of the variability of genetic characteristics in samples from the largest stocks of the Atlantic cod Gadus morhua Linnaeus, 1758 in the Northeast Atlantic (NEA) and the Northwest Atlantic (NWA) waters. The results of a pairwise estimation of the genetic differentiation, performed using allozyme and microsatellite markers, detected a significant difference between the cod sample from the New England Shelf (NWA) and the cod of the Icelandic–Greenlandic and Norwegian–Barents Sea stocks. At the same time, cod samples from areas of East and West Greenland and samples from the Barents Sea, despite considerable geographic differences, demonstrated a high level of identity according to molecular genetic markers. The peculiarities of the formation of the cod population structure in the Quaternary period are considered in connection with the dynamics of global climatic and oceanological processes.

Long‐read sequence capture of the haemoglobin gene clusters across codfish species

Combining high‐throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short‐read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long‐read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom‐made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage‐specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long‐read capture as a versatile approach for comparative genomic studies by generation of a cross‐species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.

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.

Gear sustainability assessment of the Newfoundland inshore northern cod fishery

From an ocean-basin collapse to a limited reopening, the Newfoundland northern cod fishery is challenged by ecological and economic sustainability. Pivotal factors influencing resource sustainability involve the use of gillnets as the main fishing method and the perception of cod as a low value commodity. Considering gillnetting and two other methods used in this fishery, hand-lines and Newfoundland cod pots, we identified and assessed strengths and weaknesses of each as a basis for best practices management decisions. This assessment involved multi-criteria evaluations based on “ideal gear properties” (International Council for the Exploration of the Sea) adapted to incorporate criteria specific to this fishery. An index scoring system involving 20 ecological, economic and social criteria was developed and used to assess the three gears. Catch-related data collected onboard commercial fishing vessels and structured interviews on economic and social criteria assessments with fishers were collected. Literature reviews supplemented these data.Hand-lining scored the best results on each of the three criteria, with significant advantages (minimal ecosystem impacts; economic and social incentives for an adaptive accessible fishery). Newfoundland cod pots had the second most sustainable results (benefits for cod population, interesting work conditions). Though this gear had economic disadvantages, Newfoundland cod pots ensure best catches for a quality-based fishery. Despite being the fishing gear most commonly used, bottom-set gillnets are the least sustainable method. Catch-related advantages (efficiency, size selectivity) are not adapted to a new quality-based fishery. Restriction of gillnet fishing and promotion of complementary hand-lining and pot fishing would support a best practices more sustainable approach.

Modeling the impact of hypoxia on the energy budget of Atlantic cod in two populations of the Gulf of Saint-Lawrence, Canada

Like many marine species around the globe, several stocks of Atlantic cod (Gadus morhua) live in increasingly hypoxic waters. In the Gulf of Saint Lawrence (GSL) in Canada, the deep channels traversing the semi-enclosed sea exhibit year-round hypoxia, identified as one of the limiting factor for the recovery of GSL cod in its northern part. While many individuals in the northern GSL are known to venture in deeper, warmer, and more hypoxic waters of the Gulf channels, those in the southern GSL live in a shallower, colder, and more oxygenated environment. In this study, we use the modeling framework of the Dynamic Energy Budget (DEB) theory to disentangle the effects of hypoxia, temperature and food on the life-history traits of these two populations of cod in the GSL. Following recent advances by Thomas et al. (2018, this issue) on the mechanisms for the effects of hypoxia within the context of DEB theory, we implemented a correction of ingestion depending on dissolved oxygen (DO) saturation. We successfully developed and validated a set of parameters for a GSL Atlantic cod DEB model. Using simulations of historical growth trajectories from 1990 until 2004 estimated from data collected through fisheries research surveys, we found that temperature explained about half (48%) of the difference in length and 59% of the difference in mass between the two populations. The remaining proportion was attributed to exposure to hypoxia and food input. We also used our model to explore scenarios of duration, frequency, and intensity of hypoxia on cod's life-history traits, which showed that decreasing DO linearly reduces growth and reproduction while young cod seem to avoid impairing conditions resulting in limiting effects on developmental stages.

Morphometric and meristic characteristics of poor cod, Trisopterus minutus (L. 1758), from the eastern central Adriatic Sea

Background and Purpose: Poor cod, Trisopterus minutus (Linnaeus, 1758) is a gadoid fish, which inhabits the Mediterranean and eastern Atlantic. The aim of present work was to investigate the morphological properties of poor cod in the eastern central Adriatic Sea by analyzing classical morphometric and meristic characteristics, and thereby investigating: a) whether there are morphological differences between males and females; b) the existence of possible homogenous or heterogeneous stock morphology; and c) the changes in morphometric characteristics with increase in body length.Material and methods: Samples of 410 poor cod specimens (209 females, 201 males) were collected by bottom-trawl between 2014 and 2016 from five localities in the eastern central Adriatic Sea. In order to analyze biometry of the species; fifteen morphometric and eight meristic characteristics were measured.Results and Conclusions: Total length of all specimens ranged from 8.8 to 27.1 cm. Morphological differences between males and females was not marked. Biometric analysis of the morphometric and meristic characteristics indicated a homogenous morphology stock of Trisopterus minutus in the Adriatic Sea. Changes in some morphometric characteristics obtained in conjunction with an increase in body length showed that smaller specimens have a longer head, eye diameter, ventral fins and second anal fins than adult specimens. The negative correlation recorded for the maximum and minimum body depth indicated that the body elongated with poor cod growth. Comparison of the meristic characteristics that were published earlier show some differences between the poor cod populations inhabiting the Adriatic, Black Sea and eastern Atlantic.

Climate change not to blame for cod population decline

Three decades of increasing temperature were expected to cause cod stocks to decline in the North Sea and Gulf of Maine, but they increased in the North Sea and declined in the Gulf of Maine. These trends are due to changes in fishing pressure rather than climate change.

Zoonotic Babesia microti in the northeastern U.S.: Evidence for the expansion of a specific parasite lineage.

The recent range expansion of human babesiosis in the northeastern United States, once found only in restricted coastal sites, is not well understood. This study sought to utilize a large number of samples to examine the population structure of the parasites on a fine scale to provide insights into the mode of emergence across the region. 228 B. microti samples collected in endemic northeastern U.S. sites were genotyped using published Variable number tandem repeat (VNTR) markers. The genetic diversity and population structure were analysed on a geographic scale using Phyloviz and TESS, programs that utilize two different methods to identify population membership without predefined population data. Three distinct populations were detected in northeastern US, each dominated by a single ancestral type. In contrast to the limited range of the Nantucket and Cape Cod populations, the mainland population dominated from New Jersey eastward to Boston. Ancestral populations of B. microti were sufficiently isolated to differentiate into distinct populations. Despite this, a single population was detected across a large geographic area of the northeast that historically had at least 3 distinct foci of transmission, central New Jersey, Long Island and southeastern Connecticut. We conclude that a single B. microti genotype has expanded across the northeastern U.S. The biological attributes associated with this parasite genotype that have contributed to such a selective sweep remain to be identified.

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.