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Discriminating populations of Atlantic herring mixing in the Norwegian Sea feeding ground using single nucleotide polymorphisms (SNPs)
Get PDFAtlantic herring Clupea harengus feeding in the Norwegian Sea are assumed to consist of Norwegian spring spawners (NSSH), Icelandic summer spawners (ISSH) and North Sea autumn spawners (NSAH). Putative Norwegian autumn spawners (NASH), Faroese autumn (FASH) and spring (FSSH) spawners also feed in the area. However, until there is a method to discriminate between populations in mixed samples, fishery and survey data from the Norwegian Sea will be solely attributed to the predominating NSSH, ultimately causing biased stock assessments. Hence, we evaluated if a panel of 120 single nucleotide polymorphisms (SNPs) associated with spawning characteristics and salinity preferences would be an effective discrimination tool. The overall observed levels of genetic differentiation were high (FST = 0.57, p <0.001, 95% CI: 0.51-0.62). Spawners from stocks under current management (NSSH, NSAH and ISSH) were well separated, but the putative populations were not. Discriminant analysis of principal component as well as Structure runs confirmed the differentiation observed with FST. When the SNP panels were tested on commercial fishery samples of NSSH east of Iceland, up to 16% were assigned to ISSH. This implies that catch data are seriously biased and demonstrates the potential of SNP panels as a tool to solve the problem. However, work is needed to develop improved SNP panels that effectively separate the putative populations from the managed stocks. We recommend that such a tool should be established in regular sampling of fishery and surveys in the Norwegian Sea and accounted for in future stock assessments, advice and management.publishedVersio
Nanopore sequencing provides snapshots of the genetic variation within salmonid alphavirus-3 (SAV3) during an ongoing infection in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)
Get PDFFrequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.publishedVersio
Genetic Stock Identification Reveals Mismatches Between Management Areas and Population Genetic Structure in a Migratory Pelagic Fish
Get PDFSustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population-informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn-spawning herring north of 62° N (average = 19.2%), Norwegian spring-spawning herring south of 62° N (average = 13.5%), and western Baltic spring-spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.publishedVersio
Quantifying the effects of sample size and species distribution on the precision and accuracy of abundance estimates from bottom-trawl surveys in the Gulf of Alaska
Get PDFWe assessed the effect of survey effort reduction on the accuracy and precision of estimates of abundance for 4 commercially or ecologically important species with differing distributions observed in a bottom-trawl survey conducted in the Gulf of Alaska. Simulations from a spatiotemporal generalized linear mixed model based on historical observations of catch densities were used to evaluate the statistical robustness, measured in terms of coefficient of variation, relative bias, and relative root mean square error, of the abundance estimates and their variances. These metrics were used to compare estimates between the traditional design-based estimator and the alternative estimator, based on a vector autoregressive spatiotemporal model, at 4 different sampling densities, representing 2 historical and 2 theoretical sampling effort levels on either side of the historical range. The recent reduction in the density of survey sampling from 820 to 550 stations had only a modest effect on the performance metrics for both estimators for arrowtooth flounder (Atheresthes stomias), Pacific cod (Gadus macrocephalus), and Pacific ocean perch (Sebastes alutus). However, the effect on the abundance estimates for sablefish (Anoplopoma fimbria) was substantial. We attribute this difference in results to the wider depth range utilized by sablefish, which preferentially occupy the relatively under-sampled deep strata (>500 m), and to the truncated survey area at the reduced sampling levels where the deepest strata (>700 m) have been eliminated.publishedVersio
Quantifying the Detection Sensitivity and Precision of qPCR and ddPCR Mechanisms for eDNA Samples
Get PDFEnvironmental DNA (eDNA) detection employing quantitative PCR (qPCR) and droplet digital PCR (ddPCR) offers a non-invasive and efficient approach for monitoring aquatic organisms. Accurate and sensitive quantification of eDNA is crucial for tracking rare and invasive species and understanding the biodiversity abundance and distribution of aquatic organisms. This study compares the sensitivity and quantification precision of qPCR and ddPCR for eDNA surveys through Bayesian inference using latent parameters from both known concentration (standards) and environmental samples across three teleost fish species assays. The results show that ddPCR offers higher sensitivity and quantification precision, particularly at low DNA concentrations (< 1 copy/μL reaction), than qPCR. These findings highlight the superior performance of ddPCR for eDNA detection at low concentrations, guiding researchers towards more reliable methods for effective species monitoring. Additionally, this study indicates that a two-step (detection and concentration) model increased the precision of qPCR results, useful for enhancing the robustness of eDNA quantification. Furthermore, we investigated the lower limit of quantification for ddPCR, providing insights on how such limit can be extended, which could also be applied to qPCR.publishedVersio
Diversité des parasites Anisakidae chez un cachalot pygmée, Kogia breviceps (Cetacea : Kogiidae) échoué à la limite de son aire de répartition dans l’Atlantique Nord-Est
Get PDFAnisakid nematodes are a globally distributed group of marine mammal parasites. Kogiid whales, including the pygmy sperm whale Kogia breviceps, host an assemblage of specific anisakid species. Currently, three species are known to be specific to kogiid hosts, i.e., Skrjabinisakis paggiae, S. brevispiculata, and the less studied Pseudoterranova ceticola. The aim of this study was to investigate the species diversity of anisakid nematodes sampled from a pygmy sperm whale stranded in 2013 at the edge of its distribution range in the Northeast Atlantic, specifically in the North of Scotland. Nematodes were assigned to genus level based on morphology and identified by sequence analysis of the mtDNA cox2 gene and the rDNA ITS region. The present finding represents the first observation of syntopic occurrence of adult stages of S. brevispiculata, S. paggiae, and P. ceticola in a pygmy sperm whale in the Northeast Atlantic, and represent the northernmost record of these species in this area. Skrjabinisakis brevispiculata was the most abundant species, accounting for 55% of the identified nematodes, predominantly in the adult stage. Anisakis simplex (s.s.) was also abundant, with most specimens in the preadult stage, followed by S. paggiae and P. ceticola. The pygmy sperm whale is rarely documented in Scottish waters, and its occurrence in the area could suggest expansion of its geographic range. The presence of S. brevispiculata, S. paggiae, and P. ceticola in this whale species in this region may indicate a shift in the whole host community involved in the life cycle of these parasites in northern waters. However, it is also plausible that these parasites were acquired while the whale was feeding in more southern regions, before migrating northbound.publishedVersio
An emerging pathway of Atlantic Water to the Barents Sea through the Svalbard Archipelago: Drivers and variability
Get PDFThe Barents Sea, an important component of the Arctic Ocean, is experiencing changes in its ocean currents, stratification, sea ice variability, and marine ecosystems. Inflowing Atlantic Water (AW) is a key driver of these changes. As AW predominantly enters the Barents Sea via the Barents Sea Opening, other pathways remain relatively unexplored. Comparisons of summer climatology fields of temperature from the last century with those from 2000–2019 indicate warming in the Storfjordrenna trough and along two shallow banks, Hopenbanken and Storfjordbanken, within the Svalbard Archipelago. Additionally, they indicate shoaling of AW that extends further into the “channel” between the islands of Edgeøya and Hopen. This region emerges as a pathway enabling AW to enter the northwestern Barents Sea. Moreover, 1-year-long records from a mooring deployed between September 2018 and November 2019 at the saddle of this channel show the flow of Atlantic-origin waters into the Arctic domain of the northwestern Barents Sea. The average current is directed eastwards into the Barents Sea and exhibits significant variability throughout the year. Here, we investigate this variability on timescales ranging from hours to months. Wind forcing mediates currents, water exchange, and heat exchange through the channel by driving geostrophic adjustment to Ekman transport. The main drivers of the warm-water inflow and across-saddle transport of positive temperature anomalies include persistently strong semidiurnal tidal currents, intermittent wind-forced events, and wintertime warm-water intrusions forced by upstream conditions. We propose that similar topographic constraints near AW pathways may become more important in the future. Ongoing warming and shoaling of AW, coupled with changes in large-scale weather patterns, are likely to increase warm-water inflow and heat transport through the processes identified in this study.publishedVersio
A longline survey for spurdog distribution and life history along the Norwegian coast
Get PDFTo improve spatiotemporal data collection and inform future spurdog Squalus acanthias stock assessment, a new dedicated longline survey was initiated in 2021 in coastal waters of southern Norway. The survey comprised a mixture of randomly predefined stations to facilitate unbiased abundance estimates and supplementary stations including informant putative hotspots. During 25 survey days in autumn 2021, 287 stations were sampled, of which 280 were categorized as “satisfactory” in terms of gear quality deployment. Spurdog catches (n = 954) were more abundant in southeast coastal shallower waters (19–150 m). No length, sex, or maturity stratified schooling behavior was found with increasing catches. Females were more abundant and larger than males, but males were older. Growth and reproduction parameters were within ranges reported for the stock. Our results provide valuable input for spurdog survey designs with regards to optimizing boat time, location of stations, and biological sampling protocols. The survey provides important data for monitoring the spurdog stock and other data-limited species, especially considering the newly re-opened spurdog fishery but also to study possible future effects of climatic changes on spurdog distribution.publishedVersio
Geographical distribution of close kin in southern right whales on feeding grounds
Get PDFThis study investigated the close kinship structure of southern right whales on feeding grounds during austral summer seasons. The study was based on biopsy samples of 171 individual whales, which were genotyped with 14 microsatellite DNA loci. Kinship was investigated by using the LOD (Log Odds) score, a relatedness index for a pair of genotypes. Based on a cut-off point of LODPO > 6, which was chosen to balance false positives and negatives, a total of 28 dyads were inferred. Among these, 25 were classified as parent-offspring pairs. Additional genetic (mitochondrial DNA haplotypes) and biological (estimated body length, sex) data were used to provide additional information on the inferred close kin pairs. The elapsed time between sampling varied from 0 (close kin detected in the same austral summer season) to 17 years. All the kin pairs occurred within the Antarctic Indo sector (85°-135°E) and no pair occurred between whales within and outside of this sector. Six pairs were between individuals in high (Antarctic) and lower latitudes. Results of the present analysis on kinship are consistent with the views that whales in the Indo sector of the Antarctic are related with the breeding ground in Southwest Australia, and that whales from this population can occupy different feeding grounds. The present study has the potential to contribute to the conservation of the southern right whales through the monitoring of important population parameters such as population sizes and growth rate, in addition to assist the interpretation of stock structure derived from standard population genetic analyses.publishedVersio
Genetics in the Ocean's Twilight Zone: Population Structure of the Glacier Lanternfish Across Its Distribution Range
Get PDFThe mesopelagic zone represents one of the few habitats that remains relatively untouched from anthropogenic activities. Among the many species inhabiting the north Atlantic mesopelagic zone, glacier lanternfish (Benthosema glaciale) is the most abundant and widely distributed. This species has been regarded as a potential target for a dedicated fishery despite the scarce knowledge of its population genetic structure. Here, we investigated its genetic structure across the North Atlantic and into the Mediterranean Sea using 121 SNPs, which revealed strong differentiation among three main groups: the Mediterranean Sea, oceanic samples, and Norwegian fjords. The Mediterranean samples displayed less than half the genetic variation of the remaining ones. Very weak or nearly absent genetic structure was detected among geographically distinct oceanic samples across the North Atlantic, which contrasts with the low motility of the species. In contrast, a longitudinal gradient of differentiation was observed in the Mediterranean Sea, where genetic connectivity is known to be strongly shaped by oceanographic processes such as current patterns and oceanographic discontinuities. In addition, 12 of the SNPs, in linkage disequilibrium, drove a three clusters' pattern detectable through Principal Component Analysis biplot matching the genetic signatures generally associated with large chromosomal rearrangements, such as inversions. The arrangement of this putative inversion showed frequency differences between open-ocean and more confined water bodies such as the fjords and the Mediterranean, as it was fixed in the latter for the second most common arrangement of the fjord's samples. However, whether genetic differentiation was driven by local adaptation, secondary contact, or a combination of both factors remains undetermined. The major finding of this study is that B. glaciale in the North Atlantic-Mediterranean is divided into three major genetic units, information that should be combined with demographic properties to outline the management of this species prior to any eventual fishery attempt.publishedVersio