Clupea Harengus Research Articles

The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

Chromosomal inversions are associated with local adaptation in many species. However, questions regarding how they are formed, maintained and impact various other evolutionary processes remain elusive. Here, using a large genomic dataset of long-read and short-read sequencing, we ask these questions in one of the most abundant vertebrates on Earth, the Atlantic herring. This species has four megabase-sized inversions associated with ecological adaptation that correlate with water temperature. The S and N inversion alleles at these four loci dominate in the southern and northern parts, respectively, of the species distribution in the North Atlantic Ocean. By determining breakpoint coordinates of the four inversions and the structural variations surrounding them, we hypothesize that these inversions are formed by ectopic recombination between duplicated sequences immediately outside of the inversions. We show that these are old inversions (>1 MY), albeit formed after the split between the Atlantic herring and its sister species, the Pacific herring. There is evidence for extensive gene flux between inversion alleles at all four loci. The large Ne of herring combined with the common occurrence of opposite homozygotes across the species distribution has allowed effective purifying selection to prevent the accumulation of genetic load and repeats within the inversions.

Disentangling bottom-up and top-down controls on fish consumption of key prey in the Northeast US Shelf ecosystem

Abstract Exploited forage fishes serve a dual role in marine ecosystems by supporting directed fisheries and predator productivity, and thus both harvest and predatory removals should be accounted for when developing stock assessments and evaluating management trade-offs. Predator catch and stomach content data collected on the Northeast US Shelf from 1978 to 2019 by two fisheries-independent surveys were combined within multivariate spatiotemporal models to estimate time-series of consumptive removals during spring and fall for four commercially exploited prey; Atlantic herring (Clupea harengus), silver hake (Merluccius bilinearis), butterfish (Peprilus triacanthus), and longfin squid (Doryteuthis pealeii). Seasonal consumption trends were mostly synchronous for Atlantic herring and silver hake, asynchronous for butterfish and longfin squid, and predatory removals were generally greater during fall. Consumption has increased since the 1990s for all prey except Atlantic herring and butterfish during fall, which coincides with the widespread implementation of harvest constraints meant to rebuild predator and prey populations. These time-series were linked to hypothesized drivers using state-space regression models; prey availability (bottom-up; positive relationships) and commercial catch (top-down; primarily negative relationships) were the strongest predictors of consumption. Although the mechanisms underlying these relationships remain unresolved, these linkages highlight connections among the systemic drivers of productivity on the Northeast Shelf.

Climate challenges for fish larvae: Interactive multi-stressor effects impair acclimation potential of Atlantic herring larvae

Fish early life stages are particularly vulnerable and heavily affected by changing environmental factors. The interactive effects of multiple climate change-related stressors on fish larvae remain, however, largely underexplored. As rising temperatures can increase the abundance and virulence of bacteria, we investigated the combination of a spring heat wave and bacterial exposure on the development of Atlantic herring larvae (Clupea harengus). Eggs and larvae of Western Baltic Spring-spawners were reared at a normal and high temperature ramp and exposed to Vibrio alginolyticus and V. anguillarum, respectively. Subsequently, mRNA and miRNA transcriptomes, microbiota composition, growth and survival were assessed. Both high temperature and V. alginolyticus exposure induced a major downregulation of gene expression likely impeding larval cell proliferation. In contrast, interactive effects of elevated temperature and V. alginolyticus resulted in minimal gene expression changes, indicating an impaired plastic response, which may cause cellular damage reducing survival in later larval stages. The heat wave alone or in combination with V. alginolyticus induced a notable shift in miRNA expression leading to the down- but also upregulation of predicted target genes. Moreover, both increased temperature and the Vibrio exposures significantly altered the larval microbiota composition, with warming reducing microbial richness and diversity. The outcomes of this study highlight the high sensitivity of herring early life stages towards multiple climate change-related stressors. Our results indicate that interactive effects of rapidly changing environmental factors may exceed the larval stress threshold impairing essential acclimation responses, which may contribute to the ongoing recruitment decline of Western Baltic Spring-Spawning herring.

Investigating the effects of pelagic trawling on the welfare of Atlantic herring (Clupea harengus)

The effects of pelagic trawling on the health and welfare of Atlantic herring (Clupea harengus L.) were investigated on a refrigerated seawater vessel operating in the North Sea. A total of 495 Atlantic herring (Clupea harengus L.) were sampled during five hauls from two fishing trips in September 2021 and 2022. For assessments of consciousness and mortality, a Reflex Action Mortality Predictor test (i.e. RAMP-test) was used on herring collected following trawling and pumping. Inspections for external and internal damage or wounds were performed via morphological welfare indicators and analyses of photos and radiographs. In addition, blood samples were taken and analysed for haematological indicators of stress. Following trawling and pumping, only 5% of the investigated herring showed signs of external wounds associated with the morphological indicators of welfare, and no internal damage was observed in the radiographic inspections. However, 96% of the assessed herring scored 0 on all three reflexes included in the RAMP-test and were therefore judged dead. On average, herring lost 95% of their scales, while 95% of herring had a very high degree of ruptured red blood cells (i.e. haemolysis). Extensive scale loss results in a deterioration of the skin's protective barrier function, which in turn impairs the osmoregulatory capacity of the herring. This was evident by elevated levels of plasma osmolality and circulating chloride concentrations, which could also likely explain the high occurrence of haemolysis in captured herring. Extended trawling time and larger catch size proved to be two important factors to consider, as the former led to increased plasma levels of osmolality, whereas the latter was associated with elevated plasma levels of lactate and cortisol. In conclusion, the high mortality appears to be influenced by a combination of factors such as severe stress, loss of osmoregulatory ability, crowding density within the trawl, and extended trawling times. This study provides important information on the welfare of wild Atlantic herring caught using pelagic trawls and highlights areas where improvements can be made to safeguard the welfare of fish captured in pelagic fisheries in the future.

Small pelagic fish in the shallow Wadden Sea show opportunistic feeding with a strong benthic link

Abstract Small pelagic fish (SPF) are crucial in marine food webs, transferring energy from plankton to higher trophic levels. This study focuses on herring (Clupea harengus) and sprat (Sprattus sprattus), addressing knowledge gaps in their feeding ecology in a nursery area, the Dutch Wadden Sea. We conducted a year-long, monthly survey, and used DNA metabarcoding to analyse zooplankton samples and stomach contents of two size classes of herring and sprat. Intra-, interspecific, and seasonal variations in fish condition, stomach fullness, and diet composition, along with selective feeding, were studied. Our study showed that condition and diet composition of herring and sprat, along with zooplankton density, exhibited a clear seasonal pattern. Juvenile herring and sprat displayed opportunistic feeding behaviour, rather than showing distinct prey selection. Besides copepods, we regularly observed (larvae of) benthic invertebrates in their diet. This emphasizes the crucial role of SPF as energy transfer agents, not solely between trophic levels, but also from benthic to pelagic habitats. Furthermore, fish post-larvae were part of the diet of larger herring (10–15 cm). Because of its unprecedented temporal and taxonomical detail, this study advances the understanding of seasonal dynamics of dominant components at the base of the Wadden Sea food web.

Northeast Arctic haddock (Melanogrammus aeglefinus) spawning grounds and drift to nursery areas in the Barents Sea

AbstractThe Northeast Arctic stock of haddock (Melanogrammus aeglefinus) is the most northerly stock of the species. It is one of the largest haddock stocks but not the most studied. Similar to the more extensively studied sympatric cod (Gadus morhua) and herring (Clupea harengus) stocks, it relies on Atlantic currents for egg and larvae transportation from spawning grounds to nursery areas in the Barents Sea. The exact locations of the spawning grounds have not been known and the maps that have been published differ substantially. Here, we present results from the first survey dedicated to exploring the spawning habitat of Northeast Arctic (NEA) haddock, and a particle drift and larvae growth model with physical forcing from a high‐resolution ocean model. Gadoid eggs, later identified as haddock by DNA analyses, as well as spawning individuals were sampled at the survey. Spawning haddock was found in Atlantic water in temperatures 3.6–6.2°C and depths of 240–560 m. Sampled eggs were mostly in early development stages, suggesting that they were largely spawned in the surveyed area. Using the drift model, we found that most of the modelled particles released as eggs at our surveyed area ended up in the nursery area in the Barents Sea. A crude estimate of the spawning stock biomass based on the survey suggests that the most updated spawning ground map of NEA haddock might be too restricted in its extent. Particle drift and growth with physical forcing for the years 2012–2022 indicated small interannual variation in aberrant drift, and that growth driven by ambient temperature could be important in explaining interannual variation in haddock recruitment.

Quantifying global redundant fisheries trade to streamline seafood supply chains.

Seafood plays an important role in sustainably feeding the world and is one of the most traded food products globally. However sustainability improvements are often focused on its production (e.g., aquaculture, fishing) rather than trade. Here, we quantify the magnitude and extent of global 'redundant two-way' seafood trade-the exchange of the same quantity of the same taxonomic species between two countries-to examine its prevalence and potential implications across the seafood supply chain. We focused on wild-caught seafood trade and found that redundant two-way trade has increased by 43%, between 2000 and 2015, making up 3.2% (7.7 Mt) of global seafood trade during that period. Although most countries were involved in redundant two-way seafood trade (111 of 212 analyzed), the majority occurred between five trade partners: Canada and the United States (15%), Germany and the Netherlands (11.8%); Denmark and Sweden (10.6%); Germany and Denmark (7.1%); and France and Norway (7%). Nearly 50% of redundant trade is made up of just four species including Atlantic herring, Atlantic cod, Skipjack tuna and Atlantic mackerel. While deficiencies in global seafood trade data mask seasonal and product heterogeneity, redundant trade could have implications for meeting conservation and sustainable development goals. Future research should build upon these findings to explore specific environmental, economic, and social implications associated with redundant two-way trade to benefit producers and consumers within the seafood supply chain.

Mercury exposure and trophic ecology of urban nesting black-legged kittiwakes from France

Seabirds are increasingly used as bioindicators for assessing the chemical contamination of marine ecosystems, including by mercury (Hg) worldwide. However, some geographical areas are still poorly documented, as metropolitan France that is home to 28 seabird species including the black-legged kittiwake Rissa tridactyla, in the part of the southern limit of the North Atlantic range of the species. Here, we investigated Hg contamination and trophic ecology of black-legged kittiwakes breeding in the harbour of Boulogne-sur-Mer, Northern France. Mean blood Hg concentration was 4.81 ± 1.20 μg g−1 dw (dry weight), 3.66 ± 0.75 μg g−1 dw and 0.43 ± 0.07 μg g−1 dw for adult males, adult females, and chicks, respectively. According to Hg toxicity benchmarks for avian blood, 30% of the sampled adults were considered to be at moderate risk to Hg toxicity. Stable isotope and food analyses showed that highest δ15N values (reflecting a higher trophic position) were related to highest blood Hg concentrations in adult birds, and that Atlantic herring (Clupea harengus) and Atlantic mackerel (Scomber scombrus) were the main prey. Adult kittiwakes from Boulogne-sur-Mer showed Hg levels three times higher than those found in Arctic nesting kittiwakes, where sublethal effects have been documented. This study provides a first description of Hg contamination of black-legged kittiwakes breeding in France and calls for future ecotoxicological research to assess the vulnerability of this species in the southern part of its distribution range.

Discriminating populations of Atlantic herring mixing in the Norwegian Sea feeding ground using single nucleotide polymorphisms (SNPs)

Atlantic 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.

Stay or go? Changing breeding conditions affect sexual difference in colony attendance strategies of Atlantic puffins Fratercula arctica.

Male and female birds have different roles in reproduction and, thereby in their reproductive investment, which in turn may increase negative effects of poorer breeding conditions caused by e.g., climate change or ecosystem regime shifts. By using a 33-year time series of resightings of Atlantic puffins Fratercula arctica individually colour-ringed as breeders in previous years, we showed that the difference in colony attendance of male and female birds depended on the environmental conditions for raising young, proxied by the average duration of the chick period and size of the herring Clupea harengus fed to the chicks in the colony each year. The longer the chick period, the more was the sex ratio of adults sitting visibly in the colony biased in favour of males. An increase in herring size, indicating better feeding conditions for raising chicks, led to more observations of both sexes. Additionally, we found that birds were observed less with age and females more so than males. We discuss the results in relation to general life-history theory on sexual differences in trade-offs between individual investment in breeding and own survival. Our results suggest that females are increasingly more willing than males to invest in provisioning for the chick the more and longer the chick needs such care.

Dynamics of mercury stable isotope compounds in Arctic seals: New insights from a controlled feeding trial on hooded seals Cystophora cristata

Accurate interpretation of mercury (Hg) isotopic data requires the consideration of several biotic factors such as age, diet, geographical range, and tissue metabolic turnover. A priori knowledge of prey-predator isotopic incorporation rates and Hg biomagnification is essential. This study aims to assess Hg stable isotopes incorporation in an Arctic species of Phocidae, the hooded seal Cystophora cristata, kept in human care for 24 months (2012–2014) and fed on a constant diet of Norwegian Spring Spawning herring Clupea harengus. We measured THg, MMHg and iHg levels, as well as Hg stable isotope composition with both mass dependent (MDF) and mass independent (MIF) fractionation (e.g. δ202Hg and Δ199,200,201,204Hg) in hooded seal kidney, liver, hair and muscle, in addition to herring muscle. We then calculated Hg MDF and MIF isotopic fractionation between hooded seals and their prey. We found a significant shift in δ202Hg between hooded seal hair (+0.80‰) and kidney (−0.78‰), and herring muscle. In hooded seals tissues δ202Hg correlated positively with MMHg percentage. These findings suggest that tissue-specific Hg speciation is the major driver of changes in Hg isotopic fractionation rates in this Arctic predator. Δ199Hg, Δ200Hg, Δ201Hg and Δ204Hg values did not vary between herring and hooded seal tissues, confirming their utility as tracers of Hg marine and atmospheric sources in top predators. To our knowledge, this represents the first attempt to assess complex Hg isotope dynamics in the internal system of Arctic Phocidae, controlling the effects of age, diet, and distribution. Our results confirm the validity of Hg stable isotopes as tracers of environmental Hg sources even in top predators, but emphasize the importance of animal age and tissue selection for inter-study and inter-species comparisons.

Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.

First detection of Ichthyophonus sp. in invasive wild pink salmon (Oncorhynchus gorbuscha) from the North Atlantic Ocean.

Pacific pink salmon (Oncorhynchus gorbuscha) were deliberately introduced to rivers surrounding the White Sea and has spread to Norway and several other countries surrounding the North Atlantic Ocean. In August 2021, a female pink salmon displaying pale gills and abnormal behaviour was captured in River Lakselva in Northern Norway and later submitted to the Norwegian Veterinary Institute (NVI) for post-mortem examination. Histological examination of organ samples revealed structures indicative of systemic ichthyophoniasis, caused by Ichthyophonus sp. The parasites appeared to be especially abundant in the heart and skeletal musculature, and local tissue responses were assessed to be absent or very mild. Sequences of the ribosomal 18S rRNA and the mitochondrial cytochrome oxidase 1 (CO1) genes confirmed the diagnosis and identified the pathogen as Ichthyophonus sp. The CO1 sequence further established that the isolate from pink salmon was most similar to sequences of Ichthyophonus sp. from Atlantic salmon, Salmo salar, from the Atlantic Ocean on the east coast of the US and from Atlantic herring, Clupea harengus, from Iceland. We here report the first detection of Ichthyophonus sp. in pink salmon in the North Atlantic Ocean.

Early arrival of spring-spawning Atlantic herring Clupea harengus at their spawning ground in the Kiel Fjord, western Baltic, relates to increasing winter seawater temperature.

The disturbance of marine organism phenology due to climate change and the subsequent effects on recruitment success are still poorly understood, especially in migratory fish species, such as the Atlantic herring (Clupea harengus; Clupeidae). Here we used the commercial catch data from a local fisher over a 50-year period (1971-2020) to estimate western Baltic spring-spawning (WBSS) herring mean arrival time Q50 (i.e., the week when 50% of the total fish catches had been made) at their spawning ground within the Kiel Fjord, southwest Baltic Sea, and the duration of the spawning season for each year. The relationship between the seawater temperature in the Kiel Bight and other environmental parameters (such as water salinity, North Atlantic and Atlantic multidecadal oscillations) and Q50 was evaluated using a general linear model to test the hypothesis that fish arrived earlier after warm than cold winters. We also estimated the accumulated thermal time to Q50 during gonadal development to estimate the effects of seawater temperature on the variations of Q50. The results of this study revealed a dramatic decrease in herring catches within the Kiel Fjord since the mid-1990s, as documented for the whole southwestern Baltic Sea. Warmer winter seawater temperature was the only factor related to an earlier arrival (1 week for one January seawater temperature degree increase) of herring at their spawning ground. The relationship was found for the first time on week 52 of the year prior to spawning and was the strongest (50% of the variability explained) from the fourth week of January (8 weeks before the mean Q50 among the studied years). A thermal constant to Q50 (~316°C day) was found when temperatures were integrated from the 49th week of the year prior to spawning. These results indicate that seawater temperature enhanced the speed of gonadal maturation during the latest phases of gametogenesis, leading to an early fish arrival under warm conditions. The duration of the spawning season was elongated during warmer years, therefore potentially mitigating the effects of trophic mismatch when fish spawn early. The results of this study highlight the altering effects of climate change on the spawning activity of a migratory fish species in the Baltic Sea where fast global changes presage that in other coastal areas worldwide.

Magnetic orientation in juvenile Atlantic herring (Clupea harengus) could involve cryptochrome 4 as a potential magnetoreceptor.

The Earth's magnetic field can provide reliable directional information, allowing migrating animals to orient themselves using a magnetic compass or estimate their position relative to a target using map-based orientation. Here we show for the first time that young, inexperienced herring (Clupea harengus, Ch) have a magnetic compass when they migrate hundreds of kilometres to their feeding grounds. In birds, such as the European robin (Erithacus rubecula), radical pair-based magnetoreception involving cryptochrome 4 (ErCRY4) was demonstrated; the molecular basis of magnetoreception in fish is still elusive. We show that cry4 expression in the eye of herring is upregulated during the migratory season, but not before, indicating a possible use for migration. The amino acid structure of herring ChCRY4 shows four tryptophans and a flavin adenine dinucleotide-binding site, a prerequisite for a magnetic receptor. Using homology modelling, we successfully reconstructed ChCRY4 of herring, DrCRY4 of zebrafish (Danio rerio) and StCRY4 of brown trout (Salmo trutta) and showed that ChCRY4, DrCRY4 and ErCRY4a, but not StCRY4, exhibit very comparable dynamic behaviour. The electron transfer could take place in ChCRY4 in a similar way to ErCRY4a. The combined behavioural, transcriptomic and simulation experiments provide evidence that CRY4 could act as a magnetoreceptor in Atlantic herring.

Implementation of Food Safety Management System FSMS (ISO 22000) in Cold Smoked Herring (Clupea harengus) Factory at AL-GHARBIA Governorate

Implementation of Food Safety Management System FSMS (ISO 22000) in Cold Smoked Herring (Clupea harengus) Factory at AL-GHARBIA Governorate

Completing the picture: using vertebrae as well as otoliths in diet analysis reveals new preferred prey of great skuas

Knowledge of the diet of marine predators such as seabirds is fundamental to understanding the ecological cascades they may influence and the impact that environmental changes may have on them. Diet analysis of seabirds frequently relies on the identification of fish otoliths in pellets. However, it is recognised that the true dietary importance of fish with small and fragile otoliths is likely underestimated, requiring an additional method. In this study, we compared the identification of otoliths with that of vertebrae in pellets to gain a more complete picture of seabird diet. We identified fish otoliths and vertebrae from 2584 great skua Stercorarius skua pellets collected between 2014 and 2017 from five colonies in Scotland. Diet varied markedly between colonies, comprising mostly fish in Shetland and mostly birds in St Kilda. 10% of pellets contained otoliths compared to 70% with fish vertebrae. Atlantic herring Clupea harengus and Atlantic mackerel Scomber scombrus were the most common fish species at all colonies when using vertebrae in contrast to being virtually absent when using otoliths. Conversely, the occurrence of Norway pout Trisopterus esmarkii and pollock Pollachius pollachius otoliths was six and eight times, respectively, higher than for vertebrae. Therefore, combining data from both otoliths and vertebrae provides a more complete profile of the fish component of seabird diet. This is fundamental to improving our understanding of the impacts of marine management policies on seabirds, as well as how changes in the population size of such seabird species might affect their prey species.

Temporal declines in fecundity: A study of southern Gulf of St. Lawrence Atlantic herring (Clupea harengus) and implications for potential reproductive output.

Individuals must reproduce to survive and thrive from generation to generation. In fish, the fecundity of individuals and estimates of total reproductive output are critical for evaluating reproductive success and understanding population dynamics. Estimating fecundity is an onerous task; therefore, many populations lack contemporary estimates of fecundity and size-fecundity relationships. However, reproductive dynamics are not static in time; therefore, it is important to develop contemporary fecundity estimates to better inform conservation and management action. To highlight the importance of contemporary fecundity estimates, we examined the fecundity of southern Gulf of St. Lawrence (sGSL) spring and fall spawning Atlantic herring in 2022, developed size-fecundity models, and compared these to historical fecundity estimates and models. Our results suggest that the average fecundity of sGSL spring and fall herring has undergone a substantial temporal decline of approximately 47% and 58%, respectively, since the 1970s and 1980s. The size-fecundity relationships for fall spawning herring have shifted, with fish of a given size exhibiting lower fecundity in 2022 compared to the 1970s. Alternatively, the size-fecundity relationships for spring spawning herring have remained relatively static. Furthermore, simulations highlighted a substantial reduction in potential reproductive output in 2022 compared to 1970 of approximately 32% and 68% for spring and fall spawners, respectively, based on a fixed number of mature females, which may have negative implications for stock rebuilding. Overall, our study provides support for periodic estimates of fecundity in fish populations to better understand temporal changes in reproductive and population dynamics.

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

BackgroundGenome-wide comparisons of populations are widely used to explore the patterns of nucleotide diversity and sequence divergence to provide knowledge on how natural selection and genetic drift affect the genome. In this study we have compared whole-genome sequencing data from Atlantic and Pacific herring, two sister species that diverged about 2 million years ago, to explore the pattern of genetic differentiation between the two species.ResultsThe genome comparison of the two species revealed high genome-wide differentiation but with islands of remarkably low genetic differentiation, as measured by an FST analysis. However, the low FST observed in these islands is not caused by low interspecies sequence divergence (dxy) but rather by exceptionally high estimated intraspecies nucleotide diversity (π). These regions of low differentiation and elevated nucleotide diversity, termed high-diversity regions in this study, are not enriched for repeats but are highly enriched for immune-related genes. This enrichment includes genes from both the adaptive immune system, such as immunoglobulin, T-cell receptor and major histocompatibility complex genes, as well as a substantial number of genes with a role in the innate immune system, e.g. novel immune-type receptor, tripartite motif and tumor necrosis factor receptor genes. Analysis of long-read based assemblies from two Atlantic herring individuals revealed extensive copy number variation in these genomic regions, indicating that the elevated intraspecies nucleotide diversities were partially due to the cross-mapping of short reads.ConclusionsThis study demonstrates that copy number variation is a characteristic feature of immune trait loci in herring. Another important implication is that these loci are blind spots in classical genome-wide screens for genetic differentiation using short-read data, not only in herring, likely also in other species harboring qualitatively similar variation at immune trait loci. These loci stood out in this study because of the relatively high genome-wide baseline for FST values between Atlantic and Pacific herring.

Broadband backscattering by Atlantic herring (Clupea harengus L.) differs when measured from a research vessel vs. a silent uncrewed surface vehicle

Abstract Broadband frequency-modulated signals are believed to improve acoustic spectral-based target classification. Efficient use of uncrewed surface vehicles (USV) for fisheries science applications, with no possibility for biological sampling, is believed to be facilitated by use of broadband signals with methods for target classification. If the broadband frequency response used to train automated target classifiers are obtained from conventional research vessels (RVs), due to potential vessel avoidance, the swimming angle distribution may be different than for USVs. This may have consequences for target classification if the model is trained with RV data. The aim of this study was to assess whether the frequency response differs between platforms due to avoidance. Broadband acoustic data were collected with a conventional RV and a small USV. The broadband frequency response of Norwegian spring spawning herring obtained with the USV and RV was found to be significantly different for shallow herring layers in the 200 kHz band. This indicates that broadband frequency response has potential as a tool for real-time monitoring of behaviour reactions to vessels and to provide insight into fish behaviour in general. When using broadband frequency response for target classification, the potential platform-dependent broadband frequency response should be considered.