Hidden but revealed: After years of genetic studies behavioural monitoring combined with genomics uncover new insight into the population dynamics of Atlantic cod in Icelandic waters

Stock structure is of paramount importance for sustainable management of exploited resources. In that context, genetic markers have been used for more than two decades to resolve spatial structure of marine exploited resources and to fully fathom stock dynamics and interactions. While genetic markers such as allozymes and RFLP dominated the debate in the early era of genetics, technology advances have provided scientists with new tools every decade to better assess stock discrimination and interactions (i.e. gene flow). Here, we provide a review of genetic studies performed to understand stock structure of Atlantic cod in Icelandic waters, from the early allozyme approaches to the genomic work currently carried out. We further highlight the importance of the generation of a chromosome-anchored genome assembly together with whole-genome population data, which drastically changed our perception of the possible management units to consider. After nearly 60 years of genetic investigation of Atlantic cod structure in Icelandic waters, genetic (and later genomic) data combined with behavioural monitoring using Data Storage Tags shifted the attention from geographical population structures to behavioural ecotypes. This review also demonstrates the need for future research to further disentangle the impact of these ecotypes (and gene flow among them) on the population structure of Atlantic cod in Icelandic waters. It also highlights the importance of whole-genome data to unravel unexpected within-species diversity related to chromosomal inversions and associated supergenes, which are important to consider for future development of sustainable management programmes of the species within the North Atlantic.

High-resolution otolith elemental signatures in eteline snappers from valuable deepwater tropical fisheries

Marine resources are often shared among countries, with some fish stocks straddling multiple Exclusive Economic Zones, therefore understanding the structure of populations is important for the effective management of fish stocks. Otolith chemical analyses could discriminate among populations based on differences in the chemical composition of otoliths. We used otoliths from two deepwater snappers (flame snapper Etelis coruscans and ruby snapper Etelis boweni) to examine the evidence for population structure across six Pacific Island countries using solution-based inductively coupled plasma mass spectrometry (ICP-MS) for otolith core and whole otolith samples and laser ablation ICP-MS (LA-ICP-MS) for core and edge areas of a cross-sectioned otolith. The inter-species comparison of these methods is important as the two species are often managed under the same regulations. For both species, the two methods demonstrated separation among the locations sampled with high classification accuracy. Smaller laser ablation spot size gave greater temporal resolution over the life-history transect. Comparing the early life-history section of the otoliths (i.e., the core), one interpretation is that young fish experienced more uniform environments in the open ocean as larvae than adults, as the elemental fingerprints had greater overlap among multiple locations. LA-ICP-MS methods had some advantages over solution-based ICP-MS and generally better discrimination for the trace elements investigated. There were substantial differences between species, but both methods suggested nonmixing populations at the regional scale. Otolith chemistry can be an effective tool in discriminating variation for deepwater marine species in multispecies fisheries, and edge measurements from LA-ICP-MS provided the greatest resolution. Although caution should be taken in interpreting the results from relatively small samples sizes, otolith chemical analyses could be useful at these spatial scales to investigate population structure. This information on separate or overlapping populations could be used in future regional fishery management plans.

Genome-wide analysis reveals the genetic stock structure of hoki (Macruronus novaezelandiae)

The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep-water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome-wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole-genome re-sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST  = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine-scale population genetic structure to inform the management of this species.

Biological Knowledge of Thornback Ray (Raja clavata) from the Azores: Improving Scientific Information for the Effectiveness of Species-Specific Management Measures

Simple Summary

Sharks, rays, and skates are increasingly being recognized as endangered due to their life-history characteristics, fishing pressure, and habitat degradation. The thornback ray Raja clavata is one of the most commercially important skates in the seas of Northwest Europe. However, due to a lack of biological knowledge about this species in Azorean waters, the types of stock evaluations that can be performed are restricted. This study expands current knowledge on vertical distribution, size-frequency distributions, growth patterns, sex ratios, mortality rates, and reproduction of this species, and provides a baseline for further fishing monitoring.

Abstract

Elasmobranchs are globally recognized as vulnerable due to their life-history characteristics, fishing pressure, and habitat degradation. Among the skates and rays caught by commercial fisheries, the thornback ray Raja clavata is one of the most economically important in Northwest European seas. However, the scarcity of biological knowledge about this species in Azorean waters has limited the stock assessment types that can be conducted. To improve information on its habitat preferences, spatial distribution and movement pattern, growth, sex ratio, mortality, and reproduction, as well as to investigate long-term changes in abundance and size, this study analyzed approximately 25 years of fishery-dependent and independent data from the Azores. Raja clavata was mainly caught at depths up to 250 m. Most of the tagged fish were recaptured near the release point. A larger–deeper trend was found, and females were larger and more abundant than males. Life-history parameters showed that R. clavata has a long lifespan, large size, slow growth, and low natural mortality. The sustainability of its population is of concern to fisheries management and, while our findings suggested a relatively healthy stock in the Azores, a thorough increase in data quality is required to better understand the stock condition and prevent overexploitation.

Contributions to Management Strategies in the NE Atlantic Regarding the Life History and Population Structure of a Key Deep-Sea Fish (Mora Moro)

Simple Summary

The growing scarcity of continental shelf and epipelagic oceanic fishes has led to commercial fishing in deeper waters. With this spatial expansion in fishing efforts, some vulnerable deep-sea species have been increasingly captured. To reduce fishing-induced impacts on these resources, information on population traits is required by fishery scientists to produce adequate management advice. In the Northeast Atlantic, the common mora Mora moro has become the main fish species caught by bottom longliners operating in deep waters between 600 and 1200 m. Information about the biology and exploitation status of this species is scarce. This study unravels and highlights important and crucial aspects of the habitat preferences, life-history traits (sex ratio, timing of reproduction, size at maturity, growth pattern, and mortality rates), size structure, and abundance of the M. moro based on scientific surveys and commercial fisheries in the Azores region. Results highlight its vulnerability to overfishing due to its large size, slow growth, low natural mortality, long life span, and late maturity.

Abstract

With the commercial fishery expansion to deeper waters, some vulnerable deep-sea species have been increasingly captured. To reduce the fishing impacts on these species, exploitation and management must be based on detailed and precise information about their biology. The common mora Mora moro has become the main deep-sea species caught by longliners in the Northeast Atlantic at depths between 600 and 1200 m. In the Azores, landings have more than doubled from the early 2000s to recent years. Despite its growing importance, its life history and population structure are poorly understood, and the current stock status has not been assessed. To better determine its distribution, biology, and long-term changes in abundance and size composition, this study analyzed a fishery-dependent and survey time series from the Azores. M. moro was found on mud and rock bottoms at depths below 300 m. A larger–deeper trend was observed, and females were larger and more abundant than males. The reproductive season took place from August to February. Abundance indices and mean sizes in the catch were marked by changes in fishing fleet operational behavior. M. moro is considered vulnerable to overfishing because it exhibits a long life span, a large size, slow growth, and a low natural mortality.

Genome-wide insights into introgression and its consequences for genome-wide heterozygosity in the Mytilus species complex across Europe

The three mussel species comprising the Mytilus complex are widespread across Europe and readily hybridize when they occur in sympatry, resulting in a mosaic of populations with varying genomic backgrounds. Two of these species, M. edulis and M. galloprovincialis, are extensively cultivated across Europe, with annual production exceeding 230,000 tonnes. The third species, M. trossulus, is considered commercially damaging as hybridization with this species results in weaker shells and poor meat quality. We therefore used restriction site associated DNA sequencing to generate high-resolution insights into the structure of the Mytilus complex across Europe and to resolve patterns of introgression. Inferred species distributions were concordant with the results of previous studies based on smaller numbers of genetic markers, with M. edulis and M. galloprovincialis predominating in northern and southern Europe respectively, while introgression between these species was most pronounced in northern France and the Shetland Islands. We also detected traces of M. trossulus ancestry in several northern European populations, especially around the Baltic and in northern Scotland. Finally, genome-wide heterozygosity, whether quantified at the population or individual level, was lowest in M. edulis, intermediate in M. galloprovincialis, and highest in M. trossulus, while introgression was positively associated with heterozygosity in M. edulis but negatively associated with heterozygosity in M. galloprovincialis. Our study will help to inform mussel aquaculture by providing baseline information on the genomic backgrounds of different Mytilus populations across Europe and by elucidating the effects of introgression on genome-wide heterozygosity, which is known to influence commercially important traits such as growth, viability, and fecundity in mussels.

Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site-associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.

Metazoan parasites of Brama australis from southern Chile: a tool for stock discrimination?

The metazoan parasites of 403 specimens of the southern ray's bream Brama australis from three localities in southern Chile (Lebu 36° 70' S; 73° 40' W, Calbuco 41° 50' S; 73° 08' W and Punta Arenas 53° 10' S; 70° 50' W) were recorded. More than 23 400 parasite specimens belonging to 12 taxa were registered. Metazoan parasites were dominated by the copepod Hatschekia conifera, constituting 97% of the total number of parasites; the larval cestode Hepatoxylon trichiuri was the second most important parasite (2·1% of the total number of parasites). The remaining 10 species constituted <1% of the metazoan parasites. Parasitological evidence, based on univariate and multivariate analysis, does not support the existence of discrete stocks in the studied zone.

Critically endangered western gray whales migrate to the eastern North Pacific

Western North Pacific gray whales (WGWs), once considered extinct, are critically endangered with unknown migratory routes and reproductive areas. We attached satellite-monitored tags to seven WGWs on their primary feeding ground off Sakhalin Island, Russia, three of which subsequently migrated to regions occupied by non-endangered eastern gray whales (EGWs). A female with the longest-lasting tag visited all three major EGW reproductive areas off Baja California, Mexico, before returning to Sakhalin Island the following spring. Her 22 511 km round-trip is the longest documented mammal migration and strongly suggests that some presumed WGWs are actually EGWs foraging in areas historically attributed to WGWs. The observed migration routes provide evidence of navigational skills across open water that break the near-shore north-south migratory paradigm of EGWs. Despite evidence of genetic differentiation, these tagging data indicate that the population identity of whales off Sakhalin Island needs further evaluation.

Post-glacial population expansion of the Monterey Spanish mackerel Scomberomorus concolor in the Gulf of California

The level of genetic homogeneity and demographic history of the Monterey Spanish mackerel Scomberomorus concolor was assessed by analyses using sequences of the mitochondrial (mt)DNA-control region of samples from the two oceanographic regions of the Gulf of California in order to define the stock structure for this exploited vulnerable species. The data were consistent with a single homogeneous population and revealed the hallmark of fluctuations in population size; these fluctuations appear to have occurred during glacial events of the middle to late Pleistocene, which may in turn be related to the colonization and expansion of S. concolor populations in the gulf.

Combining genetic and demographic information to prioritize conservation efforts for anadromous alewife and blueback herring

A major challenge in conservation biology is the need to broadly prioritize conservation efforts when demographic data are limited. One method to address this challenge is to use population genetic data to define groups of populations linked by migration and then use demographic information from monitored populations to draw inferences about the status of unmonitored populations within those groups. We applied this method to anadromous alewife (Alosa pseudoharengus) and blueback herring (Alosa aestivalis), species for which long-term demographic data are limited. Recent decades have seen dramatic declines in these species, which are an important ecological component of coastal ecosystems and once represented an important fishery resource. Results show that most populations comprise genetically distinguishable units, which are nested geographically within genetically distinct clusters or stocks. We identified three distinct stocks in alewife and four stocks in blueback herring. Analysis of available time series data for spawning adult abundance and body size indicate declines across the US ranges of both species, with the most severe declines having occurred for populations belonging to the Southern New England and the Mid-Atlantic Stocks. While all alewife and blueback herring populations deserve conservation attention, those belonging to these genetic stocks warrant the highest conservation prioritization.

Development of the first standardised panel of two new microsatellite multiplex PCRs for gilthead seabream (Sparus aurata L.)

The high number of multiplex PCRs developed for gilthead seabream (Sparus aurata L.) from many different microsatellite markers does not allow comparison among populations. This highlights the need for developing a reproducible panel of markers, which can be used with safety and reliability by all users. In this study, the first standardised panel of two new microsatellite multiplex PCRs was developed for this species. Primers of 138 specific microsatellites from the genetic linkage map were redesigned and evaluated according to their genetic variability, allele size range and genotyping reliability. A protocol to identify and classify genotyping errors or potential errors was proposed to assess the reliability of each marker. Two new multiplex PCRs from the best assessed markers were designed with 11 markers in each, named SMsa1 and SMsa2 (SuperMultiplex Sparus aurata). Three broodstocks (59, 47 and 98 breeders) from different Spanish companies, and a sample of 80 offspring from each one, were analysed to validate the usefulness of these multiplexes in the parental assignation. It was possible to assign each offspring to a single parent pair (100% success) using the exclusion method with SMsa1 and/or SMsa2. In each genotyped a reference sample (Ref-sa) was used, and its DNA is available on request similar to the kits of bin set to genotype by genemapper (v.3.7) software (kit-SMsa1 and kit-SMsa2). This will be a robust and effective tool for pedigree analysis or characterisation of populations and will be proposed as an international panel for this species.