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The neritic-oceanic squid Illex argentinus supports one of the largest fisheries in the Southwest Atlantic. It is characterized by extensive migrations across the Patagonian Shelf and complex population structure comprising distinct seasonal spawning groups. To address uncertainty as to the demographic independence of these groups that may compromise sustainable management, a multidisciplinary approach was applied integrating statolith ageing with genome-wide single-nucleotide polymorphism (SNP) analysis. To obtain complete coverage of the spawning groups, sampling was carried out at multiple times during the 2020 fishing season and covered a large proportion of the species' range across the Patagonian Shelf. Statolith and microstructure analysis revealed three distinct seasonal spawning groups of winter-, spring-, and summer-hatched individuals. Subgroups were identified within each seasonal group, with statolith microstructure indicating differences in environmental conditions during ontogeny. Analysis of >10 000 SNPs reported no evidence of neutral or non-neutral genetic structure among the various groups. These findings indicate that I. argentinus across the Patagonian Shelf belong to one genetic population and a collaborative management strategy involving international stakeholders is required. The connectivity among spawning groups may represent a "bet-hedging" mechanism important for population resilience.

Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of biodiversity. Such data is traditionally obtained as a result of research surveys through the capture and/or visual identification of organisms. Recent years have seen significant advances in the utilisation of environmental DNA (eDNA) in the marine environment in order to develop alternative cost-effective ways to gather relevant data. Such approaches attempt to identify and/or quantify the species present at a location through the detection of extra-organismal DNA in the environment. These new eDNA based approaches have the potential to revolutionise data collection in the marine environment using non-invasive sampling methods and providing snapshots of biodiversity beyond the capacity of traditional sampling. Here we present a non-technical summary of different approaches in the field of eDNA, and emphasise the broad application of this approach, with value for the governance and management of marine aquatic ecosystems. The review focuses on identifying those tools which are now readily applicable and those which show promise but are currently in development and require further validations. The aim is to provide an understanding of techniques and concepts that can be used by managers without genetic or genomic expertise when consulting with specialists to perform joint evaluations of the utility of the approaches.

In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

In a recent paper, “Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring,” Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.

The impacts of climate change on marine ecosystems can be seen in the changing distribution, migration, and abundance of species in the oceans. For some species this changing environment may be beneficial and can support population expansions. In the northeast Atlantic (NEA), the Atlantic mackerel (Scomber scombrus) is undergoing an increase in stock size accompanied by changing summer migration patterns, which have resulted in an expansion further north and north west than previously recorded. This study uses microsatellite loci to confirm the differentiation among NEA and northwest Atlantic (NWA) mackerel spawning populations and to assess the level of structuring within these populations. In addition, to enable population-specific exploitation rates to be factored into fisheries management, we identified the origin of individuals composing the expanding feeding aggregations in the central north Atlantic (Greenland, Iceland, Faroes), with all aggregations tested originating from spawning populations in the NEA. This study showed that microsatellite loci were useful to assess the contribution of NEA and NWA populations to mixed feeding aggregations across the north Atlantic for large pelagic fish stocks but were not powerful enough to evaluate the specific contribution of known stocks within NEA and NWA.

Chemosynthetic ecosystems have long been acknowledged as key areas of enrichment for deep-sea life, supporting hundreds of endemic species. Echinoderms are among the most common taxa inhabiting the periphery of chemosynthetic environments, and of these, chiridotid holothurians are often the most frequently observed. Yet, published records of chiridotids in these habitats are often noted only as supplemental information to larger ecological studies and several remain taxonomically unverified. This study therefore aimed to collate and review all known records attributed to Chiridota Eschscholtz, 1829, and to conduct the first phylogenetic analysis into the relationship of these chiridotid holothurians across global chemosynthetic habitats. We show that Chiridota heheva Pawson & Vance, 2004 is a globally widespread, cosmopolitan holothurian that occupies all three types of deep-sea chemosynthetic ecosystem—hydrothermal vents, cold seeps and organic falls—as an organic-enrichment opportunist. Furthermore, we hypothesise that C. heheva may be synonymous with another vent-endemic chiridotid, Chiridota hydrothermica Smirnov et al., 2000, owing to the strong morphological, ecological and biogeographical parallels between the two species, and predict that any chiridotid holothurians subsequently discovered at global reducing environments will belong to this novel species complex. This study highlights the importance of understudied, peripheral taxa, such as holothurians, to provide insights to biogeography, connectivity and speciation at insular deep-sea habitats.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Recent advances in genetic and genomic analysis have greatly improved our understanding of spatial population structure in marine species. However, studies addressing phylogeographic patterns at oceanic spatial scales remain rare. In Atlantic cod (Gadus morhua), existing range‐wide examinations suggest significant transatlantic divergence, although the fine‐scale contemporary distribution of populations and potential for secondary contact are largely unresolved. Here, we explore transatlantic phylogeography in Atlantic cod using a data‐synthesis approach, integrating multiple genome‐wide single‐nucleotide polymorphism (SNP) datasets representative of different regions to create a single range‐wide dataset containing 1,494 individuals from 54 locations and genotyped at 796 common loci. Our analysis highlights significant transatlantic divergence and supports the hypothesis of westward post‐glacial colonization of Greenland from the East Atlantic. Accordingly, our analysis suggests the presence of transatlantic secondary contact off eastern North America and supports existing perspectives on the phylogeographic history of Atlantic cod with an unprecedented combination of genetic and geographic resolution. Moreover, we demonstrate the utility of integrating distinct SNP databases of high comparability

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method.

Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities.

The genomic architecture underlying ecological divergence and ecological speciation with gene flow is still largely unknown for most organisms. One central question is whether divergence is genome‐wide or localized in ‘genomic mosaics’ during early stages when gene flow is still pronounced. Empirical work has so far been limited, and the relative impacts of gene flow and natural selection on genomic patterns have not been fully explored. Here, we use ecotypes of Atlantic cod to investigate genomic patterns of diversity and population differentiation in a natural system characterized by high gene flow and large effective population sizes, properties which theoretically could restrict divergence in local genomic regions. We identify a genomic region of strong population differentiation, extending over approximately 20 cM, between pairs of migratory and stationary ecotypes examined at two different localities. Furthermore, the region is characterized by markedly reduced levels of genetic diversity in migratory ecotype samples. The results highlight the genomic region, or ‘genomic island’, as potentially associated with ecological divergence and suggest the involvement of a selective sweep. Finally, we also confirm earlier findings of localized genomic differentiation in three other linkage groups associated with divergence among eastern Atlantic populations. Thus, although the underlying mechanisms are still unknown, the results suggest that ‘genomic mosaics’ of differentiation may even be found under high levels of gene flow and that marine fishes may provide insightful model systems for studying and identifying initial targets of selection during ecological divergence.

Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.