Morphological similarities between skates of the genus Dipturus in the north-eastern Atlantic and Mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as 'D. batis'). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the 'common skate', with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.

Abstract
. Background
. Elasmobranch populations are declining, predominantly driven by overfishing, and over a third of global sharks, rays, and chimeras are estimated to be threatened with extinction. In terms of trade, Brazil is ranked the eleventh-largest shark producer and the top importer of shark meat in the world. Research has shown that elasmobranchs are sold in Brazil under the name “cação” (a generic designation for cartilaginous fish) to overcome consumer resistance.
.
. Methodology and results
. This study used DNA barcoding to investigate the sale of sharks in the State of São Paulo during the COVID-19 lockdown. A total of 35 samples of “cação” were analysed, revealing six different shark species on sale, including Carcharhinus falciformis, Carcharhinus signatus, Carcharias taurus, Isurus oxyrinchus, and Isurus paucus, that are threatened with extinction according to the IUCN red list. This study demonstrates that vulnerable elasmobranchs are being commercialised under the label “cação” in the São Paulo State and Brazil.
.
. Conclusions
. Comparison of shark products traded before and during the COVID-19 pandemic showed no significant difference, suggesting lockdown did not affect patterns of species commercialisation. Effective fisheries and sale monitoring, correct product labelling legislation and increased consumer awareness that “cação” is shark are needed for appropriate conservation and management of shark populations in Brazil.
.

Mislabeling of seafood products and marketing of protected species remains a worldwide issue despite the labeling regulations set at a local, European and International level. DNA barcoding has proven to be the most popular and accurate method of detection of fraudulent seafood products. This study investigated the batoid meat market of Greece, the mislabeling rates and the protected species occurrence. A total of 114 ray products were collected from fishmongers, open markets, supermarkets, and restaurants across eight Greek cities. The cytochrome oxidase subunit I (COI) gene was used to analyze samples, and the sequences were compared against genetic databases for species identification. At least 13 species across nine genera were identified. The results did not indicate significant differences in species utilization among cities, retailers, and labels. However, in the pairwise comparisons, Athens differed from all other locations and a similar trend was followed by the label “salachi”. Moderate mislabeling levels were recorded (13.5%), while 3.5% of the identified samples belonged to species with prohibitions on landings, confirming an ongoing market for protected species. Overall, 19.8% of the samples originated from species that are locally listed in threatened categories of the IUCN Red List of species.

AbstractBatoid fishes are among the most endangered marine vertebrates, yet conservation efforts have been confounded by incomplete taxonomy. Evidence suggest that the critically endangered ‘common skate’ actually represents two species: the flapper skate (Dipturus intermedius) and the blue skate (Dipturus batis). However, knowledge of the geographic range of these two nominal species is limited. Here, DNA sequencing is used to distinguish these species, allowing their spatial distributions to be clarified. These records were also used as the basis for species distribution modelling, providing the first broad scale models for each species across the Northeast Atlantic. Samples were obtained from Iceland, the UK (specifically Shetland), the North Sea and the Azores. Results suggest that D. batis was commonly distributed in the Western Approaches and Celtic Sea, extending out to Rockall and Iceland. D. intermedius generally appears to be less abundant, but was most frequent around northern Scotland and Ireland, including the northern North Sea, and was also present in Portugal. Two individuals were also identified from seamounts in remote areas of the Atlantic around the Azores, the furthest south and west the species has been found. This supports reports that the flapper skate historically had a much wider distribution (which was also highlighted in the distribution model), emphasising the large scale over which fisheries may have led to extirpations. Furthermore, these Azorean samples shared a unique control region haplotype, highlighting the importance of seamounts in preserving genetic diversity.

In the original publication, the Supplementary Table S2 was published without accession numbers.

Food authenticity has received an increasing focus due to high profile cases of substitution/mislabeling, with many investigations identifying sales of endangered or prohibited species. At the same time, the European Union (EU) has introduced one of the most progressive sets of legislation in order to promote traceability and protect consumers. This study aims to identify shark species that are sold under the commercial term “Galeos” in Greece (which officially designates Mustelus mustelus, M. punctulatus and M. asterias), using DNA barcoding. A total of 87 samples were collected from fishmongers and markets across four cities. A combination of two mitochondrial genes, the cytochrome c oxidase subunit I (COI) and the 16S ribosomal RNA (16S), were used to analyze samples, and species were identified by reference to genetic databases. The results revealed significant differences in patterns of species utilization between cities and retailers. Across the study an extremely high level of mislabeling was identified (56%). This probably relates to some degree of unintentional misidentification and confusion surrounding the designation in Greece, but highlights how consumers are unprotected from incorrect/misleading labels. Over half of products originated from species that are locally listed as threatened by the ICUN red list, and of the mislabeled products, 23% originated from species with prohibitions on landings or CITES listings. This includes large growing sharks with little resemblance to Mustelus spp. and likely demonstrates deliberate substitution. It shows how mislabeled products are providing a route for prohibited/protected sharks to enter the supply chain and be sold to consumers.

In this work, patterns of geographical genetic diversity in Atlantic salmon Salmo salar were studied across the whole Atlantic Arc; whether these patterns (and thus genetic population structure) were affected by water temperatures was also evaluated. Salmo salar populations were characterized using microsatellite loci and then analysed with reference to ocean surface temperature data from across the region. Analysis showed the presence of a latitudinal cline of genetic variability (higher in northern areas) and water temperatures (sea surface temperatures) determining genetic population structure (the latter in combination with genetic drift in southern populations). Under the current global change scenario, northern areas of Europe would constitute refugia for diversity in the future. This is effectively the inverse of what appears to have happened in glacial refugia during the last glacial maximum. From this perspective, the still abundant and large northern populations S. salar should be considered as precious as the small almost relict southern ones and given appropriate protection. Careful management of the species, coordinated across countries and latitudes, is needed in order to avoid its extinction in Europe.

The existence of strong genetic structure is expected in species with limited ability to disperse and philopatric behaviour. These life-history traits are found in many small benthic elasmobranchs, such as in the small-spotted catshark (Scyliorhinus canicula). However, no evidence of genetic structure was found across its northeastern Atlantic (NEA) range using traditional molecular markers. Here, fine-scale genetic differentiation was detected between the British Isles and southern Iberia using 2674 single nucleotide polymorphism loci generated using 2b-restriction siteassociated DNA (2b-RAD). Geographical distance and historical demography were two major drivers shaping the distribution of genetic diversity of S. canicula along the NEA. Significant positive spatial autocorrelation of allelic frequencies was detected, with genetic differentiation generally increasing with geographical distance. However, marked genetic divergence of the Celtic Sea and South Portugal collections from their closest neighbours resulted in geographically constrained genetic breaks south of the British Isles and off southwestern Iberia. Historical demographic reconstruction of population pairs across these genetic breaks suggested a scenario of historical isolation before secondary contact, probably related to distinct northern and southern glacial refugia. These results provide new insights into the population structure of S. canicula along the NEA and serve as a reference for benthic elasmobranchs with similar distribution ranges.

Many shark populations are in decline, primarily due to overexploitation. In response, conservation measures have been applied at differing scales, often severely restricting sales of declining species. Therefore, DNA barcoding was used to investigate sales of shark products in fishmongers and fish and chip takeaways in England. The majority of samples were identified as Spiny Dogfish (Squalus acanthias), which is critically endangered in the Northeast Atlantic and landings have been prohibited (although there is evidence of importation of this species). Significant differences in the species sold between retailer types were also identified, suggesting differing supply chains. The results underline issues surrounding the use of 'umbrella' sales terms where many species are labelled with the same designation. This denies consumer choice as purchasers cannot easily avoid declining species or those associated with high levels of toxicants. For the first time in Europe, minibarcodes are also used to identify species from dried shark fins. Despite a small sample size, analysis of UK wholesaler fins identified threatened sharks, including the endangered and CITES listed Scalloped Hammerhead (Sphyrna lewini). This highlights the global nature of the damaging trade in endangered shark species, in which Europe and the UK have a continuing role.

Tuna fisheries and processing represent economic activities of paramount importance around the world. Most of these products are traded for human consumption and in general are highly demanded commodities. However, not all tuna products achieve the same market price, some consumers are willing to pay a huge amount of money for certain species (i.e. Japanese market for Bluefin tuna) while other species are rather affordable (i.e. Skipjack tuna), therefore mislabelling has been observed frequently. We collected and analysed 545 tuna samples in six European countries, including fresh, frozen and canned products, and we have investigated whether or not these products were correctly labelled under European and national legislations. We found an overall mislabelling rate of 6.79%; in particular, 6.70% of the fresh and frozen tuna products and 7.84% of canned tuna were mislabelled, and only in the case of fresh and frozen tuna samples significant differences among countries were found. Mislabelling rates for Atlantic Bluefin tuna labelled products were very high, ranging from 50 up to 100%. In general, mislabelling was higher when specific names were included in the labels. The "tuna" umbrella term is a very popular one with consumers, but also one that remains vulnerable to ambiguity, hampering efforts towards market transparency and with potential negative consequences to the adequate management of tuna species stocks.

Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.

AbstractAtlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

The alpha taxonomy of the globally distributed shark genus Squalus has been under intense investigation recently, and many new species have been described over the last decade. However, taxonomic uncertainty remains about several taxa. Without consistent nomenclature and the ability to reliably distinguish between the different Squalus species, basic data collection, downstream conservation and management efforts are seriously compromised. To aid in clarifying the taxonomic status of Squalus species in the eastern Atlantic and Mediterranean, we assessed species diversity at the molecular level and evaluated the consistency in species identification in the region. Samples from all nominal Squalus species recognized in the above regions were collected in an international effort and sequenced for regions of the mitochondrial COI and ND2 genes. These data were further analysed alongside publicly available sequences, including 19 of the 26 Squalus species globally recognized, to compare the regional genus‐level diversity with that found elsewhere. Our results confirm inconsistent species identification in the eastern Atlantic and Mediterranean Squalus, particularly concerning S. blainville and S. megalops, and reinforce the need to revise the status of S. megalops and S. mitsukurii as they may include several distinct species distributed around the world. The status of S. blainville is also discussed in the light of the current findings and its problematic taxonomic history.

Concentrated chemical spills have been shown to impact adversely on fish populations and even cause localized population extinctions. Evaluating population-level impacts of sublethal exposure concentrations is, however, complex and confounded by other environmental pressures. Applying effect measures derived from laboratory-based chemical exposures to impacts in wild fish populations is constrained by uncertainty on how biochemical response measures (biomarkers) translate into health outcomes, lack of available data for chronic exposures and the many uncertainties in available fish population models. Furthermore, wild fish show phenotypic plasticity and local adaptations can occur that adds geographic and temporal variance on responses. Such population-level factors are rarely considered in the chemical risk assessment process and can probably be derived only from studies on wild fish. Molecular technologies, including microsatellite and SNP genotyping, and RNASeq for gene expression studies, are advancing our understanding of mechanisms of eco-toxicological response, tolerance, adaptation and selection in wild populations. We examine critically the application of such approaches with examples including using microsatellites that has identified roach (Rutilus rutilus) populations living in rivers contaminated with sewage effluents that are self-sustaining, and studies of stickleback (Gasterosteus aculeatus) and killifish (Fundulus heteroclitus) that have identified genomic regions under selection putatively related to pollution tolerance. Integrating data on biological effects between laboratory-based studies and wild populations, and building understanding on adaptive responses to sublethal exposure are some of the priority research areas for more effective evaluation of population risks and resilience to contaminant exposure.

Skates and rays constitute the most speciose group of chondrichthyan fishes, yet are characterised by remarkable levels of morphological and ecological conservatism. They can be challenging to identify, which makes monitoring species compositions for fisheries management purposes problematic. Owing to their slow growth and low fecundity, skates are vulnerable to exploitation and species exhibiting endemism or limited ranges are considered to be the most at risk. The Madeira skate Raja maderensis is endemic and classified as ‘Data Deficient’ by the IUCN, yet its taxonomic distinctiveness from the morphologically similar and more wide-ranging thornback ray Raja clavata is unresolved. This study evaluated the sequence divergence of both the variable control region and cytochrome oxidase I ‘DNA barcode’ gene of the mitochondrial genome to elucidate the genetic differentiation of specimens identified as R. maderensis and R. clavata collected across much of their geographic ranges. Genetic evidence was insufficient to support the different species designations. However regardless of putative species identification, individuals occupying waters around the Azores and North African Seamounts represent an evolutionarily significant unit worthy of special consideration for conservation management.

Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70%) of fish species substitution. Based on indications that the European seafood retail sector may currently be under better control than its North American counterpart, here we investigated levels of seafood labelling accuracy in sushi bars and restaurants across England. We used the COI barcoding gene to screen samples of tuna, eel, and a variety of other products characterised by less visually distinctive ‘white flesh’. Moderate levels of substitution were found (10%), significantly lower than observed in North America, which lends support to the argument that public awareness, policy and governance of seafood labels is more effective in the European Union. Nevertheless, the results highlight that current labelling practice in UK restaurants lags behind the level of detail implemented in the retail sector, which hinders consumer choice, with potentially damaging economic, health and environmental consequences. Specifically, critically endangered species of tuna and eel continue to be sold without adequate information to consumers.

AbstractCanids, particularly dogs, constitute the major source of cystic echinococcosis (CE) infection to humans, with the majority of cases being caused byEchinococcus granulosus(G1 genotype). Canine echinococcosis is an asymptomatic disease caused by adult tapeworms ofE. granulosussensu lato (s.l.). Information on the population structure and genetic variation of adultE. granulosusis limited. Using sequenced data of the mitochondrial cytochromecoxidase subunit 1 (cox1) we examined the genetic diversity and population structure of adult tapeworms ofE. granulosus(G1 genotype) from canid definitive hosts originating from various geographical regions and compared it to that reported for the larval metacestode stage from sheep and human hosts.Echinococcus granulosus(s.s) was identified from adult tapeworm isolates from Kenya, Libya, Tunisia, Australia, China, Kazakhstan, United Kingdom and Peru, including the first known molecular confirmation from Gaza and the Falkland Islands. Haplotype analysis showed a star-shaped network with a centrally positioned common haplotype previously described for the metacestode stage from sheep and humans, and the neutrality indices indicated population expansion. Low Fst values suggested that populations of adultE. granulosuswere not genetically differentiated. Haplotype and nucleotide diversities forE. granulosusisolates from sheep and human origin were twice as high as those reported from canid hosts. This may be related to self-fertilization ofE. granulosusand/or to the longevity of the parasite in the respective intermediate and definitive hosts. Improved nuclear single loci are required to investigate the discrepancies in genetic variation seen in this study.

The skate fauna in the northern Northeast (NE) Atlantic is poorly investigated, and misidentifications are common. Here, ‘DNA barcoding’ was used to analyse 105 specimens of 15 species previously reported from the area to investigate the occurrence of species. of these 15 species, three were new to the region and confirmed with voucher specimens. Three previously reported taxa were not obtained from the study area, providing a total number of 12 skate species for the northern NE Atlantic. Only one specimen of the critically endangered Dipturus batis complex was found. It occurs frequently in the literature and commercial fisheries catch records, and we argue that the vast majority of these are misidentifications. Due to striking differences in Amblyraja radiata life history parameters across the North Atlantic, cryptic species diversity has previously been suspected. A total of 80 A. radiata cytochrome c oxidase subunit I sequences from across the North Atlantic were sampled, and the highest fixation index (FST) was found when maximising geographical distance (FST = 0.133). A lower index was found when grouped according to life history (FST = 0.067). These results are not strongly supportive for the occurrence of cryptic species.

Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.

The genus Salmo was employed as a model to study introgression of genes between species due to secondary contacts. Seven microsatellite loci, the LDH-C1. locus and the 5S ribosomal DNA were studied. Results showed the mutually enhanced introgression of allochthonous genomes into southern European salmonids. This phenomenon appears to go beyond a simple consequence of the altered behaviour of domestic individuals. Invasions of autochthonous genomes by allochthonous genes would be enhanced by human activities such as stock transfers, which would simultaneously promote allochthonous and allospecific (from other species) introgressions in a synergistic process in Atlantic salmon Salmo salar and brown trout Salmo trutta. As a minor result, the data do not support the value of the microsatellite locus SsaD486 as a species-specific marker. © 2014 the Fisheries Society of the British Isles.

Glacial and postglacial processes are known to be important determinants of contemporary population structuring for many species. In Europe, refugia in the Italian, Balkan and Iberian peninsulas are believed to be the main sources of species colonising northern Europe after the glacial retreat; however, there is increasing evidence of small, cryptic refugia existing north of these for many cold-tolerant species. This study examined the glacial history of Atlantic salmon in western Europe using two independent classes of molecular markers, microsatellites (nuclear) and mitochondrial DNA variation. Alongside the well-documented refuge in the Iberian Peninsula, evidence for a cryptic refuge in northwest France is also presented. Critically, methods utilised to estimate divergence times between the refugia indicated that salmon in these two regions had diverged a long time before the last glacial maximum; coalescence analysis (as implemented in the program IMa2) estimated divergence times at around 60 000 years before present. Through the examination of haplotype frequencies, previously glaciated areas of northwest Europe, that is, Britain and Ireland, appear to have been colonised from salmon expanding out of both refugia, with the southwest of England being the primary contact zone and exhibiting the highest genetic diversity. © 2013 Macmillan Publishers Limited all rights reserved.

Abstract
. Bréchon, A. L. Coombs S. H. Sims D. W. and Griffiths A. M. 2013. Development of a rapid genetic technique for the identification of clupeid larvae in the Western English Channel and investigation of mislabelling in processed fish products – ICES Journal of Marine Science, 70: 399–407. A novel genetic technique, involving real-time polymerase chain reaction (PCR) and high-resolution melt (HRM) analysis was developed, which successfully identified four species of clupeid larvae from the Western English Channel and revealed the presence of herring (Clupea harengus). This was unexpected in a context of global warming as herring are at the southern limit of their range off southwest England, where the larvae are generally very rare. The application of the method in cases of degraded DNA, such as in processed fishery products, was also assessed, revealing a low level of misidentification or equivocal identity (8.3%). Eight-year-old formalin-preserved samples were also analysed successfully. This highlights the potentially broad applications for HRM-based approaches to species identification in marine science.

This study focuses on temporal changes in Atlantic salmon (Salmo salar) populations from the vulnerable periphery of the species range (northern Spain). Using microsatellite markers to assess population structuring and introgression of exogenous genes in four different temporal samples collected across 20 years, we have determined the relative weights of climate and stocking practices in shaping contemporary regional population genetic patterns. Climate, represented by the North Atlantic Oscillation Index, was identified as the main factor for determining the level of population genetic differentiation. Populations within the region have become homogenized through gene flow enhanced by straying of adult salmon from natal rivers and subsequent interchange of genes among rivers due to warmer temperatures. At the same time, and in line with documented changes in stock transfer strategies, evidence of genetic introgression from past stock transfers has decreased throughout the study period, becoming a secondary factor in erasing population structuring. The ability to disentangle the effects of climatic changes and anthropogenic factors (fisheries management practices)is essential for effective long-term conservation of this iconic species. We emphasize the importance of evaluating all factors which may be linked to stocking practices in vulnerable species, particularly those sensitive to climate change.

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L. population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment-specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment-specific studies of stock abundance. Implications for implementing management actions are considered. © 2010 Blackwell Publishing Ltd.

Since the 1970s, when major improvements to the water quality were made, the River Thames has been subject to a high-profile project aimed at restoring Atlantic salmon to the catchment. Whilst initially successful, with hundreds of salmon returning each year in the late 1980s, the number of adults returning to the river has declined steeply again in recent years, reaching a low in 2005 when no salmon were recorded. Using a baseline of genetic information gathered from 3830 salmon from throughout their southern European range, and incorporating samples from the hatchery fish used to stock the Thames, all 10 tagged hatchery fish captured in 2003 and all 16 returning untagged adult salmon captured between 2005 and 2008 were assigned to their most likely river of origin. The results suggest that untagged salmon currently ascending the river originate not from exogenous fish stocked into the Thames, but predominantly from other rivers in southern England. This highlights the potential for natural processes of recolonisation to operate in rivers where salmon have become locally extirpated. These findings also underscore several important considerations when undertaking species restoration projects: (i) previous causes of declines must be sufficiently ameliorated to allow new/translocated individuals to thrive, (ii) introduced individuals should originate from a stock that is closely related to the extirpated population, according to the principles of contemporary conservation biology, and (iii) dispersal and gene-flow from neighbouring populations may play a significant role in establishing new populations. © 2011 Elsevier Ltd.

BACKGROUND: Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. RESULTS: to facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. CONCLUSIONS: This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.

Serra‐Pereira, B. Moura, T. Griffiths, A. M. Gordo, L. S. & Figueiredo, I. (2010). Molecular barcoding of skates (Chondrichthyes: Rajidae) from the southern Northeast Atlantic. —Zoologica Scripta, 40, 76–84.Due to their vulnerability to fishing pressure, many species of skate (Rajidae) in the Northeast Atlantic are undergoing declines in abundance. The assessment of stock status and subsequent proposal of management measures are often complicated by high levels of species diversity and endemism, coupled with morphological and ecological conservatism, which makes distinguishing between species difficult. To improve the identification of skates and investigate the phylogenetic position of endemic species the cytochrome c oxidase subunit I (COI) was sequenced in 12 species (Dipturus oxyrinchus, Leucoraja naevus, Leucoraja circularis, Neoraja iberica, Raja brachyura, Raja clavata, Raja maderensis, Raja microocellata, Raja miraletus, Raja montagui, Raja undulata, Rostroraja alba) inhabiting the Portuguese waters. Based on sequence divergence R. maderensis and R. clavata only differ by 1% of the 652 bp COI sequence, questioning the recognition of R. maderensis (considered to be endemic to Madeira and the Azores), as a reproductively isolated species. Otherwise, there was clear phylogenetic support for the different genera and all the remaining species, although the genetic divergence was low compared to other chordates. In particular, COI analysis allowed clear identification of the morphologically similar species R. brachyura and R. montagui.

Many sharks and skates are particularly vulnerable to overfishing because of their large size, slow growth, late maturity and low fecundity. In Europe dramatic population declines have taken place in common skate (Dipturus batisL.), one of the largest demersal fish in regional shelf seas, leading to extirpations from substantial parts of its former range. Here we report the discovery of cryptic species in common skate collected from the northeast Atlantic continental shelf. Data from nuclear microsatellite markers indicated two clearly distinct clades and phylogenetic analysis of mitochondrial DNA sequences demonstrated monophyly of each one of them. Capture locations showed evidence of strong spatial segregation, with one taxon occurring mainly in waters off the southern British Isles and around Rockall, while the other was restricted to more northerly shelf waters. These apparently cryptic species showed overlapping substrate and depth preferences, but distributional limits were closely related to temperature gradients, potentially indicating thermal limits to their distributions. This discovery of hidden diversity within a large, critically endangered marine vertebrate demonstrates how marine biodiversity can be underestimated, even in such a relatively well-studied and heavily exploited region.

Salmonid fishes exhibit high levels of population differentiation. In particular, the brown trout (Salmo trutta L.) demonstrates complex within river drainage genetic structure. Increasingly, these patterns can be related to the underlying evolutionary models, of which three scenarios (member-vagrant hypothesis, metapopulation model and panmixia) facilitate testable predictions for investigations into population structure. We analysed 1225 trout collected from the River Dart, a 75 km long river located in southwest England. Specimens were collected from 22 sample sites across three consecutive summers (2001-2003) and genetic variation was examined at nine microsatellite loci. A hierarchical analysis of molecular variance revealed that negligible genetic variation was attributed among temporal samples. The highest levels of differentiation occurred among samples isolated above barriers to fish movement, and once these samples were removed, a significant effect of isolation-by-distance was observed. These results suggest that, at least in the short-term, ecological events are more important in shaping the population structure of Dart trout than stochastic extinction events, and certainly do not contradict the expectations of a member-vagrant hypothesis. Furthermore, individual-level spatial autocorrelation analyses support previous recommendations for the preservation of a number of spawning sites spaced throughout the tributary system to conserve the high levels of genetic variation identified in salmonid species. © 2009 the Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

New World screwworm populations in North and Central America have been the targets of virtually continuous eradication attempts by sterile insect technique (SIT) since the 1950s. Nevertheless, in some areas, such as Jamaica, SIT control programmes have failed. Reasons for the failure of SIT-based control programmes in some locations are unknown, but it has been hypothesized that failure may be related to mating incompatibility between sterile and wild fly populations or to the existence of sexually incompatible cryptic species. This paper outlines the development of a suite of four new microsatellite loci which can be used to study intra-specific relationships between populations of Cochliomyia hominivorax from the Caribbean and South America, which represent those populations involved in, or earmarked for, forthcoming SIT control. Cross-amplification with the secondary screwworm, Cochliomyia macellaria, was also successful with three of the new loci. We present results which suggest that populations from Trinidad and Jamaica form distinct groupings of flies and that C. hominivorax from Trinidad appears particularly distinct.

Complete sequencing of the mtDNA control region (CR) from five specimens of brown trout Salmo trutta from the Amu Darya River identified two novel haplotypes belonging to the Danubian lineage. This finding supports the long-standing hypothesis that brown trout in the Aral Sea represent a distinct genetic stock and also illustrates the benefits that complete sequencing of the CR can provide for elucidating phylogeographic relationships.

There is substantial evidence that genetic variation, at both the level of the individual and population, has a significant effect on behaviour, fitness and response to toxicants. Using DNA microsatellites, we examined the genetic variation in samples of several commonly used laboratory strains of zebrafish, Danio rerio, a model species in toxicological studies. We compared the genetic variation to that found in a sample of wild fish from Bangladesh. Our findings show that the wild fish were significantly more variable than the laboratory strains for several measures of genetic variability, including allelic richness and expected heterozygosity. This lack of variation should be given due consideration for any study which attempts to extrapolate the results of ecotoxicological laboratory tests to wild populations.