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Monitoring communities of fish is important for the management and sustainability of fisheries and marine ecosystems. Baited remote underwater video systems (BRUVs) are among the most effective nondestructive techniques for sampling bony fishes and elasmobranchs (sharks, rays, and skates). However, BRUVs sample visually conspicuous biota; hence, some taxa are undersampled or not recorded at all. We compared the diversity of fishes characterized using BRUVs with diversity detected via environmental DNA (eDNA) metabarcoding. We sampled seawater and captured BRUVs imagery at 48 locales that included reef and seagrass beds inside and outside a marine reserve (Jurien Bay in Western Australia). Eighty-two fish genera from 13 orders were detected, and the community of fishes described using eDNA and BRUVs combined yielded >30% more generic richness than when either method was used alone. Rather than detecting a homogenous genetic signature, the eDNA assemblages mirrored the BRUVs’ spatial explicitness; differentiation of taxa between seagrass and reef was clear despite the relatively small geographical scale of the study site (~35 km²). Taxa that were not sampled by one approach, due to limitations and biases intrinsic to the method, were often detected with the other. Therefore, using BRUVs and eDNA in concert provides a more holistic view of vertebrate marine communities across habitats. Both methods are noninvasive, which enhances their potential for widespread implementation in the surveillance of marine ecosystems. El monitoreo de comunidades de peces es importante para el manejo y sustentabilidad de las pesquerías y los ecosistemas marinos. Los sistemas remotos de video submarino con carnada (SRVSC) están entre las técnicas no destructivas más efectivas para el muestreo de peces óseos y elasmobranquios (tiburones, mantarrayas y rayas). Sin embargo, los SRVSC muestrean biota que es conspicua visiblemente; entonces, algunos taxones están mal muestreados o simplemente no se registran en los muestreos. Comparamos la diversidad de peces caracterizada usando SRVSC con la diversidad detectada por medio del metacódigo de barras de ADN ambiental (eDNA, en inglés). Muestreamos el agua de mar y capturamos imágenes con SRVSC en 48 localidades que incluyeron el arrecife y los pastos marinos dentro y fuera de una reserva marina (Bahía Jurien en el oeste de Australia). Se detectaron 83 géneros de peces de 13 órdenes, y la comunidad de peces descrita con el uso combinado del eDNA y el SRVSC produjo >30% riqueza más genérica que cuando cualquiera de los dos métodos se usó individualmente. En lugar de detectar una firma genética homogénea, los ensamblados de eDNA reflejaron la claridad espacial del SRVSC; la diferenciación de los taxones entre los pastos marinos y el arrecife fue clara a pesar la escala geográfica relativamente pequeña del sitio de estudio (~35 km²). Los taxones que no fueron muestreados por uno de los métodos, por causa de limitaciones y sesgos intrínsecos al método, casi siempre fueron detectados usando el otro método. Por lo tanto, el uso de SRVSC y el eDNA en concreto proporciona una visión más holística de las comunidades marinas de vertebrados en todos los hábitats. Ambos métodos son no invasivos, lo que incrementa su potencial para ser una implementación de uso amplio en la vigilancia de los ecosistemas marinos.

The longnose skates (Zearaja chilensis and Dipturus trachyderma) are the main component of the elasmobranch fisheries in the south-east Pacific Ocean. Both species are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. In this study, we used a genetic variation (560 bp of the control region of the mitochondrial genome and ten microsatellite loci) to explore population connectivity at five locations along the Chilean coast. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations (San Antonio, Valdivia), two locations in the Chiloé Interior Sea (Puerto Montt and Aysén) and Punta Arenas in southern Chile. For example, mtDNA haplotype diversity was similar across off-shore locations and Punta Arenas (h = 0.46-0.50), it was significantly different to those in the Chiloé Interior Sea (h = 0.08). These results raise concerns about the long-term survival of the species within the interior sea, as population resilience will rely almost exclusively on self-recruitment. In contrast, little evidence of genetic structure was found for D. trachyderma. Our results provide evidence for three management units for Z. chilensis, and we recommend that separate management arrangements are required for each of these units. However, there is no evidence to discriminate the extant population of Dipturus trachyderma as separate management units. The lack of genetic population subdivision for D. trachyderma appears to correspond with their higher dispersal ability and more offshore habitat preference.

Impacts of chronic overfishing are evident in population depletions worldwide, yet indirect ecosystem effects induced by predator removal from oceanic food webs remain unpredictable. As abundances of all 11 great sharks that consume other elasmobranchs (rays, skates, and small sharks) fell over the past 35 years, 12 of 14 of these prey species increased in coastal northwest Atlantic ecosystems. Effects of this community restructuring have cascaded downward from the cownose ray, whose enhanced predation on its bay scallop prey was sufficient to terminate a century-long scallop fishery. Analogous top-down effects may be a predictable consequence of eliminating entire functional groups of predators.

Resource partitioning is expected in sympatric assemblages of predators as a mechanism that reduces competition between individuals of different species or age classes, which in turn can affect population and community interactions as well as resource distribution and availability. However, for species such as benthic skates (Rajidae), the juveniles of which are cryptic and not easily sampled by traditional survey methods, there is a knowledge gap concerning the spatial and trophic ecology during early life stages. The eye lenses of vertebrates grow over their lifetime providing a chronological biochemical record that can be used to infer differences in diet and/or foraging location (trophic geography) throughout the ontogeny of the animal. For the first time, eye lenses of 4 sympatric Rajidae species from the northeast Atlantic were successfully used to recover stable isotope life histories for individual skates. Isotopic separation among species and across life stages within species suggests that habitat partitioning and differences in trophic ecology are present throughout ontogeny. Isotopic data imply that adults are separated from juveniles both spatially and in terms of their diet and the 4 species appear to partition resources more than expected based on previous studies.

Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.

Characterization of fish diets from stomach content analysis commonly involves the calculation of multiple relative measures of prey quantity (%N,%W,%FO), and their combination in the standardized Index of Relative Importance (%IRI). Examining the underlying structure of dietary data matrices reveals interdependencies among diet measures, and obviates the advantageous use of underused prey-specific measures to diet characterization. With these interdependencies clearly realized as formal mathematical expressions, we proceed to isolate algebraically, the inherent bias in %IRI, and provide a correction for it by substituting traditional measures with prey-specific measures. The resultant new index, the Prey-Specific Index of Relative Importance (%PSIRI), is introduced and recommended to replace %IRI for its demonstrated more balanced treatment of the relative measures of prey quantity, and less erroneous behavior across taxonomic levels of identified prey. As a case study, %PSIRI was used to examine the diet of the Aleutian skate Bathyraja aleutica from specimens collected from three ecoregions of the northern Gulf of Alaska (GOA) continental shelf during June-September 2005–2007. Aleutian skate were found to primarily consume the commonly abundant benthic crustaceans, northern pink shrimp Pandalus eous and Tanner crab Chionoecetes bairdi , and secondarily consume various teleost fishes. Multivariate variance partitioning by Redundancy Analysis revealed spatially driven differences in the diet to be as influential as skate size, sex, and depth of capture. Euphausiids and other mid-water prey in the diet were strongly associated with the Shelikof Strait region during 2007 that may be explained by atypical marine climate conditions during that year.

Gli autori riportano la cattura di diversi esemplari della razza norvegese Dipturus nidarosiensis (Storm, 1881) al largo delle coste algerine occidentali. Si tratta prevalentemente di esemplari di grandi dimensioni, compresi tra 141 cm e 164 cm di lunghezza totale e tra 69 cm e 71,5 cm di larghezza del disco. È probabile che questi esemplari provengano dall'Atlantico orientale e siano entrati nel Mediterraneo attraverso lo stretto di Gibilterra, il che renderebbe D. nidarosiensis una specie erculea. L'abbondanza relativamente elevata di catture al largo della costa algerina suggerisce che attualmente una popolazione vitale si sia stabilita con successo nella regione.

Habitat selection is the process by which an individual makes an active decision to make use of a particular habitat when others are available. The ability to infer habitat selection therefore requires observations of movement through space and time which can be particularly challenging for marine species that are cryptic and do not regularly visit the sea surface. Rajidae (skates) are benthic mesopredators that inhabit turbid coastal waters and exhibit site fidelity, making them an ideal group for studying habitat selection and resource partitioning using a fixed, passive acoustic receiver array in the western English Channel, UK. Using network analysis, significant differences were found in the way 4 species of Rajidae occupied different parts of the array; for example, Raja microocellata and R. clavata occupied shallower habitat than R. brachyura and R. montagui. R. montagui and R. brachyura were further separated, with each species detected more frequently at different receivers. Males and females of all 4 species were also detected at different receivers and at different times. These results demonstrate habitat selection, resource partitioning among species and sexual segregation in these 4 species of Rajidae. Our findings are important evidence for management of fisheries, such as the designation of marine protected areas, and further highlight the potential of this method for tracking other mobile marine species in temperate, open coastal regions.

Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts’ divergence times showed that the differences in microbial communities in all three body parts were related to the hosts’ divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.

Despite increased focus on ascertaining the status of elasmobranch fish, the stock units for many species are uncertain. Data from mark-recapture tagging studies undertaken from 1959–2017 were analysed for 13 batoid species. Data were most comprehensive for skates (Rajidae), with 22,374 released and 3342 (14.9%) returned. Most data related to thornback ray Raja clavata , blonde ray R. brachyura and spotted ray R. montagui . Tags were generally returned from areas less than 50 km from their release, and usually from the ICES Division in which they were released. However, straight-line distances travelled of up to 910 km ( R. brachyura ) and 772 km ( R. clavata ) were recorded, highlighting that individual skates are capable of longer-distance movements. The maximum time at liberty was 16.6 years ( R. clavata ). Whilst mark-recapture data indicated that the current stock units used by ICES are broadly appropriate, southward movements of several skate species tagged off Northern Ireland (Division 6.a) to the Irish Sea (Division 7.a) were observed. In contrast, skates tagged in the Irish Sea and Bristol Channel (Division 7.f) generally remained in that area, with only occasional recaptures from Division 6.a.