1,721,111 research outputs found
Genomic analysis of population structure of yellowfin tuna (Thunnus albacares) at the global scale
No full textGenetics of local adaptation of Atlantic Bluefin Tuna from the Mediterranean Sea.
No full textThe Atlantic Bluefin tuna (ABFT, Thunnus thynnus), one of the largest top-predator fish inhabiting the pelagic ecosystems of the North Atlantic Ocean and Mediterranean Sea, has been extensively overexploited in recent decades. However, in the Mediterranean Sea, the mixing rates between the eastern, central and western basins have not yet been resolved. Both electronic tagging, otolith and genetic markers cannot still depict a clear scenario of tuna movements and structuring, essential requirement for a proper management of ABFT fisheries. Here we used Expressed Sequence Tag-linked (EST-linked) microsatellites to explore the patterns of adaptive evolution of T. thynnus population and of its population dynamics in the Mediterranean Sea. For this purpose 16 EST-linked microsatellites were genotyped in 177 tuna individuals from the Mediterranean and several methods were used to explore population genetic structuring and estimate/detect signals of local adaptation. Bayesian clustering results indicated the presence of a single cluster, corroborated also by the Correspondence Analysis and pairwise FSTs. Similarly the two methods, used for the detection of FST outliers, did not reveal any pattern suggesting the presence of selective pressure. Our results advise that the low level of polymorphism detected in EST-SSR loci used in this study could be ascribed to the presence of relatively conserved regions flanking these microsatellites. These genomic regions are probably not involved in physiological responses to local adaptation and we were able to rule out action of divergent or balancing selection on EST-SSR polymorphism
Not all that clear cut : intraspecific morphological variability in Squalus blainville (Risso, 1827) and implications for identification of the species
Full text linkOf the three species of the genus Squalus that occur in the Mediterranean Sea, S. blainville and S. megalops are very difficult to distinguish. This study assesses the variability in morphological features that have been used to differentiate between these species. Squalus were collected from stations within the 25-nautical mile Fisheries Management Zone around the Maltese Islands; 349 specimens were dissected and categorized into male and female, mature and immature, and individuals were randomly selected from each category to make up a sample of 169 specimens. For each individual, total length and first dorsal fin parameters were measured, and morphology of denticles isolated from the laterodorsal area, of the upper and lower teeth and of the chondrocranium was analysed. The first dorsal spine was shorter that the fin base in 93% of the specimens, which is typical of S. megalops; this character was not related to either gender or maturity. Chondrocrania with one lateral process (typical of S. blainville) and two lateral processes (typical of S. megalops) were present. Teeth from the same individuals showed morphological features that overlap between S. blainville and S. megalops. Both unicuspid (typical of S. megalops) and tricuspid denticles (typical of S. blainville) were observed on the same individuals. Twelve specimens (six having one and six having two lateral chondrocranial processes) were analysed genetically by sequencing of the mtDNA marker Cytochrome Oxidase Subunit I (COI). All resulted to be S. blainville showing that intraspecific variability in supposedly diagnostic morphological features is large enough to render these unreliable to tell apart these two species, especially in the field.peer-reviewe
Species diversity and morphological stasis in skates (order Rajiformes): The challenge of skin transcriptome profiling in non-model species
No full textApproximately twenty years have passed since the beginning of concentrated investigations into the evolutionary history and ecology of skates. The evidence generated thus far suggests that skates have experienced multiple and parallel adaptive radiations at a regional scale, starting in the upper Cretaceous, which contributed to the delineation of strong phylo-geographical and population structuring. Despite the high species diversity characterising the Order Rajiformes, a strikingly stable gross morphology has been maintained on the evolutionary level. The combined use of morphometric analyses and genotyping by various panels of molecular markers on a large number of samples of widely distributed and endemic geographic populations provided efficient tools for stock identification and management. Nonetheless, the adaptive value of some phenotypic traits as, for instance, particular ornaments of the dorsal part of the body, remains poorly understood. Here, we applied transcriptome profiling of skin pictorial motifs (eyespots and dots on a uniformly coloured matrix) on recently diverged species with sibling and sister phylogenetic relationships (Raja clavata, R. straeleni and R. asterias respectively) and on species that are easily recognized by specific patterning traits and show strong monophyly (the Mediterranean R. miraletus and the South African R. ocellifera). The on-going differential expression analysis at skin transcriptome level will help to understand mechanisms of divergence, hybridisation signals and could be considered one of the tiles allowing to evaluate whether the same or alternative traits have been used in parallel adaptations to similar environments
DNA metabarcoding of trawling bycatch reveals diversity and distribution patterns of sharks and rays in the central Tyrrhenian Sea
Full text linkConservation and management of chondrichthyans are becoming increasingly important, as many species are particularly vulnerable to fishing activities, primarily as bycatch, which leads to incomplete catch reporting, potentially hiding the impact on these organisms. Here, we aimed at implementing an eDNA metabarcoding approach to reconstruct shark and ray bycatch composition from 24 hauls of a bottom trawl fishing vessel in the central Mediterranean. eDNA samples were collected through the passive filtration of seawater by simple gauze rolls encapsulated in a probe (the “metaprobe”), which already showed great efficiency in detecting marine species from trace DNA in the environment. To improve molecular taxonomic detection, we enhanced the 12S target marker reference library by generating sequences for 14 Mediterranean chondrichthyans previously unrepresented in public repositories. DNA metabarcoding data correctly identifies almost all bycaught species and detected five additional species not present in the net, highlighting the potential of this method to detect rare species. Chondrichthyan diversity showed significant association with some key environmental variables (depth and distance from the coast) and the fishing effort, which are known to influence demersal communities. As DNA metabarcoding progressively positions itself as a staple tool for biodiversity monitoring, we expect that its melding with opportunistic, fishery-dependent surveys could reveal additional distribution features of threatened and elusive
megafauna
Limitless connectivity: panmixia of Pagellus bogaraveo (Brünnich, 1768) over large distances
No full textThe intrinsic discrepancies existing between the definition of fish stock units and the structure of biological populations emphasize the need for integrating genetic data of population structure into fishery management strategies in the perspective of improving the assessment and management of valuable target species.
Population samples of Pagellus bogaraveo (Brunnich; 1768), a commercially valuable deep-water fish ineffectively exploited in the past decade, were considered in the present work. A total of 320 individuals were collected from different fishing grounds in the Atlantic Ocean and the Mediterranean Sea during surveys from the EU-funded MEDITS project and with traditional fishery along the European and African coasts. Samples were analyzed through the use of 21 microsatellite markers to estimate both genetic variability and differentiation. In general, no signal of population differentiation was detected since low levels of variation between groups were observed across multiple approaches. As a matter of fact, AMOVA revealed the highest percentage of total variation ‘within populations”. Moreover, no correlation with geographical distance was found using FST estimates. Analyses conducted using individual-based methods such as Bayesian clustering (STRUCTURE) and geometric approach (DAPC) agreed in showing a lack of structured population along the study areas. In all, the high homogeneity revealed using the molecular markers assessed suggested the absence of physical barriers between the geographical areas considered in this study. Hence, high connectivity spreads across the whole Mediterranean Sea and especially between the Atlantic and Mediterranean areas
Holistic multi-tracer assessment of stock structure for common sole (Solea solea) in the Mediterranean Sea
No full textThe data and code underlying this article are available in GitHub repository at https://github.com/RacheleCorti/Integrative_solea.The identification of biological population structure is vital for sustainable marine resource management. Misalignment between management units and actual fish populations can result in ineffective regulations, impacting the sustainability of exploited species. The common sole, Solea solea (Linnaeus, 1758), a commercially important demersal flatfish in the Mediterranean Sea, has been previously studied, but gaps remain in understanding its spatial structure within a pan-Mediterranean context. This study employed a multi-tracer holistic approach, integrating genomic and otolith data across various spatio-temporal scales using semi-quantitative methods and integrative multi-variate analysis. This holistic approach revealed the existence of at least three distinct regional stocks within the Mediterranean, highlighting a complex spatial population structure. The Stock Differentiation Index indicated a strong spatial structure, with multi-variate analysis showing consistent and complementary results across different tracers. The integration of these tracers supports the identification of distinct management units, offering a valuable uptake of the resulted information to the management strategies of common sole. Furthermore, this study advocates for the regular application of the holistic approach in the stock assessment of other fishery resources, underscoring its potential to enhance sustainable exploitation of marine resources across various species.None declared.Peer reviewe
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
- …
