Geographically Widespread Swordfish Barcode Stock Identification: A Case Study of Its Application

Background: The swordfish (Xiphias gladius) is a cosmopolitan large pelagic fish inhabiting tempered and tropical waters and it is a target species for fisheries all around the world. The present study investigated the ability of COI barcoding to reliably identify swordfish and particularly specific stocks of this commercially important species. Methodology: We applied the classical DNA barcoding technology, upon a 682 bp segment of COI, and compared swordfish sequences from different geographical sources (Atlantic, Indian Oceans and Mediterranean Sea). The sequences of the 59 hyper-variable fragment of the control region (59dloop), were also used to validate the efficacy of COI as a stockspecific marker. Case Report: This information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products. Conclusions: The NJ distance-based phenogram (K2P model) obtained with COI sequences allowed us to correlate the swordfish haplotypes to the different geographical stocks. Similar results were obtained with 59dloop. Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance. This information might speed the samples analysis in commercia

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

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Out of the Pacific and Back Again: Insights into the Matrilineal History of Pacific Killer Whale Ecotypes

Killer whales (Orcinus orca) are the most widely distributed marine mammals and have radiated to occupy a range of ecological niches. Disparate sympatric types are found in the North Atlantic, Antarctic and North Pacific oceans, however, little is known about the underlying mechanisms driving divergence. Previous phylogeographic analysis using complete mitogenomes yielded a bifurcating tree of clades corresponding to described ecotypes. However, there was low support at two nodes at which two Pacific and two Atlantic clades diverged. Here we apply further phylogenetic and coalescent analyses to partitioned mitochondrial genome sequences to better resolve the pattern of past radiations in this species. Our phylogenetic reconstructions indicate that in the North Pacific, sympatry between the maternal lineages that make up each ecotype arises from secondary contact. Both the phylogenetic reconstructions and a clinal decrease in diversity suggest a North Pacific to North Atlantic founding event, and the later return of killer whales to the North Pacific. Therefore, ecological divergence could have occurred during the allopatric phase through drift or selection and/or may have either commenced or have been consolidated upon secondary contact due to resource competition. The estimated timing of bidirectional migration between the North Pacific and North Atlantic coincided with the previous inter-glacial when the leakage of fauna from the Indo-Pacific into the Atlantic via the Agulhas current was particularly vigorous

Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids

The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology- based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases.Versión del editor4,411

Trophic Ecology of Atlantic Bluefin Tuna (Thunnus thynnus) Larvae from the Gulf of Mexico and NW Mediterranean Spawning Grounds: A Comparative Stable Isotope Study

The present study uses stable isotopes of nitrogen and carbon (δ15Nandδ13C) as trophic indicators for Atlantic bluefin tuna larvae (BFT) (6–10mm standard length) in the highly contrasting environmental conditions of the Gulf of Mexico (GOM) and the Balearic Sea (MED). These regions are differentiated by their temperature regime and relative productivity, with the GOM being significantly warmer and more productive. MED BFT larvae showed the highest δ15N signatures, implying an elevated trophic position above the underlyingmicrozooplankton baseline. Ontogenetic dietary shifts were observed in the BFT larvae from the GOM and MED which indicates early life trophodynamics differences between these spawning habitats. Significant trophic differences between the GOM and MED larvae were observed in relation to δ15N signatures in favour of the MED larvae, which may have important implications in their growth during their early life stages. These low δ15N levels in the zooplankton from the GOM may be an indication of a shifting isotopic baseline in pelagic food webs due to diatrophic inputs by cyanobacteria. Lack of enrichment for δ15N in BFT larvae compared to zooplankton implies an alternative grazing pathway from the traditional food chain of phytoplankton— zooplankton—larval fish. Results provide insight for a comparative characterization of the trophic pathways variability of the two main spawning grounds for BFT larvaeVersión del editor4,411

Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.)

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SNP identification and validation in two invasive species: zebra mussel (Dreissena polymorpha) and Asian clam (Corbicula fluminea)

Identificación y validación de PNU en dos especies invasoras: el mejillón cebra (Dreissena polymorpha) y la almeja asiática (Corbicula fluminea) El desarrollo de las plataformas asequibles de secuenciación masiva en paralelo (SMP) ha reducido el coste y el tiempo en la identificación de marcadores de polimorfismos de nucleótido único (PNU) para su uso en estudios de genética de poblaciones y de conservación. Tras la SMP, suele ser necesaria una segunda validación. El análisis de las curvas de fusión a alta resolución (HRMA en su sigla en inglés) es un método rápido y sencillo para escanear mutaciones y, por tanto, es un protocolo adecuado de validación de dichos marcadores, especialmente en especies no modelo. En este trabajo se presenta un juego de nueve marcadores polimórficos de PNU nuevos identificados mediante SMP y validados con el HRMA en dos especies invasoras (el mejillón cebra Dreissena polymorpha y la almeja asiática Corbicula fluminea), que pueden utilizarse en estudios de genética de poblaciones para evaluar y entender correctamente los episodios de invasión pasados y los que podrían ocurrir en el futuro.The development of affordable massive parallel sequencing (MPS) has reduced both time and costs of SNP identification for use in conservation and population genetic studies. After MPS, a second validation is usually required. High resolution melting analysis (HRMA) is a fast and simple method for mutation scanning, and thus a suitable validation protocol, particularly in non–model species. We present a set of nine novel polymorphic SNPs identified by MPS and validated with HRMA in two invasive species (the zebra mussel Dreissena polymorpha and the Asian clam Corbicula fluminea). These SNPs can be used in genetic studies to accurately assess and understand past and future invasion events.Identificación y validación de PNU en dos especies invasoras: el mejillón cebra (Dreissena polymorpha) y la almeja asiática (Corbicula fluminea) El desarrollo de las plataformas asequibles de secuenciación masiva en paralelo (SMP) ha reducido el coste y el tiempo en la identificación de marcadores de polimorfismos de nucleótido único (PNU) para su uso en estudios de genética de poblaciones y de conservación. Tras la SMP, suele ser necesaria una segunda validación. El análisis de las curvas de fusión a alta resolución (HRMA en su sigla en inglés) es un método rápido y sencillo para escanear mutaciones y, por tanto, es un protocolo adecuado de validación de dichos marcadores, especialmente en especies no modelo. En este trabajo se presenta un juego de nueve marcadores polimórficos de PNU nuevos identificados mediante SMP y validados con el HRMA en dos especies invasoras (el mejillón cebra Dreissena polymorpha y la almeja asiática Corbicula fluminea), que pueden utilizarse en estudios de genética de poblaciones para evaluar y entender correctamente los episodios de invasión pasados y los que podrían ocurrir en el futuro