Dataset Information

Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.

ABSTRACT: The identification of species constitutes the first basic step in phylogenetic studies, biodiversity monitoring and conservation. DNA barcoding, i.e. the sequencing of a short standardized region of DNA, has been proposed as a new tool for animal species identification. The present study provides an update on the composition of shark in the Egyptian Mediterranean waters off Alexandria, since the latest study to date was performed 30 years ago, DNA barcoding was used in addition to classical taxonomical methodologies. Thus, 51 specimen were DNA barcoded for a 667 bp region of the mitochondrial COI gene. Although DNA barcoding aims at developing species identification systems, some phylogenetic signals were apparent in the data. In the neighbor-joining tree, 8 major clusters were apparent, each of them containing individuals belonging to the same species, and most with 100% bootstrap value. This study is the first to our knowledge to use DNA barcoding of the mitochondrial COI gene in order to confirm the presence of species Squalus acanthias, Oxynotus centrina, Squatina squatina, Scyliorhinus canicula, Scyliorhinus stellaris, Mustelus mustelus, Mustelus punctulatus and Carcharhinus altimus in the Egyptian Mediterranean waters. Finally, our study is the starting point of a new barcoding database concerning shark composition in the Egyptian Mediterranean waters (Barcoding of Egyptian Mediterranean Sharks [BEMS], http://www.boldsystems.org/views/projectlist.php?&#Barcoding%20Fish%20%28FishBOL%29).

SUBMITTER: Moftah M

PROVIDER: S-EPMC3206905 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.

Moftah Marie M Abdel Aziz Sayeda H SH Elramah Sara S Favereaux Alexandre A

PloS one 20111102 11

The identification of species constitutes the first basic step in phylogenetic studies, biodiversity monitoring and conservation. DNA barcoding, i.e. the sequencing of a short standardized region of DNA, has been proposed as a new tool for animal species identification. The present study provides an update on the composition of shark in the Egyptian Mediterranean waters off Alexandria, since the latest study to date was performed 30 years ago, DNA barcoding was used in addition to classical taxo ...[more]

PMID: 22087242

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Project description:BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. METHODOLOGY/PRINCIPAL FINDINGS: Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide robust support for most morphologically based taxon concepts and also highlight key areas of taxonomic uncertainty worthy of reappraisal.

Project description:Body shape is a foundational trait on the differences between species. However, morphological measurements can be simplifying and, for many taxa, can be distorted upon preservation or are difficult to collect due to a species' habit or size. Scientific illustrations, or pictographs, provide information on a species' morphology but are rarely used as traits. Here, we demonstrate the use of pictographs using two shark clades: Lamniformes and Carcharhinidae + Sphyrnidae. After collecting 473 pictographs from 67 species across 12 sources, we used landmarking to show that measurements derived from pictographs do not substantially differ from those garnered from specimens. We then used Elliptical Fourier Analysis and principal components analysis to construct a multivariate morphospace. Using global shape measurements, we evaluated whether substantial variability in body shape was introduced by habitat association, endemism, or illustrator. We found that a species' habitat preference strongly influenced the discovery rate of pictographs and the within-species similarity. While illustrations varied within a species, only a limited set of illustrators exhibited significant systematic variability. We also demonstrated the utility of pictographs in two common applications. For ancestral trait reconstruction, we developed a simple extension to estimate body shapes from principal components and, in doing so, observed that the Lamnid body plan diverged from the rest of Lamniformes ~100 MYA. For phylogenetic generalized linear mixed models (PGLMM), we found that the pictographs had greater explanatory power than traditional morphological measurements. We used the PGLMM to show that higher endemism across Carcharhinidae + Sphyrnidae taxa correlates with body shapes that have caudal fins with small heterocercal angles and more pronounced second dorsal/anal fins. We concluded that pictographs are likely an undervalued and easy-to-digitize data source on a species' body shape with numerous established methods for comparing pictographs and assessing variability.

Project description:BACKGROUND:Accessing folk knowledge from small-scale fishers is an affordable and reliable approach to understand the dynamic and diversity of shark species worldwide, especially of those eventually caught. In this context, ethnotaxonomy (folk identification and classification) may represent an alternative to support sharks fisheries management, especially in data-poor places. This study aimed to investigate fishing and ethnotaxonomy of the main shark species caught by small-scale fisheries from the coastal waters of the Brazilian Northeast. METHODS:Semi-structured and structured interviews were conducted with fishers targeting general aspects of fishing activities and specific topics regarding ethnotaxonomy, capture, and commercialization of sharks. For species identification, an ethnobiological systematic perspective was used to analyze the folk nomenclature and classification criteria. Non-parametric statistical tests were used to verify associations between species caught, fishing gear, and harvest period. RESULTS:Fishers mentioned 73 binomial names, 21 main folk species, and eight synonymies. Some species belonging to the same scientific genus are often named and grouped by the same folk name, with no distinction between species by fishers. Sharks are most landed as bycatch and correspond to less than 5% of the total commercial fisheries in the communities, with socioeconomic value for subsistence consumption and local commercialization. Sharks were said to be mainly caught with hand line and surface long line during the rainy season, while gillnet captures were associated to the dry season. At least three of the species most mentioned by fishers are currently classified as vulnerable and endangered worldwide. CONCLUSIONS:Even though landed sharks account for a small proportion of the fishing catches, their biological and life history features place sharks among the most vulnerable organisms globally. Such an ethnobiological approach towards shark identification may contribute to generate basic information on species caught, their frequency in the landings, and how different species belonging to the same genus can be landed and sold together. This type of information can generate subsidies to the development of conservation and management plans for these fishing resources, where knowledge is scarce.

Project description:BackgroundDNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity.Methodology/principal findingsA dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species.Conclusion/significanceWe emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.

Dataset Information

Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.

Publications

Classification of sharks in the Egyptian Mediterranean waters using morphological and DNA barcoding approaches.

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