DNA Barcoding for the Assessment of the Taxonomy and Conservation Status of the Fish Bycatch of the Northern Brazilian Shrimp Trawl Fishery

Guimarães‐Costa, Aurycéia; Machado, Fabíola S.; Reis‐Filho, José Amorim; Andrade, Marcelo C.; Araújo, Rafael; Corrêa, Eglé Miranda Ramos; Sampaio, Iracilda; Giarrizzo, Tommaso

doi:10.3389/fmars.2020.566021

Cited by 16 publications

(10 citation statements)

References 52 publications

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“…The integration of morphological and molecular taxonomic approaches carried out in the present work provides a further confirmation of the appropriateness of integrated methods for the identification of copepods, as demonstrated also for other organisms (Fontaneto et al, 2015;Avó et al, 2017;Mills et al, 2017;Guimarães-Costa et al, 2020). The success of using barcoding for single-species identification depends on the presence of high-quality reference data available in public sequence libraries (Bucklin et al, 2021).…”

Section: Discussionsupporting

confidence: 62%

From Phenotypes to Genotypes and Back: Toward an Integrated Evaluation of Biodiversity in Calanoid Copepods

et al. 2022

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Zooplankton molecular analyses allow for accurate species identification with a proper molecular signature, complementing classic phenotypic-based taxonomy (α taxonomy). For the first time in the Mediterranean Sea, cytochrome oxidase I (COI) gene sequences of calanoid copepods were associated with morphological identification, HD and SEM images, using a fully integrated approach to assess taxonomic diversity. Such method was applied to selected species, generating consensus sequences from the Gulf of Naples (Central Tyrrhenian Sea, Western Mediterranean Sea) also including reference barcodes of three target species (Nannocalanus minor, Pleuromamma gracilis and the non-indigenous species (NIS) Pseudodiaptomus marinus) that are new for the Mediterranean area. The new barcodes were selected including: dominant and rare species; species that were originally described in the study area as type locality, but lacking a molecular description; emergent NIS and potential species complex. The integration between morphological and molecular identification by tree placement, using species-specific highly conserved oligonucleotides, also provided new and high-quality references of the most common and abundant copepod genera and species in the Mediterranean Sea. Our regional reference library was then integrated and analyzed with global data reference available on BOLD database to explore the presence of potential cryptic species and biogeographic patterns and links among geographically distant populations of copepods. Overall, this study provides valuable insight into the actual copepod taxonomic diversity and contributes to building baseline knowledge to monitor coastal biodiversity in neritic areas worldwide, where copepods are of paramount ecological importance, paving the way for future metabarcoding studies.

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Section: Discussionsupporting

confidence: 62%

From Phenotypes to Genotypes and Back: Toward an Integrated Evaluation of Biodiversity in Calanoid Copepods

et al. 2022

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“…(Marceniuk et al, 2019). Similarly, molecular data identified Narcine brasiliensis and Mustelus canis (Guimarães-Costa et al, 2020;Rodrigues-Filho et al, 2020) while integrative analyses based on morphological, genetic and ecological studies recorded H. berthalutzae (Pentean et al, 2020) for this region. These data highlight the importance of focusing on the diversity of elasmobranchs in the north coast of Brazil, as recent studies have identified distinct results on the species composition in this group of fishes.…”

Section: Diversity Of Elasmobranchs In the Amazon Coastmentioning

confidence: 84%

“…A potential obstacle to a proper identification of the species was the lack of whole specimens to be used as a voucher for morphological identification as well as the absence of sequences in public datasets for comparative analyses (Rodrigues-Filho et al, 2020). In recent years, studies based on molecular identification of stingray species have allowed both the identification of valid species and the registration of new occurrences and new species (Guimarães-Costa et al, 2020;Pentean et al, 2020). In a recent study, Rodrigues-Filho et al ( 2020) identified nine ray species on the Amazon coast using DNA barcodes.…”

Section: Diversity Of Elasmobranchs In the Amazon Coastmentioning

confidence: 99%

“…Fish landing occur daily in this municipality (Isaac et al, 2008) and most of products are sold in the street market of Bragança that encompasses indoor ("Mercado") and outdoor ("Feirinha") sites where a high diversity and number of species are commercialized (Freire et al, 2011;Martins et al, 2021). Over more than a decade, studies in this region have shown that Bragança lands and commercializes a large diversity of elasmobranchs with variation in the abundance and richness of sharks and rays species sold in the street market (Carmona et al, 2008;Rodrigues-Filho et al, 2009Guimarães-Costa et al, 2020;Feitosa et al, 2018;Marceniuk et al, 2019;Souza-Araujo et al, 2021). The elasmobranchs labeled as "cação" and "arraia" are among the most commercialized fish groups in this region but the lack of standard commercial common names and the mischaracterization of specimens constrain their morphological identification and justify the utilization of other methods based on molecular validation of species, like DNA barcode (Feitosa et al, 2018;Rodrigues-Filho et al, 2020;Martins et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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Intensive Commercialization of Endangered Sharks and Rays (Elasmobranchii) Along the Coastal Amazon as Revealed by DNA Barcode

et al. 2021

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Elasmobranchs represent a well-defined group, composed of about 1,150 species inhabiting diverse aquatic environments. Currently, several of these species have been classified as threaten due to overexploitation. Therefore, we used DNA barcode to identify traded species of sharks and stingrays in the municipality of Bragança (Amazon coastal region), a major fishery landing site in northern Brazil. We collected a total of 127 samples labeled into 24 commercial nomenclatures over 1-year period. Twenty species were discriminated and 13 of them are recognized under some threatening status. In relation to sharks, Carcharhinidae showed the highest number of species, half of them classified as endangered, followed by hammerhead sharks (Sphyrnidae), with four species also regarded as threatened with extinction. The Rhinopteridae and Dasyatidae rays were the most abundant groups, with trade records of the following threatened species: Rhinoptera brasiliensis, Rhinoptera bonasus, Hypanus berthalutzae, and Fontitrygon geijskesi. It is noteworthy that threatened species of elasmobranchs have been frequently and regularly exploited because of inefficient fishery management policies. Therefore, effective inspection practices need to be incorporated in fisheries, including the use of DNA barcode to enable a reliable method of species authentication and to assure the proper commercialization.

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“…In the decades since a DNA barcoding system for specimen identifications was established, numerous studies have proven that this technique is effective for identifying species (Hajibabaei et al, 2006;Ward et al, 2009;Radulovici et al, 2010). DNA barcoding has now been successfully applied in insects (Janzen et al, 2005;Smith et al, 2005), crustaceans (Costa et al, 2007;Bilgin et al, 2014;Bucklin et al, 2022), fish (Ward et al, 2005;Hubert et al, 2008;Ghouri et al, 2020;Guimarães-Costa et al, 2020;Xu et al, 2021), birds (Hebert et al, 2004), and mammals (Lorenz et al, 2005;Clare et al, 2007). These achievements have benefited from the establishment of the Barcode of Life Data Systems (BOLDSystems), which is a global public standard dataset platform with general technical rules and identification systems for animal taxonomy.…”

Section: Introductionmentioning

confidence: 99%

The Application of DNA Barcoding in Crustacean Larvae Identification from the Zhongsha Islands, South China Sea

Wang

Huang

et al. 2022

Front. Mar. Sci.

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Marine crustaceans are known as a group with high morphological diversity and great economic value. Most species have planktonic larval stages that are difficult to identify to species level using traditional approaches because of insufficient morphological diagnostic characters or taxonomic descriptions. We used DNA barcoding and molecular species identification to investigate the species diversity and distribution of crustacean larvae in the Zhongsha Islands waters, South China Sea. In total, 108 sequences were obtained from crustacean larvae collected in the Zhongsha Islands waters in 2019 using vertical hauls between the depths of 5 and 200 m. The molecular classification approach confirmed that 108 sequences represented crustaceans typical to the South China Sea, with 70 species identified, representing 43 genera, 23 families, and 4 orders. However, the cytochrome c oxidase subunit I gene sequences of only 27 species identified from the larval samples matched with available sequences taken from adults in GenBank. The comparison of K2P distances yielded a notable gap of 3.5–10.7% between intraspecific and interspecific distances across the sequence dataset. More than 80% of the crustacean larvae species belonged to the order Decapoda, and they displayed marked differences in their distributionsin the Zhongshan Islands waters. The orders Calanoida and Amphipoda were represented by the fewest species, which were recorded only at the edge of the Zhongsha Atoll.

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DNA Barcoding for the Assessment of the Taxonomy and Conservation Status of the Fish Bycatch of the Northern Brazilian Shrimp Trawl Fishery

Cited by 16 publications

References 52 publications

From Phenotypes to Genotypes and Back: Toward an Integrated Evaluation of Biodiversity in Calanoid Copepods

From Phenotypes to Genotypes and Back: Toward an Integrated Evaluation of Biodiversity in Calanoid Copepods

Intensive Commercialization of Endangered Sharks and Rays (Elasmobranchii) Along the Coastal Amazon as Revealed by DNA Barcode

The Application of DNA Barcoding in Crustacean Larvae Identification from the Zhongsha Islands, South China Sea

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