DNA Barcoding Identifies Argentine Fishes from Marine and Brackish Waters

Abstract

BackgroundDNA 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 FindingsSpecimens 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/SignificanceThis 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.

Resolving taxonomic uncertainty in vulnerable elasmobranchs: are the Madeira skate (Raja maderensis) and the thornback ray (Raja clavata) distinct species?

“…Only sequences originating from the following specialist publications were utilised to minimise inaccuracy with species identification: Spies et al (2006), Serra-Pereira et al (2011), Coulson et al (2011), Mabragaña et al (2011) and Lynghammar et al (2014. Additional sequences from the starry ray (R. asterias, a Mediterranean endemic species) were also downloaded, as this species is considered closely related to R. clavata (summarised in Table S3).…”

“…Therefore, determining the taxonomic status of R. maderensis has important implications for conservation and management. The application of genetic markers to this question seems especially appropriate, given that this approach has been highly successful in unambiguously distinguishing skates across Europe and elucidating taxonomic issues in the group (Spies et al 2006;Griffiths et al 2010;Iglésias et al 2010;Serra-Pereira et al 2011;Coulson et al 2011;Mabragaña et al 2011;Lynghammar et al 2014). In terms of IUCN assessment this study highlights polytypic nature of R. clavata, further complicating its assessment for red-listing.…”

“…In particular, the mitochondrial 'barcoding' gene, cytochrome c oxidase subunit I (COI), can reveal differentiation at fine taxonomic levels, yet usefully diverges little within species (Hebert et al 2003). COI barcoding has recently proven a successful tool for validating skate identification in a number of fisheries (Spies et al 2006;Serra-Pereira et al 2011;Coulson et al 2011;Mabragaña et al 2011;Lynghammar et al 2014).…”

Application of Computational Methods in Fish Species Identification Based on Mitochondrial DNA Sequences

“…This makes it difficult to use a single threshold level. Therefore, genetic distances vary from species to species 11,12 . Among fishes, genus Puntius/Pethia has more than 130 valid species with many hidden or species complexes 13,14 .…”

Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?

“…The second focus of this study is on labeonine cyprinid genera, where members of Crossocheilus, Hemigrammocapoeta, barcoding proved to be a powerful and reliable tool for discriminating a large range of species, including all major taxa of marine as well as freshwater fishes [e.g. 1,[5][6][7][8][9][10][11][12]. The tool has gained additional attention among biologists by having the potential to reveal cryptic diversity, especially given the enormous amount of data collected globally, which can easily be used to compare own sequence data on a regional scale.…”