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.
Highlights
Despite ongoing scientific debate concerning the role of molecular methods in taxonomy DNA barcoding has emerged as a widely accepted tool for species identification because of its enhanced focus on standardization and data validation [1]
Advocating the use of an characterized 648 bP fragment from the mitochondrial 59 region of the cytochrome c oxidase subunit I (COI) gene for animal identification, the primary goal of barcoding focuses on the assembly of reference sequence libraries derived from expert-identified voucher specimens in order to develop reliable molecular tools for species identification in nature [5]
We examined the patterns of barcode sequence divergence among 577 specimens identified as belonging to 125 fish species, representing nearly one third of the known fauna [33,35,43]
Summary
Despite ongoing scientific debate concerning the role of molecular methods in taxonomy DNA barcoding has emerged as a widely accepted tool for species identification because of its enhanced focus on standardization and data validation [1]. Barcoding [2,3,4] seeks to extend species identification capabilities by using short, standardized gene regions for the efficient and cost-effective identification of eukaryotes. Advocating the use of an characterized 648 bP fragment from the mitochondrial 59 region of the cytochrome c oxidase subunit I (COI) gene for animal identification, the primary goal of barcoding focuses on the assembly of reference sequence libraries derived from expert-identified voucher specimens in order to develop reliable molecular tools for species identification in nature [5]. DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets.
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