Abstract
BackgroundDNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world's fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea.Methodology/Principal FindingsDNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species.Conclusions/SignificanceThe present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy.
Highlights
Fishes show an astonishing diversity of shapes, sizes, and colors
Barcode divergences of 1% were used as filters to perform comparisons between units that were identified morphologically; the criterion was met in all cases except Upeneus sulphureus, Siganus guttatus, Alepes djedaba, Acentrogobius caninus, Hyporhamphus limbatus, Gymnothorax reevesii, Kumococius rodericensis, Mene maculata, Terapon jarbua, Zebrias quagga, Pennahia anea, and Mugil cephalus
The distribution of the nearest-neighbor distance (NND), namely the minimum of genetic variation between a species and its closest relative, revealed that only 3.31% of NNDs (8 cases) were lower than 1% (Fig. 4)
Summary
Fishes show an astonishing diversity of shapes, sizes, and colors. The delimitation and recognition of fish species is of interest for taxonomy and systematists, but it is a requirement in studies of natural history and ecology, fishery management, tracking the dispersal patterns of eggs and larvae, estimations of recruitment and spawn areas, and authentication of food products [1,2]. Sequence divergences within the 59 region of the mitochondrial cytochrome oxidase subunit I (COI) gene are generally much greater between species than within species. This in turn suggests that the approach is extensively applicable among phylogenetically distant animal groups [8,9,10,11,12,13,14]. DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea
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