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Background and Aims: Fishes are the main animal protein source for human beings and play a vital role in aquatic ecosystems and food webs. Fish identification can be challenging, especially in the tropics (due to high diversity), and this is particularly true for larval forms or fragmentary remains. DNA barcoding, which uses the 5' region of the mitochondrial cytochrome c oxidase subunit I (COI) as a target gene, is an efficient method for standardized species-level identification for biodiversity assessment and conservation, pending the establishment of reference sequence libraries., Materials and Methods: In this study, fishes were collected from three rivers in southeastern Nigeria, identified morphologically, and imaged digitally. DNA was extracted, PCR-amplified, and the standard barcode region was bidirectionally sequenced for 363 individuals belonging to 70 species in 38 genera. All specimen provenance data and associated sequence information were recorded in the barcode of life data systems (BOLD; www.barcodinglife.org ). Analytical tools on BOLD were used to assess the performance of barcoding to identify species., Results: Using neighbor-joining distance comparison, the average genetic distance was 60-fold higher between species than within species, as pairwise genetic distance estimates averaged 10.29% among congeners and only 0.17% among conspecifics. Despite low levels of divergence within species, we observed river system-specific haplotype partitioning within eight species (11.4% of all species)., Conclusion: Our preliminary results suggest that DNA barcoding is very effective for species identification of Nigerian freshwater fishes.

Background and Aims: Considering the promising use of DNA barcoding for species identification, the importance of the freshwater fish fauna of the Paraíba do Sul River Basin, and its advanced stage of degradation, the present study evaluated the effectiveness of DNA barcoding to identify the fish species in this basin., Materials and Methods: A total of 295 specimens representing 58 species belonging to 40 genera, 17 families, and 5 orders were sequenced., Results: The DNA barcodes discriminated all species analyzed without ambiguity. The results showed a pronounced difference between conspecific and congeneric pair-wise sequence comparisons, demonstrating the existence of a "barcode gap" for the species analyzed. The nearest-neighbor distance analysis showed only three cases with Kimura two-parameter values lower than a 2% divergence threshold. However, the patterns of divergence observed in each case remained sufficient to discriminate each species, revealing the accuracy of DNA barcoding even cases with relatively low genetic divergence. At the other extreme, three species displayed high genetic sequence divergence among conspecifics. For two cases, Characidium alipioi and Geophagus proximus, barcoding proved effective at flagging possible new species. For another case, Astyanax bimaculatus, the use of DNA barcoding of the comparison of shared freshwater fish fauna between different basins revealed itself as highly useful in disclosing that the previously identified A. bimaculatus "cluster A" probably represents the species Astyanax altiparanae., Conclusion: The present study is among the first to assess the efficiency of barcoding for the Brazilian freshwater fishes. The results demonstrate the utility of barcoding to identify the fauna from this basin, contribute to an enhanced understanding of the differentiation among species, and to help flag the presence of overlooked species.

The Fish Barcode of Life Initiative (FISH-BOL) is a concerted global research project launched in 2005, with the goal to collect and assemble standardized DNA barcode sequences and associated voucher provenance data in a curated reference sequence library to aid the molecular identification of all fish species. This article is a detailed progress report (July 2010) on the number of fish species that have been assigned a DNA barcode. Of the approximately 31,000 currently known fish species, 25% have been processed successfully, with at least one species from 89% of all families barcoded; in this report we give a progress overview by taxonomy and geographic region. Using standard analytical protocols, differences in the barcoding completion rate between orders and families are observed, suggesting a potential PCR amplification bias. Overall, between 3 and 9% of the species analyzed failed to yield a "BARCODE compliant" sequence, depending upon how the data are filtered. When species with only a single representative specimen are included, the failure rate was 9%. This might derive from several sources such as mismatched primers and degraded DNA templates. In an attempt to account for the latter, when the analysis is restricted to species with at least two specimens examined, the observed failure rate is significantly lower (3%), suggesting that template quality is a source of concern for FISH-BOL. We, therefore, conclude that using a standard protocol with several specimens per species and PCR primer cocktails is an efficient and successful approach because failures were evenly distributed among orders and families. Only six orders with low species numbers (Pristiformes, Torpediniformes, Albuliformes, Batrachoidiformes, Gobiesociformes, and Petromyzontiformes) showed failure rates between 10 and 33%. Besides outlining an overarching approach for FISH-BOL data curation, the goal of the present article is to give guidance in directing sampling campaigns toward neglected or underrepresented families in order to complete the FISH-BOL campaign most efficiently.

Background and Aims: Here we describe preliminary efforts to integrate DNA barcoding into an ongoing inventory of the Lower Congo River (LCR) ichthyofauna. The 350 km stretch of the LCR from Pool Malebo to Boma includes the world's largest river rapids. The LCR ichthyofauna is hyperdiverse and rich in endemism due to high habitat heterogeneity, numerous dispersal barriers, and its downstream location in the basin., Materials and Methods: We have documented 328 species from the LCR, 25% of which are thought to be endemic. In addition to detailing progress made to generate a reference sequence library of DNA barcodes for these fishes, we ask how DNA can be used at the current stage of the Fish Barcode of Life initiative, as a work in progress currently of limited utility to a wide audience. Two possibilities that we explore are the potential for DNA barcodes to generate discrete diagnostic characters for species, and to help resolve problematic taxa lacking clear morphologically diagnostic characters such as many species of the cyprinid genus Labeo, which we use as a case study., Results: Our molecular analysis helped to clarify the validity of some species that were the subject of historical debate, and we were able to construct a molecular key for all monophyletic and morphologically recognizable species. Several species sampled from across the Congo Basin and widely distributed throughout Central and West Africa were recovered as paraphyletic based on our molecular data., Conclusion: Our study underscores the importance of generating reference barcodes for specimens collected from, or in close proximity to, type localities, particularly where species are poorly understood taxonomically and the extent of their geographical distributions have yet to be established.

Background and Aims: The Fish Barcode of Life campaign involves a broad international collaboration among scientists working to advance the identification of fishes using DNA barcodes. With over 25% of the world's known ichthyofauna currently profiled, forensic identification of seafood products is now feasible and is becoming routine., Materials and Methods: Driven by growing consumer interest in the food supply, investigative reporters from five different media establishments procured seafood samples (n = 254) from numerous retail establishments located among five Canadian metropolitan areas between 2008 and 2010. The specimens were sent to the Canadian Centre for DNA Barcoding for analysis. By integrating the results from these individual case studies in a summary analysis, we provide a broad perspective on seafood substitution across Canada., Results: Barcodes were recovered from 93% of the samples (n = 236), and identified using the Barcode of Life Data Systems "species identification" engine ( www.barcodinglife.org ). A 99% sequence similarity threshold was employed as a conservative matching criterion for specimen identification to the species level. Comparing these results against the Canadian Food Inspection Agency's "Fish List" a guideline to interpreting "false, misleading or deceptive" names (as per s 27 of the Fish Inspection regulations) demonstrated that 41% of the samples were mislabeled. Most samples were readily identified; however, this was not true in all cases because some samples had no close match. Others were ambiguous due to limited barcode resolution (or imperfect taxonomy) observed within a few closely related species complexes. The latter cases did not significantly impact the results because even the partial resolution achieved was sufficient to demonstrate mislabeling., Conclusion: This work highlights the functional utility of barcoding for the identification of diverse market samples. It also demonstrates how barcoding serves as a bridge linking scientific nomenclature with approved market names, potentially empowering regulatory bodies to enforce labeling standards. By synchronizing taxonomic effort with sequencing effort and database curation, barcoding provides a molecular identification resource of service to applied forensics.

Background and Aims: We analyzed a small and wide geographically distributed Neotropical freshwater fish, the Piabina argentea from the Upper Paraná Basin, to check the hypothesis that this species is composed of more than one biological unit, since it has a limited dispersion, through the DNA barcode technique., Materials and Methods: Partial mitochondrial COI and CytB gene sequences were obtained for 58 specimens drawn from 13 localities., Results: Phylogenetic analysis revealed six major clusters of P. argentea. Kimura-two-parameter (K2P) genetic divergences among these six P. argentea clusters ranged from 2 to 5.6% and from 2.3 to 5.4% for COI and CytB genes, respectively, and these values were on average approximately nine times greater than intra-cluster K2P divergences. The fixation index (F(ST)) among clusters showed very high values and the haplotype network analysis displayed seven unconnected units., Conclusion: These results reinforce the hypothesis that the widely distributed P. argentea species concept as currently conceived actually represents more than one species (possibly six). These results demonstrate the efficacy of DNA barcoding for the discovery of hidden diversity in Neotropical freshwater fishes, and we conclude that barcoding is a useful tool for alpha taxonomy.

Background and Aims: The application of DNA barcoding as a global standard for fish identification is probing diverse worldwide realms (Nearctic, Australian and the Neotropics) and environments (e.g. marine and freshwater). Comparing the patterns of sequence divergence among conspecific and congeneric taxa between realms can provide valuable information on recent evolutionary histories of lineages as barcode data accumulates., Materials and Methods: Herein, we have analyzed over 100 species (around 50%) of the Neotropical fish fauna from the São Francisco River, in southeast Brazil. Our aims were to test the performance of DNA barcoding in this biodiversity-rich region, and to compare patterns of genetic divergence with previous studies., Results: The mean Kimura two-parameter distances within species, genera, families, orders, and classes were 0.5, 10.6, 21.0, 22.7, and 24.4%, respectively, with 100% of the species examined successfully differentiated by barcoding. With the exception of Astyanax bimaculatus lacustris, Piabina argentea, and Bryconamericus stramineus, all other species yield a single, cohesive cluster of barcode sequences. The average 'nearest-neighbor distance' was 11.12%, 21-fold higher than the mean within species distance of around 0.54%. In a few instances, deep lineage divergences among conspecifics (up to 10%) and congenerics (up to 22.9%) taxa were revealed., Conclusions: Reflecting possible cases of cryptic speciation and the deeper phylogeographic history of São Francisco fish fauna, with some higher clades extending back into the late Cretaceous and Cenozoic (90 mya), when much of the diversification of the Neotropical region apparently took place. In addition, barcodes also highlighted misidentifications and helped to document range extensions for known species.

DNA barcoding is a method promising fast and accurate identification of animal species based on the sequencing of the mitochondrial c oxidase subunit (COI) gene. In this study, we explore the prospects for DNA barcoding in one particular fish group, the billfishes (suborder Xiphioidei--swordfish, marlins, spearfishes, and sailfish). We sequenced the mitochondrial COI gene from 296 individuals from the 10 currently recognized species of billfishes, and combined these data with a further 57 sequences from previously published projects. We also sequenced the rhodopsin gene from a subset of 72 individuals to allow comparison of mitochondrial results against a nuclear marker. Five of the 10 species are readily distinguishable by COI barcodes. Of the rest, the striped marlin (Kajikia audax) and white marlin (K. albida) show highly similar sequences and are not unambiguously distinguishable by barcodes alone, likewise are the three spearfishes Tetrapturus angustirostris, T. belone, and T. pfluegeri. We discuss the taxonomic status of these species groups in light of our and other data, molecular and morphological.

Background and Aims: The shark fisheries of Madagascar remain largely unstudied. Remoteness makes fisheries monitoring challenging while the high value of shark fins combined with the extreme poverty in Madagascar creates intensive pressure on shark resources., Materials and Methods: We use DNA barcoding and species-specific PCR assays to characterize shark fisheries in Antongil Bay in northeastern Madagascar., Results: The 239 samples taken from individuals collected in 2001 and 2002 correspond to 19 species. The four most common species were Sphyrna lewini, Rhizoprionodon acutus, Carcharhinus brevipinna, and C. sorrah. Antongil Bay may be a breeding area for C. brevipinna, C. leucas, and S. lewini., Conclusion: Local names are generally not a useful proxy for monitoring the species harvested in the fishery. Conservation efforts should characterize species exploitation at present, create spatial and temporal fishing restrictions to protect endangered species, and restrict large mesh gillnets.

The Fish barcode of life (FISH-BOL) initiative seeks to establish a reference sequence library of short, standardized mitochondrial gene sequences derived from the 5' end of the cytochrome c oxidase subunit I gene (DNA barcodes) to facilitate the rapid, accurate, and cost-effective DNA-based identification of all fishes, regardless of life-stage, sex, or specimen condition. This task requires the participation of scientists from around the world and its success is predicated on the development and acceptance of standard protocols for the collection of specimens associated provenance data. Here, we provide guidelines for specimen collection, imaging, preservation, and archival, as well as meta-data collection and submission protocols developed for the FISH-BOL campaign in order to promote efficient participation in FISH-BOL by a broadening array of international participants.

DNA barcoding efforts involving animals have focused on the mitochondrial cytochrome c oxidase subunit I (Cox1) gene. Some authors suggest that this marker might under-diagnose young species. Herein, we examine Cox1 and control region diversity in a sample of Siberian sturgeon (Acipenser baerii), a species with an extremely wide geographic distribution in the major rivers of Siberia and in Lake Baikal. Some authors currently recognize three subspecies within this species. These subspecies are reasonable candidates for species units detectable through DNA barcoding. The Cox1 gene illustrated no variation within the species, while the control region displayed statistically significant differences among the subspecies using analysis of molecular variance (AMOVA). Given the uniformity of Cox1 sequences recovered, Cox1 is probably a good region for barcoding A. baerii at the species level. Although control region variation among subspecies was significant, diagnostic differences were not found for any of the subspecies.