Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study.

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.

DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers.

Excessive ingestion of mercury--a health hazard associated with consuming predatory fishes--damages neurological, sensory-motor and cardiovascular functioning. The mercury levels found in Bigeye Tuna (Thunnus obesus) and bluefin tuna species (Thunnus maccoyii, Thunnus orientalis, and Thunnus thynnus), exceed or approach levels permissible by Canada, the European Union, Japan, the US, and the World Health Organization. We used DNA barcodes to identify tuna sushi samples analysed for mercury and demonstrate that the ability to identify cryptic samples in the market place allows regulatory agencies to more accurately measure the risk faced by fish consumers and enact policies that better safeguard their health.

The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances.

BACKGROUND: The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. METHODOLOGY/PRINCIPAL FINDINGS: Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. CONCLUSIONS/SIGNIFICANCE: The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.

Functional richness and ecosystem services: bird predation on arthropods in tropical agroecosystems.

In agroecosystems, biodiversity correlates with ecosystem function, yet mechanisms driving these relationships are often unknown. Examining traits and functional classifications of organisms providing ecosystem functions may provide insight into the mechanisms. Birds are important predators of insects, including pests. However, biological simplification of agroforests may decrease provisioning of this pest removal service by reducing bird taxonomic and functional diversity. A recent meta-analysis of bird exclosure studies from a range of agroecosystems in Central America concluded that higher bird richness is associated with significantly greater arthropod removal, yet the mechanism remains unclear. We conducted a meta-analysis of the same data to examine whether birds demonstrate functional complementarity in tropical agroforests. We classified birds according to relevant traits (body mass, foraging strategy, foraging Strata, and diet) and then examined how design of functional classification, including trait selection, classification methods, and the functional diversity metric used affect the suitability of different classifications as predictors of ecosystem services. We determined that vegetation characteristics are not likely drivers of arthropod removal by birds. For some functional classifications, functional richness positively correlated with arthropod removal, indicating that species complementarity may be an important mechanism behind this ecosystem function. The predictive ability of functional classifications increased with the number of traits included in the classification. For the two best classifications examined, functional group richness was a better predictor of arthropod reduction than other metrics of functional diversity (FD and Rao's Q). However, no functional classification predicted arthropod removal better than simple species richness; thus other factors may be important. Our analysis indicates that the sampling effect may also play a role, as one species and two functional groups were responsible for disproportionate effects of arthropod removal.