Dataset Information

Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots.

ABSTRACT: Trade restrictions for endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, trade monitoring is challenging due to product variety and the complexity of import/export routes. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate in-situ monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 commonly encountered species (including 22 CITES-listed species) to test a recently developed real-time PCR single-assay originally developed for screening bony fish. In the absence of a bespoke elasmobranch identification online platform in the original FASTFISH-ID model, we employed a deep learning algorithm to recognize species based on DNA melt-curve signatures. By combining visual and machine-learning assignment methods, we distinguished 25/28 species, 20 of which were CITES-listed. With further refinement, this method can improve monitoring of the elasmobranch trade worldwide, without a lab or species-specific assays.

SUBMITTER: Prasetyo AP

PROVIDER: S-EPMC10300358 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature

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Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots.

Prasetyo Andhika P AP Cusa Marine M Murray Joanna M JM Agung Firdaus F Muttaqin Efin E Mariani Stefano S McDevitt Allan D AD

iScience 20230607 7

Trade restrictions for endangered elasmobranch species exist to disincentivise their exploitation and curb their declines. However, trade monitoring is challenging due to product variety and the complexity of import/export routes. We investigate the use of a portable, universal, DNA-based tool which would greatly facilitate <i>in-situ</i> monitoring. We collected shark and ray samples across the Island of Java, Indonesia, and selected 28 commonly encountered species (including 22 CITES-listed sp ...[more]

PMID: 37389182

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Project description:BackgroundThe megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.ResultsOf the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.ConclusionsOur study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

Project description:Elasmobranchs, the group of cartilaginous fishes that include sharks and rays, are especially vulnerable to overfishing due to low fecundity and late sexual maturation. A significant number of elasmobranch species are currently overexploited or threatened by fisheries activities. Additionally, several recent reports have indicated that there has been a reduction in regional elasmobranch population sizes. Brazil is an important player in elasmobranch fisheries and one of the largest importers of shark meat. However, carcasses entering the shark meat market have usually had their fins and head removed, which poses a challenge to reliable species identification based on the morphology of captured individuals. This is further complicated by the fact that the internal Brazilian market trades several different elasmobranch species under a common popular name: "cação." The use of such imprecise nomenclature, even among governmental agencies, is problematic for both controlling the negative effects of shark consumption and informing the consumer about the origins of the product. In this study, we used DNA barcoding (mtDNA, COI gene) to identify, at the species level, "cação" samples available in local markets from Southern Brazil. We collected 63 samples traded as "cação," which we found to correspond to 20 different species. These included two teleost species: Xiphias gladius (n = 1) and Genidens barbus (n = 6), and 18 species from seven elasmobranch orders (Carcharhiniformes, n = 42; Squaliformes, n = 3; Squatiniformes, n = 2; Rhinopristiformes, n = 4; Myliobatiformes, n = 3; Rajiformes, n = 1; and Torpediniformes, n = 1). The most common species in our sample were Prionace glauca (n = 15) and Sphyrna lewini (n = 14), while all other species were represented by four samples or less. Considering IUCN criteria, 47% of the elasmobranch species found are threatened at the global level, while 53% are threatened and 47% are critically endangered in Brazil. These results underline that labeling the meat of any shark species as "cação" is problematic for monitoring catch allocations from the fishing industry and discourages consumer engagement in conservationist practices through informed decision-making.

Project description:The value of natural history collections for conservation science research is increasingly recognized, despite their well-documented limitations in terms of taxonomic, geographic, and temporal coverage. Specimen-based analyses are particularly important for tropical plant groups for which field observations are scarce and potentially unreliable due to high levels of diversity-amplifying identification challenges. Specimen databases curated by specialists are rich sources of authoritatively identified, georeferenced occurrence data, and such data are urgently needed for large genera. We compared entries in a monographic database for the large Neotropical genus Myrcia in 2007 and 2017. We classified and quantified differences in specimen records over this decade and determined the potential impact of these changes on conservation assessments. We distinguished misidentifications from changes due to taxonomic remodeling and considered the effects of adding specimens and georeferences. We calculated the potential impact of each change on estimates of extent of occurrence (EOO), the most frequently used metric in extinction-risk assessments of tropical plants. We examined whether particular specimen changes were associated with species for which changes in EOO over the decade were large enough to change their conservation category. Corrections to specimens previously misidentified or lacking georeferences were overrepresented in such species, whereas changes associated with taxonomic remodeling (lumping and splitting) were underrepresented. Among species present in both years, transitions to less threatened status outnumbered those to more threatened (8% vs 3%, respectively). Species previously deemed data deficient transitioned to threatened status more often than to not threatened (10% vs 7%, respectively). Conservation scientists risk reaching unreliable conclusions if they use specimen databases that are not actively curated to reflect changing knowledge.

Dataset Information

Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots.

Publications

Universal closed-tube barcoding for monitoring the shark and ray trade in megadiverse conservation hotspots.

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