Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade

Collins, Rupert A.; Armstrong, Karen; Meier, Rudolf; Yi, Youguang; Brown, Samuel D. J.; Cruickshank, Robert; Keeling, Stephanie; Johnston, Colin

doi:10.1371/journal.pone.0028381

Cited by 141 publications

(137 citation statements)

References 84 publications

(119 reference statements)

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“…The results of Collins and colleagues [170] also indicated a high level of unrecognized diversity. Among Indonesian taxa, for example, unrecognized diversity was found in Brevibora dorsiocellata (as Rasbora in [170]), Rasbora einthovenii, Trigonostigma heteromorpha (as Rasbora in [170]), Trigonopoma pauciperforata (as Rasbora in [170], a widespread species) and Sundadanio axelrodi.…”

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 91%

“…Later, Pouyaud and colleagues reappraised the taxonomy and species richness of the family in Indonesia based on sequencing of mitochondrial DNA in combination with morphology and described five additional species [150][151][152][153][154]. Two species of Pangasiidae are reared in Indonesia [155], Pangasianodon hypophthalmus and Pangasius djambal, the former for the "unrecognized diversity" reported by Collins and colleagues [170]. Collins and colleagues [170] highlighted that mismatch between species names applied to the specimens transiting in the international ornamental trade and taxonomic assignment based on DNA barcodes are due to either taxonomic uncertainty and/or conflict due to misidentifications.…”

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

“…Two species of Pangasiidae are reared in Indonesia [155], Pangasianodon hypophthalmus and Pangasius djambal, the former for the "unrecognized diversity" reported by Collins and colleagues [170]. Collins and colleagues [170] highlighted that mismatch between species names applied to the specimens transiting in the international ornamental trade and taxonomic assignment based on DNA barcodes are due to either taxonomic uncertainty and/or conflict due to misidentifications. The authors hence caution the use of GenBank for identification purposes due to the potential absence of preserved voucher specimens and justified identifications and note that while BOLD data are generally better curated and with higher quality standards, they are also likely to suffer from misidentification to some degree.…”

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

“…Collins and colleagues [170], for instance, explored the usefulness of DNA barcodes in identifying ornamental fishes obtained from the aquarium trade. They focused on cyprinids and included several popular aquarium fishes that are regularly exported from Indonesia, mostly Sumatra and Kalimantan.…”

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

“…Among Indonesian taxa, for example, unrecognized diversity was found in Brevibora dorsiocellata (as Rasbora in [170]), Rasbora einthovenii, Trigonostigma heteromorpha (as Rasbora in [170]), Trigonopoma pauciperforata (as Rasbora in [170], a widespread species) and Sundadanio axelrodi. At the same time, Brevibora cheeya (Liao & Tan, 2011) from Terengganu, Malaysia was described and recently Brevibora exilis [171] from Kalimantan Tengah, Borneo was described and both could potentially account based on a revision of available sequence data and newly generated sequences with the aim to enable identification of potential and established invasive species outside of their native range.…”

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

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DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

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With 1172 native species, the Indonesian ichthyofauna is among the world’s most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during the last decades is posing serious threats to Indonesian biodiversity. Indonesia, however, is one of the major sources of export for the international ornamental trade and home of several species of high value in aquaculture. The development of new tools for species identification is urgently needed to improve the sustainability of the exploitation of the Indonesian ichthyofauna. With the aim to build comprehensive DNA barcode libraries, the co-authors have started a collective effort to DNA barcode all Indonesian freshwater fishes. The aims of this review are: (1) to produce an overview of the ichthyological researches conducted so far in Indonesia, (2) to present an updated checklist of the freshwater fishes reported to date from Indonesia’s inland waters, (3) to highlight the challenges associated with its conservation and management, (4) to present the benefits of developing comprehensive DNA barcode reference libraries for the conservation of the Indonesian ichthyofauna.

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Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 91%

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

Section: Border Biosecurity and Invasive Speciesmentioning

confidence: 99%

See 3 more Smart Citations

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Hubert¹,

Kadarusman²,

Wibowo³

et al. 2015

DNA Barcodes

View full text Add to dashboard Cite

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Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library

Andersen

Oboyski

Davies

et al. 2019

Ecological Applications

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New genetic diagnostic approaches have greatly aided efforts to document global biodiversity and improve biosecurity. This is especially true for organismal groups in which species diversity has been underestimated historically due to difficulties associated with sampling, the lack of clear morphological characteristics, and/or limited availability of taxonomic expertise. Among these methods, DNA sequence barcoding (also known as “DNA barcoding”) and by extension, meta‐barcoding for biological communities, has emerged as one of the most frequently utilized methods for DNA‐based species identifications. Unfortunately, the use of DNA barcoding is limited by the availability of complete reference libraries (i.e., a collection of DNA sequences from morphologically identified species), and by the fact that the vast majority of species do not have sequences present in reference databases. Such conditions are critical especially in tropical locations that are simultaneously biodiversity rich and suffer from a lack of exploration and DNA characterization by trained taxonomic specialists. To facilitate efforts to document biodiversity in regions lacking complete reference libraries, we developed a novel statistical approach that categorizes unidentified species as being either likely native or likely nonnative based solely on measures of nucleotide diversity. We demonstrate the utility of this approach by categorizing a large sample of specimens of terrestrial insects and spiders (collected as part of the Moorea BioCode project) using a generalized linear mixed model (GLMM). Using a training data set of known endemic (n = 45) and known introduced species (n = 102), we then estimated the likely native/nonnative status for 4,663 specimens representing an estimated 1,288 species (412 identified species), including both those specimens that were either unidentified or whose endemic/introduced status was uncertain. Using this approach, we were able to increase the number of categorized specimens by a factor of 4.4 (from 794 to 3,497), and the number of categorized species by a factor of 4.8 from (147 to 707) at a rate much greater than chance (77.6% accuracy). The study identifies phylogenetic signatures of both native and nonnative species and suggests several practical applications for this approach including monitoring biodiversity and facilitating biosecurity.

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Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

et al. 2021

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While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer have considered riverine systems, particularly those spanning the environmental gradients present in large river basins. Such dynamic systems are challenging for eDNA biomonitoring due to differing eDNA transport distances in rivers and the effects of river chemistry. To address this challenge, we focused on the Thames River system, UK, which has exceptional historical fish records providing a baseline to test the accuracy of eDNA metabarcoding in recovering fish community structure across both fresh and tidal zones. Two primer sets targeting 12S and CO1 regions were used to capture fish communities across the Thames catchment, from the upper freshwaters to the mid estuary. eDNA was collected at 35 sites, 14 of which were simultaneously paired with traditional fish surveys for direct comparison. We demonstrated that eDNA metabarcoding consistently detected more freshwater species than traditional methods, despite extensive sampling effort using the latter. In contrast, metabarcoding did not perform as well as traditional approaches in estuarine waters, although results included the novel detection of the protected sea lamprey. We further demonstrated that minor variations in the recovery of all approaches would not impact on the assessment of simple ecological models of community structure and, thus, some variability between approaches should not be viewed as a serious hindrance to uptake. Rather, our findings support a growing consensus that eDNA can reliably detect fish communities across dynamic freshwater habitats.

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Barcoding and Border Biosecurity: Identifying Cyprinid Fishes in the Aquarium Trade

Cited by 141 publications

References 84 publications

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

Categorization of species as native or nonnative using DNA sequence signatures without a complete reference library

Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods

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