Armstrong, K.F.

Brown, S.D.J.

Collins, R.A.

Cruickshank, R.H.

Johnston, C.

Keeling, S.

Meier, R.

Yi, Y.

PLoS ONE

PubMed

<div><h3>Background</h3><p>Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species.</p> <h3>Methodology/Principal Findings</h3><p>We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90–99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb <em>Puntius denisonii</em>.</p> <h3>Conclusions/Significance</h3><p>We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade.</p> </div

Rupert A. Collins (279572)

Karen F. Armstrong (187115)

Rudolf Meier (92763)

Youguang Yi (187121)

Samuel D. J. Brown (187128)

Robert H. Cruickshank (187135)

Suzanne Keeling (187139)

Colin Johnston (187143)

The Francis Crick Institute

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

Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species..We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade

Collins Rupert A.

Armstrong Karen F.

Meier Rudolf

Yi Youguang

Brown Samuel D. J.

Cruickshank Robert H.

Keeling Suzanne

Johnston Colin

Public Library of Science (PLOS)

BackgroundPoorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method); and (3) providing supplementary information to identify difficult species.Methodology/principal findingsWe sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90-99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank (additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii.Conclusions/significanceWe demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to confidently identify high-risk fishes in the aquarium trade

Rupert A Collins

Karen F Armstrong

Rudolf Meier

Youguang Yi

Samuel D J Brown

Robert H Cruickshank

Suzanne Keeling

Colin Johnston

Directory of Open Access Journals

Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade.

Rupert A. Collins

Karen F. Armstrong

Samuel D. J. Brown

Robert H. Cruickshank

Crossref

Background: Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic
activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications,
often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for
quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for
ornamental cyprinid fishes by: (1) expanding current barcode reference libraries; (2) assessing barcode congruence with
morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species,
choice of analytical method); and (3) providing supplementary information to identify difficult species.
Methodology/Principal Findings: We sampled 172 ornamental cyprinid fish species from the international trade, and
provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold). DNA barcodes were found to be
highly congruent with our morphological assignments, achieving success rates of 90–99%, depending on the method used
(neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold). Inclusion of data from GenBank
(additional 157 spp.) resulted in a more comprehensive library, but at a cost to success rate due to the increased number of
singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images,
morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this
nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity
within popular aquarium species, including the endangered Indian barb Puntius denisonii.
Conclusions/Significance: We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly
identifying ornamental fishes. In cases where DNA barcodes are unable to offer an identification, we improve on previous
studies by consolidating supplementary information from multiple data sources, and empower biosecurity agencies to
confidently identify high-risk fishes in the aquarium trade.This work was supported by a Ministry of Agriculture and Forestry Biosecurity New Zealand scholarship for RAC; grant R377-000-040-112 by the
Ministry of Education (Singapore) for RM and YY

Collins, RA

Armstrong, Karen

Meier, R

Yi, Y

Brown, SDJ

Cruickshank, RH

Keeling, S

Johnston, C

Lincoln University Research Archive

Barcoding and border biosecurity: Identifying Cyprinid fishes in the aquarium trade

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Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade

Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade

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The Francis Crick Institute

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Directory of Open Access Journals

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Lincoln University Research Archive

Public Library of Science (PLOS)