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Meekan, Mark G.; Wei, Nu-Wei V.; O'shea, Owen; Bradshaw, Corey; Austin, Christopher M

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Meekan, Mark G.; Wei, Nu-Wei V.; O'shea, Owen; Bradshaw, Corey; Austin, Christopher M PUBLISHED VERSION Cerutti-Pereyra, Florencia; Meekan, Mark G.; Wei, Nu-Wei V.; O'Shea, Owen; Bradshaw, Corey; Austin, Christopher M. Identification of rays through DNA barcoding: an application for ecologists PLoS ONE, 2012; 7(6):e36479 Copyright: © 2012 Cerutti-Pereyra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. PERMISSIONS http://www.plosone.org/static/policies.action#copyright 3. Copyright and License Policies Open access agreement. Upon submission of an article, its authors are asked to indicate their agreement to abide by an open access Creative Commons license (CC-BY). Under the terms of this license, authors retain ownership of the copyright of their articles. However, the license permits any user to download, print out, extract, reuse, archive, and distribute the article, so long as appropriate credit is given to the authors and source of the work. The license ensures that the authors' article will be available as widely as possible and that the article can be included in any scientific archive. Open access agreement: US government authors. Papers authored by one or more US government employees are not copyrighted, but are licensed under a Creative Commons public domain license (CC0), which allows unlimited distribution and reuse of the article for any lawful purpose. Authors should read about CC-BY or CC0 before submitting papers. Archiving in PubMed Central. Upon publication, PLoS also deposits all articles in PubMed Central. This complies with the policies of funding agencies, such as the NIH in the USA, the Wellcome Trust, and the Research Councils in the UK, and the Deutsche Forschungsgemeinschaft in Germany, which request or require deposition of the published articles that they fund into publicly available databases. http://www.plos.org/about/open-access/license/ LICENCE The Public Library of Science (PLoS) applies the Creative Commons Attribution License (CC-BY) to works we publish (read the human-readable summary or the full license legal code). Under this license, authors retain ownership of the copyright for their content, but allow anyone to download, reuse, reprint, modify, distribute, and/or copy the content as long as the original authors and source are cited. No permission is required from the authors or the publishers. Appropriate attribution can be provided by simply citing the original article (e.g., Kaltenbach LS et al. (2007) Huntingtin Interacting Proteins Are Genetic Modifiers of Neurodegeneration. PLoS Genet 3(5): e82. doi:10.1371/journal.pgen.0030082). For any reuse or redistribution of a work, users must also make clear the license terms under which the work was published. This broad license was developed to facilitate free access to, and unrestricted reuse of, original works of all types. Applying this standard license to your own work will ensure that it is freely and openly available in perpetuity. If you have a question about the Creative Commons License please use this contact form and choose “General Questions.” 21 March, 2013 http://hdl.handle.net/2440/76113 Identification of Rays through DNA Barcoding: An Application for Ecologists Florencia Cerutti-Pereyra1, Mark G. Meekan2, Nu-Wei V. Wei1, Owen O’Shea3, Corey J. A. Bradshaw4,5, Chris M. Austin6* 1 Research Institute of Environment and Livelihood, Charles Darwin University, Northern Territory, Australia, 2 Australian Institute of Marine Science, UWA Oceans Institute, Western Australia, Australia, 3 Murdoch University, Western Australia, Australia, 4 The Environment Institute and School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, South Australia, Australia, 5 South Australian Research and Development Institute, South Australia, Australia, 6 School of Science Monash University Sunway Campus, Petaling Jaya, Selangor, Malaysia Abstract DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera) of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the ‘uarnak’ complex. Two sets of problems limited the successful application of DNA barcoding: (1) the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2) insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data. Citation: Cerutti-Pereyra F, Meekan MG, Wei N-WV, O’Shea O, Bradshaw CJA, et al. (2012) Identification of Rays through DNA Barcoding: An Application for Ecologists. PLoS ONE 7(6): e36479. doi:10.1371/journal.pone.0036479 Editor: Sergios-Orestis Kolokotronis, Barnard College, Columbia University, United States of America Received November 4, 2011; Accepted April 8, 2012; Published June 11, 2012 Copyright: ß 2012 Cerutti-Pereyra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: We thank the Australian Institute of Marine Science and Charles Darwin University for financial support, and CONACYT-Me´xico for an international grant to FCP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction combination of morphometric attributes. Handling, examining and measuring individuals is often impractical, inappropriate for Taxonomic misidentification and the presence of cryptic species ethical reasons, or simply dangerous, thus exacerbating the can seriously compromise the veracity of ecological, fisheries and problem of securing accurate identification. Furthermore, even if conservation-related research and management [1–4]. These experienced taxonomists have studied the target organisms, it is problems are further compounded by the ‘greying’ of the unlikely that they can be encouraged to assist in the field, taxonomic workforce and the decline in the teaching of taxonomy especially in remote locations. Voucher specimens can be taken for and training of field biologists at universities, both issues identified subsequent lodgement in museums; however, this is often as major impediments to the conduct of biodiversity science and impractical for large species, samples obtained in remote locations conservation biology [5]. Within this context, a key question is: and studies involving multiple species. Even where voucher how much confidence can be placed in the application of correct specimens can be obtained, it will not necessarily guarantee scientific names of taxa reported in ecological studies? In a review reliable and timely identification. of high-ranking ecological journals, Bortolus [4] reported that DNA barcoding potentially offers scientists who are not expert 62.5% of papers did not provide any supporting information taxonomists a powerful tool to support the efficiency and accuracy justifying or guaranteeing the correct identification of the of field studies involving the challenging identification of diverse organisms under investigation. taxa [6]. The proponents of this approach mostly advocate the use The challenges for ecologists seeking verification of their field- of a single gene for global identification of animals based on the based identifications are not trivial. Even when adequate availability of a library of sequences linked to voucher specimens, taxonomic keys and field guides are available, it is often difficult thus making these sequences, in effect, a DNA barcode [7], [8]. A to identify organisms in the field with confidence, as ecologists can 650-base fragment of the cytochrome c oxidase I (COI, cox1)is be dealing with juveniles, undocumented geographic variants, or proposed as a ‘global’ standard because the variation in COI sexual dimorphism, such that accurate identification might require within species is lower relative to that among species. While the examination of microanatomy or measurements of a complex DNA barcoding approach has its critics when touted as a solution PLoS ONE | www.plosone.org 1 June 2012 | Volume 7 | Issue 6 | e36479 DNA Barcoding Rays to impediments presented by traditional taxonomy [9], [10], it however, detailed data on landings and by-catch
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