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      One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon

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          Abstract

          Piranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery—incorporating both tree and distance based techniques—we report between 76 and 99 species-like clusters, i.e. between 20% and 33% of a priori identified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genus Myloplus exhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of the Serrasalmus rhombeus group proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.

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          The integrative future of taxonomy

          Background Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Results Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. Conclusions We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.
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            How to fail at species delimitation.

            Species delimitation is the act of identifying species-level biological diversity. In recent years, the field has witnessed a dramatic increase in the number of methods available for delimiting species. However, most recent investigations only utilize a handful (i.e. 2-3) of the available methods, often for unstated reasons. Because the parameter space that is potentially relevant to species delimitation far exceeds the parameterization of any existing method, a given method necessarily makes a number of simplifying assumptions, any one of which could be violated in a particular system. We suggest that researchers should apply a wide range of species delimitation analyses to their data and place their trust in delimitations that are congruent across methods. Incongruence across the results from different methods is evidence of either a difference in the power to detect cryptic lineages across one or more of the approaches used to delimit species and could indicate that assumptions of one or more of the methods have been violated. In either case, the inferences drawn from species delimitation studies should be conservative, for in most contexts it is better to fail to delimit species than it is to falsely delimit entities that do not represent actual evolutionary lineages. © 2013 John Wiley & Sons Ltd.
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              DEVELOPMENT AND ENVIRONMENT. Balancing hydropower and biodiversity in the Amazon, Congo, and Mekong.

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                Author and article information

                Contributors
                rupertcollins@gmail.com
                hrbek@evoamazon.net
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                30 May 2018
                30 May 2018
                2018
                : 8
                : 8387
                Affiliations
                [1 ]ISNI 0000 0001 2221 0517, GRID grid.411181.c, Laboratório de Evolução e Genétic Animal, Departamento de Genética, , Universidade Federal do Amazonas, Av., ; General Rodrigo Otávio Jordão, 3000, 69077-000 Manaus, AM Brazil
                [2 ]ISNI 0000 0004 1936 7603, GRID grid.5337.2, School of Biological Sciences, , University of Bristol, ; Life Sciences Building, 24 Tyndall Avenue, Bristol, BS8 1TQ UK
                [3 ]ISNI 0000 0004 0427 0577, GRID grid.419220.c, Programa de Pós-Graduação em Biologia de Água Doce e Pesca Interior, , Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, ; 2936, CP 2223, Petrópolis, 69080-971 Manaus, AM Brazil
                [4 ]ISNI 0000 0001 2171 5249, GRID grid.271300.7, Programa de Pós-Graduação em Ecologia Aquática e Pesca, Instituto de Ciências Biológicas, , Universidade Federal do Pará, Av. Perimetral, ; 2651, Terra Firme, 66040-830 Belém, PA Brazil
                Author information
                http://orcid.org/0000-0002-9135-1169
                http://orcid.org/0000-0002-3573-5774
                http://orcid.org/0000-0003-3239-7068
                Article
                26550
                10.1038/s41598-018-26550-x
                5976771
                29849152
                e79df49d-165a-4e45-b2b7-80822c938dd1
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 September 2017
                : 10 May 2018
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