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      A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias

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          Abstract

          With an estimate of around 9,000 species, the Neotropical region hosts the greatest diversity of freshwater fishes of the world. Genetic surveys have the potential to unravel isolated and unique lineages and may result in the identification of undescribed species, accelerating the cataloguing of extant biodiversity. In this paper, molecular diversity within the valuable and widespread Neotropical genus Hoplias was assessed by means of DNA Barcoding. The geographic coverage spanned 40 degrees of latitude from French Guiana to Argentina. Our analyses revealed 22 mitochondrial lineages fully supported by means of Barcode Index Number, Automatic Barcode Gap Discovery and phylogenetic analyses. This mtDNA survey revealed the existence of 15 fully supported mitochondrial lineages within the once considered to be the continentally distributed H. malabaricus. Only four of them are currently described as valid species however, leaving 11 mitochondrial lineages currently “masked” within this species complex. Mean genetic divergence was 13.1%. Barcoding gap analysis discriminated 20 out of the 22 lineages tested. Phylogenetic analyses showed that all taxonomically recognized species form monophyletic groups. Hoplias malabaricus sensu stricto clustered within a large clade, excluding the representatives of the La Plata River Basin. In the H. lacerdae group, all species but H. curupira showed a cohesive match between taxonomic and molecular identification. Two different genetic lineages were recovered for H. aimara. Given the unexpected hidden mitochondrial diversity within H. malabaricus, the COI sequence composition of specimens from Suriname (the type locality), identified as H. malabaricus sensu stricto, is of major importance.

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Cryptic species as a window on diversity and conservation.

            The taxonomic challenge posed by cryptic species (two or more distinct species classified as a single species) has been recognized for nearly 300 years, but the advent of relatively inexpensive and rapid DNA sequencing has given biologists a new tool for detecting and differentiating morphologically similar species. Here, we synthesize the literature on cryptic and sibling species and discuss trends in their discovery. However, a lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups. The discovery of cryptic species is likely to be non-random with regard to taxon and biome and, hence, could have profound implications for evolutionary theory, biogeography and conservation planning.
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              Windows 95/98/NT

               Bill Buchanan (1999)
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: Writing – original draftRole: Writing – review & editing
                Role: Formal analysisRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Data curationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                13 August 2018
                2018
                : 13
                : 8
                Affiliations
                [1 ] Laboratorio de Sistemática y Biología Evolutiva, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
                [2 ] Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
                [3 ] Grupo de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
                [4 ] Fundación Bosques Nativos Argentinos para la Biodiversidad, Buenos Aires, Argentina
                [5 ] Instituto de Investigaciones en Producción Animal, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires, Argentina
                [6 ] Fundación de Historia Natural “Félix de Azara”, Departamento de Ciencias Naturales y Antropología, Universidad Maimónides, Buenos Aires, Argentina
                [7 ] Department of Herpetology and Ichthyology, Museum of Natural History, Geneva, Switzerland
                [8 ] Centro de Investigaciones Antonia Ramos, Villa Bonita, Campo Ramón, Misiones, Argentina
                National Cheng Kung University, TAIWAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Article
                PONE-D-17-43347
                10.1371/journal.pone.0202024
                6089427
                30102742
                © 2018 Cardoso 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.

                Page count
                Figures: 4, Tables: 3, Pages: 25
                Product
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002923, Consejo Nacional de Investigaciones Científicas y Técnicas;
                Award ID: PIP 11220130100339 CO
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100002923, Consejo Nacional de Investigaciones Científicas y Técnicas;
                Award ID: I-Bol Grant
                Award Recipient :
                Funded by: Universidad Nacional de Mar del Plata (AR)
                Award ID: 15/E619 EXA669/14
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100006668, Fondo para la Investigación Científica y Tecnológica;
                Award ID: PICT2014-0580
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100006668, Fondo para la Investigación Científica y Tecnológica;
                Award ID: PICT 2014-0665
                Award Recipient :
                Funded by: Fundación Bosques Nativos Argentinos para la Biodiversidad
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100000193, International Development Research Centre;
                Award Recipient :
                This work was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas: PIP 11220130100339 CO to MGC, Consejo Nacional de Investigaciones Científicas y Técnicas I-Bol Grant to JMDA, Universidad Nacional de Mar del Plata (AR) 15/E619 EXA669/14 to JMDA, Fondo para la Investigación Científica y Tecnológica, PICT2014-0580 to YPC and PICT 2014-0665 to JMDA, Fundación Bosques Nativos Argentinos para la Biodiversidad to EA, and the International Development Research Centre to JJR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
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                Custom metadata
                Newly sequenced data are stored in GenBank: MG699453-MG699576. Remaining data are publicly available in the Barcode of Life Database (BOLD) and GenBank. The complete list of BOLD and GenBank process ID and project names are presented in S1 Table. Some sequences are only available in GenBank: accessions GU688963- GU688966; KC250448- KC250469; JX112659- JX112693.

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