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      A new species of Tometes Valenciennes 1850 (Characiformes: Serrasalmidae) from Tocantins-Araguaia River Basin based on integrative analysis of molecular and morphological data

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          Abstract

          A new large serrasalmid species of Tometes is described from the Tocantins-Araguaia River Basin. Tometes siderocarajensis sp. nov. is currently found in the rapids of the Itacaiúnas River Basin, and formerly inhabited the lower Tocantins River. The new species can be distinguished from all congeners, except from T. ancylorhynchus, by the presence of lateral space between 1st and 2nd premaxillary teeth, and by the absence of lateral cusps in these two teeth. However, T. siderocarajensis sp. nov. can be differentiated from syntopic congener T. ancylorhynchus by an entirely black with mottled red body in live specimens, densely pigmented pelvic fins with a high concentration of dark chromatophores, and the presence of 39 to 41 rows of circumpeduncular scales ( vs. silvery body coloration with slightly reddish overtones on middle flank during breeding period in live specimens, hyaline to slightly pale coloration on distalmost region of pelvic fins, and 30 to 36 rows of circumpeduncular scales). Additionally, molecular sequence shows that T. siderocarajensis sp. nov. is reciprocally monophyletic, and diagnosable from all congeners by having two autapomorphic molecular characters in the mitochondrial gene COI. The phylogenetic reconstruction still show that T. siderocarajensis sp. nov. is closely related to T. trilobatus. This is the first molecular study using an integrative taxonomic approach based on morphological and molecular sequence data for all described species of Tometes. These findings increase the number of formally described species of Tometes to seven. A key to the Tometes species is provided.

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          Molecular Cloning : A Laboratory Manual

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            Spider: an R package for the analysis of species identity and evolution, with particular reference to DNA barcoding.

            Spider: SPecies IDentity and Evolution in R is a new R package implementing a number of useful analyses for DNA barcoding studies and associated research into species delimitation and speciation. Included are functions essential for generating important summary statistics from DNA barcode data, assessing specimen identification efficacy, and for testing and optimizing divergence threshold limits. In terms of investigating evolutionary and taxonomic questions, techniques for assessing diagnostic nucleotides and probability of reciprocal monophyly are also provided. Additionally, a sliding window function offers opportunities to analyse information across a gene, essential for marker design in degraded DNA studies. Spider capitalizes on R's extensible ethos and offers an integrated platform ideal for the analysis of both nucleotide and morphological data. The program can be obtained from the comprehensive R archive network (CRAN, http://cran.r-project.org) and from the R-Forge package development site (http://spider.r-forge.r-project.org/). © 2012 Blackwell Publishing Ltd.
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              Identifying Canadian Freshwater Fishes through DNA Barcodes

              Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                19 April 2017
                2017
                : 12
                : 4
                : e0170053
                Affiliations
                [1 ]Universidade Federal do Pará, Cidade Universitária Professor José Silveira Netto, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Ecologia Aquática e Pesca, Laboratório de Biologia Pesqueira e Manejo dos Recursos Aquáticos, Belém, Pará, Brazil
                [2 ]Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazônia Legal, Rede Bionorte, Laboratório de Evolução e Genética Animal, Manaus, Amazonas, Brazil
                [3 ]Institut de Recherche pour le Développement, Biologie des Organismes et Ecosystèmes Aquatiques, UMR BOREA, Laboratoire d´Icthyologie, Muséum national d’Histoire naturelle, MNHN, CP26, 43 rue Cuvier, Paris, France
                Institute of Botany, CHINA
                Author notes

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

                • Conceptualization: MCA VNM MJ IPF TG.

                • Data curation: MCA VNM MJ IPF.

                • Formal analysis: MCA VNM MJ IPF.

                • Funding acquisition: TG MJ IPF.

                • Investigation: MCA VNM MJ.

                • Methodology: MCA VNM MJ IPF TG.

                • Project administration: MCA.

                • Resources: TG MCA MJ IPF.

                • Supervision: MCA VNM MJ IPF TG.

                • Validation: MCA VNM MJ IPF TG.

                • Visualization: MCA VNM MJ IPF TG.

                • Writing – original draft: MCA VNM.

                • Writing – review & editing: MCA VNM MJ IPF TG.

                Author information
                http://orcid.org/0000-0002-3573-5774
                Article
                PONE-D-16-15891
                10.1371/journal.pone.0170053
                5396854
                28422969
                c50b0091-e8cf-4132-a2f8-05b67ff5e1c1
                © 2017 Andrade 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.

                History
                : 19 April 2016
                : 24 December 2016
                Page count
                Figures: 9, Tables: 1, Pages: 21
                Funding
                Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (BR)
                Award ID: 6666/2015-9
                Award Recipient :
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR)
                Award ID: 308278/2012-7
                Award Recipient :
                Funded by: Fundação de Amparo a Pesquisa do Estado do Pará
                Award ID: 011/2015
                Award Recipient :
                MCA: Coordenação de Aproveitamento de Pessoal de Nível Superior # grant 6666/2015-9. TG: Conselho Nacional de Desenvolvimento Científico e Tecnológico # grant 308278/2012-7, Coordenação de Aproveitamento de Pessoal de Nível Superior, Programa Nacional de Pós Doutorado, Fundação Amazônia de Amparo a Estudos e Pesquisa do Pará # grant 011/2015. IPF: Conselho Nacional de Desenvolvimento Científico e Tecnológico # CNPq/PRONEX/FAPEAM. This research was supported by PROPESP-UFPA (# grant 23073.004649/2017-06).
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