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      Molecular phylogeny of Planaltina Böhlke (Characidae: Stevardiinae) and comments on the definition and geographic distribution of the genus, with description of a new species

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          Abstract

          A molecular phylogeny of Planaltina, including the three previously described species and an undescribed species, is presented. The monophyly of the genus, included in Diapomini, is strongly supported. Its sister group, the remaining Diapomini, includes only species without modified caudal-fin squamation in the present analysis (species of Diapoma with caudal organs were not sampled). Creagrutus is sister to Planaltina plus remaining Diapomini instead of Planaltina being sister to Creagrutus plus Diapomini, as a previous analysis had suggested. Species of Planaltina form two clades: P. britskii plus the new species, with low support (< 50%); and P. myersi plus P. glandipedis, with higher support. Planaltina is rediagnosed from all Characidae based on the morphology of the caudal organ, the absence of a humeral spot and the presence of a complete lateral line. Comments on the caudal-fin squamation of Diapoma and Lepidocharax burnsi, on the type-series of L. burnsi and on the geographic distribution of Planaltina and Lepidocharax species are provided. Finally, a formal description of the aforementioned new species and a novel identification key to Planaltina are presented.

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          An index of substitution saturation and its application.

          We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables researchers to quickly judge whether a set of aligned sequences is useful in phylogenetics. We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE.
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            Phylogeny of the family Characidae (Teleostei: Characiformes): from characters to taxonomy

            The family Characidae is the most diverse among Neotropical fishes. Systematics of this family are mainly based on pre-cladistic papers, and only recently a phylogenetic hypothesis for Characidae was proposed by the author. That phylogeny was based on 360 morphological characters studied for 160 species, including representatives of families related to Characidae. This paper is based on that phylogenetic analysis, with the analyzed characters described herein and documented, accompanied by comparisons of their definition and coding in previous papers. Synapomorphies of each node of the proposed phylogeny are listed, comparisons with previous classifications provided, and autapomorphies of the analyzed species listed. Taxonomic implications of the proposed classification and the position of the incertae sedis genera within Characidae are discussed. A discussion of the phylogenetic information of the characters used in the classical systematics of the Characidae is provided.
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              Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot

              Background The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. Results We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. Conclusions We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: 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
                16 May 2018
                2018
                : 13
                : 5
                : e0196291
                Affiliations
                [1 ] Programa de Pós-Graduação em Ecologia de Ambientes Aquáticos Continentais, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
                [2 ] Departamento de Biologia, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
                [3 ] Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
                [4 ] Instituto de Biociências, Departamento de Morfologia, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, São Paulo, Brazil
                National Cheng Kung University, TAIWAN
                Author notes

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

                Author information
                http://orcid.org/0000-0002-5520-9763
                Article
                PONE-D-17-30323
                10.1371/journal.pone.0196291
                5955486
                29768420
                1fd1f320-eca8-48eb-b9e2-67c62305807a
                © 2018 Deprá 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
                : 17 August 2017
                : 8 April 2018
                Page count
                Figures: 8, Tables: 1, Pages: 26
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001807, Fundação de Amparo à Pesquisa do Estado de São Paulo;
                Award ID: 2014/26508–3
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004612, Fundação Araucária;
                Award ID: covenant #471/2013, protocol #36204
                Award Recipient :
                We thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, cnpq.br) for scholarship to GCD and grants to CSP and Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, www.fapesp.br) for providing grant (proc. 2014/26508–3) to CO. WJG is partially supported by a research grant from the Fundação Araucária (Secretaria da Ciência, Tecnologia e Ensino Superior do Paraná, www.fappr.pr.gov.br; covenant #471/2013, protocol #36204). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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