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      Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

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          Abstract

          Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.

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          Isolation of plant DNA from fesh tissue

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            The conditioned reconstructed process.

            We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have n extant species today, we look at the tree distribution of the reconstructed trees--i.e. the trees without the extinct species. Whereas the tree shape distribution is well-known and actually the same as under the pure birth process, no analytic results for the speciation times were known. We provide the distribution for the speciation times and calculate the expectations analytically. This characterizes the reconstructed trees completely. We will show how the results can be used to date phylogenies.
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              Cryptic animal species are homogeneously distributed among taxa and biogeographical regions

              Background Cryptic species are two or more distinct but morphologically similar species that were classified as a single species. During the past two decades we observed an exponential growth of publications on cryptic species. Recently published reviews have demonstrated cryptic species have profound consequences on many biological disciplines. It has been proposed that their distribution is non-random across taxa and biomes. Results We analysed a literature database for the taxonomic and biogeographical distribution of cryptic animal species reports. Results from regression analysis indicate that cryptic species are almost evenly distributed among major metazoan taxa and biogeographical regions when corrected for species richness and study intensity. Conclusion This indicates that morphological stasis represents an evolutionary constant and that cryptic metazoan diversity does predictably affect estimates of earth's animal diversity. Our findings have direct theoretical and practical consequences for a number of prevailing biological questions with regard to global biodiversity estimates, conservation efforts and global taxonomic initiatives.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                peerj
                peerj
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                22 March 2019
                2019
                : 7
                Affiliations
                [1 ]Laboratory of Animal Genetics and Evolution (LEGAL), Federal University of Amazonas , Manaus, Amazonas, Brazil
                [2 ]Graduate Program in Genetics, Conservation, and Evolutionary Biology, National Institute of Amazonian Research (INPA) , Manaus, Amazonas, Brazil
                [3 ]Wildlife Laboratory, Brazilian Agricultural Research Corporation (EMBRAPA) Pantanal , Corumbá, Mato Grosso do Sul, Brazil
                [4 ]Graduate Program in Freshwater Biology and Inland Fisheries, National Institute of Amazonian Research (INPA) , Manaus, Amazonas, Brazil
                [5 ]Chico Mendes Institute for Biodiversity Conservation (ICMBio) , Boa Vista, Roraima, Brazil
                [6 ]Laboratory of Zoology Applied to Conservation, Federal University of Amazonas (UFAM) , Manaus, Amazonas, Brazil
                [7 ]Institut Pasteur de la Guyane , Cayenne, French Guiana
                [8 ]Association Kwata , Cayenne, French Guiana
                Article
                6580
                10.7717/peerj.6580
                6433001
                ©2019 Bittencourt et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                Funding
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
                Award ID: 575603/2008-9
                Award ID: 400813/2012-2
                Award ID: 482662/2013-1
                Award ID: 470383/2007-0
                Award ID: 479179/2014
                Funded by: CNPq/SISBIOTA- BioPHAM
                Award ID: 563348/2010
                Funded by: Empresa Brasileira de Pesquisa Agropecuaria Pantanal (Macroprograma 3)
                Funded by: Instituto Nacional de Pesquisas da Amazônia (INPA), Parque Nacional Viruá
                Funded by: Fundação de Apoio ao Desenvolvimento do Ensino
                Funded by: Ciência e Tecnologia do Estado do Mato Grosso do Sul (Fundect/CNPq grant PRONEX 006/2015), Norte Energia, Tractebel Energia
                Funded by: O Boticário Foundation, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) and Santo Antônio Energia
                Funded by: Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM)
                This study was financed by the following grants: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq grant no. 575603/2008-9) and CNPq/SISBIOTA- BioPHAM (CNPq grant no. 563348/2010) awarded to Izeni Pires Farias, CNPq grant no. 400813/2012-2 and 482662/2013-1 to Tomas Hrbek, and grant no. 470383/2007-0 and 479179/2014 to Zilca Campos. Additional financial and logistical support were also financed by Empresa Brasileira de Pesquisa Agropecuaria Pantanal (Macroprograma 3), Instituto Nacional de Pesquisas da Amazônia (INPA), Parque Nacional Viruá, Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado do Mato Grosso do Sul (Fundect/CNPq grant PRONEX 006/2015), Norte Energia, Tractebel Energia, O Boticário Foundation, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) and Santo Antônio Energia. Pedro Senna Bittencourt was supported by a Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM), and Izeni Pires Farias and Tomas Hrbek by a grant from CNPq. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Biodiversity
                Biogeography
                Evolutionary Studies
                Genetics
                Population Biology

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