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      A new reproductive mode in anurans: Natural history of Bokermannohyla astartea (Anura: Hylidae) with the description of its tadpole and vocal repertoire

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          Abstract

          Anurans have the greatest diversity of reproductive modes among tetrapod vertebrates, with at least 41 being currently recognized. We describe a new reproductive mode for anurans, as exhibited by the Paranapiacaba Treefrog, Bokermannohyla astartea, an endemic and poorly known species of the Brazilian Atlantic Forest belonging to the B. circumdata group. We also describe other aspects of its reproductive biology, that are relevant to understanding the new reproductive mode, such as courtship behavior, spawning, and tadpoles. Additionally, we redescribe its advertisement call and extend its vocal repertoire by describing three additional call types: courtship, amplectant, and presumed territorial. The new reproductive mode exhibited by B. astartea consists of: (1) deposition of aquatic eggs in leaf-tanks of terrestrial or epiphytic bromeliads located on or over the banks of temporary or permanent streams; (2) exotrophic tadpoles remain in the leaf-tanks during initial stages of development (until Gosner stage 26), after which they presumably jump or are transported to streams after heavy rains that flood their bromeliad tanks; and (3) tadpole development completes in streams. The tadpoles of B. astartea are similar to those of other species of the B. circumdata group, although with differences in the spiracle, eyes, and oral disc. The vocal repertoire of B. astartea exhibits previously unreported acoustic complexity for the genus. Bokermannohyla astartea is the only bromeligenous species known to date among the 187 known species within the tribe Cophomantini. We further discuss evolutionary hypotheses for the origin of this novel reproductive mode.

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          NIH Image to ImageJ: 25 years of image analysis

          For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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            BLAST+: architecture and applications

            Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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              Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

              Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: SupervisionRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Funding acquisitionRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: 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
                17 February 2021
                2021
                : 16
                : 2
                : e0246401
                Affiliations
                [1 ] Núcleo São Sebastião, Parque Estadual da Serra do Mar, Fundação para a Conservação e a Produção Florestal do Estado de São Paulo, São Sebastião, São Paulo, Brazil
                [2 ] Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
                [3 ] Programa de Pós-Graduação em Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
                [4 ] Programa de Pós-Graduação em Biologia Comparada, Departamento de Biologia/FFCLRP, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
                [5 ] División Herpetología, Museo Argentino de Ciencias Naturales-CONICET, Buenos Aires, Argentina
                [6 ] Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
                [7 ] Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo, Brazil
                Universitat Trier, GERMANY
                Author notes

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

                Author information
                https://orcid.org/0000-0003-0065-6029
                https://orcid.org/0000-0002-5154-154X
                https://orcid.org/0000-0002-4789-7033
                Article
                PONE-D-20-19802
                10.1371/journal.pone.0246401
                7888631
                33596209
                61ff4c08-7696-43e5-94d0-0b64c12f5bca
                © 2021 Malagoli 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
                : 26 June 2020
                : 19 January 2021
                Page count
                Figures: 7, Tables: 3, Pages: 30
                Funding
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
                Award ID: grants #141259/2014-0, #202081/2015-0, #306623/2018-8, #312795/2018-1, and #310301/2018-1
                Funded by: São Paulo Research Foundation (FAPESP)
                Award ID: grants #2008/54472-2, #2008/50928-1, #2013/50741-7, #2014/50342-8, #2014/23677-9, #2017/27137-7, #2017/26162-8, and #2018/15425-0
                Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for PROTAX fellowship
                Award ID: grant #440665/2015-9
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100003074, Agencia Nacional de Promoción Científica y Tecnológica;
                Award ID: ANPCyT PICT 2015-820
                Funding: This work was part of L. R. M.’s PhD degree. L. R. M. thanks Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) for doctoral fellowship (grant #141259/2014-0). For financial support, we thank São Paulo Research Foundation (FAPESP) (grants #2008/54472-2, #2008/50928-1, #2013/50741-7, #2014/50342-8, and #2014/23677-9). T. L. P. thanks Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) for PROTAX fellowship (grant #440665/2015-9) and CNPq for “Ciência Sem Fronteiras” fellowship (grant #202081/2015-0). D. L. B. thanks FAPESP for doctoral fellowship (grant #2017/27137-7). J. F. thanks Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT PICT 2015-820), and FAPESP (grant #2018/15425-0). M. L. L. thanks FAPESP for fellowship (grant #2017/26162-8). J. G. R. G. thanks CAPES for doctoral fellowship (Financing Code 001). C. F. B. H., R. J. S and P. C. A. G. thanks CNPq for research productivity fellowship (grants # 306623/2018-8, #312795/2018-1, #310301/2018-1, respectively). 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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