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      Identification of the taxonomic status of Scinax nebulosus and Scinax constrictus (Scinaxinae, Anura) based on molecular markers Translated title: Identificação do status taxonômico de Scinax nebulosus e Scinax constrictus (Scinaxinae, Anura), baseado em marcadores moleculares

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          Abstract

          Abstract The validation of many anuran species is based on a strictly descriptive, morphological analysis of a small number of specimens with a limited geographic distribution. The Scinax Wagler, 1830 genus is a controversial group with many doubtful taxa and taxonomic uncertainties, due a high number of cryptic species. One example is the pair of species Scinax constrictus and Scinax nebulosus, which share a similar morphology. Scinax constrictus is restricted to the Brazilian Cerrado savanna, while S. nebulosus is widely distributed throughout northern South America. Despite the validation of many anuran species, discriminations based only on morphological traits is quite difficult due to the high conservative morphology of some groups. In this context, the present study uses mitochondrial and nuclear genes to provide a more consistent diagnosis and test the validity of S. constrictus as a distinct species from S. nebulosus, as well as evaluate the position of these taxa within the Scinax genus. The topologies obtained herein uphold the monophyletic status of Scinax based on all molecular markers assessed in this study, in all analytical approaches, with high levels of statistical support.

          Translated abstract

          Resumo A validação de muitas espécies de anuros é baseada em uma análise morfológica e descritiva de um pequeno número de espécimes com uma distribuição geográfica limitada. O gênero Scinax Wagler, 1830 é um grupo controverso com muitos táxons duvidosos e incertezas taxonômicas devido ao grande número de espécies crípticas. Um exemplo são as espécies, Scinax constrictus e Scinax nebulosus, que compartilham uma morfologia similar. Scinax constrictus é restrito à savana do Cerrado brasileiro, enquanto S. nebulosus é amplamente distribuído pelo norte da América do Sul. Apesar da validação de muitas espécies de anuros, a discriminação baseada apenas em características morfológicas é bastante difícil, devido à alta morfologia conservadora de alguns grupos. Neste contexto, o presente estudo utiliza genes mitocondriais e nucleares para fornecer um diagnóstico mais consistente e para testar a validade de S. constrictus como uma espécie distinta de S. nebulosus, bem como avaliar a posição destes táxons dentro do gênero Scinax. As topologias obtidas confirmaram o status monofilético de Scinax com base em todos os marcadores moleculares, em todas as abordagens analíticas, com altos níveis de suporte estatístico.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

            We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
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              MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

              Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d N /d S rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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                Author and article information

                Journal
                bjb
                Brazilian Journal of Biology
                Braz. J. Biol.
                Instituto Internacional de Ecologia (São Carlos, SP, Brazil )
                1519-6984
                1678-4375
                December 2021
                : 81
                : 4
                : 855-866
                Affiliations
                [02] Belém Pará orgnameUniversidade Federal do Pará orgdiv1Centro de Estudos Avançados da Biodiversidade orgdiv2Programa de Pós-graduação em Ecologia Aquática e Pesca Brazil
                [03] Bragança Pará orgnameUniversidade Federal do Pará orgdiv1Instituto de Estudos Costeiros orgdiv2Laboratório e Filogenomica e Bioinformatica Brazil
                [01] São Luís orgnameUniversidade Federal do Maranhão orgdiv1Departamento de Biologia orgdiv2Laboratório de Ecologia e Sistemática de Peixes Brazil
                [04] Porto Seguro Bahia orgnameUniversidade Federal da Bahia orgdiv1Centro de Formação em Ciências Ambientais orgdiv2Instituto Sosígenes Costa de Humanidades, Artes e Ciências Brazil
                Article
                S1519-69842021000400855 S1519-6984(21)08100400855
                10.1590/1519-6984.225646
                d56401e2-2f11-45b5-ac96-bddc7f805bf6

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                : 26 June 2019
                : 04 May 2020
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 43, Pages: 12
                Product

                SciELO Brazil

                Categories
                Original Article

                marcadores moleculares,phylogeny,molecular markers,cryptic species,espécies crípticas,Scinax,filogenia,anuros,anurans

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