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      Notes on the distribution, morphology, and phylogenetics of Platyrrhinus incarum (Chiroptera: Phyllostomidae) in Brazil, and confirmation that Platyrrhinus helleri does not occur in the country

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          Abstract

          ABSTRACT Changes in Neotropical bat taxonomy in the past two decades have caused significant shifts in our understanding of the diversity and distribution of the group. Taxonomic revisions have shown that the once widespread Platyrrhinus helleri (Peters, 1866) represented a species complex, which resulted in the elevation of Platyrrhinus helleri incarum (Thomas, 1912) to the species level for cis-Andean South America and the restriction of P. helleri to Central America and northern South America west of the Andes. Nevertheless, some studies still mention P. helleri for Brazil. Aiming to investigate if P. helleri occurs in Brazil, we collected specimens of small-sized Platyrrhinus in the Cerrado and Pantanal ecosystems, and revised vouchers in museum collections. Based on DNA sequence data and analysis of the pelage and craniodental morphology, we confirm that the only small Platyrrhinus species occurring in Cerrado and Pantanal of central Brazil corresponds to P. incarum. This is the first study to provide sequence data for Brazilian P. incarum. We also provide new records of P. incarum, extending its range by 390 km to southeast and 480 km to the east in Brazil.

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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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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              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

                Journal
                zool
                Zoologia (Curitiba)
                Zoologia (Curitiba)
                Sociedade Brasileira de Zoologia (Curitiba, PR, Brazil )
                1984-4670
                1984-4689
                2024
                : 41
                : e23044
                Affiliations
                [7] Glenside Pennsylvania orgnameArcadia University orgdiv1Department of Biology United States
                [8] New York New York orgnameAmerican Museum of Natural History orgdiv1Department of Mammalogy United States
                [5] Vairão orgnameUniversidade do Porto orgdiv1Campus de Vairão orgdiv2BIOPOLIS Program in Genomics, Biodiversity and Land Planning Portugal
                [2] Cuiabá Mato Grosso orgnameUniversidade Federal de Mato Grosso orgdiv1Instituto de Biociências orgdiv2Laboratório de Mastozoologia Brazil
                [1] Viçosa Minas Gerais orgnameUniversidade Federal de Viçosa orgdiv1Departamento de Biologia Animal orgdiv2Museu de Zoologia João Moojen Brazil
                [4] Porto orgnameUniversidade do Porto orgdiv1Faculdade de Ciências orgdiv2Departamento de Biologia Portugal
                [3] Vairão orgnameUniversidade do Porto orgdiv1Campus de Vairão orgdiv2InBIO Laboratório Associado Portugal
                [6] São Paulo São Paulo orgnamePrefeitura Municipal de São Paulo orgdiv1SMS orgdiv2Divisão de Vigilância de Zoonoses Brazil
                Article
                S1984-46702024000100508 S1984-4670(24)04100000508
                10.1590/s1984-4689.v41.e23044
                4dc45e66-f351-41df-ab45-3253e706b312

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

                History
                : 23 November 2023
                : 01 August 2023
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 40, Pages: 0
                Product

                SciELO Brazil

                Categories
                Research Article

                phylogeny,Stenodermatinae,Pantanal,Cytochrome b,Cerrado,broad-nosed bat,Atlantic Forest

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