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      A new species of Thinouia ( Paullinieae , Sapindaceae ) from the Amazon and its phylogenetic placement

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          Abstract

          Thinouia is a Neotropical genus of lianas with approximately 12 species and is the only genus in tribe Paullinieae with actinomorphic flowers. During a taxonomic revision of the genus and fieldwork in south-western Amazonia, we found a new species that appears similar to Thinouia trifoliata (ex Allosanthus ) because of its racemiform inflorescence. However, before describing the new species, we had to confirm that Allosanthus was congeneric with Thinouia so we could place the new species in the correct genus. The results of the phylogenetic analysis, based on molecular data ( trnL intron and ITS sequences), show that Allosanthus should be included in Thinouia . Thus, the new taxon is described here as Thinouia cazumbensis sp. nov. The new species is described, illustrated and phylogenetic trees showing relationships within supertribe Paulliniodae and Thinouia and the congeneric Allosanthus are given.

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          MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

          Fredrik Ronquist, Maxim Teslenko, Paul van der Mark … (2012)
          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

            Matthew Kearse, Richard Moir, Amy Wilson … (2012)
            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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              MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.

              K Katoh (2002)
              A multiple sequence alignment program, MAFFT, has been developed. The CPU time is drastically reduced as compared with existing methods. MAFFT includes two novel techniques. (i) Homo logous regions are rapidly identified by the fast Fourier transform (FFT), in which an amino acid sequence is converted to a sequence composed of volume and polarity values of each amino acid residue. (ii) We propose a simplified scoring system that performs well for reducing CPU time and increasing the accuracy of alignments even for sequences having large insertions or extensions as well as distantly related sequences of similar length. Two different heuristics, the progressive method (FFT-NS-2) and the iterative refinement method (FFT-NS-i), are implemented in MAFFT. The performances of FFT-NS-2 and FFT-NS-i were compared with other methods by computer simulations and benchmark tests; the CPU time of FFT-NS-2 is drastically reduced as compared with CLUSTALW with comparable accuracy. FFT-NS-i is over 100 times faster than T-COFFEE, when the number of input sequences exceeds 60, without sacrificing the accuracy.
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                Author and article information

                Contributors
                Herison Medeiros
                Journal
                Journal ID (nlm-ta): PhytoKeys
                Journal ID (iso-abbrev): PhytoKeys
                Journal ID (publisher-id): 3
                Journal ID (index): urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                Title: PhytoKeys
                Publisher: Pensoft Publishers
                ISSN (Print): 1314-2011
                ISSN (Electronic): 1314-2003
                Publication date Collection: 2020
                Publication date (Electronic): 28 October 2020
                Volume: 165
                Pages: 115-126
                Affiliations
                [1 ] Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, 05508-090 São Paulo, SP, Brazil Jardim Botânico do Rio de Janeiro Rio de Janeiro Brazil
                [2 ] Department of Botany, MRC-166 Smithsonian Institution, P.O. Box 37012, Washington D.C. 20013-7012, USA Universidade de São Paulo São Paulo Brazil
                [3 ] Jardim Botânico do Rio de Janeiro, Pacheco Leão, 915, 22460-030, Rio de Janeiro, Rio de Janeiro, Brazil Department of Botany Washington United States of America
                Author notes
                Corresponding author: Herison Medeiros ( medeiros.herison@ 123456gmail.com )

                Academic editor: Marc Appelhans

                Author information
                https://orcid.org/0000-0002-0946-8668
                https://orcid.org/0000-0002-8366-0738
                Article
                Accession ID: PMC7642129 Pmcid ID: PMC7642129 Pmc-uid ID: 7642129 Publisher ID: 57341
                DOI: 10.3897/phytokeys.165.57341
                PMC ID: 7642129
                PubMed ID: 33192150
                SO-VID: 9646e4ad-b405-4938-86f4-f9ea3e512849
                License:

                This is an open access article distributed under the terms of the CC0 Public Domain Dedication.

                History
                Date received : 07 August 2020
                Date accepted : 02 October 2020
                Funding
                Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico 501100003593 http://doi.org/10.13039/501100003593
                Categories
                Subject: Research Article
                Subject: Sapindaceae
                Subject: Amazon Basin
                Subject: Americas
                Subject: South America

                Keywords: Sapindaceae ,neotropical biodiversity,Amazonia, Sapindales , Thinouia ,taxonomy, Allosanthus ,Brazil, Paullinieae ,Paulliniodae,lianas
                Data availability:
                Keywords: Sapindaceae , neotropical biodiversity, Amazonia, Sapindales , Thinouia , taxonomy, Allosanthus , Brazil, Paullinieae , Paulliniodae, lianas

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