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      Leucheria cantillanensis (Nassauvieae, Asteraceae), a new species endemic to Central Chile

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          Abstract

          A new species, Leucheria cantillanensis sp. nov., endemic to the coastal mountain range of Central Chile, is described. By using both nDNA and cpDNA, phylogenetic relationships of the new species were investigated. This new species belongs to the acaulescent/subacaulescent clade of Leucheria , which is congruent with the morphology of the species. A detailed description, distribution map, insights about its habitat, conservation status, and illustrations are provided. An updated key for acaulescent/subacaulescent species of Leucheria from Central Chile is also given.

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          Most cited references 32

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          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              Universal primers for amplification of three non-coding regions of chloroplast DNA.

              Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.
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                Author and article information

                Contributors
                Journal
                PhytoKeys
                PhytoKeys
                3
                urn:lsid:arphahub.com:pub:F7FCE910-8E78-573F-9C77-7788555F8AAD
                PhytoKeys
                Pensoft Publishers
                1314-2011
                1314-2003
                2020
                08 December 2020
                : 169
                : 99-117
                Affiliations
                [1 ] Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Avenida Libertador B. O’Higgins 340, Santiago, Chile Pontificia Universidad Católica de Chile Santiago Chile
                [2 ] Instituto de Ecología y Biodiversidad (IEB), Universidad de Chile, Las Palmeras 3425, Santiago, Chile Pontificia Universidad Católica de Chile Santiago Chile
                Author notes
                Corresponding author: Nicolás Lavandero ( nglavand@ 123456uc.cl )

                Academic editor: P. de Lange

                Article
                57532
                10.3897/phytokeys.169.57532
                7738470
                Nicolás Lavandero, Benito Rosende, Maria Fernanda Pérez

                This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Funding
                Funded by: Fondo Nacional de Desarrollo Científico y Tecnológico 501100002850 http://doi.org/10.13039/501100002850
                Categories
                Research Article
                Asteraceae
                Molecular Systematics
                Phylogeny
                Taxonomy
                Chile
                South America

                Plant science & Botany

                taxonomy, rupicolous flora, leucheria , cantillana, asteraceae

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