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      Phylogenetics of Paepalanthus (Eriocaulaceae), a diverse Neotropical monocot lineage

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          Abstract

          Paepalanthus is a diverse monocot genus with remarkable diversity distributed in the Neotropical highlands of South America. The genus comprises 410 species arranged in subgenera, sections, subsections and series. Added to this complex classification, Paepalanthus shows considerable morphological heterogeneity and includes three other genera in it, Actinocephalus (Körn.) Sano, Lachnocaulon Kunth and Tonina Aubl. A broadly sampled phylogenetic inference for the genus is still missing, precluding a better understanding of its delimitation and further studies in the group. Here we present the most comprehensive phylogenetic study for Paepalanthus to date, as well as morphological survey of characters that delimit the main lineages found. We assembled a morphologically and geographically representative sampling of Paepalanthus and associated genera comprising 356 accessions in a combined dataset of plastid (trnL-F, psbA-trnH) and nuclear (ITS, ETS) regions. Bayesian inference and maximum likelihood methods were used for phylogenetic reconstruction. We found that Paepalanthus and 16 of its 28 infrageneric categories are not monophyletic, as well as the closely related genus Actinocephalus. Thirty-six well-supported clades are recognized. Morphological characters show high levels of homoplasy, and concepts traditionally used in the classification of Paepalanthus were found to be inconsistent. We confirmed that Paepalanthus as currently circumscribed is not monophyletic and revealed several new relationships in Eriocaulaceae. To make Paepalanthus monophyletic, the genus must be re-circumscribed. These results also provide a foundation for future investigations of the diversification and evolution of flora of the Neotropical highlands of South America.

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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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              jModelTest: phylogenetic model averaging.

              jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.). It implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion," the "Bayesian information criterion," and a "decision-theoretic performance-based" approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.
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                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Botanical Journal of the Linnean Society
                Oxford University Press (OUP)
                0024-4074
                1095-8339
                January 01 2021
                January 01 2021
                September 03 2020
                January 01 2021
                January 01 2021
                September 03 2020
                : 195
                : 1
                : 34-52
                Affiliations
                [1 ]Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
                [2 ]Instituto Tecnológico Vale, Belém, Pará, Brazil
                [3 ]Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, Distrito Federal, Brazil
                [4 ]Keller Science Action Center, Field Museum of Natural History, Chicago, Illinois, United States
                [5 ]Departamento de Ciências Biológicas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
                Article
                10.1093/botlinnean/boaa070
                34311590-bb87-4e02-93c8-10bf2155c428
                © 2020

                https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model

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