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      Phylogeny and species delimitation in Silene sect. Arenosae (Caryophyllaceae): a new section

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          Abstract

          A putatively monophyletic group of annual Silene species is revised taxonomically and described as the new section S. sect. Arenosae . The species of this section were previously treated as a part of a widely circumscribed and polyphyletic S. sect. Rigidulae . Silene sect. Arenosae as circumscribed here consists of nine species. Members of the section show a predominantly E Mediterranean to SW Asian distribution pattern from Turkey southward to Egypt and eastward to Iran and Pakistan, although most of the species have a limited distribution range. The species of S. sect. Arenosae are characterized by narrowly lanceolate calyx teeth, which are often highly polymorphic, and lanceolate to oblanceolate (non-spathulate) basal leaves. The provided taxonomic revision is based on morphological characters and supported by phylogenetic analyses of two nuclear loci (nrITS and an intron of the RPB2 gene) and one chloroplast locus (the intron of the rps16 gene). The species descriptions are formalized using a novel implementation of the Prometheus Description Model.

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          Most cited references 32

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          Molecular mechanisms of polyploidy and hybrid vigor.

          Hybrids such as maize (Zea mays) or domestic dog (Canis lupus familiaris) grow bigger and stronger than their parents. This is also true for allopolyploids such as wheat (Triticum spp.) or frog (i.e. Xenopus and Silurana) that contain two or more sets of chromosomes from different species. The phenomenon, known as hybrid vigor or heterosis, was systematically characterized by Charles Darwin (1876). The rediscovery of heterosis in maize a century ago has revolutionized plant and animal breeding and production. Although genetic models for heterosis have been rigorously tested, the molecular bases remain elusive. Recent studies have determined the roles of nonadditive gene expression, small RNAs, and epigenetic regulation, including circadian-mediated metabolic pathways, in hybrid vigor, which could lead to better use and exploitation of the increased biomass and yield in hybrids and allopolyploids for food, feed, and biofuels. Copyright 2010 Elsevier Ltd. All rights reserved.
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            A General System for Coding Taxonomic Descriptions

             M. Dallwitz (1980)
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              Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent.

               Graham Jones (2017)
              The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori assignment of individuals to species, and no guide tree. The method is implemented in a package called STACEY for BEAST2, and is a extension of the author's DISSECT package. Here we demonstrate considerable efficiency improvements by using three new operators for sampling from the posterior using the Markov chain Monte Carlo algorithm, and by using a model for the population size parameters along the branches of the species tree which allows these parameters to be integrated out. The correctness of the moves is demonstrated by tests of the implementation. The practice of using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al. in Syst Biol 63:263-271. doi: 10.1093/sysbio/syt106 , 2014). The same simulated data set is used to demonstrate the accuracy and improved convergence of the present method. We also compare performance with *BEAST for a fixed delimitation analysis on a large data set, and again show improved convergence.
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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
                04 September 2020
                : 159
                : 1-34
                Affiliations
                [1 ] Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
                [2 ] Centre of Excellence in Phylogeny of Living Organisms, and Department of Plant Science, School of Biology, College of Science, University of Tehran, 14155–6455, Tehran, Iran
                [3 ] Department of Biological and Environmental Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
                [4 ] Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
                [5 ] Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
                [6 ] Gothenburg Global Biodiversity Centre, University of Gothenburg, P.O. Box 461, 40530 Göteborg, Sweden
                Author notes
                Corresponding author: Farzaneh Jafari ( jafari_far1435@ 123456ut.ac.ir ); Bengt Oxelman ( bengt.oxelman@ 123456bioenv.gu.se )

                Academic editor: G. Giusso del Galdo

                Article
                51500
                10.3897/phytokeys.159.51500
                7486315
                Frida Eggens, Farzaneh Jafari, Mikael Thollesson, Simon Crameri, Shahin Zarre, Bengt Oxelman

                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.

                Categories
                Research Article
                Angiospermae
                Caryophyllaceae
                Molecular Systematics
                Phylogeny
                Taxonomy
                Africa
                Asia
                Europe

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