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      Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi ( Bryoria sect. Implexae, Parmeliaceae)

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          Abstract

          In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

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          AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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            MRBAYES: Bayesian inference of phylogenetic trees.

            The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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              Analyzing the mosaic structure of genes.

              Some genes in prokaryotes consist of a mosaic of regions derived from different ancestors by horizontal gene transfer. A method is described for demonstrating the statistical significance of such mosaic structure and for locating the crossover points separating different regions.
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                Author and article information

                Journal
                Persoonia
                Persoonia
                Persoonia
                Persoonia : Molecular Phylogeny and Evolution of Fungi
                Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
                0031-5850
                1878-9080
                23 August 2018
                June 2019
                : 42
                : 75-100
                Affiliations
                [1 ]Departamento de Farmacología, Farmacognosia y Botánica (U.D. Botánica), Facultad de Farmacia, Universidad Complutense, Plaza de Ramón y Cajal s/n, Madrid 28040, Spain
                [2 ]Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf 8903, Switzerland.
                [3 ]Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland.
                [4 ]Research and Collections, Canadian Museum of Nature, Ottawa, ON K1P 6P4, Canada.
                [5 ]Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.
                [6 ]Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; and Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, United Kingdom.
                Author notes
                corresponding author e-mail: Carlos G. Boluda, carlgala@ 123456ucm.es .
                Article
                10.3767/persoonia.2019.42.04
                6712543
                31551615
                b0cdf92f-3a3d-4cbb-8bb0-d718c222fc93
                © 2019 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute

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                History
                : 21 December 2017
                : 18 June 2018
                Categories
                Research Article

                Plant science & Botany
                chemotypes,cryptic species,haplotypes,incomplete lineage sorting,integrative taxonomy,microsatellites,speciation,species concepts

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