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      Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales)

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      BMC Evolutionary Biology

      BioMed Central

      Laetiporus, Wood rot fungi, Phylogeny, Biogeography, Molecular clock

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          Abstract

          Background

          The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU).

          Results

          Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area.

          Conclusions

          Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

          Electronic supplementary material

          The online version of this article (doi:10.1186/s12862-017-0948-5) contains supplementary material, which is available to authorized users.

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          Most cited references 58

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          RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

          RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. icwww.epfl.ch/~stamatak
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            MrBayes 3: Bayesian phylogenetic inference under mixed models.

            MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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              Confidence Limits on Phylogenies: An Approach Using the Bootstrap

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                Author and article information

                Affiliations
                ISNI 0000 0001 1456 856X, GRID grid.66741.32, Institute of Microbiology, , Beijing Forestry University, ; P.O. Box 61, 35#, Qinghua East Road, Haidian District, Beijing, 100083 People’s Republic of China
                Contributors
                super_jasone@yahoo.com
                +86-10-62336309 , baokaicui2013@gmail.com
                Journal
                BMC Evol Biol
                BMC Evol. Biol
                BMC Evolutionary Biology
                BioMed Central (London )
                1471-2148
                20 April 2017
                20 April 2017
                2017
                : 17
                948
                10.1186/s12862-017-0948-5
                5397748
                28424048
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31422001, 31170018
                Funded by: Fundamental Research Funds For the Central Universities
                Award ID: 2016ZCQ04
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Evolutionary Biology

                laetiporus, molecular clock, biogeography, phylogeny, wood rot fungi

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