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      Biogeographic history of a large clade of ectomycorrhizal fungi, the Russulaceae, in the Neotropics and adjacent regions

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          Summary

          • The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae.

          • We inferred a supertree of 3285 operational taxonomic units, representing worldwide internal transcribed spacer sequences. We reconstructed biogeographic history and diversification and identified lineages in the Neotropics and adjacent Patagonia.

          • The ectomycorrhizal Russulaceae have a tropical African origin. The oldest lineages in tropical South America, most with African sister groups, date to the mid‐Eocene, possibly coinciding with a boreotropical migration corridor. There were several transatlantic dispersal events from Africa more recently. Andean and Central American lineages mostly have north‐temperate origins and are associated with North Andean uplift and the general north–south biotic interchange across the Panama isthmus, respectively. Patagonian lineages have Australasian affinities. Diversification rates in tropical South America and other tropical areas are lower than in temperate areas.

          • Neotropical Russulaceae have multiple biogeographic origins since the mid‐Eocene involving dispersal and co‐migration. Discontinuous distributions of host plants may explain low diversification rates of tropical lowland ectomycorrhizal fungi. Deeply diverging neotropical fungal lineages need to be better documented.

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          MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

          We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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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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                Author and article information

                Contributors
                j.hackel@kew.org
                Journal
                New Phytol
                New Phytol
                10.1111/(ISSN)1469-8137
                NPH
                The New Phytologist
                John Wiley and Sons Inc. (Hoboken )
                0028-646X
                1469-8137
                30 July 2022
                October 2022
                : 236
                : 2 ( doiID: 10.1111/nph.v236.2 )
                : 698-713
                Affiliations
                [ 1 ] Royal Botanic Gardens, Kew Richmond‐upon‐Thames TW9 3AE UK
                [ 2 ] Laboratoire Evolution et Diversité Biologique (UMR 5174) Université Toulouse III – Paul Sabatier/CNRS/IRD 31062 Toulouse cedex 9 France
                [ 3 ] Department of Biological Sciences California State Polytechnic University, Humboldt Arcata CA 95521 USA
                [ 4 ] Faculté de Pharmacie, Laboratoire des Sciences Végétales et Fongiques (LGCgE, ER4) Université de Lille 59006 Lille France
                [ 5 ] Department of Biology Ghent University 9000 Gent Belgium
                [ 6 ] Centro Universitário de João Pessoa PB 58053‐000 João Pessoa Brazil
                [ 7 ] Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS Sorbonne Université, EPHE, Université des Antilles 75231 Paris cedex 05 France
                [ 8 ] Departamento de Botânica Universidade Federal de Santa Catarina SC 88040‐900 Florianópolis Brazil
                [ 9 ] Microbiología Ambiental–School of Microbiology, Laboratory of Taxonomy and Ecology of Fungi–Institute of Biology University of Antioquia 050010 Medellín Colombia
                [ 10 ] Departamento de Sistemática e Ecologia Universidade Federal da Paraíba PB 58051‐970 João Pessoa Brazil
                [ 11 ] UMR Ecologie des Forêts de Guyane AgroParisTech/CIRAD/CNRS/Université des Antilles/Université de la Guyane/INRA 97379 Kourou cedex French Guiana
                [ 12 ] Institut Agronomique néo‐Calédonien (IAC), Equipe Sol & Végétations (SolVeg) BP18239 98848 Nouméa New Caledonia
                [ 13 ] Instituto de Bioquímica y Microbiología Universidad Austral de Chile 5049000 Valdivia Chile
                [ 14 ] Instituto Franco‐Argentino para el Estudio del Clima y sus Impactos (UMI IFAECI/CNRS‐CONICET‐UBA‐IRD) Universidad de Buenos Aires C1428EGA Ciudad Autonoma de Buenos Aires Argentina
                Author notes
                [*] [* ] Author for correspondence:

                Jan Hackel

                Email:j.hackel@ 123456kew.org

                Author information
                https://orcid.org/0000-0002-9657-5372
                https://orcid.org/0000-0001-9760-8837
                https://orcid.org/0000-0003-4783-3643
                https://orcid.org/0000-0002-6266-3091
                https://orcid.org/0000-0001-6824-5280
                https://orcid.org/0000-0002-1810-4890
                https://orcid.org/0000-0003-0539-9711
                https://orcid.org/0000-0003-4930-565X
                https://orcid.org/0000-0002-9139-920X
                https://orcid.org/0000-0001-8283-9413
                https://orcid.org/0000-0001-7153-8455
                https://orcid.org/0000-0001-5907-6999
                https://orcid.org/0000-0002-4565-2331
                Article
                NPH18365 2022-40512
                10.1111/nph.18365
                9795906
                35811430
                f528315a-4cf4-4b6d-bcbe-5392af708b34
                © 2022 The Authors. New Phytologist © 2022 New Phytologist Foundation.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 22 June 2022
                : 23 June 2022
                Page count
                Figures: 6, Tables: 2, Pages: 16, Words: 15310
                Funding
                Funded by: Agence Nationale de la Recherche , doi 10.13039/501100001665;
                Award ID: ANR‐10‐LABX‐25‐01
                Funded by: National Geographic Society , doi 10.13039/100006363;
                Award ID: 6679‐99
                Award ID: 7435‐03
                Funded by: National Science Foundation , doi 10.13039/100000001;
                Award ID: DEB‐0918591
                Award ID: DEB‐1556338
                Funded by: Special Research Fund Ghent University
                Award ID: B/13485/01
                Award ID: BOF‐PDO‐2017‐001201
                Funded by: BBSRC , doi 10.13039/501100000268;
                Award ID: BB/S019669/1
                Funded by: CNRS Nouragues Research Station
                Categories
                Full Paper
                Research
                Full Papers
                Custom metadata
                2.0
                October 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.3 mode:remove_FC converted:28.12.2022

                Plant science & Botany
                boreotropical migration,dispersal,diversification,ectomycorrhizal fungi,neotropics,patagonia,russulaceae,vicariance

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