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      Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

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          Abstract

          Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA‐sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae. Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well‐known refugia. We hypothesize that low light requirements evolved when species persisting in cold‐stage refugia were forced into marginal habitats by more competitive warm‐stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.

          Abstract

          Saxifraga sect. Saxifraga subsect. Arachnoideae is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats. Based on phylogenetic relationships, the geographical distribution of species in relation to refugial areas in the Alps and a reconstruction of ecological preferences we hypothesize that low light requirements evolved when species persisting in cold‐stage refugia were forced into marginal habitats by more competitive warm‐stage vegetation.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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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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              MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

              The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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                Author and article information

                Contributors
                kadereit@uni-mainz.de
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                09 January 2023
                January 2023
                : 13
                : 1 ( doiID: 10.1002/ece3.v13.1 )
                : e9728
                Affiliations
                [ 1 ] Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg‐Universität Mainz Germany
                [ 2 ] Institut für Biologie, AG Systematische Botanik und Pflanzengeographie, Freie Universität Berlin Berlin Germany
                [ 3 ]Present address: Systematik, Biodiversität und Evolution der Pflanzen Ludwig‐Maximilians‐Universität München Munich Germany
                Author notes
                [*] [* ] Correspondence

                Joachim W. Kadereit, Systematik, Biodiversität und Evolution der Pflanzen, Ludwig‐Maximilians‐Universität München, Menzinger Str. 67, D‐80638 München, Germany.

                Email: kadereit@ 123456uni-mainz.de

                Author information
                https://orcid.org/0000-0002-9274-3359
                Article
                ECE39728 ECE-2022-12-01822
                10.1002/ece3.9728
                9829489
                36636428
                ef12a686-cbeb-4587-8841-05c8117f51ca
                © 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                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
                : 12 December 2022
                : 23 December 2022
                Page count
                Figures: 9, Tables: 2, Pages: 22, Words: 12260
                Funding
                Funded by: Deutsche Forschungsgemeinschaft , doi 10.13039/501100001659;
                Award ID: KA 635/21‐1
                Categories
                Phylogenetics
                Research Article
                Research Articles
                Custom metadata
                2.0
                January 2023
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.3 mode:remove_FC converted:09.01.2023

                Evolutionary Biology
                adaptive evolution,alps,hybseq,indicator values,quaternary,rear edge
                Evolutionary Biology
                adaptive evolution, alps, hybseq, indicator values, quaternary, rear edge

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