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      Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

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          Abstract

          Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.

          Abstract

          Water availability dictates patterns of global phylogenetic beta diversity in tropical plants.

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          Most cited references194

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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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            Fast and accurate short read alignment with Burrows–Wheeler transform

            Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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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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                Journal
                Science Advances
                Sci. Adv.
                American Association for the Advancement of Science (AAAS)
                2375-2548
                February 17 2023
                February 17 2023
                : 9
                : 7
                Affiliations
                [1 ]Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland.
                [2 ]Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil.
                [3 ]Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil.
                [4 ]Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil.
                [5 ]Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil.
                [6 ]Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia.
                [7 ]School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.
                [8 ]School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
                [9 ]Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France.
                [10 ]Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada.
                [11 ]School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA.
                [12 ]Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK.
                [13 ]Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.
                [14 ]Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil.
                [15 ]Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil.
                [16 ]Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina.
                [17 ]Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina.
                [18 ]Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina.
                [19 ]Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA.
                [20 ]United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA.
                [21 ]Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia.
                [22 ]School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK.
                [23 ]Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK.
                [24 ]Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK.
                [25 ]Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland.
                [26 ]Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland.
                Article
                10.1126/sciadv.ade4954
                acc32d35-ba27-4934-a9ef-c6a92c7b61f6
                © 2023
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