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      Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies

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      1 , 2 , 3 , , 4 , 3 , 5 , 6 , 7 , 3 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 14 , 8 , 15 , 16 , 11 , 17 , 6 , 8 , 18 , 11 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 15 , 26 , 2
      Nature Communications
      Nature Publishing Group UK
      Biodiversity, Biogeography, Macroecology, Phylogenetics, Biodiversity

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          Abstract

          The global increase in species richness toward the tropics across continents and taxonomic groups, referred to as the latitudinal diversity gradient, stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluate several of these hypotheses to explain spatial diversity patterns in a butterfly family, the Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal, and also the extent to which these processes differ among regions at the same latitude. We generate a time-calibrated phylogeny containing 2,866 nymphalid species (~45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the latitudinal diversity gradient among regions because temporal diversification dynamics differ greatly across longitude. The Neotropical diversity results from low extinction rates, not high speciation rates, and biotic interchanges with other regions are rare. Southeast Asia is also characterized by a low speciation rate but, unlike the Neotropics, is the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, combined with tropical niche conservatism, played a major role in generating the modern latitudinal diversity gradient of nymphalid butterflies.

          Abstract

          A phylogeny of Nymphalidae butterflies unveils the origin of the latitudinal diversity gradient. This study showed that the modern pattern of species richness emerged from dynamics of dispersal and diversification that varied through time and across regions, and that global climate change throughout the Cenozoic probably played a major role in generating the biodiversity pattern.

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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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            Bayesian Phylogenetics with BEAUti and the BEAST 1.7

            Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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              PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

              PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.
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                Author and article information

                Contributors
                chazotn@gmail.com
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                29 September 2021
                29 September 2021
                2021
                : 12
                : 5717
                Affiliations
                [1 ]GRID grid.6341.0, ISNI 0000 0000 8578 2742, Department of Ecology, , Swedish University of Agricultural Sciences, ; Ulls väg 16, 75651 Uppsala, Sweden
                [2 ]GRID grid.4514.4, ISNI 0000 0001 0930 2361, Systematic Biology Group, Department of Biology, , Lund University, ; Lund, Sweden
                [3 ]GRID grid.8761.8, ISNI 0000 0000 9919 9582, Gothenburg Global Biodiversity Centre, ; Gothenburg, Sweden
                [4 ]GRID grid.4444.0, ISNI 0000 0001 2112 9282, CNRS, UMR 5554 Institut des Sciences de l’Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), ; Place Eugene Bataillon, 34095 Montpellier, France
                [5 ]GRID grid.270240.3, ISNI 0000 0001 2180 1622, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, ; Seattle, WA USA
                [6 ]GRID grid.10800.39, ISNI 0000 0001 2107 4576, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, ; Lima, Peru
                [7 ]GRID grid.462378.c, ISNI 0000 0004 1764 2464, IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, , Indian Institute of Science Education and Research Thiruvananthapuram, ; Thiruvananthapuram, India
                [8 ]Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
                [9 ]GRID grid.256304.6, ISNI 0000 0004 1936 7400, Department of Life and Earth Sciences, Perimeter College, Georgia State University, ; 33 Gilmer Street, Atlanta, GA 30303 USA
                [10 ]GRID grid.463994.5, ISNI 0000 0004 0370 7618, ISYEB, CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, ; 57 rue Cuvier, Paris, 75005 France
                [11 ]GRID grid.15276.37, ISNI 0000 0004 1936 8091, McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, ; Gainesville, FL 32611 USA
                [12 ]GRID grid.212340.6, ISNI 0000000122985718, City College of New York and Graduate Center, CUNY, ; New York, NY USA
                [13 ]National Museum of Natural History, Manila, Philippines
                [14 ]GRID grid.266835.c, ISNI 0000 0001 2179 5031, Department of Biological Sciences, , University of New Orleans, ; New Orleans, LA USA
                [15 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Department of Zoology, , Stockholm University, ; 10691 Stockholm, Sweden
                [16 ]GRID grid.438303.f, ISNI 0000 0004 0470 8815, Australian Museum, ; 6 College Street, Sydney, NSW 2010 Australia
                [17 ]GRID grid.411087.b, ISNI 0000 0001 0723 2494, Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, ; Av. Candido Rondom, 400, 13083-875 Campinas, SP Brazil
                [18 ]GRID grid.5522.0, ISNI 0000 0001 2162 9631, Nature Education Centre, Jagiellonian University, ; ul. Gronostajowa 5, 30-387 Kraków, Poland
                [19 ]GRID grid.412188.6, ISNI 0000 0004 0486 8632, Departamento de Química y Biología, , Universidad del Norte, ; Barranquilla, Colombia
                [20 ]GRID grid.507636.1, ISNI 0000 0004 0424 5398, Institut de Biologia Evolutiva (CSIC‐UPF), ; Barcelona, Spain
                [21 ]GRID grid.35937.3b, ISNI 0000 0001 2270 9879, Department of Life Sciences, Natural History Museum, ; London, SW7 5BD UK
                [22 ]GRID grid.9759.2, ISNI 0000 0001 2232 2818, Durrell Institute of Conservation and Ecology (DICE), University of Kent, ; Canterbury, CT2 7NR UK
                [23 ]GRID grid.189504.1, ISNI 0000 0004 1936 7558, 5 Cummington Street, Department of Biology, Boston University, ; Boston, MA 02215 USA
                [24 ]GRID grid.5335.0, ISNI 0000000121885934, Department of Zoology, , University of Cambridge, ; Downing St., Cambridge, CB2 3EJ UK
                [25 ]GRID grid.438006.9, ISNI 0000 0001 2296 9689, Smithsonian Tropical Research Institute, ; Gamboa, Panama
                [26 ]GRID grid.411087.b, ISNI 0000 0001 0723 2494, Departamento de Biologia Animal, , Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), ; 13083-862 Campinas, SP Brazil
                Author information
                http://orcid.org/0000-0003-1673-9910
                http://orcid.org/0000-0002-1564-1738
                http://orcid.org/0000-0002-2885-4919
                http://orcid.org/0000-0002-0689-2906
                http://orcid.org/0000-0002-6423-424X
                http://orcid.org/0000-0003-3663-522X
                http://orcid.org/0000-0002-2447-4388
                http://orcid.org/0000-0002-7809-062X
                http://orcid.org/0000-0002-5763-4990
                http://orcid.org/0000-0002-1259-3363
                Article
                25906
                10.1038/s41467-021-25906-8
                8481491
                34588433
                6a648738-93ca-4c0e-a0e8-7ebb5026df2f
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 May 2020
                : 7 September 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100003252, Lunds Universitet (Lund University);
                Funded by: FundRef https://doi.org/10.13039/501100001665, Agence Nationale de la Recherche (French National Research Agency);
                Award ID: ANR-10-LABX-25-01
                Award ID: ANR-16-CE02-0012
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000854, Human Frontier Science Program (HFSP);
                Award ID: RGP0014/2016
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100000155, NSF | BIO | Division of Environmental Biology (DEB);
                Award ID: DEB-1541557
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/100006363, National Geographic Society;
                Award ID: WW-227R-17
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000275, Leverhulme Trust;
                Funded by: FundRef https://doi.org/10.13039/501100004359, Vetenskapsrådet (Swedish Research Council);
                Award ID: 2015-04441
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                biodiversity,biogeography,macroecology,phylogenetics
                Uncategorized
                biodiversity, biogeography, macroecology, phylogenetics

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