Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication

Frontiers in Plant Science

Plant Science

Jérôme Munzinger¹  Katharina Nargar²  Lars Nauheimer³  Darren M. Crayn³  Martin W. Callmander⁴  José R. Pirani⁵  Marcelo F. Devecchi⁵  Milton Groppo⁵  Sven Buerki⁶  Carolina M. Siniscalchi⁷  Andrea Weeks⁸  Jurriaan M. de Vos⁹  Alexandra N. Muellner-Riehl^1,10  Marc S. Appelhans^1,11  Julien B. Bachelier^1,12  Porter P. Lowry^1,13  Hervé Sauquet^1,14  John Mitchell^1,15  Martin Cheek^1,16  William J. Baker^1,16  Alexandre R. Zuntini^1,16  Olivier Maurin^1,16  Félix Forest^1,16  Ilia J. Leitch^1,16  Caroline M. Pannell^1,17  Harvey K. Orel^1,18  Michael J. Bayly^1,18  Kevin R. Thiele^1,19  Elizabeth M. Joyce^2,20  Susan K. Pell^2,21 

[1] AMAP, Université Montpellier, Institut de Recherche pour le Développement (IRD), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Centre National de la Recherche Scientifique (CNRS), Institut national de la recherche agronomique (INRAE), Montpellier, France;Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia;National Research Collections Australia, Commonwealth Industrial and Scientific Research Organization (CSIRO), Canberra, ACT, Australia;College of Science and Engineering, James Cook University, Cairns, QLD, Australia;Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia;Conservatoire et Jardin botaniques de la Ville de Genève, Geneva, Switzerland;Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil;Department of Biological Sciences, Boise State University, Boise, ID, United States;Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, United States;Department of Biology, George Mason University, Fairfax, VA, United States;Department of Environmental Sciences, University Basel, Basel, Switzerland;Department of Molecular Evolution and Plant Systematics & Herbarium, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany;German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany;Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Goettingen, Germany;Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States;Institut für Biologie, Freie Universität Berlin, Berlin, Germany;Missouri Botanical Garden, St. Louis, MO, United States;Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France;National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia;New York Botanical Garden, New York, NY, United States;Royal Botanic Gardens, Kew, Richmond, United Kingdom;Royal Botanic Gardens, Kew, Richmond, United Kingdom;Department of Biology, Oxford University, Oxford, United Kingdom;Marine Laboratory, Queen’s University Belfast, Portaferry, United Kingdom;School of BioSciences, The University of Melbourne, Parkville, VIC, Australia;School of Biological Sciences, University of Western Australia, Perth, WA, Australia;Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Munich, Germany;College of Science and Engineering, James Cook University, Cairns, QLD, Australia;Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia;United States Botanic Garden, Washington, DC, United States;

关键词: Cenomanian-Turonian Thermal Maximum;    phylogenomics;    target enrichment;    sequence capture;    HybSeq;    paralogy;   

DOI  :  10.3389/fpls.2023.1063174

 received in 2022-10-06, accepted in 2023-01-31,  发布年份 2023

来源: Frontiers

【 摘 要 】

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order’s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.

【 授权许可】

Unknown   
Copyright © 2023 Joyce, Appelhans, Buerki, Cheek, de Vos, Pirani, Zuntini, Bachelier, Bayly, Callmander, Devecchi, Pell, Groppo, Lowry, Mitchell, Siniscalchi, Munzinger, Orel, Pannell, Nauheimer, Sauquet, Weeks, Muellner-Riehl, Leitch, Maurin, Forest, Nargar, Thiele, Baker and Crayn