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Serna-Sánchez MA, Pérez-Escobar OA, Bogarín D, Torres-Jimenez MF, Alvarez-Yela AC, Arcila-Galvis JE, Hall CF, de Barros F, Pinheiro F, Dodsworth S, Chase MW, Antonelli A, Arias T. Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution. Sci Rep 2021; 11:6858. [PMID: 33767214 PMCID: PMC7994851 DOI: 10.1038/s41598-021-83664-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/30/2020] [Indexed: 11/29/2022] Open
Abstract
Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth-death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.
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Affiliation(s)
- Maria Alejandra Serna-Sánchez
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
- Biodiversity, Evolution and Conservation, EAFIT University, Cra. 49, No. 7 sur 50, Medellín, Colombia
| | | | - Diego Bogarín
- Jardín Botánico Lankester, Universidad de Costa Rica, P. O. Box 302-7050, Cartago, Costa Rica
- Endless Forms Group, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - María Fernanda Torres-Jimenez
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Astrid Catalina Alvarez-Yela
- Centro de Bioinformática y Biología Computacional (BIOS), Ecoparque Los Yarumos Edificio BIOS, Manizales, Colombia
| | - Juliana E Arcila-Galvis
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia
| | - Climbie F Hall
- Instituto de Botânica, Núcleo de Pesquisa Orquídario Do Estado, Postal 68041, São Paulo, SP, 04045-972, Brasil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquídario Do Estado, Postal 68041, São Paulo, SP, 04045-972, Brasil
| | - Fábio Pinheiro
- Instituto de Biologia, Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, SP, 13083-862, Brazil
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Alexandre Antonelli
- Royal Botanic Gardens Kew, London, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Gothenburg, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Tatiana Arias
- Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB), Cra. 72 A No. 78 B 141, Medellín, Colombia.
- Centro de Bioinformática y Biología Computacional (BIOS), Ecoparque Los Yarumos Edificio BIOS, Manizales, Colombia.
- Tecnológico de Antioquia, Calle 78B NO. 72A - 220, Medellín, Colombia.
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