Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
AuthorsSerna-Sánchez, Maria Alejandra
Pérez-Escobar, Oscar A.
Torres-Jimenez, María Fernanda
Alvarez-Yela, Astrid Catalina
Arcila-Galvis, Juliana E.
Hall, Climbie F.
de Barros, Fábio
Chase, Mark W.
AffiliationCorporación Para Investigaciones Biológicas
Royal Botanic Gardens Kew
Universidad de Costa Rica
Naturalis Biodiversity Center
University of Gothenburg
Ecoparque Los Yarumos Edificio BIOS
Instituto de Botânica, Núcleo de Pesquisa Orquídario Do Estado
Universidade Estadual de Campinas
University of Bedfordshire
University of Oxford
Tecnológico de Antioquia
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AbstractRecent 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.
CitationSerna-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 (2021) 'Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution', Scientific Reports, 11 (1) 6858.
PubMed Central IDPMC7994851
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