Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

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 eforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confrmed 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 frst 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 diferent 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.

• Autores: Serna Sánchez, María Alejandra; Pérez Escobar, Óscar Alejandro; Bogarín Chaves, Diego Gerardo; Torres Jiménez, María Fernanda; Álvarez Yela, Astrid Catalina; Arcila Galvis, Juliana Estefanía; Ferreira Hall, Climbiê; De Barros, Fábio; Pinheiro, Fábio; Dodsworth, Steven; Chase, Mark Wayne; Antonelli, Alexandre; Arias Garzón, Tatiana
• Tipo de recurso: Article of investigation
• Fecha de publicación: 2021
• Institución: Tecnológico de Antioquia
• Repositorio: Repositorio Tdea
• Idioma: eng
• OAI Identifier: oai:dspace.tdea.edu.co:tdea/2788
• Acceso en línea: https://dspace.tdea.edu.co/handle/tdea/2788
• Palabra clave: Orchidaceae; Filogenética; Phylogenetics; Plastids; Plastídeos; Familia de las Orquídeas; Orquidáceas; Orchidaceae; Plastidios; Genoma de Plastidios; Genome, Plastid; Genomas de Plastídeos
• Rights: openAccess
• License: https://creativecommons.org/licenses/by/4.0/