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
MetadataShow full item record
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
The following license files are associated with this item:
- Creative Commons
Except where otherwise noted, this item's license is described as Green - can archive pre-print and post-print or publisher's version/PDF
- Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.
- Authors: Li YX, Li ZH, Schuiteman A, Chase MW, Li JW, Huang WC, Hidayat A, Wu SS, Jin XH
- Issue date: 2019 Oct
- Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
- Authors: Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ
- Issue date: 2021 Jul
- Plastid phylogenomics improves resolution of phylogenetic relationship in the Cheirostylis and Goodyera clades of Goodyerinae (Orchidoideae, Orchidaceae).
- Authors: Tu XD, Liu DK, Xu SW, Zhou CY, Gao XY, Zeng MY, Zhang S, Chen JL, Ma L, Zhou Z, Huang MZ, Chen SP, Liu ZJ, Lan SR, Li MH
- Issue date: 2021 Nov
- Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification.
- Authors: Freudenstein JV, Chase MW
- Issue date: 2015 Mar
- Phylogenetic relationships within Orchidaceae based on a low-copy nuclear coding gene, Xdh: Congruence with organellar and nuclear ribosomal DNA results.
- Authors: Górniak M, Paun O, Chase MW
- Issue date: 2010 Aug