Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
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 h...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-83664-5 |
| _version_ | 1818430811256389632 |
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| author | Maria Alejandra Serna-Sánchez Oscar A. Pérez-Escobar Diego Bogarín María Fernanda Torres-Jimenez Astrid Catalina Alvarez-Yela Juliana E. Arcila-Galvis Climbie F. Hall Fábio de Barros Fábio Pinheiro Steven Dodsworth Mark W. Chase Alexandre Antonelli Tatiana Arias |
| author_facet | Maria Alejandra Serna-Sánchez Oscar A. Pérez-Escobar Diego Bogarín María Fernanda Torres-Jimenez Astrid Catalina Alvarez-Yela Juliana E. Arcila-Galvis Climbie F. Hall Fábio de Barros Fábio Pinheiro Steven Dodsworth Mark W. Chase Alexandre Antonelli Tatiana Arias |
| author_sort | Maria Alejandra Serna-Sánchez |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-14T15:39:20Z |
| format | Article |
| id | doaj.art-8dfa9db3560b4cb2ad7fb70f35811e3d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-14T15:39:20Z |
| publishDate | 2021-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-8dfa9db3560b4cb2ad7fb70f35811e3d2022-12-21T22:55:40ZengNature PortfolioScientific Reports2045-23222021-03-0111111110.1038/s41598-021-83664-5Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolutionMaria Alejandra Serna-Sánchez0Oscar A. Pérez-Escobar1Diego Bogarín2María Fernanda Torres-Jimenez3Astrid Catalina Alvarez-Yela4Juliana E. Arcila-Galvis5Climbie F. Hall6Fábio de Barros7Fábio Pinheiro8Steven Dodsworth9Mark W. Chase10Alexandre Antonelli11Tatiana Arias12Laboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB)Royal Botanic Gardens KewJardín Botánico Lankester, Universidad de Costa RicaGothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of GothenburgCentro de Bioinformática y Biología Computacional (BIOS), Ecoparque Los Yarumos Edificio BIOSLaboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB)Instituto de Botânica, Núcleo de Pesquisa Orquídario Do EstadoInstituto de Botânica, Núcleo de Pesquisa Orquídario Do EstadoInstituto de Biologia, Departamento de Biologia Vegetal, Universidade Estadual de CampinasSchool of Life Sciences, University of BedfordshireRoyal Botanic Gardens KewRoyal Botanic Gardens KewLaboratorio de Biología Comparativa, Corporación Para Investigaciones Biológicas (CIB)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.https://doi.org/10.1038/s41598-021-83664-5 |
| spellingShingle | Maria Alejandra Serna-Sánchez Oscar A. Pérez-Escobar Diego Bogarín María Fernanda Torres-Jimenez Astrid Catalina Alvarez-Yela Juliana E. Arcila-Galvis Climbie F. Hall Fábio de Barros Fábio Pinheiro Steven Dodsworth Mark W. Chase Alexandre Antonelli Tatiana Arias Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution Scientific Reports |
| title | Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| title_full | Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| title_fullStr | Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| title_full_unstemmed | Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| title_short | Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| title_sort | plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution |
| url | https://doi.org/10.1038/s41598-021-83664-5 |
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