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...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8dfa9db3560b4cb2ad7fb70f35811e3d
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spelling	oai:doaj.org-article:8dfa9db3560b4cb2ad7fb70f35811e3d2021-12-02T16:35:55ZPlastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution10.1038/s41598-021-83664-52045-2322https://doaj.org/article/8dfa9db3560b4cb2ad7fb70f35811e3d2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83664-5https://doaj.org/toc/2045-2322Abstract 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.Maria Alejandra Serna-SánchezOscar A. Pérez-EscobarDiego BogarínMaría Fernanda Torres-JimenezAstrid Catalina Alvarez-YelaJuliana E. Arcila-GalvisClimbie F. HallFábio de BarrosFábio PinheiroSteven DodsworthMark W. ChaseAlexandre AntonelliTatiana AriasNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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
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.
format	article
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
title	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_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_sort	plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8dfa9db3560b4cb2ad7fb70f35811e3d
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Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

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