RT Journal Article
SR Electronic
T1 Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 774018
DO 10.1101/774018
A1 Maria Alejandra Serna-Sánchez
A1 Oscar A. Pérez-Escobar
A1 Diego Bogarín
A1 María Fernanda Torres
A1 Astrid Catalina Alvarez-Yela
A1 Juliana E. Arcila
A1 Climbie F. Hall
A1 Fábio de Barros
A1 Fábio Pinheiro
A1 Steven Dodsworth
A1 Mark W. Chase
A1 Alexandre Antonelli
A1 Tatiana Arias
YR 2020
UL http://biorxiv.org/content/early/2020/11/03/774018.abstract
AB 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 nodes). 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.Competing Interest StatementThe authors have declared no competing interest.