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

Maria Alejandra Serna-Sánchez,Oscar A Pérez-Escobar,Diego Bogarín,Climbie F Hall,Astrid Catalina Alvarez-Yela,Fábio De Barros,Juliana E Arcila-Galvis,Alexandre Antonelli,Tatiana Arias,Fábio Pinheiro,Mark W Chase,María Fernanda Torres-Jimenez,Steven Dodsworth

doi:10.1038/s41598-021-83664-5

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.

Highlights

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes
Phylogenomic approaches have been implemented to infer relationships between major orchids clades in deep and recent time[2,10,12,13,22,23], but extensive uncertainties remain regarding the phylogenetic placement of several subtribes[24]
The results reported here provide a robust framework for the orchid family and new insights into relationships at both deep and shallow phylogenetic levels

Summary

Introduction

Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. 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. Phylogenomic approaches have been implemented to infer relationships between major orchids clades in deep and recent time[2,10,12,13,22,23], but extensive uncertainties remain regarding the phylogenetic placement of several subtribes[24] This knowledge-gap stems from a dearth of both taxonomic and genomic sampling efforts that would be required to comprehensively cover all major orchid clades (subtribes/groups of genera). Previous efforts to disentangle the phylogenetic relationships in the subfamily have mostly relied on a small set of nuclear and plastid m arkers[34], and more recently on extensive plastid coding sequence data[2]

Methods

Results

Discussion

Conclusion