Skip to search boxSkip to navigationSkip to main content

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
    ,
  • María Fernanda Torres-Jimenez
    ,
  • Astrid Catalina Alvarez-Yela
    ,
  • Juliana E. Arcila-Galvis
  • Corporación para Investigaciones Biológicas
    ,
  • Universidad EAFIT
    ,
  • Royal Botanic Gardens, Kew
    ,
  • University of Costa Rica
    ,
  • Naturalis Biodiversity Center
    ,
  • University of Gothenburg
Research Output: Contribution to journal Article Peer-review

Open access

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.

Publication Information

Output type

Research Output: Contribution to journal Article Peer-review

Original language

English

Article number

6858

Pages from-to (Number of pages)

Pages 6858

Journal (Volume, Issue Number)

Scientific Reports (Volume 11, Issue 1)

Publication milestones

  • Accepted/In press - 30/12/2020
  • Published - 25/03/2021

Publication status

Published - 25/03/2021

External Publication IDs

  • handle.net: 10547/624908
  • Scopus: 85103432146

Access to documents

Publication metrics

Metrics

Download statistics
Download count
8

PlumX, opens in new tab

Mentions
2
55
Social media
26
Captures
95