ArticleAmerican journal of botany2021
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
Article in American journal of botany, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Orchid genome evolution and trait innovation.Journal of integrative plant biology · 2026Review
- Unraveling the Genome of Epidendrum Fulgens: Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid.Genome biology and evolution · 2026Article
- Metaviromic insights into the viral community associated with Dendrobium catenatum.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- The multichromosomal structure evolution ofFrontiers in plant science · 2026Article
- Selective regime shifts and intracellular gene transfer in the organellar genomes of the mycoheterotrophic orchidFrontiers in plant science · 2026Article
- Reticulate evolutionary history underpins a revised generic circumscription of Paphiopedilum (Orchidaceae): insights from integrative phylogenomics and historical biogeography.BMC plant biology · 2025Article
- Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.Annals of botany · 2025Article
- Plastome and transcriptome analysis reveals a degenerated photosynthesis-related pathway in the mycoheterotrophic vanilloid orchid Cyrtosia lindleyana.BMC plant biology · 2025Article
- Biosilicification in monocots: Comparative analysis highlights contrasting patterns of deposition.American journal of botany · 2025Article
- Discordance Down Under: Combining Phylogenomics and Fungal Symbioses to Detangle Difficult Nodes in a Diverse Tribe of Australian Terrestrial Orchids.Systematic biology · 2025Article
- Orchid phylogenetics and evolution: history, current status and prospects.Annals of botany · 2025Review
- Unveiling a Meaningful Form ofPlants (Basel, Switzerland) · 2025Article
- From Phenotypes to Genotypes: Enhancing the Identification ofPlants (Basel, Switzerland) · 2025Article
- Phylogenetic placement of the mysterious Malagasy genusFrontiers in plant science · 2025Article
- Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes.Plant systematics and evolution = Entwicklungsgeschichte und Systematik der Pflanzen · 2025Article
- Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia.Annals of botany · 2024Article
- Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium.Annals of botany · 2024Article
- Phylogenomic insights into NeotropicalHeliyon · 2024Article
- Progress in systematics and biogeography of Orchidaceae.Plant diversity · 2024Review
- Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales.BMC plant biology · 2024Article
Corrections and comments
- Erratum issuedCorrigendum.2022
Authors and funding
22 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
premiseThe inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed.
methodsWe inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses.
resultsPhylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes.
conclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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