Claim · model-written summary
Combining genomic and transcriptomic data can mislead phylogeny locally in heavily RNA-edited taxa.
- Taxon
- heavily RNA-edited taxae5
- Treatment
- combining genomic and transcriptomic data sourcese5
- Outcome
- phylogenye5
- Direction
- misleade5
- Qualifier
- locallye5
Not reportedMaterialGeneCompoundOrgan / stageInteractorInteractor roleSecond interactorSecond interactor roleComparatorSettingValue
Verbatim
e5“I show that combining genomic and transcriptomic data sources can mislead phylogeny locally for heavily RNA-edited taxa, but that excluding putative edit sites restores cases of unexpected non-monophyly to monophyly”
Title
Systematics of deep and recent lineages of bryophytes using phylogenomic approaches
Bell, David cIRcle (University of British Columbia) 2022. doi:10.14288/1.0394088
Other claims from this paper (17)
- Observation Plastid and mitochondrial phylogenomic analyses give conflicting relationships among embryophytes across analyses.
- Observation The conflicts among embryophyte analyses mask an underlying unrooted tree that is consistent with most published studies.
- Observation Relationships within the major bryophyte clades largely agree across analyses and between the two organellar genomes.
- Intervention effect Excluding putative RNA edit sites restores unexpected non-monophyly to monophyly in heavily RNA-edited taxa.
- Observation In the mycoheterotrophic liverwort Aneura mirabilis, relaxed purifying selection affects multiple plastid genes.
- Observation In the putatively mycoheterotrophic moss Buxbaumia, relaxed purifying selection does not affect plastid genes.
- Observation Plastid genome structure is nearly invariant across autotrophic bryophytes.
- Observation The tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.
- Observation The broad phylogeny of Andreaeaceae was reconstructed from phylogenetic and nuclear phylogenomic data sets.
- Observation Andreaeaceae relationships are largely congruent across disparate molecular data sources.
- Observation Phylogenetic inferences in Andreaea conflict with the traditional infrageneric classification.
- Observation Andreaea wilsonii is deeply nested in Andreaea and is not a distinct genus.
- Recommendation An updated infrageneric classification of Andreaea with three new sections is proposed.
- Observation Analyses demonstrate an incomplete understanding of species diversity in Herbertus.
- Observation Herbertus names are widely misapplied because of imperfect morphological species concepts.
- Observation Reassessment of Herbertus data highlights overlooked species diversity and cryptic species.
- Observation The reassessment of Herbertus data helps delineate taxa.