A large phylogenetic tree for euphyllophytes

Premise Molecular datasets for estimating phylogenetic trees increasingly include more species and gene regions, and trees are often constructed using backbone phylogenies, subtrees, and other techniques to address the challenges of large dataset size. Currently, there is no established approach to integrate these rapidly expanding datasets. Methods We generated a phylogenetic tree (and 1000 bootstrap trees) with divergence times that span euphyllophytes. To do this, we integrated taxonomically broad dated backbone phylogenies with species‐level trees generated from phylogenetic analysis of individual clades. Datasets for species‐level trees were assembled using PyPHLAWD. Results The resulting dated phylogenetic tree includes 121,641 angiosperm species, 1026 gymnosperms, and 5603 ferns. This is the largest euphyllophyte phylogenetic tree constructed to date. Topological uncertainty spikes at the start of the Cretaceous and gradually increases during the Cenozoic. Uncertainty in age estimates gradually increases in the Cenozoic but increases dramatically in the most recent 5 Myr. Discussion This dated phylogenetic framework can underpin evolutionary studies spanning euphyllophytes and enable the integration of insights from the recent to the distant past. Our approach also enables the tree to be easily updated in the future to reflect increases in data availability, as well as systematic and taxonomic advances within specific clades.