Revisiting the phylogeny of royal ferns (Osmundales) through the lens of character dependence and restudied fossil taxa questions existing family and subfamily concepts

The royal ferns (Osmundales) are a morphologically diverse group of leptosporangiate ferns, the fossil record of which dates back to the Permian. Despite there being numerous described permineralized species, the phylogenetic relationships between extinct species remain contentious. Although several analytical approaches have been applied to infer well-resolved phylogenetic hypotheses-even methods that are arguably conceived to be better at dealing with data conflict and uncertainty, many taxa have not been assigned to specific taxonomic categories. Here, we evaluate the phylogenetic affinities in Osmundales by reanalysing a dataset comprising an extensive taxon sampling of fossil Osmundalean rhizomes. The impact of both character dependence and weighting characters against homoplasy on the inferred topologies is also evaluated. Our analyses cast doubts on the monophyly of Osmundaceae and Guaireaceae. Subfamily Itopsidemoideae was rendered monophyletic when inferences were conducted by considering character dependence and downweighting characters. The subfamily Osmundoideae was retrieved monophyletic only under one concavity value and using character dependence while the remaining subfamilies included fossils with uncertain affinities within Osmundales. The position of Osmundacaulis, for instance, was recovered as a sister taxon to guaireoid fossils. To recover the monophyly of the categories below the subfamily level, incorporating character dependence and/or weighting against homoplasy was necessary. Consistent with previous studies, multiple taxa were unstable, leaving their phylogenetic affinities unclear. Our analyses underline the impact of accounting for both character dependence and weighting against homoplasy, especially when considering the contribution of missing data to observed homoplasy. Ultimately, these considerations yield markedly different topologies that imply contrasting classification schemes, highlighting the complexity inherent in resolving the evolutionary history of royal ferns.