Taxonomy in the light of incongruence: An updated classification of Malvales and Malvaceae based on phylogenomic data

Abstract Malvales is a diverse order of flowering plants, economically and ecologically relevant, and it is known for its broad morphological variability. Recent phylogenomic studies have revealed a complex evolutionary history for the order, including localised phylogenetic discordances among nuclear loci. However, since the late 1990s, Malvales classification has largely been neglected. This study aims to address this gap by revisiting the classification of Malvales, with a focus on its largest family, Malvaceae. By integrating phylogenomic and morphological datasets, our primary goals are to provide an updated phylogeny for the order and to map key traits supporting a revised suprageneric classification, while accounting for gene and species tree conflicts. Our molecular dataset included 194 genera and 309 nuclear genes, obtained through target sequence capture using Angiosperms353 probes. This dataset covers approximately half of the known genera in the order, representing all families and subfamilies, as well as nearly all tribes, and all subtribes. A coalescent approach utilising nuclear gene trees was used to infer phylogenetic relationships. A morphological matrix with 50 characters relevant for suprageneric classification was compiled, and character‐state distributions for selected traits were mapped against the phylogenetic tree to identify and discuss diagnostic features for clades. Phylogenetic relationships and the monophyly of most groups aligned closely with previous studies. Morphological traits that define key clades varied significantly across Malvales, with differences observed in growth habit, leaf structure, pollen type, floral features, and fruit/seed morphology. In Malvaceae, we resolved uncertainties in the early Malvoideae lineages, and we describe a new tribe, Pentaplareae tr. nov., which clarifies the taxonomic placement of a previously uncertain genus. Additionally, we propose the recognition of a new subfamily, Matisioideae subfam. nov., elevated from its former status as a tribe, and positioned as the sister group to Malvoideae. This study highlights how taxonomic frameworks can be refined even in the face of conflicting phylogenomic data, demonstrating the importance of integrating molecular and morphological evidence in revising classifications.