A robust phylogenomic framework supports a revised intrafamilial classification of Urticaceae

Over the past decade, phylogenomics has significantly enhanced our understanding of relationships among numerous angiosperm lineages. However, comprehensive phylogenetic studies combining broad sampling of both genomic sequences and taxa within the nettle family (Urticaceae) are still lacking. Here, we reconstructed the phylogeny of Urticaceae (345 species across 89% of accepted genera) using concatenated and coalescent analyses from plastome and nuclear ribosomal DNA sequences. Different plastid datasets and tree inference methods yielded a consistent phylogenetic backbone, with 98% of nodes achieving > 90% bootstrap support - a significant improvement compared to 54% of nodes in the latest published phylogenetic study of Urticaceae. Plastid and nuclear phylogenetic relationships were largely congruent, with several exceptions that warrant further study. In the context of the updated phylogenetic relationships, we propose dividing the family into seven tribes that correspond to seven major clades or subclades, including a newly established tribe, Sarcochlamydeae stat. nov. Our phylogenetic analysis indicates that Debregeasia and Phenax are non-monophyletic. By combing morphological, molecular and distributional evidence, we describe a new genus Chiajuia gen. nov. Additionally, we propose synonymizing the following genera: Cypholophus (to Boehmeria), Haroldiella (to Pilea), Hemistylus, Neodistemon, Rousselia (all to Pouzolzia), Hesperocnide (to Urtica), and Pellionia (to Elatostema), while recognizing Elatostematoides, Gonostegia, Leptocnide, Margarocarpus, Scepocarpus, and Sceptrocnide as distinct genera. This robust phylogenomic framework and revised classification lays a foundation for future studies on the evolution and ecology of Urticaceae. The approach applied here may also serve as an important reference for other large plant families in angiosperms.