Phylogenomics and classification of Cactaceae based on hundreds of nuclear genes.

Phylogenetic classification based on evolutionary relationships is the standard approach in systematics, but Cactaceae has posed significant challenges due to the signature of its rapid radiation: low sequence divergence hindering phylogenetic resolution and enormous species diversity hindering attempts to adequately reflect phylogenetic diversity. Previous classifications mostly relied on joint assessment of multiple phylogenetic studies and/or intuition on morphological evolution, lacking comprehensive genomic analysis. Here, we propose a revised phylogenetic classification of Cactaceae, based on the Angiosperms353 set of phylogenomic markers, including 170 species, covering close to 90% of genera and common segregates. Coalescent-based gene tree-species tree reconciliation reveals a well-resolved phylogenetic backbone, mostly congruent with a previous plastid DNA-based summary phylogeny. Some unresolved areas surrounding the subfamilies Cactoideae and Pereskioideae remain however, where gene concordance analyses reveal complex evolutionary histories. We formally recognize the four traditional subfamilies Pereskioideae, Opuntioideae, Maihuenioideae, and Cactoideae, plus Blossfeldioideae and Leuenbergerioideae. Four subfamilies are monogeneric, while within Opuntioideae, we recognize three tribes (Opuntieae, Cylindropuntieae, and Pterocacteae) and within Cactoideae, we recognize eight tribes: Lymanbensonieae, Copiapoeae, Cacteae (incl. subtribes Echinocactinae, Ferocactinae, Cactinae), Phyllocacteae (incl. subtribes Corryocactinae, newly recognized Leptocereinae, Hylocereinae, Echinocereinae), Fraileae, Rhipsalideae, Notocacteae, and Cereeae (incl. subtribes Aylosterinae, Rebutiinae, Gymnocalyciinae, Cereinae, newly recognized Reicheocactinae, Trichocereinae). Our completely revised classification for all clades includes full generic synonymy accepting 155 genera. Overall, the phylogenetic structure of Cactaceae mirrors the angiosperm-wide pattern of enigmatic, species-poor lineages dispersed amongst clades that are orders of magnitude more species rich, revealing a mix of nested, 'explosive' radiations and orphan lineages. Supplementary Information: The online version contains supplementary material available at 10.1007/s00606-025-01948-z.