Acantholimon is an important component of the subalpine steppe flora in the northeastern Iranian region and the second largest genus of the Plumbaginaceae with about 317 cushion-forming subshrubby species. Yet, it has been poorly represented in previous molecular phylogenetic studies and the consequence is that important taxonomic and phylogenetic matters such as the circumscription and monophyly of the genus have not been addressed within a solid evolutionary framework. We have assembled datasets of sequences from the Nuclear (nrDNA ITS) and the plastid (trnT-Y, trnL-F) DNA for 102 accessions of Acantholimon, encompassing the major areas of occurrence of the genus in Central Asia, with a special emphasized on northeastern Iran. Bayesian and maximum likelihood analyses of our molecular data showed that northeastern Iranian Acantholimon species do not represent a single monophyletic group and instead formed several lineages which intermingled with the Central Asian counterparts. With the exception of A. sects. Platystegia and Pterostegia, each with two species, the remaining sections (Acantholimon, Acmostegia, Armeriopsis, Glumaria, Inermia, and Tragacanthina) are not monophyletic. The nuclear and plastid gene trees are conflicting (cytonuclear discordance) on the position of a couple of species (e.g., A. acmostegium, A. inerme, A. erinaceum). This might be caused by chloroplast capture through hybridization and introgression or incomplete lineage sorting. The present study revealed that acantholimons of Northeastern Iran evolved independently several times from Central Asian allies. Our comprehensive analysis has shed light on the taxonomic complexities within Acantholimon and providing valuable insights into its phylogeny.

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