Abstract
Clinopodium is a morphologically highly diverse and taxonomically intricate genus. Molecular studies have demonstrated high divergence within the genus, and there is no consensus on the taxonomic treatment of some groups classified as Clinopodium. The current phylogenetic understanding of the genus relies almost exclusively on the analysis of the trnK and trnL-trnF sequences. In Clinopodium s.s., there is no phylogenetic backbone based on nuclear sequences. Therefore, in this study, we included a larger number of plastid and nuclear markers to better understand the diversification of natural populations of the genus Clinopodium from the Balkans. We encompassed the wild-growing taxa from former genera that have now been integrated into Clinopodium: Calamintha, Acinos, and section Pseudomelissa from the genus Micromeria. The markers that displayed the highest informativeness in the in silico analysis were selected. Four nuclear loci (ITS1, 5.8S rDNA, ITS2, ETS) and seven plastid loci (rps16-trnK(UUU), rpl32-trnL(UAG), rps15-ycf1, psbA-trnH(GUG), rps16-trnQ(UUG), petN-psbM, psbK-trnS(UGA)) were used to analyse the phylogenetic relationships between the Balkan species and subspecies currently classified into Clinopodium. Phylogenetic reconstructions showed the divergence of the two lineages with different diversification patterns. Nuclear markers have shown that the three groups within the clade Clinopodium s.s. have evolved separately, which is consistent with earlier phenetic systems.