Molecular Diversification of the Genus Clinopodium (Lamiaceae) from the Balkans with an Emphasis on the Transferred Groups Calamintha, Acinos, and the Sect. Pseudomelissa

<i>Clinopodium</i> 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 <i>Clinopodium</i>. The current phylogenetic understanding of the genus relies almost exclusively on the analysis of the <i>trn</i>K and <i>trn</i>L-<i>trn</i>F sequences. In <i>Clinopodium s.s.</i>, 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 <i>Clinopodium</i> from the Balkans. We encompassed the wild-growing taxa from former genera that have now been integrated into <i>Clinopodium</i>: <i>Calamintha</i>, <i>Acinos</i>, and section <i>Pseudomelissa</i> from the genus <i>Micromeria</i>. 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 (<i>rps</i>16-<i>trn</i>K^UUU, <i>rpl</i>32-<i>trn</i>L^UAG, <i>rps</i>15-<i>ycf</i>1, <i>psb</i>A-<i>trn</i>H^GUG, <i>rps</i>16-<i>trn</i>Q^UUG, <i>pet</i>N-<i>psb</i>M, <i>psb</i>K-<i>trn</i>S^UGA) were used to analyse the phylogenetic relationships between the Balkan species and subspecies currently classified into <i>Clinopodium</i>. Phylogenetic reconstructions showed the divergence of the two lineages with different diversification patterns. Nuclear markers have shown that the three groups within the clade <i>Clinopodium s.s.</i> have evolved separately, which is consistent with earlier phenetic systems.