*3.7. Phylogenetic Analysis*

The analysis was conducted based on the complete chloroplast genome sequences of nine Capparaceae taxa, six species and three varieties, *C. farinosa,* MN603027, *C. glandulosa*, MN603028, *M. crassifolia,* MN603029, *M. oblongifolia,* MN603030, *Capparis spinosa*, MT041701, *Capparis spinosa* var. *spinosa*, MK639365, *Capparis spinosa* var. *herbacea*, MK639366, *Capparis spinosa* var. *ovata*, MK637690 and *Capparis decidua* MT948186, two Cloemaceae species, eight species of Brassicaceae and two species of Malvaceae, as an outgroup. All sequences were aligned using MAFFT software [81] with default settings. The phylogenetic trees were reconstructed based on maximum parsimony analysis using PAUP software (version 4.0b10) [82], utilizing tree bisection and reconnection branch swapping, with MulTrees on, saving a maximum of 1000 trees per replicate. Missing characters were treated as gaps. The bootstrap analysis confidence was based on 1000 replicates. MrBayes version 3.2.6 [83] was used to conduct Bayesian analysis and jModelTest version 3.7 [84] was used to select the appropriate model.
