Phylogenetic tree dataset of vascular plants from Surkhandarya Region, Uzbekistan

The phylogenetic tree was generated using the R package U.PhyloMaker (Jin & Qian, 2023) under scenario S3. The analysis was based on the dated mega-phylogeny GBOTB (Smith & Brown, 2018) and its extended version GBOTB.extended.TPL.tre (Jin & Qian, 2022), which served as the backbone phylogeny for vascular plants. Species present in the backbone phylogeny were retained at the species level. Species absent from the backbone tree were inserted according to their taxonomic hierarchy following scenario S3, with taxa lacking molecular phylogenetic information placed at the genus or family level as polytomies. In total, 795 species were directly matched with the backbone phylogeny, 1,297 species were inserted at the genus level, and 110 species were inserted at the family level.