Data from: Population genomics reveal deep divergence and strong geographical structuring in the Hengduan Mountains

We used restriction site-associated DNA sequencing to generate 1,907 single nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing the diversification of G. hexaphylla in the HM. Here, the SNP data and plastid sequence alignments are provided.