The double-digest restriction site-associated DNA (ddRAD) sequence data of ten Diploderma lizards and one Acanthosaura lizard

For each species, we obtained 2 to 16 toe-clipping tissues; the detailed locality information was listed in Supplementary Table S5. Genomic DNA was extracted using the MolPure Cell/Tissue DNA kit (Yeasen, Shanghai) for each sample. We conducted double-digest restriction site-associated DNA (ddRAD) sequencing to obtain individual genotypes. The RAD library was prepared according to the standard protocol (Peterson et al., 2012) with modifications (Yang et al., 2018), and then sequenced on the Illumina NovaSeq platform (Novogene, Beijing).