Diversity, Phylogeny, and Biogeography of the Subgenus Japonigekko (Gekkonidae: Gekko)

This dataset contains genomic and mitochondrial sequence data used for phylogenetic analyses of Gekko species. The nuclear dataset includes a set of aligned single-copy loci extracted from whole-genome resequencing data, while the mitochondrial dataset includes two commonly used markers for gekkonid systematics (16S–12S and ND2). Together, these datasets support phylogenomic reconstruction and species delimitation within Gekko. Files included: nuclear_loci.zip Contains MAFFT-aligned nuclear loci recovered from whole-genome resequencing data. Each FASTA file represents one single-copy nuclear gene, with sequences from multiple Gekko species. These loci were used for nuclear phylogenomics and species tree estimation. 12S_rRNA_tRNA-Val_16S_rRNA.fas Mitochondrial 16S–12S fragment for sampled Gekko species. Useful for traditional mitochondrial phylogeny, species identification, and comparison with previous studies. Gekko_ND2.fas ND2 mitochondrial gene sequences for the same set of Gekko species. Commonly used in gecko systematics for phylogenetic inference and divergence estimation. Summary of data processing:Nuclear loci were extracted from genome resequencing assemblies, filtered to retain single-copy orthologs, and aligned using MAFFT. Mitochondrial sequences (16S–12S and ND2) were obtained from assembled whole-genome or mitochondrial reads and curated manually. All alignments are provided in standard FASTA format. Usage:These datasets can be used to reproduce phylogenetic analyses, conduct downstream comparative or evolutionary studies, or integrate with additional molecular datasets for gekkonid taxonomy and species delimitation.