Data from: Three new species reveal an unrecognised clade of rock monitors (Varanidae; Varanus) from the eastern Australian savannas

mtDNA.zipDescription: This folder contains files associated with the mitochondrial DNA (mtDNA) analyses.1. ND4_663bp.fasta – A 663 bp alignment comprising 600 bp of the ND4 gene and 63 bp of the adjacent tRNA-His region.2. ND4_p-distances.csv – A spreadsheet reporting average uncorrected p-distances for all pairwise species comparisons based on the ND4_663bp.fasta alignment. AHE.zipDescription: This folder contains subdirectories associated with analyses of Anchored Hybrid Enrichment (AHE) sequence data.1. AHE-303-loci – Contains 303 individual FASTA alignments, one for each AHE locus retained for phylogenomic analysis.2. BPP – Contains two subfolders (A01 and A00) corresponding to separate BPP analyses. Each subfolder contains the alignment (phylip format), the imap file, and the control file used for the analysis. Both analyses used identical alignments and imap files. Each subfolder also includes all associated outputs, including the seed file, MCMC file, and output log.3. StarBEAST3 – Contains 100locifinal.xml, which includes the alignment and all model specifications and priors, and starbeast3.log, the log file generated during the run.4. IQTREE – Contains three subfolders associated with analyses performed using IQ-TREE3:concatenated-analysis – Contains inputs and outputs from maximum likelihood phylogenetic inference using the concatenated alignment of 303 AHE loci. The file AHE-303-concat.fasta in this directory was used for both ML and gene-tree inference.gene-trees – Contains inputs and outputs from gene-tree inference across all 303 loci. The output AHE-303-clean.treefile was used as input for the Weighted ASTRAL (wASTRAL) analysis.gcf – Contains inputs and outputs associated with gene concordance factor analyses. phylogenies.zipDescription: This folder contains five phylogenetic trees in newick format.1. IQTREE_ND4.newick – Maximum likelihood tree inferred from mtDNA sequence data using IQ-TREE3.2. IQTREE_AHE-concatenated.newick – Maximum likelihood tree inferred from 303 concatenated AHE loci using IQ-TREE3.3. wASTRAL-AHE.newick – Species tree inferred from 303 AHE gene trees using Weighted ASTRAL (wASTRAL).4. StarBeast3_AHE.newick – Time-calibrated multi-species coalescent tree inferred from 100 AHE loci using StarBEAST3.5. BPP_AHE-A00.newick – Multispecies coalescent tree for the 7-taxon subset inferred from 303 AHE loci using BPP (A00 analysis).