README *DRYAD data files for Evolution manuscript 21-0608 titled "Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago" *Data Accessibility: Sequence data for the ND4 mitochondrial gene have been submitted to the GenBank database under accession numbers MW291696–291940. Sequencing data from the exon‐capture experiment have been submitted to the NCBI sequence read archive under accession number PRJNA682772. File: Sphenomorphus melanopogon-MVZ292954 Lembata_annotated transcript.fasta Description: Annotated transcriptome from liver tissue of a Sphenomorphus melanopogon (MVZ:Herp:292954) from Lembata Island, Indonesia. 1,200 of these loci were used to design probes for an MYbaits exon capture kit. File: Sphenomorphus melanopogon-MVZ293067 Sumbawa_annotated transcript.fasta Description: Annotated transcriptome from liver tissue of a Sphenomorphus melanopogon (MVZ:Herp:293067) from Sumbawa Island, Indonesia. 1,200 of these loci were used to design probes for an MYbaits exon capture kit. File: Sphenomorphus_Adegenet (PCA) 171751snps.txt Description: Input file for the R program Adegenet containing 171,751 informative nucleotide polymorphisms. File: Sphenomorphus_Adegenet sample ID key.txt Description: Collector numbers and lineages for sample IDs in the Adegenet input file "Sphenomorphus_Adegenet (PCA) 171751snps.txt" File: Sphenomorphus_ASTRAL-III_input.tre Description: Maximum Likelihood gene trees for 1,064 loci to be used as the input for the summary coalescent species tree software ASTRAL-III. File: Sphenomorphus_ASTRAL-III_map file.txt Description: Species designations of Sphenomorhus samples for ASTRAL-III species tree analysis. File: Sphenomorphus_BPP4 control file A00.ctl Description: Control file for BPP A00 analyses to estimate divergence times (tau) and population sizes (thetas) for species given a pre-defined tree topology. File: Sphenomorphus_BPP4 input.txt Description: ALignments for 1,154 nuclear loci for BPP analyses. File: Sphenomorphus_concatenated exome alignment.phylip Description: The concatenated sequence data from 1,154 nuclear loci. See the file "Sphenomorphus_concatenated exome alignment partitions.txt" for locus positions. File: Sphenomorphus_concatenated exome alignment partitions.txt Description: Partition file for the concatenated alignment in the file "Sphenomorphus_concatenated exome alignment.phylip". File: Sphenomorphus_G-PhoCS input.aln Description: Sequence alignments for 500 intron loci (flanking sequence) used as the input for the coalescent isolation with migration program G-PhoCS. File: Sphenomorphus_index numbers, G-PhoCS sample key.txt Description: Index numbers associated with each sample. Name key for the G-PhoCS input file "Sphenomorphus_G-PhoCS input.aln". File: Sphenomorphus_mitochondrial genome partitions.txt Description: Separate gene and coding position partitions for the mitochondrial genome alignment file "Sphenomorphus_mitochondrial genomes.fas". File: Sphenomorphus_mitochondrial genomes.fas Description: Mitochondrial genomes assempled from non-targeted bycatch from the targeted capture experiment. File: Sphenomorphus_mitochondrial ND4.fas Description: Mitochondrial ND4 gene alignment. File: Sphenomorphus_MYbaits 120bp probe design 3X tiling.fas Description: Targeted capture probe design produced by MYbaits. See supplementary methods in the "Sphenomorphus_Supporting Information.pdf" file for details. File: Sphenomorphus_Supporting Information.pdf Description: The supporting methods, figures, and tables for the main manuscript. File: Sphenomorphus-BioGeoBEARS_areas.txt Description: Pre-defined geographic areas for the biogeographical model testing software BioGeoBEARS. File: Sphenomorphus-BioGeoBEARS_distances between areas.txt Description: Minimum straight-line distances between geographical areas for the biogeographical model testing software BioGeoBEARS. Distances determined in Google Earth. File: Sphenomorphus-BioGeoBEARS_PAIC dispersal modifier.txt Description: Dispersal probability modifier for the PAIC model in the biogeographical model testing software BioGeoBEARS. File: Sphenomorphus-BioGeoBEARS_stepping stone dispersal modifier.txt Description: Dispersal probability modifier for the stepping-stone model in the biogeographical model testing software BioGeoBEARS. File: Sphenomorphus-BioGeoBEARS_tree.txt Description: StarBEAST2 guide tree used for the biogeographical model testing software BioGeoBEARS.