Supplemental Materials

Supplemental Materials

Orthologous groups

Orthologous groups predicted by OrthoMCL. Datasets included: 35 Sceloporus species, plus the Anolis carolinensis, Gallus gallus, and human proteins

Sceloporus GFF3 annotation files

Annotation, gene ontology, and genomic sequences in GFF3 forma

Loci

Targeted sequence capture data for horned lizards (Phrynosoma). The file contains nexus data files for 584 loci, as well as a concatenated data file containing partition information

Alignment of mitochondrial DNA

Nexus file containing aligned DNA sequences for mitochondrial 12S and 16S ribosomal RNA genes, and intervening transfer RNA gene for Valin

anomalous_skinks_data.tar

Data files and results from analyses for the 429 loci used. These results were used for summaries presented in the paper

Simulation files

The zipped folder contains the simulated SNP data in xml format for conducting species delimitation analysis

Gecko SNP data

Empirical SNP data for the Hemidactylus fasciatus complex. The zipped folder contains xml files for conducting species delimitation using the alternative models described in the paper

Triplet Data

Phylip alignments for Sceloporus triplets

BPP control file

Control file used in BPP for species delimitation