TRANSCRIPTOMES folder includes: (1) The transcriptome assembly for each of the 18 reptile individuals sequenced (e.g. file name: SM1_centroids_nucleotides.fasta), see list below. These contain the longest open reading frames (ORFs) produced by Trinity, which were then clustered by UCLUST into centroids to reduce redundancy within a single species' transcriptome. A centroid may have collapsed multiple isoforms, truncated transcripts, and alleles from a gene, but it may also have collapsed very recent paralogs. Files are named by sequence identifier (e.g. SM) listed below. (2) The Trinotate annotation databases for each transcriptome (e.g. file name: trinotate_annotation_report_SM1.xls). The prot_id corresponds to the centroid sequence in the transcriptome .fasta file. (3) An ortholog key file (Ortholog_Key_3_20_2014.xlsx) that contains a list of each putative ortholog clustered by OrthoMCL, the best blast hit to uniprot, the number of species that were included in the ortholog, and the centroid IDs of those species (corresponding the the transcriptome assembly .fasta files). OrthoMCL was ran on 74 total species, and we excluded form our alignments 8 species with very poor representation (for a maximum of 66 species contained within the alignments analysed for the paper). Sequence ID, Common Name, Species ID SM1, Snapping turtle, Cheyldra serpentina SM2, Anolis lizard, Anolis sagrei SM3, California alligator lizard, Elgaria multicarinata SM4, African House, Lamprophis fuliginosus SM5, Cottonmouth, Agkistrodon piscivorus SM6, Sunbeam snake, Xenopeltis unicolor SM7, Alligator, Alligator mississippiensis SM8, Fence Lizard, Sceloporus undulatus SM9, Bearded dragon, Pogona vitticeps SM10, Stinkpot turtle, Sternotherus odoratus SM11, Sideneck turtle, Pelusios castaneus SM12, Skink, Scincella lateralis SM13, Box turtle, Terrapene ornata SM14, Viper Boa, Candoia aspera SM15, Gecko, Eublepharis macularius TC, Western aquatic garter snake, Thamnophis couchii HS08, Western terrestrial garter snake –lakeshore (fast-living) ecotype, Thamnophis elegans HS11, Western terrestrial garter snake –meadow (slow-living) ecotype, Thamnophis elegans