Table 7. Genes under accelerated evolution across chelonians and genes with fixed differences between species in the Gopherus desert tortoise species complex according to this study.

Gene	Gene symbol	Locus*
Genes under accelerated evolution across chelonians
Hematopoietic progenitor cell antigen	CD34	gopAga1_00002251
Cystatin-A	CSTA	scaffold10781 (XM_005291323)
Short Chain Dehydrogenase/Reductase Family 16c Member 5	SDR16C5	gopAga1_00014840
Selenoprotein S	VIMP	gopAga1_00004579
Superoxide dismutase 1	SOD1	scaffold518 (XM_005283906)
Free fatty acid receptor 4	FFAR4	gopAga1_00009948
C-x-c motif chemokine ligand 11	CXCL11	gopAga1_00011528
Interleukin 10	IL10	gopAga1_00002900
Nfat activating protein with itam motif 1	NFAM1	gopAga1_00016407
Tumor necrosis factor superfamily member 4	TNFSF4	scaffold21701 (XM_007061249)
Interferon gamma	IFNG	gopAga1_00016782
Peptidoglycan recognition protein 1	PGLYRP1	gopAga1_00017264
Bcl2 related protein a1	BCL2A1	gopAga1_00011769
Granzyme A	GZMA	gopAga1_00003655
Genes with fixed differences in the Gopherus species complex
Cryptochrome-1	CRY1	gopAga1_00014628
Casein kinase i isoform delta	CSNK1D	gopAga1_00008116
DNA excision repair protein ercc-6	ERCC6	gopAga1_00012364
Hyaluronidase-2	HYAL2	gopAga1_00019510
Peptidyl-prolyl cis-trans isomerase d	PPID	gopAga1_00006436
Ubiquitin-conjugating enzyme e2 b	UBE2B	gopAga1_00015001
Ubiquitin carboxyl-terminal hydrolase 28	USP28	gopAga1_00008255
Tyrosine-protein kinase abl1	ABL1	gopAga1_00009847
Histone-arginine 8 methyltransferase carm1	CARM1	gopAga1_00007934
Protein kinase c delta type	PRKCD	gopAga1_00004289
Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 2	RPN2	gopAga1_00010670
Transforming growth factor beta-1	TGFB1	gopAga1_00017303
Casein kinase I isoform delta	CSNK1D	gopAga1_00008116

*Identification number of annotated Gopherus agassizii protein, otherwise G. agassizii scaffold and RefSeq accession number of mapped locus from LASTZ (see Methods).