Table 8.

Hindgut QTL candidate genes

Gene ID	Gene name	Divergence from Rio Choy			Divergence from Rascn
		Pachn	Tinaja	Molino	Pachn	Tinaja	Molino
ENSAMXG00000007067	gpr119	0.71	0.44	0.53	0.41	0.1	0.53
ENSAMXG00000007167	cbf2	0.81	0.93	0.65	0.79	0.93	0.65
ENSAMXG00000007196	cbf1	0.95	0.94	0.93	0.94	0.94	0.93
ENSAMXG00000007233	rbm14a	0.29	0.1	0.11	0.18	0.01	0.11
ENSAMXG00000007243	rin1a	0.47	0.3	0.18	0.22	0.12	0.18
ENSAMXG00000007297	mark2a	0.2	0.27	0.23	0.32	0.34	0.23
ENSAMXG00000007312	zgc:110782	0.82	0.38	0.32	0.79	0.29	0.32
ENSAMXG00000007379	adssl	0.86	0.85	0.11	0.47	0.5	0.11
ENSAMXG00000007382	rce1b	0.85	0.76	0.72	0.81	0.76	0.72
ENSAMXG00000007446	tenm2	0.47	0.47	0.56	0.11	0.13	0.56
ENSAMXG00000025170	spry3	0.13	0.3	0.49	0.5	0.39	0.49
ENSAMXG00000025173	zgc:77262	0.73	0.55	0.58	0.25	0.05	0.58
ENSAMXG00000002865	lsm14b	0.82	0.60	0.61	0.82	0.69	0.47
ENSAMXG00000011121	fam65b	0.65	0.73	0.56	0.67	0.72	0.62
ENSAMXG00000011858	Txnla	0.64	0.50	0.29	0.73	0.45	0.60
ENSAMXG00000008444	adck5	0.42	0.26	0.28	0.29	0.14	0.35
ENSAMXG00000008359	rfx5	0.24	0.63	0.29	0.82	0.60	0.73
ENSAMXG00000008485	cpsf1	0.22	0.20	0.16	0.23	0.12	0.21

Shown in the table are the proportion of genes in the genome falling below the specified gene for D_xy when comparing indicated surface and cave populations. Some gene IDs from Pachn cavefish genome Ensembl database version 89 may be depreciated in most current Ensembl database. See Additional file 4 for updated gene IDs