Table 1.

Genes in DRs

DRs	Gene name	Predicted functions related to adaptation and speciation c
DR1a	diaphanous	Developmental process, cell movement, auditory
DR2a	ventral anterior homeobox 2	Development of retina
DR3a	prostaglandin d2 receptor 2	Unknown
	G-protein coupled receptor 4 (GPR4)	Adaptive to different oxygen concentration
	UDP-glucuronosyltransferase 2b15	Unknown
DR4	hemicentin-1	Unknown
DR5a	long wavelength-sensitive opsin (LWS)	Speciation by sensory drive
DR6a	netrin receptor UNC5c	Brain development
DR7	general transcription factor IIH subunit 1	Unknown
DR8a	intestinal mucin	Host-specific microbiota composition
DR9a	hepatocyte growth factor receptor	Morphogenesis for the muscles of fins, affecting mobility
DR10a	tbx3b (30 kb downstream from DR10)	Developmental process
DR11a	ap-4 complex subunit epsilon	Unknown
	cytochrome p450 aromatase type II	Sexual differentiation of the brain and reproductive behavior
	gliomedin	Unknown
DR12a	melanopsin A	Photic regulation of circadian clocks
DR13	No gene	–
DR14	Uncharacterized protein	–
	Uncharacterized protein	–
DR15	Uncharacterized ncRNA	–
DR16a	aryl hydrocarbon receptor nuclear translocator	Adaptive to different oxygen concentrations
DR17	UDP-n-acetylglucosamine transporter	Unknown
	U3 small nucleolar ribonucleoprotein protein imp3	Unknown
DR18a	peptidyl-prolyl cis-trans isomerase H	Unknown
	transcription initiation factor TFIID subunit 10	Early embryonic development
	G-protein coupled receptor 160	Unknown
DR19a	type II cytoskeletal 5	Epidermis development
DR20a	hydroperoxide isomerase aloxe3	Epidermis development
	macrophage mannose receptor 1	Unknown
DR21a	Ras-related protein rab-11a	Unknown
	RNA-binding protein mex3a	Brain aging

^aDRs contained genes with predicted roles for adaptation and speciation

^bThis DR did not contain a gene, but tbx3 was located 30 kbp downstream from this DR

^cReferences are listed in Additional file 6: Table S1