Table 2.

Ranking and statistical analyses of reference genes in oral and pharyngeal jaws across all of the haplochromine species from three East African lakes

	Oral jaw						Pharyngeal jaw
	BestKeeper		geNorm		NormFinder		BestKeeper		geNorm		NormFinder
	Ranks	SD	Ranks	M	Ranks	SV	Ranks	SD	Ranks	M	Ranks	SV
1	rpl18	0.581	ssrp1	0.605	rpl18	0.272	rpl18	0.654	abcf1	0.619	rpl18	0.321
2	tmem59	0.639	rpl18	0.615	ube2l3	0.324	tmem59	0.813	rpl18	0.631	ube2l3	0.322
3	pdia6	0.640	abcf1	0.632	abcf1	0.376	actb1	0.984	ube2l3	0.633	ssrp1	0.331
4	ube2l3	0.649	pdia6	0.678	pdia6	0.398	twf1	1.016	actb1	0.672	actb1	0.412
5	actb1	0.663	twf1	0.683	twf1	0.424	rps18	1.026	pdia6	0.710	pdia6	0.442
6	twf1	0.688	rps18	0.687	actb1	0.448	pdia6	1.101	rps18	0.717	abce1	0.472
7	ssrp1	0.695	actb1	0.691	rps18	0.467	ssrp1	1.106	twf1	0.755	twf1	0.477
8	rps18	0.700	abce1	0.767	ssrp1	0.478	abcf1	1.106	ssrp1	0.764	abcf1	0.480
9	abcf1	0.717	ube2l3	0.773	abce1	0.513	ube2l3	1.150	abce1	0.769	rps18	0.517
10	abce1	0.720	tmem59	0.806	tmem59	0.587	abce1	1.151	tmem59	0.785	tmem59	0.577
11	tbp	1.031	tbp	0.900	tbp	0.639	tbp	1.328	tbp	0.896	tbp	0.665
12	elf1a	1.717	elf1a	1.579	elf1a	1.324	elf1a	2.162	elf1a	1.558	elf1a	1.257

SD indicates a ranking calculation based on standard deviation generated by BestKeeper, whereas SV, stability value, and M, mean expression stability value, are calculated by geNorm and NormFinder, respectively. In all of the ranking methods lower values represent more stably expressed reference genes