Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

Table 1 Nonparametric Relative Rate Tests of the C and D ParaHox paralogons

			Nucleotide Sequence (first and second codon position)			Amino Acid Sequence
species	para-logons	gene^a	sites	unique differences	signifi-cance^b	sites	unique differences	signifi-cance^b
T. nigroviridis	Ca-Cb	kita	1674	134	*	837	43	*
		*kitb*		176			68
T. rubripes		kita	1208	74	***	603	30	***
		*kitb*		140			75
O. latipes		kita	1524	163	0.166	761	63	0.391
		*kitb*		189			73
G. aculeatus		kita	1450	168	0.628	724	64	0.604
		*kitb*		177			70
D. rerio		kita	1864	154	*	931	64	*
		*kitb*		192			93
T. nigroviridis		clock	1574	114	***	787	55	***
		*clock3*		217			113
T. rubripes		clock	1635	107	***	816	51	***
		*clock3*		222			111
O. latipes		*clock*	1562	177	*	780	112	**
		clock3		143			67
D. rerio		clock	1592	73	***	795	32	***
		*clock3*		203			116
T. nigroviridis	Da-Db	*cdx1a*	428	121	***	213	62	***
		cdx1b		39			15
T. rubripes		*cdx1a*	452	116	***	225	62	***
		cdx1b		55			22
O. latipes		*cdx1a*	224	30	*	111	11	0.134
		cdx1b		17			5
T. nigroviridis		pdgfrb1	1966	222	***	982	90	***
		*pdgfrb2*		328			164
T. rubripes		pdgfrb1	2032	249	**	1015	98	***
		*pdgfrb2*		323			173
O. latipes		pdgfrb1	1999	254	***	998	97	***
		*pdgfrb2*		405			207
A. burtoni		pdgfrb1	2025	216	***	1011	72	***
		*pdgfrb2*		301			158
T. nigroviridis		csf1ra	1864	228	***	904	54	***
		*csf1rb*		692			323
T. rubripes		csf1ra	1842	187	**	920	59	***
		*csf1rb*		258			105
O. latipes		csf1ra	1810	208	**	904	67	***
		*csf1rb*		279			119
A. burtoni		csf1ra	1856	192	**	927	62	*
		*csf1rb*		247			93
G. aculeatus		csf1ra	1782	183	***	890	65	***
		*csf1rb*		306			141

^a Genes that show statistically significant increase in rate of molecular evolution are indicated in bold.
^b χ² tests: *P < 0.1, **P < 0.01, *** P < 0.001.

ISSN: 1471-2164