Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds

BMC Genomics

Table 1 Site-selection tests for the avian and mammalian opsins

Gene	ωB	ωM	E[p]	Odd score
RH1	0.061**	0.064*	0.411	1.429
RH2	0.080
OPN1sw1	0.041*	0.178**	0.261	2.822
OPN1sw2	0.050*
OPN1lw	0.024*	0.135	0.215	3.654
TMT	0.220*
TMT2	0.118
OPN3	0.101*	0.310**	0.210	3.761
PIN	0.230**
VA	0.265**
RGR	0.148**	0.193	0.316	2.166
RRH	0.155**	0.273**	0.333	2.000
OPN5	0.112	0.089	0.497	1.013
OPN4x	0.171**
OPN4m	0.203	0.239**	0.470	1.128

ω values were calculated using the ω categories and the respective proportions under the statistcally significant site-selection model: (**) positive selection, (*) negative selection or neutral evolution (unmarked). p is the probability of a sampled ωB category being higher than a sampled ωM category. E[p] is the expected value of p using the bootstrap technique for 100 000 bootstraps. The odd score is the (1 - p)/p ratio and indicates the likelihood ωM categories are higher than the ωB categories

ISSN: 1471-2164