Table 2.
Results of PAML analysis for LW and UV opsin genes
| Gene | Parametersb | |||||||
|---|---|---|---|---|---|---|---|---|
| Modela | lnL | ω0/p (p0) | ω1/q (p1) | ω2/ωP (p2) | Null | LRT | df | |
| LW opsin | M0 (one rate) | −6550.53 | 0.07 | |||||
| Branch | H1 (N vs D)c | −6548.44 | 0.07 | 0.10 | M0 | 4.17* | 1 | |
| Free | −6432.33 | see Figure S11 | M0 | 236.40* | 37 | |||
| Sites | M1a (neutral) | −6348.90 | 0.04 (0.75) | 1 (0.25) | M0 | 403.26* | 1 | |
| M2a (selection) | −6302.40 | 0.04 (0.91) | 1 (0.09) | 999d (0.0003) | M1a | 92.99* | 2 | |
| M3 (discrete) | −6285.76 | 0.02 (0.84) | 0.49 (0.16) | 999d (0.0003) | M0 | 529.54* | 4 | |
| M7 (beta) | −6329.70 | 0.14 | 0.48 | |||||
| M8 (beta, selection) | −6277.28 | 0.15 | 1.22 | 243.12 (0.001) | M7 | 104.85* | 2 | |
|
| ||||||||
| UV opsin | M0 (one rate) | −7241.40 | 0.05 | |||||
| Branch | H1 (N vs D)c | −7236.91 | 0.05 | 0.09 | M0 | 8.98* | 1 | |
| Free | −7151.25 | see Figure S11 | M0 | 180.31* | 37 | |||
| Sites | M1a (neutral) | −7111.53 | 0.04 (0.80) | 1 (0.20) | M0 | 259.74* | 1 | |
| M2a (selection) | −7060.18 | 0.04 (0.94) | 1 (0.06) | 999d (0.0004) | M1a | 102.71* | 2 | |
| M3 (discrete) | −7031.77 | 0.02 (0.83) | 0.34 (0.17) | 999d (0.0003) | M0 | 419.26* | 4 | |
| M7 (beta) | −7093.36 | 0.14 | 0.62 | |||||
| M8 (beta, selection) | −7028.47 | 0.18 | 2.08 | 443.45 (0.0006) | M7 | 129.78* | 2 | |
a
Best models within a nested set of models (branch, site: selection, discrete, beta) are shown in bold
b
For branch models, ω0 (background branches) and ω1 (branches of interest); for site models M1a-M3, ωx and px (proportion of sites) in each class (0, 1, 2); for site models M7 and M8, p and q describe the shape of the beta distribution, ωP is the value of ω for the positively selected site class, and p2 gives the proportion of sites in this class.
c
Nocturnal versus diurnal branches
d
A value of 999 indicates an ω2 greater than 1, but unable to be precisely estimated
*
p < 0.05