## Table 3 |
|||||||||

Branch-site models: estimated parameters and log-likelihood ratio tests |
|||||||||

Model (k) |
np |
LogL |
LRT |
P-value |
prop |
clade |
ω |
||

M_{3} (2) |
58 | −2375.94 | |||||||

Lax2/Lax4 |
M_{D} (2) |
59 | −2369.54 | vs. M_{3} (2) |
12.8** | 3.47 10^{-4} |
0.76 | 0.00 | |

0.24 | Lax2 |
0.15 | |||||||

Lax4 |
0.52 | ||||||||

M_{3} (3) |
60 | −2375.94 | |||||||

M_{D} (3) |
61 | −2361.85 | vs. M_{3} (3) |
28.17** | 1.11 10^{-7} |
0.77 | 0.005 | ||

0.03 | 0.97 | ||||||||

0.20 | Lax2 |
0.55 | |||||||

Lax4 |
0.97 | ||||||||

M_{3} (2) |
61 | −3411.03 | |||||||

Pg11/Pg3 |
M_{D} (2) |
62 | −3407.95 | vs. M_{3} (2) |
6.16* | 0.01 | 0.68 | 0.09 | |

0.32 | Pg3 |
0.74 | |||||||

Pg11 |
1.35 | ||||||||

M_{3} (3) |
63 | −3400.58 | |||||||

M_{D} (3) |
64 | −3399.59 | vs. M_{3} (3) |
1.98 | 1.16 | ||||

M_{3} (2) |
40 | −2216.23 | |||||||

Pg11a/Pg11c |
M_{D} (2) |
41 | −2214.01 | vs. M_{3} (2) |
4.45* | 0.03 | 0.79 | 0.12 | |

0.21 | Pg11a |
1.54 | |||||||

Pg11c |
3.13 | ||||||||

M_{3} (3) |
42 | −2210.38 | |||||||

M_{D} (3) |
43 | −2209.37 | vs. M_{3} (3) |
2.01 | 0.16 |

Note. Models: for M_{3} (discrete model), ω is free to take the number of values indicated in brackets (k);
these values are homogenous in all branches of the tree; for M_{D}, as explained in Figure 1 (b), one category of ω is allowed to differ between the two paralogous genes clades
of the tree [33]. np: number of free parameters; log*L*: log-likelihood; LRT: likelihood ratio test statistic between indicated models; one
(respectively two) asterisk indicates that the probability of observing such an LRT
or higher under the compared model is <0.05 (respectively <0.01), assuming that the
LRT follows a χ^{2} distribution with the difference of free parameters between the compared models as
the number of degrees of freedom.

Ho-Huu * et al.*

Ho-Huu * et al.* *BMC Evolutionary Biology* 2012 **12**:195 doi:10.1186/1471-2148-12-195