Table 1

Comparison of the log-likelihood for the three hypotheses with each model

Concatenate or separate model

Substitution model

Tree

< ln L > (Δ ln L ± SE)

KH

wSH

BP

#p

AIC

Concatenate model

GTR + Γ₈

1

-117.2 ± 31.1

0.000

0.000

0.0

2

-147.3 ± 29.7

0.000

0.000

0.0

3

< -4,076,316.3 >

100.0

26

8,152,684.6

Codon + Γ₄

1

< -3,828,351.7 >

88.1

81

7,656,865.4

2

-77.8 ± 64.5

0.112

0.185

11.3

3

-142.7 ± 65.0

0.014

0.026

0.6

JTT-F + Γ₈

1

< -1,905,933.9 >

51.6

37

3,811,941.8

2

-84.1 ± 37.4

0.014

0.028

0.2

3

-1.7 ± 41.9

0.478

0.637

48.2

Separate model (among 2,789 genes)

GTR + Γ₈

1

< -3,963,489.9 >

86.2

72,514

8,072,007.8

2

-117.4 ± 72.3

0.050

0.092

4.1

3

-91.4 ± 72.7

0.104

0.174

9.7

Codon + Γ₄

1

< -3,621,322.1 >

89.6

225,909

7,694,462.2

2

-128.0 ± 103.2

0.107

0.164

10.4

3

-527.9 ± 96.3

0.000

0.000

0.0

JTT-F + Γ₈

1

< -1,799,245.4 >

93.4

103,193

3,804,876.8

2

-134.9 ± 88.5

0.064

0.112

6.6

3

-317.6 ± 85.5

0

0.000

0.0

Maximum likelihood (ML) trees varied depending on the substitution model used for the concatenate analysis, whereas the separate model analyses consistently supported tree 1. The log-likelihood of the ML tree is given in angled brackets, and the differences in the log-likelihoods of alternative trees from that of the ML tree ± 1 standard error were estimated using the formula of Kishino and Hasegawa [28]. Numbering of the trees corresponds to that shown in Figure 1. KH and wSH denote P values derived using by the test of Kishino and Hasegawa [28] and the weighted test of Shimodaira and Hasegawa [27], respectively, calculated by the CONSEL program [47]. AIC, the Akaike Information Criterion [29]; #p, number of parameters of the model.

Nishihara et al. Genome Biology 2007 8:R199   doi:10.1186/gb-2007-8-9-r199