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

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