Table 2 |
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|
Comparison of BPs among trees 1 to 3 analyzed with concatenate and separate models |
||||||||||
|
Model |
#c |
Ln L |
#p |
#s |
#s/#p |
AIC |
AICc |
Tree 1 |
Tree 2 |
Tree 3 |
|
|
||||||||||
|
Nucleotide (GTR + Γ8) |
1 |
-4,076,316.3 |
26 |
1,011,870 |
38,918.1 |
8,152,684.6 |
8,152,684.6 |
0.0 |
0.0 |
100.0 |
|
5 |
-4,059,904.9 |
130 |
1,011,870 |
7,783.6 |
8,120,069.8 |
8,120,069.8 |
0.0 |
0.0 |
100.0 |
|
|
10 |
-4,058,547.6 |
260 |
1,011,870 |
3,891.8 |
8,117,615.2 |
8,117,615.3 |
0.0 |
0.0 |
100.0 |
|
|
56 |
-4,055,469.5 |
1,456 |
1,011,870 |
695.0 |
8,113,851.0 |
8,113,855.2 |
0.1 |
0.0 |
99.9 |
|
|
100 |
-4,053,634.1 |
2,600 |
1,011,870 |
389.2 |
8,112,468.2 |
8,112,481.6 |
0.1 |
0.0 |
99.9 |
|
|
200 |
-4,049,237.9 |
5,200 |
1,011,870 |
194.6 |
8,108,875.8 |
8,108,929.5 |
0.2 |
0.0 |
99.8 |
|
|
558 |
-4,035,535.0 |
14,508 |
1,011,870 |
69.7 |
8,100,086.0 |
8,100,508.1 |
1.7 |
0.0 |
98.3 |
|
|
930 |
-4,022,303.0 |
24,180 |
1,011,870 |
41.8 |
8,092,966.0 |
8,094,150.0 |
3.6 |
0.0 |
96.4 |
|
|
1,395 |
-4,006,623.4 |
36,270 |
1,011,870 |
27.9 |
8,085,786.8 |
8,088,483.7 |
25.0 |
0.7 |
74.3 |
|
|
2,789 |
-3,963,489.9 |
72,514 |
1,011,870 |
14.0 |
8,072,007.8 |
8,083,203.5 |
86.2 |
4.1 |
9.7 |
|
|
|
||||||||||
|
Codon (+ Γ4) |
1 |
-3,828,351.7 |
81 |
337,290 |
4,164.1 |
7,656,865.4 |
7,656,865.4 |
88.1 |
11.3 |
0.6 |
|
5 |
-3,810,589.3 |
405 |
337,290 |
832.8 |
7,621,988.6 |
7,621,989.6 |
94.3 |
5.1 |
0.7 |
|
|
10 |
-3,808,198.7 |
810 |
337,290 |
416.4 |
7,618,017.4 |
7,618,021.3 |
93.3 |
5.9 |
0.8 |
|
|
56 |
-3,802,941.9 |
4,536 |
337,290 |
74.4 |
7,614,955.8 |
7,615,079.5 |
93.0 |
5.2 |
1.7 |
|
|
100 |
-3,799,324.6 |
8,100 |
337,290 |
41.6 |
7,614,849.2 |
7,615,247.9 |
94.0 |
4.9 |
1.1 |
|
|
200 |
-3,791,928.7 |
16,200 |
337,290 |
20.8 |
7,616,257.4 |
7,617,892.2 |
91.0 |
8.1 |
1.0 |
|
|
558 |
-3,766,336.0 |
45,198 |
337,290 |
7.5 |
7,623,068.0 |
7,637,056.1 |
96.7 |
2.9 |
0.3 |
|
|
930 |
-3,741,173.9 |
75,330 |
337,290 |
4.5 |
7,633,007.8 |
7,676,332.8 |
98.0 |
1.7 |
0.3 |
|
|
1,395 |
-3,712,084.5 |
112,995 |
337,290 |
3.0 |
7,650,159.0 |
7,764,009.4 |
96.2 |
3.8 |
0.0 |
|
|
2,789 |
-3,621,322.1 |
225,909 |
337,290 |
1.5 |
7,694,462.2 |
8,610,876.3 |
89.6 |
10.4 |
0.0 |
|
|
|
||||||||||
|
Amino acid (JTT-F + Γ8) |
1 |
-1,905,933.9 |
37 |
337,290 |
9,115.9 |
3,811,941.8 |
3,811,941.8 |
51.6 |
0.2 |
48.2 |
|
5 |
-1,879,320.4 |
185 |
337,290 |
1,823.2 |
3,759,010.8 |
3,759,011.0 |
63.4 |
0.2 |
36.5 |
|
|
10 |
-1,877,405.7 |
370 |
337,290 |
911.6 |
3,755,551.4 |
3,755,552.2 |
63.9 |
0.3 |
35.9 |
|
|
56 |
-1,875,094.5 |
2,072 |
337,290 |
162.8 |
3,754,333.0 |
3,754,358.6 |
56.6 |
0.1 |
43.2 |
|
|
100 |
-1,873,607.4 |
3,700 |
337,290 |
91.2 |
3,754,614.8 |
3,754,696.9 |
58.7 |
0.5 |
40.9 |
|
|
200 |
-1,870,213.5 |
7,400 |
337,290 |
45.6 |
3,755,227.0 |
3,755,559.0 |
59.8 |
0.2 |
40.1 |
|
|
558 |
-1,858,842.6 |
20,646 |
337,290 |
16.3 |
3,758,977.2 |
3,761,669.7 |
81.2 |
1.1 |
17.7 |
|
|
930 |
-1,847,528.8 |
34,410 |
337,290 |
9.8 |
3,763,877.6 |
3,771,696.4 |
81.6 |
6.5 |
11.9 |
|
|
1,395 |
-1,834,624.0 |
51,615 |
337,290 |
6.5 |
3,772,478.0 |
3,791,129.7 |
87.1 |
10.9 |
2.0 |
|
|
2,789 |
-1,799,245.4 |
103,193 |
337,290 |
3.3 |
3,804,876.8 |
3,895,855.7 |
93.4 |
6.6 |
0.0 |
|
|
|
||||||||||
|
Maximum likelihood (ML) analyses with nucleotide, codon, and amino acid substitution models and comparison of bootstrap probabilities (BPs) among trees 1 to 3. Concatenate (#c = 1) and separate analyses were performed for each dataset. The #c, #p, and #s represent the number of categories separated according to the total branch length of the 2,789 genes, the number of parameters, and the number of characters (or sites), respectively. AIC is the Akaike Information Criterion, and AICc is the AIC with second order correction. AIC with #s/#p > 40 and AICc with #s/#p < 40 are shown in italics. The best models based on AIC or AICc are shown in bold. |
||||||||||
|
Nishihara et al. Genome Biology 2007 8:R199 doi:10.1186/gb-2007-8-9-r199 |
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