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Table 2 Comparison of BPs among trees 1 to 3 analyzed with concatenate and separate models

From: Rooting the eutherian tree: the power and pitfalls of phylogenomics

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

  1. 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.
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