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Table 6 Results of applying LRT-1 and LRT-3 to the set of 21 real Streptococcus sequence alignments

From: Improved inference of site-specific positive selection under a generalized parametric codon model when there are multinucleotide mutations and multiple nonsynonymous rates

Gene

   

under-fit models

over-fit models

M2a vs. G2a13

NC

NS

TL

LRT-1:

M1a vs. M2a

M2a

MLEs

LRT-3:

G1a13 vs. G2a13

G2a13

MLEs

2Δl

1

892

19

6.98

N.S.

ω+ = 1.0

p+ = 0.026

N.S.

ω+ = 1.02

p+ = 0

881.3

2

639

16

6.37

N.S.

ω+ = 1.0

p+ = 0.15

P < 0.0001

ω+ = 4.9

p+ = 0.028

504.2

3

228

11

3.74

N.S.

ω+ = 1.0

p+ = 0.046

N.S.

ω+ = 1.2

p+ = 0

152.1

4

577

9

8.49

N.S.

ω+ = 1.0

p+ = 0.05

N.S.

ω+ = 1.18

p+ = 0

466.1

5

390

9

5.16

N.S.

ω+ = 1.0

p+ = 0.19

P < 0.0001

ω+ = 11.7

p+ = 0.03

109.6

6

348

11

4.5

N.S.

ω+ = 1.0

p+ = 0.04

N.S.

ω+ = 3.11

p+ = 0

113.7

7

184

10

0.37

P < 0.0001

ω+ = 5.29

p+ = 0.24

P < 0.0001

ω+ = 4.36

p+ = 0.29

71.7

8

169

6

30

N.S.

ω+ = 1.0

p+ = 0.001

N.S.

ω+ = 8.46

p+ = 0.02

130.9

9

227

10

5.46

N.S.

ω+ = 1.0

p+ = 0.25

N.S.

ω+ = 20.5

p+ = 0.14

50.3

10†§

450

10

2.2

N.S.

ω+ = 1.0

p+ = 0.06

N.S.

ω+ = 1

p+ = 0

14.3

11

444

7

4.6

N.S.

ω+ = 1.0

p+ = 0.31

N.S.

ω+ = 1.03

p+ = 0

109.7

12

473

9

0.45

N.S.

ω+ = 1.0

p+ = 0.21

N.S.

ω+ = 10.6

p+ = 0.007

17.3

13

427

8

0.05

0.10 > P > 0.05

ω+ = 15.7

p+ = 0.006

N.S.

ω+ > 99

p+ = 0.02

6.2

14

632

7

0.09

0.10 > P > 0.05

ω+ = 15.3

p+ = 0.016

N.S.

ω+ = 22.5

p+ = 0.03

25.1

15†

209

7

10.3

N.S.

ω+ = 1.0

p+ = 0.05

N.S.

ω+ = 1

p+ = 0

164.5

16

232

6

0.43

0.10 > P > 0.05

ω+ = 9.4

p+ = 0.29

N.S.

ω+ = 2.3

p+ = 0.37

49.1

17

661

5

3.3

N.S.

ω+ = 1.0

p+ = 0.27

P = 0.051

ω+ = 1.0

p+ = 0.33

220.6

18

564

5

7.7

N.S.

ω+ = 1.0

p+ = 0.5

N.S.

ω+ = 1.3

p+ = 0

171.4

19

261

4

9.5

N.S.

ω+ = 1.0

p+ = 0.04

N.S.

ω+ = 1.0

p+ = 0

113.6

20

201

4

2.2

N.S.

ω+ = 1.0

p+ = 0.03

N.S.

ω+ = 17.8

p+ = 0.04

40.4

21†

166

4

2.7

N.S.

ω+ = 2.15

p+ = 0.20

N.S.

ω+ = 17.8

p+ = 0.017

34.69

  1. NC is the number of codons in the sequence alignment after removal of sites with ambiguities or indels. NS is the number of gene sequences in the alignment. TL is the total tree length estimated under codon model M0 as the mean number of substitution per codon. N.S. indicates a non-significant LRT. The dagger symbol (†) indicates a gene for which likelihood optimization under a G-series model did meet convergence criteria. The two-fold s symbol (§) indicates that the MLEs were obtained by removing tip branches having near-zero lengths and re-fitting the model. The gene names, along with the sequence alignments, are provided in the DRYAD repository [51]
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BMC Ecology and Evolution

ISSN: 2730-7182

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