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Table 4 False positive rates (null scenarios) and true positive rates (alternative scenarios) for three LRTs when the evolutionary process includes DT nucleotide substitutions between codons, ω variability among sites, and MNRs

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

    

SNR (\( {e}^{\beta_{HI}} \) = 1)

High MNR (\( {e}^{\beta_{HI}} \) = 0.05)

ω 0

ω 1

ω 2

LRT-1

LRT-2

LRT-3

LRT-1

LRT-2

LRT-3

Null scenarios

False positives

3a

0.05

1.0

1.0

0.55

0.02

0.03

0.0

0.06*

0.10*

Alternative scenarios

True positives

3b

0.05

0.5

2.0

0.95

0.87

0.92

0.01

0.44

0.26

3c

0.05

1.0

2.0

0.99

0.47

0.46

0.0

0.27

0.18

  1. LRT-1 compares M1a to M2a (under-fit models). LRT-2 compares G1ax to G2ax (perfect-fit models). LRT-3 compares G1a13 to G2a13 (over-fit models). The asterisk symbol (*) indicates that the results are based on < 100 replicates due to convergence problems with some datasets when there was high MNRs. For LRT-2 case 3a is based on 99 replicates. LRT-3 case 3a is based on 91 replicates
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BMC Ecology and Evolution

ISSN: 2730-7182

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