Skip to main content

Table 2 False positive rates under a strictly neutral evolutionary process with DT nucleotide substitutions between codons

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

Simulation

LRT false positive rate

median ω+ and p+ MLEs

M1a - M2a

G1aDT - G2aDT

M2a

G2aDT

1a (simple, 5 taxa)

0.49

0.04

ω+ = 6.08

ω+ = 1.16

  

p+ = 0.37

p+ = 0.33

1b (complex, 5 taxa)

0.22

0.04

ω+ = 10.9

ω+ = 1.37

  

p+ = 0.28

p+ = 0.20

1c (complex, 10 taxa)

0.48

0.04*

ω+ = 1.35

ω+ = 1.02

  

p+ = 0.49

p+ = 0.35

  1. One hundred replicates (sequence length = 300 codons) were simulated for each scenario. Simulation 1a is based on a simple model (equal DNA exchangeabilities and equal codon frequencies) evolved over a 5-taxon tree. Simulation 1b is based on a more complex generating process using DNA exchangeabilities and codon frequencies derived from a real dataset. Simulation 1b was extended to the case of a 10-taxon tree. Codon models fitted to simulation 1a assumed equal codon frequencies (fequal), and those fitted to simulation 1b used GY94-style F3 × 4 codon frequencies. The asterisk symbol (*) indicates that the results for simulation 1c under the 10-taxon tree is based on 97 replicates due to convergence problems with some datasets
Back to article page