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. 2019 Jan 14;19:22. doi: 10.1186/s12862-018-1326-7

Table 2.

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

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

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