Table 2 PCG identification of putative positively selected codons according to site models performed in PAML.

From: Comparative analysis of the mitochondrial genomes of the soft-shelled turtles Palea steindachneri and Pelodiscus axenaria and phylogenetic implications for Trionychia

PCG

Model code

ℓ

Estimate parameter

Positively selected codon

posterior mean ± SE for ω

PP (ω > 1)

cytb

M0 (one-ration)

− 6715.6

ω = 0.0539

43 A

1.197 ± 0.473

0.596

M1a (nearly neutral)

− 6561.86

p0 = 0.9046, p1 = 0.0954

ω0 = 0.0262

350 T

1.919 ± 1.056

0.988*

M2a (positive selection)

− 6561.86

p0 = 0.9046, p1 = 0.0744, p2 = 0.0211

ω0 = 0.0262

361 T

1.157 ± 0.587

0.553

M7 (beta)

− 6505.59

p = 0.1651, q = 1.5616

   

M8 (beta & ω)

− 6496.15

p0 = 0.9922, p1 = 0.0078, p = 0.1705

q = 1.9541

ω = 1.3587

   
  1. *Indicates codons identified as positively selected with posterior probability > 0.95 estimated by Bayes empirical Bayes (BEB) analysis. The parameters are shown for only PCGs in which positive selection codons were identified. All 13 PCG results are listed in Supplementary Table S4. The numbers in the positively selected codon column indicate the position of the codon, and the capital letter represents the codon abbreviation. Other abbreviations: ℓ, log likelihood score; PP, posterior probability.
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