Table 3

rbcL dataset: estimates per codon position for the nucleotide frequencies, among-site rate variation distribution and relative rates (for the GTR123123+CP123+F123+FF16+3F model).

Frequencies


CP

A

C

G

T

CP123


1

0.2202

[0.19; 0.26]

0.2484

[0.22; 0.28]

0.3536

[0.31; 0.40]

0.1778

[0.15; 0.21]

0.1948

[0.15; 0.26]

0.2802

[0.23; 0.34]

2

0.2712

[0.22; 0.32]

0.2558

[0.20; 0.31]

0.2071

[0.16; 0.26]

0.2660

[0.22; 0.32]

0.0465

[0.00; 0.11]

0.1212

[0.09; 0.16]

3

0.2200

[0.18; 0.26]

0.2152

[0.19; 0.25]

0.0634

[0.05; 0.08]

0.5014

[0.46; 0.54]

2.6956

[1.92; 3.84]

2.5986

[2.53; 2.66]


Shown are mean estimates of 100.000 MCMC iterations, discarding the first 20.000 iterations as the burn-in, and the corresponding 95% credibility intervals. The values in the table clearly illustrate the different substitution dynamics at the three codon positions. There are many differences with the estimates of the atpB dataset, shown in Table 1. The most notable differences are the among-site rate variation distribution parameter and the nucleotide frequencies for the third codon position.

Baele et al. BMC Evolutionary Biology 2011 11:145   doi:10.1186/1471-2148-11-145

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