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Table 3 Results of a Bayesian estimation of nucleotide substitution rates

From: A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

Parameter

Mean ± S.E.

ESS

95% HPD (lower – upper)

-ln (likelihood) Deep divergences

−10921.7241 ± 0.201

2463.419

−10921.3095 – –10902.1831

-ln (likelihood) Most recent divergences

−10924.1375 ± 0.1375

5406

−10944.6406 – –10905.5067

Mean substitution rate (cox1) First codons

0.70605 ± 0.0031356

4740.8697

0.37368 – 1.1606

Mean substitution rate (cox1) First codons

0.14204 ± 0.0014602

2164.1316

0.057033 – 0.2659

Mean substitution rate (cox1) Second codons

0.087271 ± 0.00046307

4523.76

0.036775 - 0.14957

Mean substitution rate (cox1) Second codons

0.017227 ± 0.00016606

2703

0.0055299 – 0.033703

Mean substitution rate (cox1) Third codons

25.54 ± 0.06864

4361.6091

17.16 – 34.53

Mean substitution rate (cox1) Third codons

7.2543 ± 0.079013

1418.9629

2.7901 – 13.05

Mean substitution rate (cox1) All Sites

2.1253 ± 0.033205

818.4771

0.8405 – 3.9242

Mean substitution rate (rrnL)

1.2869 ± 0.0038937

3539.2582

0.79066 – 1.854

Mean substitution rate (rrnL)

0.27031 ± 0.0021339

2703

0.12723 – 0.47463

Mean substitution rate indels

0.73603 ± 0.0033437

3539.2582

0.37765 – 1.094

Mean substitution rate indels

0.14923 ± 0.0012716

2703

0.06371 – 0.26997

  1. The mean substitution rate is expressed per 100 bases per Ma. ESS, effective sample size (i.e., size corrected for auto-correlation); HPD, the 95% highest posterior probability density (equivalent to a confidence interval); SE, standard error of the mean. The substitution rates are given for the more recent divergences runs followed by the data for the deep divergences runs in italics. The rate for cox1 all sites was obtained from the initial test runs.