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After the removal of 10,000 trees as burn-in, we merged both runs and inferred a maximum credibility phylogeny using TreeAnnotator [ 45].
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Optimising adult intestinal configuration patterns onto the maximum clade credibility phylogeny indicated that the ontogenetic development of increased intestinal complexity has evolved independently on three occasions in terapontid fishes.
Time of coexistence was estimated as the length of overlapping edges in a maximum clade credibility phylogeny (e.g., the region labeled "t" in fig. 1 B) from a Bayesian posterior distribution of phylogenies using the ribosomal protein sequences described earlier under an uncorrelated log-normal relaxed molecular clock (Drummond et al. 2006).
A maximum credibility tree was subsequently produced using TreeAnnotator v1.6.1.
A maximum credibility tree was generated from the combined trees in TreeAnnotater [ 83].
A maximum credibility tree was then produced using TreeAnnotator v1.5.3 [ 21].
Trees were combined into maximum credibility trees using TreeAnnotator version 1.8.1.
The posterior set of trees produced from BEAST was used to estimate the maximum clade credibility (MCC) phylogeny, including its posterior probabilities.
Maximum Clade Credibility (MCC) phylogeny and information about common ancestors' state were obtained using Tree Annotator.
(A ) Maximum clade credibility (MCC) phylogeny showing the BE92-WU95 antigeniclusterer transition, reconstructed from sequences spanning years 1993 1997.
The divergent time used to calculate absolute substitution rates was extracted from a recently published time-calibrated maximum clade credibility (MCC) phylogeny for all birds [ 67].
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