Figure 3.

Displaying multiple annotations and assigning element formats automatically. The tree in this contrived example contains several annotations including ancestral divergence times (node heights; expressed as branch lengths in an ultrametric tree), DNA substitution rates, posterior clade probabilities as they could have been imported by TreeGraph 2 from, e.g., a tree file generated with help of TreeAnnotator after a BEAST analysis. As in a typical chronogram view, the age of the nodes (in million years ago) is expressed by the scale bar at the bottom. In addition, TreeGraph 2 was asked to automatically assign branch widths and line colors to illustrate the mean evolutionary rates for each branch, while the accuracy of each rate estimate was illustrated by a filled rectangular label icon above and an unfilled one below each branch (the branch width extended by the size of the upper icon describes the highest rate in e.g. a 95% confidence interval and the branch width reduced by the size of the lower icon describes the lowest rate in the interval). Text labels have been used to show the posterior clade probabilities (above the branches, bold) and the absolute substitution rates in substitutions per site per billion years (below the branches). Furthermore, this example tree contains star and cross icon labels that could be used, e.g., to highlight specific character state transitions (such as orange stars indicating "number to character" shifts (filled) or vice versa (not filled), and blue crosses representing "upper case to lower case" shifts).