Xml Input File
Assign Branch Lengths
Ancestral State Reconstruction
SIMMAP 1.5 offers the option to calculate ancestral states. The method used is a Bayesian, either empirical or heirarchical, approach (see Huelsenbeck and Bollback, 2001, Sys. Biol. 50:351-366.). The approach is an indirect approach in which the tree(s) and model parameters used are derived from an external program (e.g., MrBayes) or defined a priori by the user. Ancestral states can be calculated for nucleotides and morphological/standard characters.
Performing an ASR Analysis
As with a standard mutational analysis an ancestral state analysis requires that a model be configured as described here.
To configure an ancestral states analysis open the Analysis window (Figures 1 and 2) by selecting Analysis->Configure Analysis... from the main menu. Once configured, to run the analysis use the keyboard shortcut, cmd-R, or select Analysis->Run Analysis... from the main menu.
The first step (see Figure 1) is to select (check) Ancestral states in the Analysis Type box. Next, select the characters to be used in the analysis in the Characters box (see Figure 1).
Next select the Sampling tab. Select the Trees and Parameters (molecular data only) to be used in the analysis (see Figure 2). Values in the Sampling box have no affect on the ASR analysis as the posteriors reported are the marginal values.
Interpreting an ASR Analysis
Once the analysis is configured select Run Analysis... from the Analysis menu item, or use the Cmd-R keyboard shortcut. The analysis should begin first by preparing for the run (this step identifies all possible unique clades in the selected trees) followed by the actual analysis as indicated by a progress indicator showing the status of the run should appear. When the analysis is complete open the Ancestral States window by selecting either:
Statistics->Nucleotides->Ancestral States, or
The following window should open displaying the results (Figure 3):
The window has two tabs: the Results and Bipartition Table. The Results tab displays the results for each character which can be selected in the Site table located on the left side of the window. The Clade ID column in the results table shows the ID associated with each unique clade in the analysis. Translating these IDs to "actual" clades in the trees used in the analysis can be decoded using information in the Bipartition Table tab (see below for a description). The Sample Size column reflects the number of trees in which that clade exists. The remaining columns reflect the marginal posterior probability of each state at the ancestral node for the clade.
To identify the clades select the Bipartition Table tab (see Figure 4).
While this may seem complicated it is quite simple. First each Clade ID represents the IDs in the Results tab. The Bipartition column shows a list of 0s and 1s. Each 0/1, left to right, represents a species/sequence as defined by the translate command (tag) in the input file. For example, if a species has a translate ID of 5 then it is found as the fifth element (shown in red) in the bipartition (0010100010001110). In this example species/sequence IDs 3,5,9,13,14, and 15 represent a monophyletic clade.
Saving the Results of an ASR Analysis
To save the results of an analysis simply select Save Results... button at the lower right corner of the window. Next select a location and file name and select the Save button. The output saves the bipartition table and the results by clade and character.