Taxa, Trees, Characters ˇ


Mesquite's Charts

Charts compile and display values for a series of objects or items, whether taxa, trees, characters, or matrices. Mesquite has two primary styles of charts:

Most of Mesquite's charts are available through the first few submenus of the Analysis menu.

We suspect the greatest challenge to the user will be learning what chart to choose and how to set it up. For instance, how can one create a chart summarizing the estimated rate of a character's evolution according to each of a series of trees? Does one choose New Bar & Line Chart For>Characters because the value concerns a character? No, one chooses New Bar & Line Chart For>Trees because the numerous objects being summarized are trees, as the question concerns just one character but many trees. For each tree, what is being calculated is a value that relates to a character.


Chart Wizard

The first item in the Analysis window, Chart Wizard, helps you make charts. It asks you a series of questions to determine what type of chart you want. We provide this because it is sometimes difficult to decide how to start building a chart. Alternatively, you can use the New Bar & Line Chart for and New Scattergram for submenus to build a chart.

Selection of objects in charts

Most bar & line charts and scattergrams depict the values of objects— characters, taxa, trees — that can be selected. If you select these objects elsewhere in Mesquite, for example by selecting a column (character) in the Character Matrix Editor, then this selected objects will be highlighted in the chart. You can select the objects directly in the chart by clicking and dragging with the arrow cursor.

When objects are selected in the chart, and Copy is selected, then a list of the selected data points is copied to the clipboard. Otherwise if no objects are selected, then Copy puts the list of all data points into the clipboard.


By default, charts are recalculated whenever Mesquite detects that the data or assumptions underlying the chart have changed. If the chart calculation takes a long time, then this can lead to many delays if you need to make many changes in the data or assumptions. You can temporarily turn off the automatic chart recalculation by deselecting the Auto-recalculate menu item in the Chart or Scattergram menu. You can also request to Force Recalculation in the Chart menu.

Bar & Line Charts

The bar & line charts available via the Analysis menu are:

Tables as output

In addition to the graphical chart, you can obtain a text table representation of the chart in several ways:


Robustness of estimated bias in character evolution — Suppose a biologist estimated the bias in the rates of gains versus losses in a character's evolution on a given tree. How might the estimate depend on accuracy of the tree's branch lengths? To answer this, one could see how the estimate varies when noise is added to the branch lengths of the given tree. First have a tree window available with the given tree showing. Then:

Compositional bias along a sequence — A biologist with DNA sequence data wants to see how the relative frequences of A, C, G and T vary along the length of the sequence. To see this:
Above is an example of how the chart may appear. Some sections of the chart are red because those characters were indicated as belonging to a distinct character group or partition. In this chart, the introns (marked in red) have a stronger AT bias.

Calculation and Formatting options

The following menu items can be found in the Chart menu:


The scattergrams available in the Analysis menu are:
These scattergrams show the values of two variables for the objects of concern. For some scattergrams, a choice is given as to whether the Same or Different calculations should be shown on the two axes. By "Same" is meant that the same calculation is done but with a different parameter value. For instance, if the scattegram is a Taxa scattergram, it could show the character state in continuous character 1 on the Y axis, and the state in character 2 on the X axis. These represent the same calculation (continuous character state value), differing only in the character used. By "Different" is meant an entirely different calculation, such as the asymmetry of a tree on the Y axis and its likelihood score for a character on the X axis.


Canonical Variates Analysis — For a sample of specimens measured for a series of variables, how can the measurements be combined to best distinguish predefined groups? Multivariate analyses such as these can be done using modules in the Rhetenor package. Each specimen will be treated as a taxon. A continuous data matrix of the measurements should first be entered, and the taxa be assigned to groups. Next:
Correlation between variability and hydrophobicity — Do amino acid positions in proteins tend to evolve more quickly or more slowly depending on how hydrophobic they typically are? Mesquite does not yet have a direct way to estimate rates for protein characters, but we can approximately compare relative rates by comparing the number of parsimony steps for characters on a tree. First, begin with a file containing a protein data matrix and an open tree window showing a tree. Next:

The following scattergram shows the results of such an analysis, with two additions. First, the dots are colored by a third variable, the mean molecular weight of amino acids at that site. This can be done by selecting Color by Third Value from the Color menu, and in the dialog box "Values by which to color spots in the scattergram" asking for secondary choices.
Second, the analysis assistant Scattergram Regression Diagnostics (part of the PDAP package) is in use, and shows the regression line. The text view of the window shows the details of the analysis. The correlation is highly significant.

Calculating and formatting options

The following menu items can be found in the Scattergram menu:

In addition, if the scattergram is of characters, a Color menu will appear that allows you to color the dots according to a third value of the characters.