CAFCA manual: Chapter 5 - User Tree Evaluation

In a user-tree evaluation we have one or more cladograms available for which we want to know how well they fit a particular data matrix. These cladograms may, for instance, represent our intuitive ideas about the historical relations for the taxa or areas or hosts in our study group. A user-tree evaluation, then, provides a tool for comparing, in terms of selection criteria, our intuitive insights with those produced by, for instance, a group compatibility analysis of the same data.

The cladogram can also come from the literature. They are then usually based on a different set of characters than we ourselves have available. In that case we apply a user-tree evaluation as a tool for comparing the effect of different data sets.

Another possible use of user-tree evaluation may result from running a primary analysis on a data matrix containing the 'better' characters that, however, do not give a completely resolved cladogram. After saving, this cladogram can be entered as a user-tree and evaluated against another data matrix containing the 'weaker' characters, and consequently subjected to a secondary analysis on the basis of the 'weaker' characters.

User-tree evaluation can also be applied in the study of coevolution for those cases where independent cladograms are available for hosts and parasites (or genes and taxa: molecular vs morphological data).

User-trees must be available as ASCII (TEXT) files, either in parentheses format (in CAFCA spaces instead of commas are allowed, but the closing semicolon must be present), or as a binary matrix with the tree topology presented in additive binary coding (see example below).

= ((1,2),(3,(4,5)));

We can also copy a cladogram matrix from a CAFCA OutputFile to use as a user-tree. Such a cladogram already has the format of a binary matrix.

On the other hand, it may also be very likely that you use PAUP 3.0 for the Macintosh to run your phylogenetic analyses, but that occasionally you get more than one most parsimonious tree and you want CAFCA to calculate the Redundancy Quotients for these trees. In that case you export your data matrix to file in simple text format by means of the PAUP File menu and you save your trees to file (include a translation table, but leave out any comments) by means of the PAUP Trees menu. Table 5.1 shows an example of the Second data matrix, and the tree file as exported by PAUP, ready to be used in a user-tree evaluation by CAFCA.

Aus 10000110011
Bus 10000110110
Cus 01000001100
Dus 01001001100
Eus 00100000100
Fus 00010100111
Gus 00010100001
Hus 00010110010
Ius 00101000110
Anc 00000000000

#NEXUS 

begin trees;  [Treefile saved Monday, June 8, 1992  6:04 PM]
[!Heuristic search settings:
 
   1 tree(s) held at each step during stepwise addition
   Tree-bisection-reconnection (TBR) branch-swapping performed
   MULPARS option in effect
   Steepest descent option not in effect
   Initial MAXTREES setting = 100
   Branches having maximum length zero collapsed to yield polytomies
   Topological constraints not enforced
   Trees are rooted
   Total number of rearrangements tried = 968
   Length of shortest tree found = 18
   Number of trees retained = 3
   Time used = 1.12 sec
]
translate
1 Aus,
2 Bus,
3 Cus,
4 Dus,
5 Eus,
6 Fus,
7 Gus,
8 Hus,
9 Ius,
10 Anc
;
tree PAUP_1 = ((((1,2),((6,7),8)),((3,4),(5,9))),10);
tree PAUP_2 = (((((1,2),8),(6,7)),((3,4),(5,9))),10);
tree PAUP_3 = ((((((1,2),8),6),7),((3,4),(5,9))),10);
endblock;

Table 5.1 Example of a data matrix as exported by PAUP (top) and a tree file (bottom) resulting from a save trees to file operation in PAUP, both based on the data matrix as used in chapter 4 on secondary analyses in CAFCA.

Tutorial

Select User-tree Evaluation from the Run menu.
We will assume that there is no data matrix present in your workspace. That's why the following dialog appears. If, however, there is a data matrix present because you did first run another analysis, either primary, secondary or biogeographic, CAFCA continues with step 6.

Click OK for the default value 1 (Copy from ASCII file).
In the next file selector box select Second.bin from the example data on your distribution disk and click Load File.
Enter 'SecondEval' (without quotation marks!), for example, as a name for your data matrix in the next dialog box.
Take the first option (default) in the next dialog for entering a partitioning vector for the columns in your data matrix.
The next dialog prompts you to change the number of characters or taxa to include in the analysis. Click No and OK.
The basic elements (data matrix, partitioning vector, taxon namelist) are present. All you need now is the user-tree. The next dialog prompts for the source of this user-tree. Click OK for the default value 1 (User-tree from ASCII file).
Select the appropriate file name for the user-tree (Second.pau.trees in this example) and click Load File in the next dialog.
As your tree file contains more than one tree (see table 5.1) CAFCA asks whether you want to use all the trees or just some of them.
Click Yes (default) and OK in the dialog prompting for a view of the user-tree. Do not do this if you have many trees to evaluate (say, 10 or more).
In the CAFCA window a text (non-graphic) representation of the user-tree(s) will appear. You can use the scroll bar to view them all. Press the space bar or click the mouse to continue.
After pressing the SPACE bar a dialog appears prompting to confirm the correctness of the user-tree on display. Click OK for the default Yes
You will not see the standard CAFCA parameter dialog as most entries are irrelevant now. However, you must indicate whether zero's in the data matrix are to be interpreted as ancestral or not. Click OK for the NO in the dialog, as we did not interpret zero's to be forced on the root in the primary and secondary analysis either.
You must also indicate whether empty branches must be collapsed in the computation of the Redundancy Quotient. We take the default No here, as in the standard primary or secondary analysis empty branches were not collapsed either.
Evaluation of the user-tree will now start. Its progress is indicated on the screen.

When the evaluation of the user-tree is finished, READY will appear on the screen. You can now print the results.
Select Diagram Evaluation... from the Print menu.
As a data matrix etc.. is present in the workspace, CAFCA can not know whether you want to print the results of a primary analysis you could have been running, or the results of a user-tree evaluation. Click OK for 2 (User-tree evaluation in the next dialog.
Click 1 (Screen) or 3 (File) in the Select Print Device dialog box.

Discussion of Results

There is not much to discuss as the output of the cladogram evaluation looks the same as in a primary analysis. Note, however, that you can recognize by the name of the data matrix that these results are from a user-tree evaluation. This name is identical with the name you entered in the dialog (tutorial step 4), except for the addendum tree.

Selection criteria for cladograms of: SecondEvaltree
Column numbers refer to numbers of cladograms
---------------------------------------------
Row 1 : Total number of homoplasous events
Row 2 : Total number of single origins (Support)
Row 3 : Corrected Extra Length (x1000; CEL: Turner + Zandee)
Row 4 : Total number of state changes (S: Steps)
Row 5 : Redundancy Quotient (x1000; RQ: Zandee + Geesink)
Row 6 : Rescaled Redundancy Quotient (x1000; RQc)
Row 7 : Consistency Index (x1000; CI), with autapomorphy correction
Row 8 : Rescaled Consistency Index (x1000; RC: Farris)
Row 9 : Average Unit Character Consistency (x1000; AUCC: Sang)
Row 10: Homoplasy Distribution Ratio (x1000; HDR: Sang)
Row 11: Compatible Character State Index (x1000; CCSI: Zandee)

         1     2     3 
    ------------------ 
 1 |     6     6     6 
 2 |     7     7     7 
 3 |  7197  7197  7220 
 4 |    18    18    18 
 5 |   521   521   512 
 6 |   147   147   133 
 7 |   611   611   611 
 8 |   417   417   417 
 9 |   742   742   742 
10 |   338   338   338 
11 |   273   273   273 

No-Order Limit for Steps, Extra Steps, RQ, and CI:

   S   ES   RQ   CI
-------------------
  33   22  438  333

Table 5.2: Result of the evaluation of the user-trees from the file Second.pau.trees

Looking at the result of the cladogram evaluation listed in table 5.2 we notice that cladograms number 1 and 2 (fig 5.1) have the highest value of RQ and the lowest for CEL. Comparing this result with that obtained in the secondary analyses we also notice that all cladograms from the PAUP analysis are among the cladograms generated by CAFCA in its primary and secondary analyses on the same data matrix, as shown in chapter 5. PAUP, however, finds these different most parsimonious solutions very quickly and direct (contrary to the indirect nature of the secondary analysis by CAFCA) with either the branch & bound or the exhaustive search option.

Figure 5.1. Two cladograms from PAUP analysis on Second, used as user-trees, with highest RQ.

CAFCA Manual

V. User-tree evaluation

Contents [of manual]

Introduction

Tutorial

Discussion of Results