Testing for homogeneity

Use the partition homogeneity/incongruence-length difference test implemented in PAUP to determine if different partitions of the data (typically different loci) have significantly different signals. To do this, you should first have a PAUP data file with a character partition defined. Then, choose Partition Homogeneity Test under the Analysis window to perform the test. Alternatively, you could use the following batch file, which will start a log and perform the test. You should replace [name] with the name of your partition (remove the brackets).

#nexus
Begin PAUP;
log file=ildtest.log;
hompart partition=[name] nreps=100 / start=stepwise addseq=random nreps=10 savereps=no randomize=addseq rstatus=no hold=1 swap=tbr multrees=yes;
log stop;
end ;

This batch file sets the number of ILD replicates at 100, with the number of random taxon addition replicates at 10 per ILD replicate. As in everything else on this page, these are just starting suggestions, not necessarily the best numbers for your data.

If the test is non-significant, there is no significant conflict between the partitions.

If the test is significant, and you are working with more than two partitions, first create all possible charpartitions to compare pairs of loci. Then do the ILD test again for each charparitition, excluding charsets not in the charpartition being examined. For example, if we have three charsets called 28s, coI, and ef1, a batch file would be:

#nexus
begin paup;
log file=pairwiseILD.log;
charpartition noef1 = 28s:28s, coI:coI;
charpartition no28s = coI:coI, ef1:ef1;
charpartition nocoI = 28s:28s, ef1:ef1;
exclude ef1 /only;
[!ILD between 28S and COI]
hompart partition=noef1 nreps=100;
exclude 28s /only;
[!ILD between COI and EF1]
hompart partition=no28s nreps=100;
exclude coI /only;
[!ILD between 28S and EF1]
hompart partition=nocoI nreps=100;
include all;
log stop;
end;

Note that the comments in brackets which start with an exclamation point will be displayed when PAUP gets to that part of the batch file.