cpDNA-vs-nDNA congrence testing

Byron J. Adams bjadams at ucdavis.edu
Tue Aug 17 16:28:22 EST 1999


>I have two data sets, one nuclear (ITS) and one cp (matK). I wish to test to
>see if they are incongruent or congruent. I think I'm up to speed on the
>literature etc. but I cannot find a description of how to implement the test
>in a programme, e.g. PAUP.
>Can any one point me to either
>i) a paper with details
>ii) a web site? (the PAUP site doesn't have details)
> or, iii) tell me how to do it.
>
>many thanks in advance
>
>Julian

Hi Julian -

In addition to Mary's suggestions for testing alternative tree topologies
(which is also pretty easy to do under the Treescores menu in PAUP*), you
could try the partition homogeneity test, which is implemented in PAUP*,
provided you stick the pertinent commands in the right place in your nexus
file.

To do this, combine the ITS and matK data sets and then try using NEXUS
syntax that looks something like this (after the endblock that follows the
data block);

	Begin sets;
		CharPartition ITSplusmatK=ITS:1-785, matK:786-1455;
	End;

Where <ITSplusmatK> is a name you give the partitioned data set
<ITS> is the name of the first partition
<1-785> is the number of nucleotides contained in the first partition
<matK> is the name of the second partition
<786-1455> is the number of nucleotides contained in the second partition

Then, once the file is executed, in the pull down menu you should be able
to select "partition homogeneity test".

These and other nuances of the NEXUS format are dealt with in:
Maddison, D. R., D. L. Swofford, and W. P. Maddison.  1997.  NEXUS:  An
extensible file format for systematic information.  Systematic Biology
46:590-621.

Cheers,

Byron

__________________________
Byron J. Adams
Department of Nematology
One Shields Avenue
University of California
Davis, CA 95616-8668
Phone: (530) 752-1404
fax: (530) 752-5809 




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