Program for testing incongruences

Thomas K. Dibenedetto tdib at umich.edu
Sat Apr 27 10:07:35 EST 1996

Guy Hoelzer (hoelzer at unr.edu) wrote:
: > tdib said:
: > the two phylogenies are the same or they are not. Why would you need to 
: > prove anything in order to combine the two data-sets?

: The means or variances of any two data sets can
: differ due to sampling error or because they actually represent different
: populations (i.e., different phylogenies).  Phylogenetic data are no
: different.  They, too, are samples of taxa, of the extant variation within
: those taxa, of characters, etc.  Furthermore, the extant taxa and variation
: is a sample of historic taxa and variation.  Therefore, when you have two
: data sets, even when they contain samples from identical sets of taxa, they
: may differ either due to sampling error or because they are actually
: samples of different phylogenies (e.g., sequences from two different genes
: in the same set of individuals may have different phylogenetic histories
: (see Pamilo & Nei 1988)).  

So far I'm with you. 

: Therefore, it is important to know whether the
: data sets really contain conflicting phylogenetic signals prior to
: combining the data.

This is where I start wondering.... Why the "therefore"? What difference 
does it make WHY the phylogenies are different at this point in the analysis?

: It has been argued that combining data sets with conflicting phylogenies,
: caused by the use of different characters, is still a useful way to get at
: the phylogenetic relationships of the whole taxa, rather than just of the
: set of characters in a particular data set.  The basic idea is that the
: areas of conflict will become noise and the remaining phylogenetic signal
: will better represent the organismal relationships.  

I would agree with this. It seems to be one of the more basic concepts in 

: Others argue that it is inappropriate to combine statistically 
: different data sets.  


: In this
: case, one should examine the set of distinct trees available for the taxa
: under study.  The differences among them might be informative 

of what?

: and the similarities are likely to indicate real patterns in the 
: history of the whole taxa.  

The similarities would certainly show up in a combined analysis, no?

: BTW, subsets of what is collected as a single 
: data set can also contain significantly distinct phylogenetic signals; 
: so, the question of combining data sets is identical to the question of 
: searching for conflicting signals within any one data set.  

But would those who advocate _not_ combining data-sets actually break up a 
single data set simply because partitions of it may support different 
topologies? If not, then why would it be justified to "combine" 
conflicting data in an originally singular data-set, but not to combine 
two conflicting data-sets? If they do break up originally singular 
data-sets, where does it stop? What stops the deconstruction before it 
reaches single contradictory characters?

: To state my answer to the question posed above (Why would you need to prove
: anything in order to combine the two data-sets?) more directly; you don't
: need to prove anything, but you might be missing out on interesting and
: important information. 

I dont see the relevance of knowing  whether the conflicts are caused by 
sampling error or by different character trees until you arrive at a final 
assessment of the overall phylogeny, something I have a hard time 
imagining emerging from anything but a total evidence analysis of all the 
relevant taxa (IOW, just go ahead and combine them, add in all other 
evidence, and _then_ see how things can be interpreted).
Tom diBenedetto
Fish Division
University of Michigan Museum of Zoology

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