Program for testing incongruences

Thomas K. Dibenedetto tdib at umich.edu
Thu May 9 09:33:16 EST 1996

Andrew J. Roger (aroger at ac.dal.ca) wrote:
	tdib said:
: >Well gee, if I could _know_ that a gene came from elsewhere, I might go 
: >along, but how do you get to know this, before you do the analysis?

: Your point is well taken. In the absence of knowledge about the organism's
: phylogenetic position, you cannot distinguish lateral transfer from 
: vertical descent. Fortunately, most of the time one has some idea of
: phylogenetic position. [snip]

Fine, I go along with all this. It is true that we often have knowlege of 
relationships at higher and lower levels than what we are studying, and I 
am not averse to using that knowledge. It just strikes me that most of 
the problematical situations (lat. transfers) are either at a pretty gross 
level (not really in need of a statistical significance test), or may be 
operative at the (species) level in question (the level of relationships 
which one is attempting to determine), and thus not the ones we can easily 
: >
: >Would you care to point me toward those 
: >sources of evidence which have led you to conclude 
: >that "anomolous" gene trees are anywhere near as common as would be 
: >necessary to upset a total evidence analysis?

: They are probably not very common in a lot of cases. There is one
: fundamental case where they might be. Recently Golding and Gupta
: published a paperin Molecular Biology and Evolution where they
: described comparisons of eukaryote/archaebacteria/gram positive/
: gram negative homologs of roughly 2 dozen genes. They found that
: about 1/3 of the genes gave a significantly different relatioship of
: these groups to roughly 1/2 of the dataset. The rest of the genes
: did not resolve relationships very well. 

thanks, I'll check it out. (did they explain this with "chimaerism"?)

: However, the point is
: that the fundamental relationships between eukaryotes, archaebacteria
: and eubacterial groups are unknown and the data significantly
: conflict in their answers.  Total evidence on this dataset
: would mean nothing.

Do you mean that total evidence would _indicate_ nothing? If so, i guess 
I would say Good! Total evidence does not guarantee an answer, nor does 
it (most significantly) give you the false security of an answer when in 
fact the evidence is ambiguous. It is a "method" which derives from the 
rather simple principle that there really is no good reason in science to 
ignore evidence relevant to a particular question.
Tom diBenedetto
Fish Division
University of Michigan Museum of Zoology

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