Program for testing incongruences

Thomas K. Dibenedetto tdib at umich.edu
Sun May 5 07:46:32 EST 1996

Andrew J. Roger (aroger at ac.dal.ca) wrote:
: Have you heard of lateral gene transfer? In case you haven't,,,,,

Howdy Andrew! Long time, no read! 
Yeah, I sorta, kinda heard about this stuff. But you know, it _still_ 
doesnt strike me as all that much different from any other character 
which may be misleading....

: Now if you were trying to work out the phylogenetic position of an organism
: and you used all of the genes available from this organism and related
: ones, 

_all_ the genes available?
then you would probably not be misled by a case of lateral transfer...
Glad to see you inching up on the "total evidence" bandwagon!  :)

: including a gene which this organism picked up from another lineage
: (which the other taxa in the dataset did not), you would be including
: a datum which will be positively misleading about the phylogenetic 
: relationships of this organism (if you were interested in the 
: relationships which are the result of vertical descent rather than 
: lateral transfer of one of its genes).
: The need to keep data like these separate seems so obvious to me
: that I cannot conceive why you might object to it. Can you enlighten me?

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?
The original poster had two conflicting (or potentially conflicting) 
datasets and wondered if they should be combined. If they were 
"significantly different", would this necessarily indicate lateral 
transfer? Partitions of a single dataset (one gene) can be different right?
Thus, there must be other reasons why one discovers incongruence, no?
Do you think conflicting data should never be combined, irrespective of 
the reason?

: If we are dealing at the level of molecular data then one must try to
: think of what patterns of conflicting data will be indicative of true
: chimaerism as opposed to "noisy" data. 

Well, noisy data (as you point out) is unpatterned. I am asking you, are 
there other factors which might pattern data besides "chimaerism" or the 
true history? 

: Thus it is clear in principle and in practice in this case how you
: would destinguish between noisy data and real gene chimaerism.

You may be distinguishing noise from pattern, but why must it be chimaerism?
I guess it just strikes me as a backwards approach. You start with a 
process, predict a pattern it may produce, then identify any such discovered
patterns as resulting from that process. This doesnt really consider 
alternative explanations for the pattern.
In my little corner of systematics, we usually nail down the patterns 
first, then go searching for explanations.

re. my total evidence, lump it all together argument:
: This would be fine if you could be certain that a significant portion
: of your dataset were derived from vertical descent only. But it is
: possible that your total dataset may contain a large portion of
: data which is postively conflicting. The result may be a phylogeny
: which makes no sense at all because it is derived from multiple
: datasets which had different histories. 
: The success of total evidence depends on the anomalous phylogenies
: being in the minority...and that the true phylogeny will "come out
: in the wash".  I wouldn't be comfortable with this assumption.

Well, I dont know why not. 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?
Tom diBenedetto
Fish Division
University of Michigan Museum of Zoology

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