Tree construction: parsimony versus distance-based

Lee F. FrankKolakowski lfk at receptor.mgh.harvard.edu
Tue May 24 11:47:43 EST 1994

On 24 May 1994 07:58:00 -0700,
> Both parsimony and distance-based methods are completely wrong
> and can be used only for approximate estimations of tree
> topology. They are based on homology (similarity) evaluations.
> In the best cases, for SUBsequences.

Read the recent Science paper by David Hillis and colleagues.
Parsimony and other methods are *not neccesarially correct*, but can
often provide useful analyses as to a process that has left no
fossils. What do you suppose, that molecular phylogentics is going to
wait for zillions of higher order characters while genome efforts are
speeding a long a millions of bases per year?

> Any discussions about parsimony or distance-based methods are
> applicable only for multiple alignments (good fast food for 
> experimentators). Implications to the evolutionary consequences
> as well as attempts to find/explain correlations between
> "phylogenetic" trees and archeological (real evolution) facts
> seemed to be incorrect and in some cases even pseudo-scientific.

Like all science, when it is practiced by uninformed untrained
individuals, it is garbage. When the questions posed are thought about
carefully, molecular phylogenetics is *good* science. It is all up to
the practictioner.

> And even for multiple alignments, similarity comparisons does
> not work well: remember need to exclude gap penalties, recent
> findings of structure similarity without same at sequence level
> (so many such regions are present in 3D-align database files
> which contain these alignments) etc.

> Nothing to discuss - take any method if you do alignments
> or generally reconstruct ALL results way if you 
> try to build something evolutionary.

What does this mean? We need trees for lots of different purposes, not
just for the evolution of life. Trees are good ways of classifying
gene families, functional propoerties, sequences, organisms,
planets. The method has to suit the problem. Are you flat out saying
that you do not trust sequence dervived trees for displaying the
factual evolutionary processes? If so good, because, I dont think
anyone should do quite that. Do trees provide a reasonable assesment
of some biologically relevant processes? Yes.

There are lots of points to this discussion, and as such I have
redirected followups to bionet.molbio.evolution.

Frank Kolakowski

O Email: lfk at receptor.mgh.harvard.edu                                  O
O        kolakowski at helix.mgh.harvard.edu                              O
O        lfk at eastman1.mit.edu                                          O
O US Mail: Lee F. Kolakowski        Renal Unit, 8th Flr.               O
O Massachusetts General Hospital    Charlestown Navy Yard              O
O 149 13th Street                   FAX       :  1-617-726-5669        O
O Charlestown, MA 02129             Phone AT&T:  1-617-726-5666        O
O     The home of the G-Protein-Coupled Receptor Database (GCRDb)      O
O Email help to gcrdb at receptor.mgh.harvard.edu and in WWW format at    O
O<A HREF="http://receptor.mgh.harvard.edu/GCRDBHOME.html">GCRDb-WWW</A>O

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net