[Taxacom] base alignment

pierre deleporte pierre.deleporte at univ-rennes1.fr
Tue Aug 29 12:25:11 CDT 2006

A 12:28 29/08/2006 -0400, John Grehan wrote:
>I am just giving my impression of what I have
>read so far. For example, one paper I read stated that alignment uses
>distance measures which to my understanding is not cladistic.

Alignment can effectively be done on the basis of overall similarity. But 
please note that this is not data analysis, just primary homology 
assessment, and also please read other papers, and check for "alignment 
corrected by hand", or other more or less sophisticated alignment methods.
"By hand" means that molecularists are using fairly the same criteria as 
morphologists for homology assessment: detecting optimal "connections" in a 
molecular sequence, like for connections of a bone in a squeleton. After 
all one could state that squeletons of different species are "aligned by 
overall similarity" some way, with some corrections (a bone is likely 
missing here, some are likely fused there...)...
You certainly can see that if you really want.

>In the sense that parsimony is the shortest tree then that is a concept
>not restricted to cladistics.

Finding the shortest tree and rooting on outgroups is merely the computing 
shortcut for finding exactly the optimal cladistic tree you are obtaining 
by hand on your morphological data (be it with compatibility or standard 
parsimony methods).
You can also see that if you really want (just check basic courses in 
cladistics, or even simply the user's guide of PAUP to start with).

>  I am not saying that molecular trees cannot be correct, just
>that they are not necessarily correct just because they use DNA
>sequences, and that morphology is not necessarily wrong when it does not
>corroborate molecular trees.

OK but this is clearly not the point at stake when you are globally 
charging all cladistic molecular analyses of being "phenetic" - a nonsense 
in itself.
Beside your esoteric acception of "cladistic characters" (= surviving a 
compatibility analysis), hence of "phenetic characters" by the way (= any 
other kind of data set), your charge that molecular phylogenies are always 
based on overall similarity is flatly wrong.
Ze fact iz zat cladistic ones are cladistic, you know... yes, exactly like 
for morphological data... I'm pretty sure you can see that (if only...).


Pierre Deleporte
CNRS UMR 6552 - Station Biologique de Paimpont
F-35380 Paimpont   FRANCE
Téléphone : 02 99 61 81 63
Télécopie : 02 99 61 81 88

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