[Taxacom] base alignment
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
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
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...).
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