[Taxacom] base alignment

John Grehan jgrehan at sciencebuff.org
Tue Aug 29 18:31:28 CDT 2006


From: taxacom-bounces at mailman.nhm.ku.edu on behalf of pierre deleporte
Sent: Tue 8/29/2006 1:25 PM
To: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] base alignment

>"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.

Perhaps I will. The potential problem with equating the two (base alignment, and morphological character comparison) is that the alignment involves making judgements about an overall equivalence between necessary gaps and substitutions to get the best fit of all positions rather than being able to take each character (base position) individually. I have had one off list molecular correspondent state that compulational alignment is phenetic, but manual alignment for sequences of identifical length is cladistic although I have not seen the actual steps yet.

>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).

Rooting represents the cladistic part, but without that polarization the parsimony analysis will just represent the best fit between conflicting patterns. As I have mentioned before, if the character states are treated as derived when they really are not there is a problem and if alignment determines homologies based on overall simialrity then I find it problematic to make a cladistic phylogney from characters that are phenetic.

PAUP to start with).

That might be useful. Does PAUP provide sequences of different lengths to show how the alignments are determined or does it just use pre-aligned sequences?

>  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.

If molecular analyses are indeed phenetic analyses dressed up in cladistic terminology and techniques then there is reason to find that molecular phylogenies are just as open to question as are morphological phylogenies.

>your charge that molecular phylogenies are always
based on overall similarity is flatly wrong.

We shall see. As already mentioned, there are some cladists who share a similar suspicion.

>Ze fact iz zat cladistic ones are cladistic, you know... yes, exactly like
for morphological data... 

Only by imitation perhaps.

John Grehan

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