[Taxacom] base alignment

John Grehan jgrehan at sciencebuff.org
Tue Aug 29 11:28:32 CDT 2006


Karl,

If I am wrong then fine. 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.

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

None of this means that molecular people have necessarily been wasting
their time. 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
corroborte molecular trees.

John Grehan


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Karl Magnacca
> Sent: Tuesday, August 29, 2006 12:20 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] base alignment
> 
> On 29 Aug 2006 at 9:28, John Grehan wrote:
> > > But for
> > > everybody I know "phenetic" means classifying on the basis of
overall
> > > similarity of taxa, not selecting compatible characters.
> >
> > I agree with this definition. And according to that definition
cladistic
> > analysis of molecular characters appears to be an analysis of
characters
> > established through overall similarity of base substitutions and
gaps.
> 
> How ya figure?
> 
> All the molecular cladists I know (myself included) would be very
> surprised to hear that they have been doing phenetics all these years.
> I guess they wasted all that time aligning sequences in order to
> establish homologies.  I think Dave Swofford would also be interested
to
> hear that parsimony becomes phenetic when run on a molecular matrix.
> 
> Karl
> =====================
> Karl Magnacca
> UC-Berkeley, ESPM Dept.
> 137 Mulford Hall #3114
> Berkeley, CA 94720
> 
> 
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