Faith in parsimony

[Richard.Zander at MOBOT.ORG]

The Bayesian MCMC software MrBayes has implemented, so I understand, the
morphological analysis method of:
Lewis, P. O. 2001. A likelihood approach to estimating phylogeny from
discrete morphological character data. Systematic Biology 50:913-925.  I
think there are Bayesian examples but can't dredge one up. You might try
searching the Web.

A tutorial for MrBayes is at:
http://mrbayes.csit.fsu.edu/wiki/index.php/Tutorial
and can download the latest version at:
http://mrbayes.csit.fsu.edu/download.php

See also
http://hydrodictyon.eeb.uconn.edu/people/plewis/research.php
for good stuff on Bayesian methods.

Your interest, Robert, at this time is a bit late since attempted analysis
of evolution by following incremental accumulations of point mutations is
obsolete, useless, futile, ineffective and worthless as far as advancing our
understanding of evolution over the morphological studies of the past
decades. In a couple years, the money now spent on phylogeneticists'
salaries, students, grants, and special parking spaces will be going to
evo-devo types, who will divert the money river into their own labs, to some
large extent justified. As taxonomists, however, we must expect to be again
marginalized. In the absence of really clear mechanistic descriptions of how
molecular evolution dovetails with interaction of populations with the
environment and attendant speciation, I think the best evidence for tracking
shared homologies remains phenetic: such as cluster analysis of
morphological traits.

I could be wrong.

______________________
Richard H. Zander
Bryology Group, Missouri Botanical Garden
PO Box 299, St. Louis, MO 63166-0299 USA
richard.zander at mobot.org <mailto:richard.zander at mobot.org>
Voice: 314-577-5180;  Fax: 314-577-9595
Websites
Bryophyte Volumes of Flora of North America:
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Res Botanica:
http://www.mobot.org/plantscience/resbot/index.htm
Shipping address for UPS, etc.:
Missouri Botanical Garden
4344 Shaw Blvd.
St. Louis, MO 63110 USA


-----Original Message-----
From: Robert Mesibov [mailto:mesibov at SOUTHCOM.COM.AU]
Sent: Friday, July 22, 2005 6:37 PM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] Faith in parsimony

[snip]
Richard Zander wrote:

"Both maximum parsimony and Bayesian analysis can be used for morphological
data sets."

Can you point to a Bayesian example? I'm particularly interested in what
sorts of prior modeling of morphological evolution were done before a Markov
chain Monte Carlo simulation was attempted.