Important paper on practical phylogenetics (was RE: 11th specimen of Archaeopteryx)

["Thomas R. Holtz, Jr." <tholtz@umd.edu>]

> From: owner-DINOSAUR@usc.edu [mailto:owner-DINOSAUR@usc.edu] 
> On Behalf Of Mickey Mortimer

[Tremendous snippage]

> When you run an analysis like this, certain characters need 
> to be "ordered". 

This reminds me: a paper that all interested in actually doing morphological 
phylogenetics have to read is:

http://onlinelibrary.wiley.com/doi/10.1111/j.1095-8312.2011.01755.x/full

BRAZEAU, M. D. (2011), Problematic character coding methods in morphology and 
their effects. Biological Journal of the Linnean
Society, 104: 489?498. doi: 10.1111/j.1095-8312.2011.01755.x

Abstract

The effects of different coding practices in morphological phylogenetic 
analysis are well documented. In many cases, we can
determine that certain practices can be regarded as undesirable and should be 
avoided. Certain coding practices do not correctly
translate the expected information to the cladistic algorithm. It may go 
unnoticed that expressions of character information in
character lists, which may be entirely logical to any reader, do not 
necessarily reflect the mathematics employed by a phylogenetic
algorithm. Despite a wealth of literature on coding procedures and 
documentation of these issues, problematic character coding
practices are still common. A review is provided of different coding and 
character formulation practices, particularly relating to
multistate character information that may either: (1) lead to a failure to 
capture grouping information implied in the character
list; (2) cause problematic weighting or spuriously high certainty in 
particular optimizations; and (3) impose congruence
artificially, by linking more than one variable character to a particular 
state. Each of these is reviewed and presented with a
hypothetical example. Recommendations for avoiding these pitfalls are described 
in light of how parsimony algorithms work with
character data. Character lists must be drawn up not only to present character 
variation logically, but also with consideration for
how computer algorithms implement cladistic logic. The widespread use of 
problematic character coding procedures may account for
some of the perceived problems with morphological data. Therefore, an 
exploration of the effects of these methods and
standardization of methods should be a goal for the very near future. 

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A guide to problems (and strategies for avoiding them) in the coding of 
characters of various sorts.

Thomas R. Holtz, Jr.
Email: tholtz@umd.edu   Phone: 301-405-4084
Office: Centreville 1216                        
Senior Lecturer, Vertebrate Paleontology
Dept. of Geology, University of Maryland
http://www.geol.umd.edu/~tholtz/
Fax: 301-314-9661               

Faculty Director, Science & Global Change Program, College Park Scholars
http://www.geol.umd.edu/sgc
Fax: 301-314-9843

Mailing Address:        Thomas R. Holtz, Jr.
                        Department of Geology
                        Building 237, Room 1117
                        University of Maryland
                        College Park, MD 20742 USA