[Mesquitelist] Question about using Mesquite in an Introductory Biology Laboratory

[David Fitch]

Hi Rob,

while Mesquite is a great program, it is not so user friendly for  
first-time users, and I would not recommend it for a high school (or  
even undergrad) intro bio class.  MacClade is much more user  
friendly, and Sinauer (the publisher) is willing to offer a nice  
license package for classes.

Actually, I use MacClade even in my graduate course (along with  
PAUP*).  But before we do that, we test alternative phylogenetic  
hypotheses by HAND.  The sample morphological matrix "Vertebrates"  
that comes with MacClade is excellent for this, but you can also use  
sample molecular sequences.  I use a matrix with 5 taxa and 10  
nucleotide positions for students to use with UPGMA and parsimony  
methods by hand (limiting the analysis to 5 taxa allows students to  
test all 15 possible unrooted hypotheses--a good exercise in applying  
scientific method as well!).

An alternative to real organisms is to use cyber-organisms such as  
those generated by Richard Dawkins' Watchmaker program.  These  
"creatures" have very simple "body plans" and students can easily  
parse them into characters with discrete states.  In fact, this is a  
major skill that is important for students to develop--defining the  
characters and filling in the matrix with data.  Each group of  
students can use the phylogeny function of Watchmaker to "evolve" a  
set of taxa.  The pictures of these taxa can then be given to other  
groups of students to see if they can infer the correct phylogeny.

Taking the students through all these steps of systematics analysis-- 
from organism to characters to phylogeny (and even using the  
phylogeny to infer the evolution of other characters)--provides the  
students with a deeper appreciation for the science than just having  
them infer phylogenies from data already given to them.

good luck!
David Fitch

On Aug 20, 2008, at 2:29 PM, Robert E. Loeb wrote:

> Colleagues,
>
>
>
> I am new to the list, so please excuse my ignorance if the  
> questions I ask have been answered before.
>
>
>
> The introductory Biology class (first semester course) I will teach  
> for the first time this semester provides an overview of phylogeny  
> for about a third of the course.  I was introduced to Mesquite at a  
> program on Cladistics offered by the American Museum of Natural  
> History for High School Teachers and want to incorporate the use of  
> Mesquite in the laboratory. Has anyone developed laboratory  
> exercises for an Introductory Biology course using Mesquite that  
> you (they) would be willing to share?
>
>
>
> Another related question, since my small campus has few specimens,  
> I wanted to use Excel spreadsheets containing morphological (in the  
> case microbes, cytological) characteristics for groups so that the  
> students could use for analysis in Mesquite.
>
>
>
> In advance, thanks for your assistance.
>
>
>
> Best,
>
> Rob
>
>
>
> Robert Loeb, Ph.D.
>
>
>
> Kenan Fellow
>
> National Tropical Botanical Gardens
>
>
>
> Associate Professor of Biology and Forestry
>
> Penn State DuBois
>
> College Place
>
> DuBois, PA 15801
>
> 814-375-4707
>
> 814-375-4724 (FAX)
>
> Personal Web Site: http://www.personal.psu.edu/rxl5/
>
>
>
> _______________________________________________
> Mesquitelist mailing list
> Mesquitelist at mesquiteproject.org
> http://mesquiteproject.org/mailman/listinfo/mesquitelist

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~    ~       -   -
~ David H. A. Fitch            ~   \  /       /   /
~ Associate Professor          ~    \/       /   /
~ Department of Biology        ~     \      /   /
~ New York University          ~      []   /   /
~ Main Building, Room 1009     ~       \  /   /
~ 100 Washington Square East   ~        \/   /
~ New York, NY  10003          ~         \  /
~ U S A                        ~          \/
~ Tel.:  (212) 998-8254        ~           \
~ Fax:   (212) 995-4015        ~            \
~ e-mail:  david.fitch at nyu.edu ~             \
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

     http://www.nyu.edu/projects/fitch/




-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mesquiteproject.org/pipermail/mesquitelist/attachments/20080820/7b32141a/attachment.html