This project was prepared as part of a BioQUEST faculty development workshop entitled Implementing Bioinformatics in Introductory Undergraduate Biology Courses:
Exploring Microbiology, Molecular Data and Visualization
at San Diego Supercomputing Center in January 2007. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

Upcoming events               BEDROCK Problem Spaces

Seeing the Trees Through the Forest : Arthropod phylogeny based on morphology and molecular data
Authors          Audiences          Overview           Materials          Resources           Future Directions



Dawne Page
Point Loma Nazarene University

Buran Haidar
San Diego Miramar College

Michael Alfieri
Viterbo University

Kerry Fulcher
Point Loma Nazarene University


Possible Audiences:

Advanced High School Biology courses.
University courses in introductory biology, genetics, molecular biology, evolution  


Brief Overview:

This project’s goals are to create a flexible and expandable problem space that can be used at the majors level ranging from introductory to upper division courses. This can be used as a stand alone resource for individual courses or for a layered series of activities that can expand across multiple courses in the biology curriculum. This problem space will be centered around a rich data set from arthropods that contains 8 molecular markers and 303 character traits (Giribet et al. 2001).

Part 1: Introduction to Phylogenetic Trees

A good, concise summary of the terms and procedures used in making and understanding phylogenentic trees can be found in this Phylogenetic Primer by Douglas Theobald.

Part 2: Interpreting Phylogeneic Trees

Part 3: Creating Phylogenetic Trees Using Hennig's Cladistic Method (by hand)

     A. Hypothetical example

     B. Arthropod example

Part 4: Creating Phylogenetic Trees Using Computers

     A. Introduction to Biology Workbench

     B. Controlled Example

     C. Simple Unknown Example

Part 5: Advanced Open Ended Exercises



Project Materials:

List of morphological traits of select arthropods (to be attached)
List of gene bank accession numbers for molecular data (attached)
Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
Biology WorkBench is a web-based resource for analyzing and visualizing molecular data developed at NCSA (the National Center for Supercomputing Applications).  


Resources and References:

Information about Arthropods from the University of California Museum of Paleontology and the Tree of Life Arthropods section.
Original data and analysis found in a 2001 Nature paper by Gonzalo Giribet, Gregory D. Edgecombe and Ward C. Wheeler (2001) Arthropod phylogeny based on eight molecular loci and morphology Nature 413, 13, 157-161  


Future Directions:

Students search for other morphological traits and/or molecular data to add new organisms or traits to their analysis. Assign subsets of data for small group projects. Rich data set available for upper-level student projects.  



- COI subset cleaned data.txt
- Tree_Thinking_Challenge1.pdf
- ArthropodData.xls
- MorphologicalCharactersKey.doc
- H3 subset cleaned data.txt
- Arthro tree.ppt
- H3COICombinedDataClean.txt