An Introduction to Phylogenetic Analysis - Association for Biology ...
An Introduction to Phylogenetic Analysis - Association for Biology ...
An Introduction to Phylogenetic Analysis - Association for Biology ...
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<strong>An</strong> <strong>Introduction</strong> <strong>to</strong> <strong>Phylogenetic</strong> <strong>An</strong>alysis<br />
Robert J. Kosinski<br />
Department of Biological Sciences<br />
132 Long Hall<br />
Clemson University<br />
Clemson, SC 29634-0314<br />
Voice: (864) 656-3830 FAX: (864) 656-0435<br />
rjksn@clemson.edu<br />
Abstract: This exercise introduces students <strong>to</strong> analysis of evolutionary relationships both by analysis of<br />
molecular similarity and by cladistic techniques. The molecular analysis uses both paper-and-pencil and<br />
bioin<strong>for</strong>matics comparison of the amino acid sequence of the hemoglobin beta chain of eight<br />
vertebrates. The cladistic exercises introduce students <strong>to</strong> cladistic principles, and then allow students <strong>to</strong><br />
solve hypothetical problems both with and without homoplasy. Students then test their cladistic ability<br />
by analyzing published data on the flightless birds. Finally, students solve an entertaining problem<br />
using “organisms” made out of nuts and bolts.<br />
Keywords: cladistics, cladogram, phylogram, phylogeny, phylogenetic, evolution, taxonomy,<br />
bioin<strong>for</strong>matics<br />
©2006 Robert J. Kosinski<br />
Contents:<br />
Student Outline 58<br />
Classifying Based on Molecular Similarity<br />
Exercise A—Molecular Similarity (manual exercise) 58<br />
Exercise B—Molecular Similarity (bioin<strong>for</strong>matics exercise) 61<br />
Classifying Using Cladistic <strong>An</strong>alysis 65<br />
Exercise C—Solving Cladistic Problems 69<br />
Exercise D—The Flightless Birds 77<br />
Exercise E—The “Boltidae” 78<br />
Notes <strong>for</strong> the Instruc<strong>to</strong>r 79<br />
Literature Cited 85<br />
About the Author 85<br />
Instruc<strong>to</strong>r Appendices<br />
Appendix A—Student Problem Handouts 86<br />
Appendix B—Student Solution Handouts 94<br />
Appendix C—Instruc<strong>to</strong>r Solution Pages 98<br />
Appendix D—Flightless Birds Solution (transparency master) 106