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A Laboratory Class Exploring Microbial Diversity and Evolution Using Online Databases, the Biology Workbench, and Phylogenetics Software

By Sarah Boomer1, Kelly Shipley1, Bryan Dutton1, Daniel Lodge2

1. Western Oregon University 2. University of Oregon

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Abstract

Students assemble and align bacterial datasets using DNA information downloaded from the National Center for Biotechnology Information website and Biology Workbench.  Specifically, they compare unknown original DNA sequences (from, in our case, hot spring communities) to a backbone of diverse bacterial control sequences representing 11 different phyla.  Students use aligned datasets to obtain phylogenetic trees with Phylogenetic Analysis Using Parsimony.  In performing this exercise, students form predictions about bacterial phylogenetic relationships, enhance their understanding of bacterial diversity, and better appreciate the large body of research about bacterial diversity using DNA information.

Cite this work

Researchers should cite this work as follows:

  • Boomer, S., Shipley, K., Dutton, B., Lodge, D. (2005). A Laboratory Class Exploring Microbial Diversity and Evolution Using Online Databases, the Biology Workbench, and Phylogenetics Software. ASM Microbe Library. Retrieved from http://www.microbelibrary.org/library/resources/3950-a-laboratory-class-exploring-microbial-diversity-and-evolution-using-online-databases-the-biology-workbench-and-phylogenetics-software. 

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