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

  • Authors: Sarah Boomer1, Kelly Shipley2, Bryan Dutton3, Daniel Lodge4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Natural Sciences and Math, Western Oregon University; 2: Western Oregon University; 3: Natural Sciences and Math, Western Oregon University; 4: University of Oregon
  • Citation: Sarah Boomer, Kelly Shipley, Bryan Dutton, Daniel Lodge. 2005. A laboratory class exploring microbial diversity and evolution using online databases, the biology workbench, and phylogenetics software.
  • Publication Date : November 2005
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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.

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