Poster Presentation Society for Molecular Biology and Evolution Conference 2016

DNA Sequence Evolution Simulation and Phylogenetic Reconstruction Using Pen and Paper (#377)

Nicole T Perna 1 , Jeremy D Glasner 1
  1. University of Wisconsin - Madison, Madison, WI, United States

Tree-thinking is an approach to emphasizing evolution as a fundamental unifying concept in biology backed by a growing body of educational research. Many curricular resources related to phylogenetics are available for secondary school and undergraduate biology instruction. Most focus on interpretation of trees, or phylogenetic reconstruction using morphological or molecular characters. Few active-learning exercises link phylogeny to the process of mutation, and fewer yet address the role of data simulation in evolutionary biology. The exercise presented here fills this gap, while not requiring computational resources sadly still limited in many U.S. schools.

We developed a 4-part pen and paper DNA sequence evolution simulation and phylogenetic reconstruction lesson. Part 1 involves instruction in tree interpretation and includes a short formative assessment tool. In Part 2, students are given a 5-taxon tree topology with nodes calibrated in millions of years, and a 10 bp ancestral DNA sequence. They use two polyhedral dice (one 10-sided, one 4-sided) to simulate sequences at each descendant node under a model where each lineage experienced one fixed mutation per million years. In part 3, students are asked to reconstruct the tree using simulated sequences without any algorithmic instruction. Part 4 involves instruction about distance matrices and application of UPGMA.

An instructor’s guide and student handouts are freely available (Creative Commons License). These include teaching tips and readings to engage students to consider how modeling and simulation can be used to test hypotheses about evolutionary processes and examine the performance of analysis methods. The modularity of the lesson accommodates a variety of class formats and educational levels. We field tested the exercise in undergraduate courses and professional development workshops aimed at secondary school teachers in Wisconsin, USA. It is amenable to implementation elsewhere.