The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization

Abstract

Experimental evolution is a powerful method for studying the relationship between genotype and phenotype by observing how populations genetically adapt to controlled selective pressures. In educational settings, this approach also offers a dynamic way for students to engage with molecular genetics. One such educational effort, known as "yEvo" (yeast evolution), introduces experimental evolution into high school classrooms, allowing students to evolve the bakers yeast Saccharomyces cerevisiae under various stressors and investigate the resulting genetic changes. While the hands-on experiments have been successful in fostering student interest and understanding of evolution, the downstream data analysis (interpreting whole-genome sequencing results of evolved yeast compared to the ancestor) remains a challenge. Students often struggle to grasp the significance of their mutated genes and lack the broader context to determine which mutations are most phenotypically relevant. To address these issues, we developed the yEvo Mutation Browser, an intuitive web tool designed to assist students and researchers alike in visualizing and contextualizing genome sequencing data. Developed using R Shiny, this tool features an interactive chromosome map displaying mutated genes, graphs categorizing mutation types, a gene viewer illustrating specific mutation sites within genes, and a protein view that maps specific mutations onto protein structures. The app also features an option for non-yEvo-affiliated users to upload their own experimental evolution or genetic screen datasets and compare them with all yEvo data collected since 2018. The yEvo Mutation Browser streamlines data interpretation, helping students understand how organisms employ diverse genetic strategies to adapt to environmental stress. In the future, this framework could be adapted for use with other model organisms, offering a valuable resource for both genetics research and education. SignificanceBringing novel research into the classroom can transform how students learn science. The yEvo project engages high school students in experimental evolution, enabling them to witness natural selection in action and connect genetic mutations to evolutionary outcomes. By providing an accessible web-based tool, the "yEvo Mutation Browser," this work lowers barriers to interpreting genome sequencing data, allowing students, teachers, and researchers alike to explore how yeast populations adapt to diverse stress conditions. This resource not only strengthens STEM education by making cutting-edge genetics more approachable, but also builds a shared dataset that enriches the broader yeast genetics community.