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Professor Heather Waye and her colleagues conducted a pilot study in 2014 to measure genetic diversity and dispersal pattern in a population of tiger salamanders in west-central Minnesota. The ultimate goal of this research was to analyze the genetic differences between tiger salamander larvae captured in breeding ponds within Pepperton Waterfowl Production Area to understand the population structure and movement patterns. They expected that ponds closer to each other would have more similar genetic information, and that genetic differences between ponds would increase with geographic distance. However, the initial analysis using standard techniques failed to uncover useful patterns in the data. Reorganization of the data and other quantitative approaches are needed to discover any significant patterns in this sample. In my research, I attempted a different modeling method to determine whether re-manipulating samples will uncover hidden patterns of genetic variation. In order to investigate this process, I learned how to install and utilize a software pipeline called Stacks which uses a standard UNIX- like environment operating system called Ubuntu. This software pipeline is a new methodological approach that we are using to build ‘loci’, fixed positions of genetic markers on chromosomes, from short-read sequences to map the relationship between individual tiger salamanders. We hope this technique that interrogates DNA fragments will provide the potential genetic differences between individuals in the sample. My results improve understanding of how to use advanced statistical and computational methods tailored to complex problems with real-world data.
Genetics--Research--Statistical methods, Statistics
Dongmin Kim, Dennis, "Developing Methods of Processing and Analyzing Genetic Data to Examine Tiger Salamander Population Structure" (2018). Undergraduate Research Symposium 2018. 8.