This is a repo for our class project re-analyzing some of the data from Liu et al (2014) "Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears."
This paper did cool things like 1) estimate when polar bears and brown bears diverged, 2) infer the joint demographic history of the two species, and 3) detect genes under positive selection in polar bears. For any such study, the first step is population genetics analyses to look at how similar/different two populations/species are. We attempted to re-create the LD Decay, PCA, and STRUCTURE analyses, efforts documented here.
Notes on what we did are on the following hackmd documents. The individual "documents" folder in this repo has .rmd files of data manipulation in r and .pdfs of hackmd documents, and "data_output" contains results. The "data" folder in this repo does not contain data, as all data files were too large to store on GitHub.
Documents in order of our process:
Basics of Farm: https://hackmd.io/s/ByFxwWRPz
PCA: https://hackmd.io/s/BkUv3Xjwz