GumCreek2012

Steve Pederson & Nina Schwensow

Analysis of GBS dataset obtained from the Rabbit population at Gum Creek in both 2012 and 1996. Rabbit samples from 1996 were killed in the first outbreak of RHDV and contain a sample of the rabbit genome in the area pre-exposure to RHDV.

The dataset consisted of:

• 55 Samples taken from Gum Creek in 1996
• 53 Samples taken from Gum Creek (Oraparinna) in 2012
• An additional 37 samples taken from a Turretfield population of rabbits in 2010. These samples were included only for use as a phylogenetic outgroup

Analytic Code

All code is available at https://uofabioinformaticshub.github.io/GumCreek2012/

• [01 Data Pre-processing]
• 02 Selection of SNPs for Genetic Analysis
• 03 Analysis of Filtered SNPs
• 04 Association of SNPs with Genes and Gene Ontologies
• 05 Simulation of Genetic Drift
• S1 FLK Analysis