CONSERVATION GENETICS (BIOL5542)
Assessing population structure and genetic diversity
Complete the analyses on the Golden Bandicoot, using the data and scripts provided.
Provide answers to all questions. There is no need to write a formal report (Abstract, Introduction, etc). Written answers should be supported with statistical analyses, Tables and/or Figures. Answers should include a description on how the analyses were performed.
1. One of the first things people do with SNP data is run a Principal components analysis to visualise clustering in the species. For the Golden Bandicoot, write one interpretation of a distinct cluster in the PCA that cannot be supported by the analysis. Then explain the potential causes of the cluster using a combination of the knowledge of the species recent decline/translocation history, and the principles of Hardy-Weinberg Equilibrium.
2. When running population structure analyses on all populations vs just in the Kimberley, do you receive different answers? Why does this context change the answer? Hint: look at whether the actual answers change by comparing different K values in both analyses. These references will help: https://onlinelibrary.wiley.com/doi/full/10.1111/mec.14187, https://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2007.03329.x.
3. The Golden Bandicoot currently has a variety of different subspecies, a taxonomic delineation that generally means that subspecies should not be mixed. The authors of the paper did not make any explicit comment on whether the subspecies are supported or not supported. Using your analyses and the history of the species, assign the correct conservation units to/across the existing populations. Justify your answer; this reference will help https://doi.org/10.3389/fevo.2018.00165 .
4. Write out your expectations of what genetic diversity will look like in a population established through an island translocation. Be specific – will it be the same or different from the souce population in a population structure analysis, and why? What are your expectations for genetic diversity (i.e. heterozygosity, inbreeding, fixed differences)? Then for either Barrow Island or Marchinbar Island, discuss whether they meet these expectations. If not, assess why that might not be the case.