Population genomics of Sussex LHM Drosophila melanogaster

Input data, code, output data, summary plots, and run logs for investigation of the population genetics of the Drosophila melanogaster Sussex LHM sample.

For output graphs, see popgen_plots.png

Input data are 'plink binary' format.

Code is a unix/linux shell script containing commands for Plink to perform population genetic tests.

The two R scripts contain i. a short command for making a subpopulation file, ii. commands for plotting the output data. Both are initated in the shell script.

Platform and version information are available in the log files. Other information available in the shell and R scripts.

Broad observations are that the allele frequency disibribution is normal except a few humps around MAF 0.2-0.3 in the autosomes.

Linkage disequilbrium, on average, levels-out after ~200bp but there can still be some at distances of 300Kb.

The population appears to be divided into four genetically distinct groups (on the IBD-PCA scatter plot), with Fst analysis indicating that this is caused by genetic variation around the centromeres. This is possibly caused by historic admixture, and low centromeric recombination.