PCA with populations

Re-run the PCA tool on the newly prepared dataset (not shown). The summary information now includes some statistics on the differences between populations; here the significance shows pretty good P-values for all population pairs that don't involve the singleton F2 (blue boxes).

The new plot indicates the population membership of the individuals by using different colors and symbols for each population we defined. Specifying populations does not affect the PCA computation [double check that this is correct]; however leaving out the F1 individual has produced more separation between the E and S populations, and has clustered F2 with F3-5.