PCAs with maf=0.01

I redid the PCAs using an missing allele frequency of 0.01. This led to a few changes in the PCA. First, the two W pond clones now look divergent from the other populations, which makes much more sense. (They used to just be in the middle of the PCA). However, there are also three D10 individuals that now look divergent from the rest of D10.

I then reran the PCA dropping the W individuals. You can again see the three divergent D10 individuals.

I then ran the PCA again, with super clones subset (one individual per super clone per year/pond), and again excluding W pond clones. Again, those 3 D10 individuals stand out. Not sure what is going on with them.

Same PCA as above, but just graphing without the D10 pond to zoom in a bit on the Dorset ponds. These overall look fairly similar, not changed too much by dropping the maf to 0.01.

I then reran the PCA only on the Dorset ponds (not including any D10 or W clones). Interestingly, in this PCA the DBunk clones no longer look intermediate to the D8 super clones. Why would this be?

Same PCA as above, but looking just at D8 and DBunk