Karen's Lab Notebook

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 ...

Now I am taking an initial look at the 2012 Pooled data. Here I am looking at read depth and proportion reference allele for each site, by population. Again, this is using the trimmed SNP data set. I will also go back and redo this using all sites. First looking at D8. Here we see a nice distribution of read depth. Interestingly, when looking at the proportion reference allele graph, we see a strong peak at 1, but in contrast to the 2017 data, there is no peak at 0. Thus, it seems that our reference genome clone, D8.4A, is very representative of the Daphnia in D8 at this sampling time point. Perhaps there is only a single clone (or clonal lineage) present? D8 Now looking at D10. A similar distribution of read depth. For proportion reference allele we now see a small peak at 0, and also a more pronounced trimodal distribution overall. D10 Now looking at the remaining ponds. First I am showing the ponds where the distribution of read depths doesn't seem that di...

I am working on moving the pooled data forward. I started with the Sp2017 pooled data. There are pools of individual from the second sampling point (early May). Here is the distribution of read depth per site with all populations pooled. There is a bimodality to this distribution. So let's look at it by a population to population basis. These first three populations all look similar, and probably contain only (or mostly) D. pulex. D8 D Bunk D Oily We know that D Barb appears to contain a different species from the single clone we have sequenced. And we do see in the distribution below that there appear to be an excess of low coverage sites, likely due to the reduced mapping. D Oak shows a similar distribution, which is not surprising given that we also thought D Oak was a different species. D Barb D Oak Last we have D Mud. This distribution looks even more different than D Barb and D Oak. It is strongly bimodal. Do you think this suggests th...

With Cory's help I finally got my data into the correct format to get it into Admixture (took several hours of hitting my head against the wall). I ran Admixture on two different datasets. Both datasets involved using only SNPs that had been filtered for Good contigs, over 2.5kb, and filtered with maf=0.15 and for LD. In the first dataset I included all individuals we have so far (minus the 6 I dropped for low coverage and also not including the individual from D Barb). The second dataset included only one individual per super clone/pond/season (super clones subset). According to the Admixture manual the way to determine your best K is to look at CV error, and choose the K where that value is lowest. First I ran the Admixture analysis using Ks of 1-12 on the full dataset. Here is the distribution of CV error as well as log likelihood. For both of these you can see that there is a change in the curve at K=3. However, the CV error continued to get lower and never went back up ...