Initial look at 2012 Pooled Data

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 different from that in D8 and D10, but the distribution of reference allele frequencies are all strongly bimodal, with peaks at 0 and 1.

B1

SoF

W1

W6

These last three ponds have distributions read depth that are starting to get a bit to very bimodal, with an excess of sites with 0 read depth. Distributions of proportion reference allele are similar to the ponds above: bimodal distributions with peaks at 0 and 1. Are these not the same species? How sure are we that what we do have in D8 and surrounding ponds is D. pulex versus a closely related species? Or are there just divergent populations of D. pulex?

Stav

NM2

Bag