Karen's Lab Notebook

In working on the chromosome painting I noticed there seem to be a really high number of SNPs between SCA and SCB in 1982, like we had observed before. So I did a PCA using just the SNPs from 1982, and only the section of 1982 that is past the large indel, so that should not be influencing what we see. I also included D Barb for perspective. First, here is a PCA using only the SNPs from 951, one of our largest scaffolds. You can see that D Barb is very different from everyone else, and that the W ponds, D10, and D8/surrounding all cluster together. However, the story is very different when you look at the SNPs from 1982. Also, interestingly, there appear to be three clusters, with hybrids between some of these. Would love to hear your thoughts on this. Further support for something interesting going on on this scaffold? Of course, maybe other scaffolds would also look this way if I did a PCA on their SNPs? I guess I need to test more to see if this is really something unique? I kn...

Ok, I finally figured out what I was doing wrong with the chromosome painting. Here is the results for scaffold 1982 (the divergent one I focused on in lab meeting). First looking at all ponds (D8 and surrounding, D10, and W ponds). Super clone A clones are on the bottom, then super clone B clones are next. Now focusing on just the D8 and surrounding ponds. Again, super clone A clones are on the bottom, then super clone B clones are next. You can see that A and B are pretty divergent from one another. It also looks like a lot of the other clones are hybrids of the two (lots of green), while some of the others look like B. Not too many that look like A. Similar graphs but now looking at another scaffold, first 5000 SNPs on scaffold 951, just for comparison. See a similar pattern, except clones that looked heterozygous or B in 1982, don't necessarily look the same for 951. Sometimes clones are heterozygous or B in both, but sometimes they are heterozygous in one, but B i...

Here is the tree with the additional pulex/pulicaria added. The US pulex/pulicaria still fall out separate/reciprocally monophyletic from the UK D. pulex. Also, the Tucker2013bdw is the D. obtusa sample. It is an American obtusa clone. You can see it does fall out with D. Barb, but the branch lengths are pretty long between them. Maybe that is because it is US versus European obtusa? Still not sure if D Barb is obtusa or not, but at least it seems related. Still need to figure out coloring the labels/tips according to pond/superclone/something.

When doing my initial attempts at chromosome painting, I was interested not only in the apparent deletion on scaffold 1982, but also the areas of high heterozygosity. Notice the block of high heterozygosity immediately following the deletion. I decided to look into this block in a bit more detail. In this section there is an average of 1 SNP every 25 bp (276 SNPs over 7048 bps). I blasted this section on NCBI's blast X, and from this, it appears to cover the majority of the HEAT repeat containing protein 1. I then looked at this region of the scaffold in tview, and I noticed that the read depth appeared higher in this region. I then graphed the distribution of read depth along scaffold 1982. Here is that distribution for a super clone B individual, D8_125 That really high peak towards the beginning of the scaffold corresponds to that high heterozygosity block. You can see another peak farther down the scaffold. Thus, it looks like this region of high heterozygos...