Karen's Lab Notebook

Driving question: Are blocks of the genome that show elevated divergence between SCA and SCB in D8 2017 in terms of fixed SNPs, more likely to be maintained at intermediate frequencies in other ponds? I took the windows that showed the highest divergence between SCA and SCB, and then graphed the distribution of the alternate allele frequency for all SNPs within those same windows versus a randomly chosen set of windows (matched sample size, but not matched beyond that). Here is the result for D8 2012. We do see a shift in the expected direction (towards 0.5) in the divergent set of windows. Here are the results for DBunk and DOily 2017. Again, we see a shift in the right direction, though both sets are farther from 0.5 to start with. Maybe because there are more lineages (or species) contributing to this pooled data. DBunk  Doily However, once I look at D10, or more distant ponds (Bag, B1, W1, W6 so far), I don't see any signal. However, I think that it is ...

Updated prop SCA SCB figure for DBunk (top) and DOily (bottom) using 100,000 window with a 10,000 step size. Graphing prop SCA and SCB against number of fixed snps between A and B DBunk geom_point() DBunk geom_count() Doily geom_point()  Doily geom_count() Maybe there is a narrowing towards intermediate frequencies in DBunk? Not so much Doily? Looking at correlations between DBunk and Doily for prop SCA and SCB prop SCA prop SCB

So it turns out I made a mistake when making the genome wide graph in our meeting yesterday. It wasn't, in fact, genome wide. So here are the correct graphs. First, the graph using only SNPs that are fixed between A and B,F,K. Then, the graph with all SNPs genome wide. DBarb, DOak, and DMud, are not included in the second graph (to speed up computation), sorry that it makes things a bit more confusing. Things to take away from this: 1) The pattern of prop alt for SNPs that are fixed between A and B,F,K, is different than the patterns of genome wide prop alt, mostly for the Dorset ponds (compare top panel of each graph). The SNPs fixed between A and B,F,K tend to be more modal. 2) Overall the distribution of the 1982 SNPs looks distinctly different (more modal) than the distribution of the genome wide SNPs for the Dorset ponds, supporting the idea that something is keeping these 1982 haplotypes in balance and/or from recombining.  3) If you look at DBunk and DOil, 198...