Initial look at Sp2017 Pooled Samples - distributions of read depth and allele frequency

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 there is a mix of species in D Mud?

D Mud

Next some distributions of reference allele frequency by site. Again, separated out by population.

D8

D Bunk

D Oily

Definitely some interesting patterns here. It looks like in D8 most sites are either fixed for ref or alt, or they are at 50% frequency. This would fit with two super clones and F1 hybrids? Something like that? D Bunk and D Oily have a very different distribution. Suggesting more recombination? More interbreeding?

D Barb

D Oak

D Barb and D Oak show all fixed reference or alternate alleles, and no heterozygotes. I guess this could be due in part to the mapping issues, but could it also suggest that they are only reproducing clonally?

D Mud

Again some multi-modality to this distribution. We see some of the fixed reference and alternate alleles like we do in D8, DBarb, and DOak, but also a bimodal distribution of intermediate frequencies. Again, would we get this if there was a mix of species in this population?