We now have a new lentil adapted line. Samples were saved every generation during the early stages of adaptation. The goal of this project is to analyze patterns of allele frequency change during this initial period of adaptation at a fine scale to (a) identify genetic regions likely associated with lentil adaptation and (b) determine whether these regions showed consistent patterns of selection/change during this period (alternatively, change could have plateaued at some point, or selection could have only kicked in after change in other regions). The new line (L14) was actually split, so we can also ask about consistency after the split. Finally, my plan (assuming things look interesting) is to sequence whole genomes from the beginning and end of the experiment and from L1-L3 to ask about consistency at a greater scale and get at overall patterns of change (the GBS data could miss some causal variants and thus some components of change).
My analyses of these data are below, but Alex will be working on them too. Here is a link to his work on the project.
Parsing L14 GBS data - Nov 06, 2016 3:40:55 AM
C. maculatus, ABC for L14 - Feb 08, 2017 3:51:9 AM