Post date: Nov 16, 2017 3:31:30 PM
Genetic story
There are likely different loci affecting GB versus RG aspects of color - check out the two attached Gemma plots - where the peak around 52000 for RG is not there for GB - other plots and Genabel tell a similar story. So, this is related to the idea that variation is multi-oligo-genic in T.chumash but adds the detail that really we have two axes of variation and from the phenotypic side T.chumash really does show these axes (there is a green to blue spectrum for the 'regular' common bugs and then some darker ones pull away from these towards the red).
The region harboring these loci was likely inverted in the south to create chromosomal races (T. bart, T. pod – but note here we do not appear to have the indel – this is clear in T. bart with all three genotypes to compare but also likely in T. pod given hets and the one existing homozygote appear similar-ish in coverage). So, the first event was likely restricting recombination in this region to create more discrete morphs, but no indel.
The next event appears to be a single origin of the indel in North to really lock things up - loss of function - note that the greens have deletion and that in the North the species are really ‘green’ – this is supported by phenotypic data (graph attached).
So, the story may be rather simple really - few loci affecting a few traits (GB vs RG), locked up by restricted recombination, then locked up further by deletion.
Now, why did this all occur...
Ecological story
Here the idea is that the crypsis stuff will start A PRIORI motivated by natural history observations. Finesse writing to make it not overly strong - so not a true, highly replicated test of a hypothesis, but rather quantification of some trends that emerged from natural history observations (inductive rather than deductive approach). The observations - oak has all kinds of colors, which is associated with T.chum having more continuous variation, high recombination. Pine has dead and live needles (T. bart more discrete, strange red-head morph), Ceanothus and Adenostoma have classic between host trade-off with twist of light bark of this particular species of Ceanothus (T. pod has discrete green versus brown morphs). So, what Clarissa would focus on would be just quantifying these contrasts from photos - no need to do everything with every plant, but focus on these three contrasts (many oak leaves, dead vs live needles, C vs A hosts).