Post date: Oct 06, 2015 5:0:11 PM
Doro found interesting evidence of pronounced Fst between pattern morphs (striped, green, melanic) on much of LG8 that is suggestive of one or more inversions. I am using the whole genome data from the survivors of the Ecology Letters experiment to see whether this holds there too. This analysis and files are in /labs/evolution/projects/timema_speciation/timema_wgexperiment/popgen/morhps/. I used splitPops.pl to (hopefully) generate genotype likelihood files for the striped vs. green (we don't have melanic) bugs. I am then used estpEM (EM algorithm for ML of p) to infer allele frequencies for each morph. Here is the code:
cd /labs/evolution/projects/timema_speciation/timema_wgexperiment/popgen/morhps/
estpEM -i timemaStripe0.gl -o p_timemaStripe0.txt -e 0.0001 -m 20 -h 0
cd /labs/evolution/projects/timema_speciation/timema_wgexperiment/popgen/morhps/
estpEM -i timemaStripe1.gl -o p_timemaStripe1.txt -e 0.0001 -m 20 -h 0
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