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I have have measured the trait frequency for a "mountain" associated allele across a number of sites and years. In my (glmer) model I have summarized the allele frequency by site and year as the dependent (binomial) variable and specified site and year as random effects. The fixed effects are...

I have binomial frequency data for an allele associated with populations living in mountainous. These mountains run north to south where sites are nearly fixed for this allele and lowland sites to the east that lack the allele. At the south end of the mountains is a hybrid zone. Despite the...