Exploring the coalescent

I’ve just posted Lab 7. You’ll find it in the usual places, i.e., from the Lab Schedule page or from the direct link below. As you’ll see, this lab exercise will allow you to explore the coalescent by comparing the time to coalescence of all alleles in a sample as a function of the rate of migration, the number of populations exchanging genes, and the migration model, i.e., either the finite island model you explored in last week’s exercise or the one-dimensional stepping stone. As noted in the exercise itself, the run_simulation() function will run 1000 samples by default. I recommend picking a smaller number first, say 50 or 100, to get a sense of how long a full run will take before you start the simulation. It shouldn’t be surprising that simulations take longer the more populations that you specify. There’s no need to try simulating more than 100 populations. You’ll see any patterns associated with differing numbers of populations by the time you get to that many.

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