Simulating population structure using island and stepping-stone models
We will now simulate population structure. Let's start with an island model and then create a one-dimensional stepping-stone model. We will also study FST and distinguish between deme-level statistics and meta-population level statistics. Strictly speaking, we will simulate fragmentation models by splitting into islands or stepping-stones.
Getting ready
Read the first recipe (Introducing forward-time simulations) as it introduces the basic programming framework. If you are using notebooks, the content is in 04_PopSim/Pop_Structure.ipynb.
How to do it…
Take a look at the following steps:
Let's start with some basic code from the first recipe:
from __future__ import division from collections import defaultdict, OrderedDict from copy import deepcopy import simuPOP as sp from simuPOP import demography num_loci = 10 pop_size = 50 num_gens = 101 num_pops = 10 migs = [0, 0.005, 0.01, 0.02, 0.05, 0.1] init_ops = OrderedDict() pre_ops...