Changing size of outgroup population in pyslim recapitation

[mshpak76]

I simulated a demographic history in slim with population genealogy p1,(p2,(p3,p4)), where the 3,4 split occurred ~300 generations ago, the 2,(3,4) split ~1000 generation ago, and the 1,(2,(3,4)) split 4000 generations ago. Selection occurs in target population p4. The complication is that there is a twofold change in population size (from 20K to 10K) that occurred in p1 12K generations prior to the 2,3,4 split. I do not wish to simulate this in slim because of the long runtime, so I'm only simulating the 1000 generations of the last two splits.

How can I indicate the generation time at which this change occurred when recapitating in pyslim? I can use

rts = pyslim.recapitate(ts_new, recombination_rate = 1.14e-8, gene_conversion_rate = 5.9e-8, gene_conversion_tract_length = 100, ancestral_Ne=10000, random_seed = ancestry_seed)

to indicate that the ancestral population (wrt p1) is 10K rather than 20K, but this would set the population size to 10K at t=1000. I want to have p1 at 20K in the recapitation up until time 12K. Is there some way to "import" a msprime type of command to do this, e.g.

 orig_ts = tskit.load("Demog_FixC.trees")

demography = msprime.Demography.from_tree_sequence(orig_ts)
demography.add_population_parameters_change(time=12000, population="p1", initial_size=10000,growth_rate = 0.0)

I'm not sure if something like this will give me what I want, i.e. in slim I defined p1 as the ancestral/outgroup population - will this maintain the population at 20K until time 12000 generations, and then continue to use 10K as the ancestral poulation size? As it stands, population="p1" isn't recognized even though in slim the outgroup population was set to p1.

[petrelharp]

Something like that will definitely give you what you want! You just need to figure out how to set up the demographic model in msprime to do what you want - have a look at https://tskit.dev/pyslim/docs/latest/tutorial.html#recapitation-with-migration-between-more-than-one-population for an example.

[mshpak76]

Thank you, the example was quite helpful.