Evolving with tree sequence recording

Note

The function described in this section has many kwargs specifying various advanced features. Some of these will be the subject of later vignettes.

Future releases are likely to change these arguments to be kwarg only. It is also possible that we will move them into a class that can be pickled, added to tskit tree files, etc..

The function fwdpy11.evolvets() evolves a population with tree sequence recording.

Our model

By way of example, let’s use the following model:

import fwdpy11

pop = fwdpy11.DiploidPopulation(500, 1.0)

rng = fwdpy11.GSLrng(54321)

GSSmo = fwdpy11.GaussianStabilizingSelection.single_trait(
    [
        fwdpy11.Optimum(when=0, optimum=0.0, VS=1.0),
        fwdpy11.Optimum(when=10 * pop.N - 200, optimum=1.0, VS=1.0),
    ]
)

rho = 1000.

des = fwdpy11.GaussianS(beg=0, end=1, weight=1, sd=0.1,
    h=fwdpy11.LargeEffectExponentiallyRecessive(k=5.0))

p = {
    "nregions": [],
    "gvalue": fwdpy11.Additive(2.0, GSSmo),
    "sregions": [des],
    "recregions": [fwdpy11.PoissonInterval(0, 1., rho / float(4 * pop.N))],
    "rates": (0.0, 1e-3, None),
    "prune_selected": False,
    "demography": fwdpy11.ForwardDemesGraph.tubes([pop.N], burnin=10),
    "simlen": 10 * pop.N,
}
params = fwdpy11.ModelParams(**p)

The tables recording the genetic ancestry of the population are empty. For example, there are no edges:

len(pop.tables.edges)

0

Now, we can call our function to evolve our population. We will apply the table simplification algorithm of [KTAR18] every 100 generations.

fwdpy11.evolvets(rng, pop, params, simplification_interval=100) 

Now, the edge table is populated:

import numpy as np

np.array(pop.tables.edges, copy=False)[:10]

array([(0.        , 0.30459662, 1000, 303),
       (0.        , 0.30459662, 1000, 757),
       (0.93025801, 1.        , 1001, 145),
       (0.93025801, 1.        , 1001, 246),
       (0.        , 0.93025801, 1002, 145),
       (0.        , 0.57626909, 1002, 246),
       (0.        , 1.        , 1002, 899),
       (0.        , 1.        , 1002, 932),
       (0.15737727, 0.25823389, 1003, 244),
       (0.15737727, 0.25823389, 1003, 681)],
      dtype=[('left', '<f8'), ('right', '<f8'), ('parent', '<i4'), ('child', '<i4')])