Coalescence with purifying selectionHow positive selection affects genealogies is demonstrated by the script genealogies_with_selection.py and discussed on page Genealogies 1. Here, we extend this discussion to purifying selection. Instead of an infinite sites model, we now use a finite sites model. Recurrent mutations with are injected with rate U. The population will settle at a state where the influx of deleterious mutations is balanced by rare back-mutations. Hence this approximates a state where the majority of mutations are deleterious. Mutations have effect size s. The entire script can be viewed genealogies_with_selection.html or downloaded genealogies_with_selection.py.
Everything is more or less the same as in the example on positive selection, only that the per site mutation rate is set as
N = 10000 #population size s = -1e-2 #single site effect U = 0.1 #genome wide mutation rate r = 0.0 #outcrossing rate
No sex, frequent deleterious mutationsThe following shows three trees sampled from a large asexual population suffering from many deleterious mutations.
The genealogies are strongly distorted and show long terminal branches and uneven branching.
Outcrossing reduces interferenceTo demonstrate how outcrossing reduces interference, the following shows the genealogy in an obligate outcrossing population with a maplength 10. The population size was reduced to N=1000 to speed up the simulation.
Coalescence takes much longer than in the asexual example, even though the population size is smaller by a factor of 10. Open the script in your favorite text editor, change parameters, and rerun to explore.