Stdpopsim: add selfing rate

Created on 8 Apr 2021  路  1Comment  路  Source: popsim-consortium/stdpopsim

Many species are partial selfers; for instance C. elegans (see #834) has a selfing rate of about 99.9%. SLiM has a "selfing rate" option that we can use directly; for msprime we'd need to rescale things (see for instance Nordborg & Donnelly. So, maybe we need to

  • [ ] add selfing_rate as a new attribute to Species objects
  • [ ] modify engines to use this information

Note it's a little tricky to "use this information" in an engine because for instance selfing rate s multiplies Ne by (2-s)/2; this suggests we'd want to simulate with msprime using Ne = population_size * (2-selfing_rate)/2... however, estimates of Ne are probably based on genetic diversity and so probably already have this factor included.

enhancement

Most helpful comment

FYI, demes includes a selfing_rate (and a cloning_rate).

>All comments

FYI, demes includes a selfing_rate (and a cloning_rate).

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