diff --git a/stdpopsim/catalog/AraTha/__init__.py b/stdpopsim/catalog/AraTha/__init__.py index 8ec56e2ad..3a3ee4fa2 100644 --- a/stdpopsim/catalog/AraTha/__init__.py +++ b/stdpopsim/catalog/AraTha/__init__.py @@ -4,4 +4,5 @@ from . import species # noqa: F401 from . import genetic_maps # noqa: F401 from . import demographic_models # noqa: F401 +from . import dfes # noqa: F401 from . import annotations # noqa: F401 diff --git a/stdpopsim/catalog/AraTha/dfes.py b/stdpopsim/catalog/AraTha/dfes.py new file mode 100644 index 000000000..fbcbdd092 --- /dev/null +++ b/stdpopsim/catalog/AraTha/dfes.py @@ -0,0 +1,58 @@ +import stdpopsim + +_species = stdpopsim.get_species("AraTha") + +########################################################### +# +# DFEs +# +########################################################### + + +def _HuberDFE(): + id = "Gamma_H18" + description = "Deleterious Gamma DFE" + long_description = """ + Return negative (no neutral, in this case) MutationType()s + representing an Arabidopsis DFE. From Huber et al. (2018). + Gamma parameters are based on Supplementary Table 4, + the genome-wide, additive-only model for A. LYRATA- due to + challenges with simulating with selfing for A. thaliana. + The Supplementary Table 4 DFEs are not noted to contain + any neutral mutations (in contrast, Supplementary Table 3 + notes neutral proportions for two other DFEs), and in the + main text including neutral mutations seems like a + supplementary analysis rather than the main strategy. + """ + citations = [ + stdpopsim.Citation( + author="Huber et al.", + year=2018, + doi="https://doi.org/10.1038/s41467-018-05281-7", + reasons=stdpopsim.CiteReason.DFE, + ) + ] + neutral = stdpopsim.MutationType() + gamma_shape = 0.27 # shape + gamma_mean = -0.0004 # expected value + h = 0.5 # dominance coefficient + negative = stdpopsim.MutationType( + dominance_coeff=h, + distribution_type="g", # gamma distribution + distribution_args=[gamma_mean, gamma_shape], + ) + + return stdpopsim.DFE( + id=id, + description=description, + long_description=long_description, + mutation_types=[neutral, negative], + proportions=[ + 0, + 1.0, + ], + citations=citations, + ) + + +_species.add_dfe(_HuberDFE()) diff --git a/stdpopsim/catalog/HomSap/dfes.py b/stdpopsim/catalog/HomSap/dfes.py index fd6cfca91..866d0c777 100644 --- a/stdpopsim/catalog/HomSap/dfes.py +++ b/stdpopsim/catalog/HomSap/dfes.py @@ -68,7 +68,7 @@ def _HuberDFE(): author="Huber et al.", year=2017, doi="https://doi.org/10.1073/pnas.1619508114", - reasons="to be defined", # include the dfe_model reason + reasons=stdpopsim.CiteReason.DFE, ) ] neutral = stdpopsim.MutationType()