Sus scrofa demography from Piecewise size model for wild boar (Wang et al. 2025) #1752
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- Coverage 99.81% 99.38% -0.43%
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Lines 4863 4884 +21
Branches 470 470
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AprilYUZhang
changed the title
| long_description = """ | ||
| This demographic model is a piecewise size model for wild boar | ||
| from Zhang et al. (2022). Effective population sizes were estimated by | ||
| PSMC with parameters Tmax = 20, n = 64 (4 + 50*1 + 4 + 6) |
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n here is PSMC parameter. We likely don't need this level of detail here.
| long_description = """ | ||
| This demographic model is a piecewise size model for wild boar | ||
| from Wang et al. (2025). Effective population sizes were estimated by | ||
| MSMC with parameters n = 64 (4 + 50*1 + 4 + 6), generation time (g) = 5 years, and |
| long_description = """ | ||
| This demographic model is a piecewise size model for wild boar | ||
| from Zhang et al. (2022). Effective population sizes were estimated by | ||
| PSMC with parameters Tmax = 20, n = 64 (4 + 50*1 + 4 + 6) |
There was a problem hiding this comment.
@AprilYUZhang PSMC is run on just one genome (as far as I know), but you state n=64, so I am confused. Will read the paper, but you might get back to this comment faster.
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Reading the paper shows that PSMC was run on each sample, but then also MSMC2 was used, but this data was not shared by the authors.
| PSMC with parameters Tmax = 20, n = 64 (4 + 50*1 + 4 + 6) | ||
| """ | ||
| populations = [ | ||
| stdpopsim.Population(id="EUW", description="European wild boar"), |
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@petrelharp with PSMC we get just one population model. @AprilYUZhang has here combined 4 populations into one model. Is this ok or should we have 4 separate models from one study?
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I am happy to work with @AprilYUZhang on revising this PR and the follow-up QC |
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Tagging the issue that this PR addresses #1312 |
| _species.add_demographic_model(_WildBoar_4Z22()) | ||
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| _WangEtAl = stdpopsim.Citation( | ||
| doi="https://doi.org/10.1101/2025.02.05.636574", |
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This DOI points to pre-print at https://www.biorxiv.org/content/10.1101/2025.02.05.636574v1, but the corresponding paper has now been published at https://doi.org/10.1016/j.xgen.2025.100954. Best to use the latter DOI.
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| def _WildBoar_4Z22(): | ||
| id = "WildBoar_4Z22" | ||
| description = "Piecewise size model for wild boar (Zhang et al. 2022)" |
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| description = "Piecewise size model for wild boar (Zhang et al. 2022)" | |
| description = "Piecewise size model for wild boar (pig) (Zhang et al., 2022)" |
| generation_time=3, | ||
| mutation_rate=3.6e-9, | ||
| population_configurations=[ | ||
| stdpopsim.PopulationConfiguration( |
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@AprilYUZhang there is a lot of code here due to many timesteps. I suggest you follow the style from https://github.com/popsim-consortium/stdpopsim/blob/main/stdpopsim/qc/BosTau.py
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