Analysis of Capsella bursa-pastoris#

Code for all analyses of Capsella can be found in the capsella/ folder in the GitHub repo.

Main Scripts#

  • run_*.py: Scripts used to run demographic inference under the allotetraploid_bottleneck and segtetraploid_bottleneck models.

  • capsella_*.csv: Results of the independent optimization runs for each model.

  • analyze_capsella_results.py: Script to analyze all of the results for the maximum likelihood parameter estimates under each model, as well as code for estimating confidence intervals using the Fisher information Matrix and propogation of uncertainty.

  • douglas_et_al_comparison.py: Code for running a comparison of the segtetraploid_bottleneck model with the model used in the original Douglas et al. (2015) paper. The comparison is run with both 2D frequency spectra and the collapsed version of the SFS we introduce in our paper.

SFS Data#

The SFS data file is also in the repo and is named Capsella_intergene_4fold_corr_4pop_4_DSFS.fs. It can be read into Python as a dadi.Spectrum object using the code below:

Read the Capsella SFS file into Python as a dadi.Spectrum object.#
import dadi
fs = dadi.Spectrum.from_file("Capsella_intergene_4fold_corr_4pop_4_DSFS.fs")