Rapid speciation in small populations challenges the dominance of ecological speciation

Summary This is a modelling tool for the speciation dynamics under an assumption of reproductive isolation based on the genetic distance between individuals. The HAL model was originally proposed in: Gavrilets, S. (1999). A Dynamical Theory of Speciation on Holey Adaptive Landscapes. The American Naturalist, 154(1), 1–22. doi: 10.1086/303217 Project architecture Each folder with scripts contains a README with more details compare_simulation_predictions/: compare simulations under the HAL model with the deterministic prediction correlation_time_popsize_DILS/: correlation between speciation time and population sizes from the DILS data examples/: figures used in this README. fig/: figures of the main publication fig_gz/: plots of the grey zone (GZ) for each scenario tested with the fit to a sigmoid output/: directory containing the results of the deterministic predictions scripts/: main scripts implementing the HAL model (simulation and deterministic predictions) style/: matplotlib configuration for the figures Scripts: 1-predictions_neutral.py: makes the predictions in the neutral allopatric case 2-migr_bifurc_diag.py: calculates the equilibrium of the HAL dynamical system with migration and finds the bifurcation points 3-prediction_migr.py and 4-prediction_migr_nospec.py: make the predictions in the parapatric neutral case (in the cases with and without speciation) 5-predictions_la.py: makes the predictions in the case with local adaptation 6-plot_speciation_time_polymorphism.py: plots the speciation time and the polymorphism of the previous predictions with the parameters 7-predictions_asymmetric.py: runs predictions when population sizes are different 8-plot_predictions_asymmetric.py: plots the results of predictions 7 9-plot_grey_zone_temp_div.py: plot the characteristics of the grey zone of speciation from the predictions in the 3 scenarios plot_example_HAL.py: plot an illustration of the HAL framework plot_illustration_R.py: make a plot to illustrate the dependance of R (fixation coefficient) on the parameters of the model HAL_predictions.py: function to run the HAL deterministic prediction directly in command line HAL_simulations.py: function to run the HAL stochastic simulations directly in command line