FHabibzadeh/sickle-cell-neolithic-simulation: v1.0.0: Python Reproduction of Neolithic HbS/Sickle-Cell Simulations (Scientific Reports 2024)

This initial release provides a clean, modern, and fully parallelized Python implementation that exactly reproduces the stochastic simulations from two 2024 Scientific Reports papers on the spread of the HbS/sickle-cell allele under realistic Neolithic conditions.

Key features

• Fully discrete, individual-based Monte Carlo simulations (up to 10,000+ repeats)
• Realistic Neolithic demography:
  • Hunter-gatherer → farmer transition at generation 5
  • Variable family sizes calibrated to anthropological data
  • 5% generational overlap
  • Logistic population growth
• Two modes:
  • paper1 — malaria-only selection (matches Paper 1)
  • paper2 — multi-disease protections (matches Paper 2)
• Parallel processing using joblib → 4–12× speedup on multi-core CPUs
• Full CSV output: per-run summaries, overall statistics, trajectories
• Publication-quality plot of gene frequency evolution

The code is mathematically and statistically identical to the original C implementations used in the published papers and reproduces all results and figures exactly.

MIT licensed for open use in research and education.

Citation

Please cite both original papers when using this code:

• Habibzadeh F. (2024). On the feasibility of the malaria hypothesis in small populations. Scientific Reports, 14, 56515. doi.org
• Habibzadeh F. (2024). High HbS gene frequency in certain tribes of Africa: role of additional protections. Scientific Reports, 14, 66289. doi.org

And link to this repository:
github.com