Simulation scenario

Reich and Lander Reich2001a proposed a population genetics framework to model the evolution of allelic spectra (the number and population frequency of alleles at a locus). The model is based on the fact that human population grew quickly from around 10,000 to 6 billion in 18,000 -150,000 years. His analysis showed that at the founder population, both common and rare diseases have simple spectra. After the sudden expansion of population size, the allelic spectra of simple diseases become complex; while those of complex diseases remained simple.

This example is a simplified version of the simuCDCV.py script that simulates this evolution process and observe the allelic spectra of both types of diseases. The complete script is available at http://simupop.sourceforge.net/cookbookthe simuPOP online cookbook. The results are published in Peng2007, which has much more detailed discussion about the simulations, and the parameters used.