title: Fast stochastic algorithm for simulating evolutionary population dynamics.
abstract: BACKGROUND
  Many important aspects of evolutionary dynamics can only be addressed through simulations. However, accurate simulations of realistically large populations over long periods of time needed for evolution to proceed are computationally expensive. Mutants can be present in very small numbers and yet (if they are more fit than others) be the key part of the evolutionary process. This leads to significant stochasticity that needs to be accounted for. Different evolutionary events occur at very different time scales: mutations are typically much rarer than reproduction and deaths.
  
  
  RESULTS
  We introduce a new exact algorithm for fast fully stochastic simulations of evolutionary dynamics that include birth, death and mutation events. It produces a significant speedup compared to direct stochastic simulations in a typical case when the population size is large and the mutation rates are much smaller than birth and death rates. The algorithm performance is illustrated by several examples that include evolution on a smooth and rugged fitness landscape. We also show how this algorithm can be adapted for approximate simulations of more complex evolutionary problems and illustrate it by simulations of a stochastic competitive growth model.
authors.affiliation: Department of Bioengineering, University of California-San Diego, CA 92093, USA.
authors.forename: William H
authors.initials: WH
authors.lastname: Mather
authors.forename: Jeff
authors.initials: J
authors.lastname: Hasty
authors.forename: Lev S
authors.initials: LS
authors.lastname: Tsimring
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000166:cytology* / Q000235:genetics / Q000254:growth & development; D005075:Biological Evolution; D003198:Computer Simulation; D009154:Mutation