2012/10/05 by Mikkel Meyer Andersen, Andersen, Mikkel Meyer, Poul Svante Eriksen +1
Computer Science · #62-04 #Algorithms and Data Compression #Bayesian Methods and Mixture Models #Computation (stat.CO) #Data Management and Algorithms #FOS: Biological sciences #FOS: Computer and information sciences #G.3 #Other Statistics (stat.OT) #Populations and Evolution (q-bio.PE)
paper · pdf · doi:10.48550/arxiv.1210.1773
openalex publication_date 2012/10/05 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics, the haplotypes can for example consist of lineage markers such as short tandem repeat loci on the Y chromosome (Y-STR). A dominating model for describing population dynamics is the simple, yet powerful, Fisher-Wright model. We describe an efficient algorithm for exact forward simulation of exact Fisher-Wright populations (and not approximative such as the coalescent model). The efficiency comes from convenient data structures by changing the traditional view from individuals to haplotypes. The algorithm is implemented in the open-source R package 'fwsim' and is able to simulate very large populations. We focus on a haploid model and assume stochastic population size with flexible growth specification, no selection, a neutral single step mutation process, and self-reproducing individuals. These assumptions make the algorithm ideal for studying lineage markers such as Y-STR.