Stochastic Modeling and Simulation of Ascertainment Bias in Population Genetics of Inter-Species Studies

• Activity Number: 138
• Type: Contributed
• Date/Time: Monday, August 1, 2011 : 8:30 AM to 10:20 PM
• Sponsor: Section on Statistical Computing
• Author(s): Biao Li*+ and Marek Kimmel
• Companies: Rice University and Rice University
• Keywords: ascertainment bias ; population genetics ; inter-population variability ; microsatellites ; coalescence ; forward-time simulation

Abstract

In population genetics studies, investigators often calculate the inter-population variability at certain homologous loci, e.g. microsatellites and single nucleotide polymorphisms (SNPs), in closely related species. Ascertainment bias arises when a polymorphic locus is selected under a biased discovery process in species 1 and then typed in another species 2. However, allele variability can be influenced, besides the ascertainment bias, by genetic forces such as drift and mutation as well as time-variable demography. Based on the application of stochastic process and Wright-Fisher-Coalescence theory with constant genetic factors, we construct a model to discern ascertainment bias from effects of other forces and aim to implement it to more realistic demographic scenarios with changeable factors. We also use simuPOP, an individual-based forward-time population genetics simulation environment, to test the validity of the model. Simulation results agree very well with the modeling results. By fitting the model to experimental data, we characterize the effect of the ascertainment bias and estimate the impact of demography and genetic forces in inter-species studies.