Evol Ecol Res 14: 859-879 (2012) Full PDF if your library subscribes.
The consequences of the unlikely but critical assumption of stepwise mutation in the population genetic software, MSVAR
Søren Faurby1,2 and Cino Pertoldi1,3,4
1Department of Bioscience, Aarhus University, Aarhus, Denmark, 2Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA, 3Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark and 4Aalborg Zoo, Aalborg, Denmark
Correspondence: S. Faurby, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8200 Aarhus, Denmark. E-mail: email@example.com
Background: MSVAR is a software package for simulating and analysing microsatellite evolution. It assumes that all mutations lead to alleles exactly one repeat longer or shorter than the original (the stepwise mutation model) but many actual mutations lead to size changes of several repeats.
Question: How reliable are the conclusions of microsatellite analyses using the software MSVAR if we assume realistic violations of its stepwise mutation assumption?
Mathematical methods: Simulate microsatellite evolution using forward simulations, under various demographic scenarios. Use different degrees of departure from the pure stepwise mutation model. Then analyse the results using a GLM approach.
Key assumption: Regardless of starting conditions, microsatellite size attains equilibrium or near equilibrium conditions after 5Ne generations (where Ne is effective population size).
Results: Absolute values of past and present Ne, the magnitude of Ne change or the time frame of the demographic changes from the output of MSVAR cannot be trusted in the presence of realistic deviations from the assumed (stepwise) mutation model. Ancestral population sizes will be severely overestimated while current populations will be underestimated but to a lesser extent. The extent of bias produced by a given degree of model deviation is only slightly influenced by demography. The relative differences in Ne between populations of the same species will therefore generally be reliable.
Keywords: demographic changes, effective population size, microsatellites, Ne, stepwise mutation model.
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