Estimation of the population scaled mutation rate from microsatellite data.

IN a recent issue of Genetics, RoyChoudhury and Stephens (2007) showcased a new method for estimating the population scaled mutation rate u from microsatellite data; u is equivalent to four times the effective population size times the mutation rate per generation and can also be viewed as the scaled population size. Their approximation delivered impressively accurate results with little bias. They compared their results with several other commonly available programs. Their study is a good example of how comparisons with other programs should be presented; but I was not impressed by the bias and median absolute error reported for my own program MIGRATE (Beerli and Felsenstein 2001). RoyChoudhury and Stephens (2007) used the defaults of MIGRATE and wondered, given the large observed biases, how more difficult population models would fare when MIGRATE 1.7.3 has difficulties estimating a single parameter. On my request, A. RoyChoudhury sent me their data sets, so that I could check whether the current version of MIGRATE (2.3; http://popgen.scs.fsu.edu) suffers from the same problem as the tested version. The data sets, which contained 50 unlinkedmicrosatellite loci for sample sizes of 10, 20, 40, and 80 gene copies from a single population of size uT of 2, 8, and 32, were simulated using the coalescent simulator of Paul Fearnhead (RoyChoudhury and Stephens 2007). I ran these data sets through MIGRATE 2.3 using default settings with the stepwise mutation model and the Brownian motion approximation. A comparison of my Figure 1 with Figure 1 in their article shows clearly that the current version of MIGRATE is much less biased. In fact, the results are very similar to the approximatemethod of RoyChoudhury and Stephens. My Figure 1 includes their results for uT 1⁄4 32 as a reference. The Brownian motion approximation in MIGRATE, already available in version 1.7.3, delivers similar results much faster; the runtime for the largest single locus data set was "30 sec on a 2 Ghz