Check here to estimate the number of founding populations and variance of the estimate across a range of threshold values for increasing number of genetic markers1.
The number of populations and its variance is computed for a range of increasing thresholds a × m^η (where η=1/3) obtained by using a range of coefficient values of a and for an increasing set of markers S1 ⊂ S2 ⊂ S3, … ⊂ {1, … , m}, where m is the total number of markers. Then, the estimated number of populations and its empirical variance are both plotted versus the coefficient a. An useful practical criteria to estimate the number of populations is to use the value of population number for which the second interval of variance is small (Hallin and Liska, 2007)
Leek, J. T. 2011. Asymptotic conditional singular value decomposition for high-dimensional genomic data. Biometrics 67: 344–52.
Hallin M, Liska R. 2007. Determining the number of factors in the general dynamic factor model. Journal of the American Statistical Association. 102: 603–617.