Allele size standardization
Genotype data from different studies obtained with the aforementioned
six microsatellite sets were combined after standardizing allele sizes
using the Genalex add-in for Excel (version 6.503) (Peakall & Smouse,
2006; Peakall & Smouse, 2012). Standardization was necessary, because
allele size estimates have been observed to differ up to 7 bp among
platforms (LaHood, Moran, Olsen, Grant, & Park, 2002). In our case they
differed up to 11 bp (microsatellite set B relative to set A:BM3517 : 8 bp, INRA006 : 11 bp, ≤5 bp in the remaining
cases). For various populations, two microsatellite sets were available
(sets A-D in Tables 1 and 2), which permitted standardization by
shifting allele sizes by a constant amount in one of the two sets. With
two microsatellites sets (sets E and F in Tables 1 and 2)
standardization was only possible in comparison with another
microsatellite set applied to another population. The size shift we used
was the one that resulted in the highest Pearson correlation in allele
frequencies and lowest F ST between two sets.
Given large enough sample sizes, their values are expected to be close
to 1 and 0, respectively. Generally, the obtained Pearson correlations
were >0.8 and the F ST values
<0.01. Using the standardized data to regress pairwise
multilocus F ST values on geographic distance
explained 78% of the genetic variation among populations in East and
southern Africa (Figure S1), thereby providing further support for the
accuracy of the allele size standardization. A detailed description of
the allele size standardization is given in Text S1.