Allele size statistics¶
The following statistics make use of the allele size. They are available
from ComputeStats()
(all methods), but require that an
alphabet with alleles coded as integers is provided. The allele values
are interpreted as allele sizes (even if negative values are found: in
that case it is assumed that allele sizes are shifted).
Code 
Definition 
Equation 

V 
Allele size variance 

Ar 
Allele range 

M 
Garza and Williamson's M 

Rst 
Slatkin's \(R_{ST}\) 
If \(k\) is the number of alleles, \(A_i\) if the size of allele \(i\), \(p_i\) is the frequency of this allele and \(n = \sum p_i\) is the number of samples, the allele size variance is computed as a sample variance:
The allele range is simply:
Garza and Williamson’s \(M\) (Mol. Ecol. 2001 10:305318) is computed as:
Finally, Slatkin’s \(R_{ST}\) (Genetics 1995 139:457462) is computed as shown below, considering only samples from populations with at least 2 samples. Note that when computing the value for several sites the value of \(R_{ST}\) is computed as the ratio of the sums of the different terms (rather than the average of the persite values). \(\bar{V}\) is the average of withinpopulation allele size variance.