Genetic distance is defined as the total difference in allele values of different genetic markers between two individuals. The smaller the value of the genetic distance, the closer two individuals are related, and the more recently they shared a common ancestor (TMRCA). The method used to determine genetic distance for four different Y-DNA STR marker types is explained below.

A. Calculation of genetic distance for single-copy markers

For single-copy markers, the calculation is straightforward. The genetic distance for each single copy marker between two individuals is the absolute value of the difference between the value of the markers:

The total genetic distance between two individuals is the sum of the genetic distances of all markers compared.

B. Calculation of genetic distance for multi-copy markers Markers DYS385, DYS459, DYS464 and YCAII are multi-copy Y-STR markers.

For most multi-copy markers, genetic distance can be calculated by adding the differences in allele values for each of the two copies.

C. Calculation of genetic distance for multi-copy marker DYS464 - using Infinite allele model

Assuming mutations at different copies of the same marker took place in a single generation, the Infinite allele method counts the total difference between all copies of the same marker as 1, despite the fact that more than one mutation exists.

The genetic distance for DYS464 is calculated using this method.

D. Calculation of genetic distance for DYS389i/ii

DYS389i is embedded in DYS389ii; therefore, the DYS389i values are included in DYS389ii values. Genetic distance can be determined by adding up two differences: differences in DYS389i values and differences in the second part of DYS389ii values, which are obtained by subtracting the DYS389ii values by DYS389i values.