Understanding Y-DNA Genetic Distance

Genetic Distance (GD) refers to the total number of differences in the STR values of two different people. For example, if we look at 12 STRs and two people have the same values for all 12 markers, they have a GD of 0. 

There are two methods to determine the GD. These are the Step-Wise Mutation Model and the Infinite Allele Model.

Step-Wise Mutation Model

Most mutations only cause a single repeat within an STR marker to be added or lost. For these markers, we use the Step-Wise Mutation Model.

In this model, the GD for an STR marker between two people is the numerical difference in the marker. For example, if Person A has DYS19=15 and Person B has DYS19=17, then it counts as a GD of 2. 

Infinite Allele Model

In some cases, an entire marker is added or deleted instead of a single repeat within a marker. This is believed to represent a single mutation in the same way that the addition or subtraction of a repeat is a single mutation event. For this reason, we use the Infinite Allele Model in these cases.

In the Infinite Allele Model, the GD for an STR marker between two people is counted as “1” regardless of the numerical difference. This is most frequently used in null values and multi-copy markers.

Null Values

When an STR simply does not exist in an individual, this is called a null value. When a marker is missing, the value is listed as 0. 

For example, if Person A has DYS19=15 and Person B has DYS19=0, then using the Step-Wise Mutation Model would report this as a GD of 15. This would be inaccurate as the deletion happened only once. Instead, we use the Infinite Allele Model and count this null value as a GD of 1.

Multi-Copy markers

Multi-copy markers appear in more than one place on the Y chromosome. These are reported as the value found at each location, separated by hyphens. For example, you may see DYS464=15-15-15-16. This means that DYS464 has a unique number of repeats in each location. These locations are usually referred to as DYS464a, DYS464b, DYS464c, etc.

Within multi-copy markers, there are two types of mutations, or changes, that can occur: marker changes and copy changes. 

Marker Changes

Marker changes (changes in how many repeats are within a marker) are counted with the Step-Wise Mutation Model. 

Copy Changes

Copy changes (changes in the number of markers, regardless of how many repeats are in each) are counted with the Infinite Allele Model. 

To better understand how we use both marker changes and copy changes in calculating GD for multi-copy markers, let’s look at an example:

In this example, Person B has one extra repeat in DYS464c. This was probably added in a  single mutation event, so we count this GD as 1.

Person B also has one extra marker, named DYD464e. Since Person A does not have this at all, then it was either deleted in Person A in a single mutation event, or it was added to Person B in a single mutation event. It would make more sense to count the GD as 1 for that repeat than to count all 16 repeats. Counting it as 16 would imply that it mutated 16 times, which is highly unlikely. This means we apply the Infinite Allele Model for this extra repeat.

When we add these two separate changes together, we get an overall GD for this marker of 2.

For a more in-depth look at what this means and why they are calculated this way, see the Multi-Copy Markers topic. 

Calculating GD

When comparing two people, we use the Step-Wise Mutation Model for all markers with the exception of null values and multi-copy markers. Null values use the Infinite Allele Model and multi-copy markers use a combination of the Step-Wise Mutation Model and the Infinite Allele Model as described above.

Adding together the GD for each marker in two people provides the overall GD for those two people. When a GD becomes too great, it is unlikely that the two people share a common ancestor within a genealogical timeframe, so each testing level has an upper limit of GD for matching.