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Genetic Distance

This page is to explain what genetic distance (as used by Family Tree DNA) means. Genetic distance is often abbreviated "GD".

It is taken from the FTDNA FAQ #s 915, 916 & 939, as of 14 February 2013.

The unit of genetic distance is "steps", the left-hand column of FTDNA match lists.

Basic Genetic Distance

What is genetic distance? faq id: 915

Alert: As of 12 Dec 2012, the way Family Tree DNA calculates genetic distance for palindromic STR markers and NULL allele values has changed. This will change the degree of matching for some customers.

When talking about two or more Y-chromosome STR (short tandem repeat) haplotypes, genetic distance is the total number of differences, or mutations, between two sets of results. In general, it is found by summing the differences between each STR marker.

Example: Genetic Distance = 1
Kit Surname Hg D
Y
S
3
9
3
D
Y
S
3
9
0
D
Y
S
1
9
D
Y
S
3
9
1
D
Y
S
3
8
5
a
D
Y
S
3
8
5
b
D
Y
S
4
2
6
D
Y
S
3
8
8
D
Y
S
4
3
9
D
Y
S
3
8
9
|
1
D
Y
S
3
9
2
D
Y
S
3
8
9
|
2
B291 Didmoe L 12 23 14 10 17 18 11 12 11 12 14 29
B125 Didmoe L 12 23 14 10 17 18 11 12 11 12 14 28
B322 Ditmee L 12 22 13 10 17 18 11 12 10 12 14 29

For example, kit B291 and B125 have allele values of 29 and 28 respectively at DYS389-2. This is a difference of 1 {29-28= 1}. Because this is the only difference in their Y-DNA12 profiles (haplotypes) their genetic distance is 1.

 

Example: Genetic Distance = 3
Kit Surname Hg D
Y
S
3
9
3
D
Y
S
3
9
0
D
Y
S
1
9
D
Y
S
3
9
1
D
Y
S
3
8
5
a
D
Y
S
3
8
5
b
D
Y
S
4
2
6
D
Y
S
3
8
8
D
Y
S
4
3
9
D
Y
S
3
8
9
|
1
D
Y
S
3
9
2
D
Y
S
3
8
9
|
2
B291 Didmoe L 12 23 14 10 17 18 11 12 11 12 14 29
B125 Didmoe L 12 23 14 10 17 18 11 12 11 12 14 28
B322 Ditmee L 12 22 13 10 17 18 11 12 10 12 14 29

In this example, kits B291 and B322 have differences at DYS390, DYS19, and DYS439. The difference for each is calculated {DYS390: 23-22= 1, DYS19: 14-13= 1, DYS439: 11-10= 1}. The differences are added together. The total number of differences the Y-DNA12 haplotypes is 3 {1+1+1= 3 }. Their genetic distance at 12 STR markers is then 3.

 

See also: How is genetic distance calculated for NULL values? and How does the infinite allele comparison method work for palindromic markers?


Null Values

A null value is shown by a zero (0) in the table of results. It may be due to either deletion of a marker through mutation or inability to replicate sufficient quantity of the marker's DNA for detection. Null values are reasonably rare.

How is genetic distance calculated for NULL values? faq id: 916

For matching, genetic distance is calculated as a single NULL causing event. The NULL value causing event is treated as a single step event with a genetic distance of one.


Palindromic (Multicopy) Markers

Multi-copy markers are found on palindromic regions of the Y chromosome; they include the markers labeled with "a", "b", "c", etc. on the end of the marker name. The short way to explain this is with this simplified* diagram:

diagram of a palindromic region
Notice that the two arms leading into and/or out of the P1/P2 loop read the same. Also notice the extra copies of markers (e.g., DYS464) on the arms.

* Taken from a diagram in Thomas Krahn's presentation.
How does the infinite allele comparison method work for palindromic markers? faq id: 939

For palindromic markers, the infinite allele method counts a difference for two types of changes: a mismatch and a copy number change. Mismatches are any time the compared markers do not match. For example, the first man might have DYS464 = 14-15-15-16 and the other man might have DYS464 = 14-15-16-18. This counts as a single difference toward the two men's genetic distance. Palindromic copy number changes are when one person has more copies of the STR marker than the other. For example, one man might have DYS464 = 14-15-16-17 and the other might have 14-15-15-16-16-17. This also counts as a single difference toward the two men's total genetic distance.

When two men are compared and they show both a mismatch and a copy number change, it is counted as a genetic distance of two. For example, one might have DYS464 = 14-14-15-16 and the second person DYS464 = 14-15-15-16-16-17.


Editor's Note:

What the above means is that, as of December 2012, genetic distance for most markers is the absolute value of their differences. Exceptions to this general rule are

  1. Null Values: A null value in one person but not both is counted as GD=1, i.e., infinite alleles treatment; a null value in both is counted as GD=0.
     
  2. Palindromic (multi-copy) markers:
    • Each copy is treated by infinite alleles, i.e., each copy differing in values represents a GD=1.
    • A difference in number of copies is a GD=1.
    • If there is a difference in number of copies AND in values, each is a separate step of GD.

The genetic distance for each marker compared is summed to get total steps of genetic distance. Prior to December 2012, FTDNA made no exceptions for null values and multi-copy markers.

Using genetic distance

Genetic distance is only a rough guide to the degree of similarity between two haplotypes and thus the probability of sharing a common ancestor within a specified number of generations. A more precise guide uses mutation-rate adjustments to gauge haplotype similarity. An example is the FTDNA TiP (Time Predictor) algorithm.

Genetic distance is meaningful only if the number of markers across which it occurs is specifically stated. A GD=2 for 12 markers is not the same as GD=2 for 67 markers; the former suggests no relationship, the latter a fairly close relationship.