mtDNA Testing for Genetic Genealogy

Maternal Lineage mtDNA Testing

MtDNA testing (mitochondrial DNA testing) is used for maternal genealogy. MtDNA is passed from a mother to her children. Thus, it traces a direct maternal line. Both men and women can take mtDNA tests. Perfect matches are evidence that two people share a common maternal ancestor.

There are three reasons to take an mtDNA test. The first is for genealogy evidence. The second is for ethnic origins. The third is for random match discovery. That is, genealogy match fishing. MtDNA testing does well for the first two. It is not as good at the last one.

What is tested by mtDNA testing

MtDNA has many variants, also known as single nucleotide polymorphisms (SNPs). These variants are tested and used for matching.

There are two ways mtDNA can be tested to help with your genealogy. The first is direct mtDNA testing. This method sequences the entire mitochondrial genome (mtGenome). Results include all variants that exist there. It’s the best method for finding new variants. With direct testing, one can best understand matches. The second is targeted testing. It tests a set of known variants. These are picked from variant databases and from known haplogroups.

FamilyTreeDNA and YSeq both do direct testing. Microarray chips may be used for targeted mtDNA testing. Companies that use microarray chips like 23andMe, the Genographic Project, and Living DNA use targeted testing.

For genealogy, direct testing of the mtDNA genome (mtGenome) is best. At times, targeted testing may be OK to prove a hypothesis wrong.

Understanding mtDNA testing results

mtDNA Testing of the mtGenome - Wikipedia
mtDNA Genome – Wikipedia

The mtDNA genome

Current science splits mtDNA into two parts. These are the control region and the coding region.

The control region
The control region is used in DNA replication to prevent copy errors. It does not contain genes. Scientists also call the control region the d-loop.

It is further split into the first hypervariable region (HVR1), and the second hypervariable region (HVR2).

This area is known for a high rate of new variants.

The coding region

The coding region contains some genes. Variants occur less often inside genes. This is because variants inside genes can change the way genes function. Changes in gene function can impact our health.

Outside of the genes, the rest of the coding region may have the same new variant rate as the control region.

mtGenome structure

MtDNA forms a circle. In the picture on the right, the blue part is the control region. The rest of the circle is the coding region.

By convention, mtDNA numbering starts at HVR2. HVR2 numbering is 00001 to 00576. Next is the coding region. Coding region numbering is 00577 to 16023. Last is HVR1. HVR1 numbering is 16024 to 16569.

mtDNA reference sequences

mtDNA results are returned as comparisons to a reference sequence. There are two reference sequences in use. They are the RSRS and the rCRS.

The newer one is the RSRS. It was introduced by scientists in 2012. This is the sequence that used by Phylotree to build the human maternal tree. It represents the likely sequence of the common maternal ancestor of all people alive today.

The older one is the rCRS. It was created when the first mtGenome was sequenced. Later it was revised when the sample was retested. It represents a rare branch under the H2 part of the maternal tree.

Forensic (criminal) DNA researchers may still prefer the rCRS. This is because their criminal profile databases were created using it.


In 2018, most testing for genealogy uses all three parts of the mtDNA. Below are examples of how mtDNA results might be presented.

mtDNA testing results
mtDNA test results

Understanding matches

Some DNA testing companies offer mtDNA matching. If you have test two potential cousins, this is how you check for a match.

You may also find many new cousins through matching. However, exact matches on the mtGenome may be 15 or more generations in the past. Thus, these matches are best used to understand your ethnic origins for the maternal line tested.

mtDNA testing inheritance and testing strategy

mtDNA Testing
mtDNA Inheritance

MtDNA is passed by a mother to her children. Thus, both men and women can test for their mother’s mtDNA profile.

Who you test depends on your goals. To know your ancestry on your direct maternal line, you may test yourself. To know if two people descend from the same woman, both people must test.

Hypothesis testing

Genealogists use mtDNA for hypothesis testing. One first forms a hypothesis. Second, one finds cousins from the right branches to test. Third, one tests the cousins. Finally, one analysis test results.

Ethnic origins

mtDNA testing - mtDNA 5 Generation Chart
mtDNA 5 Generation Chart

The second use is for ethnic background testing.

MtDNA follows a direct line. Ancient ancestry for these lines covers both recent and distant parts of the human journey.

MtDNA testing is good for determining ethnic origins and ancient history. However, for a full picture of your ancestry, you need to test as many of your mtDNA lines as possible.

The chart on the left shows the maternal lines for a five generation pedigree. Those who do this type of testing often contact many cousins.

Database matching

FamilyTreeDNA offers mtDNA matching to others in their database. Results can then be used for match fishing. That is, finding recent cousins through random testing. MtDNA exact matches may be 15 or more generations in the past. This is often before genealogy records. Therefore, match fishing is not the best use of mtDNA testing results.

mtDNA testing – Sources & Resources

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