By: Katy Rowe-Schurwanz

Editor’s Note: This is part one of a five-part series about what mtDNA is, what mtDNA can tell you, and how to apply mtDNA results to your genealogy. Continue reading the series here:

In the world of genetic genealogy, mitochondrial DNA (mtDNA) plays a crucial role in tracing maternal lineages. mtDNA is passed down exclusively from mothers to both sons and daughters and offers valuable insights into our ancestral heritage.

In this blog, we’ll explore the history and importance of mtDNA testing, from its early days to its current significance in genetic genealogy research.

So, what is mtDNA?

You may remember from biology class that the mitochondria are “the powerhouse of the cell” because they generate energy for the cell. DNA is also found within the mitochondria, and because of its unique inheritance pattern, mitochondrial DNA, or mtDNA, can be used for genetic genealogy to provide information about your direct maternal line (your mom, her mom, her mom, and so on).

What is mtDNA

Mitochondrial DNA is DNA found outside the nucleus of the cell in the mitochondria. With only 16,569 base pairs, or SNPs (single nucleotide polymorphisms), the amount of DNA found in the mitochondria is small compared to nuclear DNA (chromosomes 1-22, the X chromosome, and the Y chromosome).

mtDNA, just like other DNA, is made up of pairs of the nucleotide bases guanine (G), adenine (A), thymine (T), and cytosine (C). At each position, there is a base pair of G, A, T, or C. Each position is assigned a number.

Because of the atomic structure of these four chemicals, normally, the nucleotide bases will be paired with each other in a specific way, with A and T paired together and C and G paired together.

When did mtDNA testing start?

FamilyTreeDNA was one of the first direct-to-consumer DNA testing companies to offer testing for genetic genealogy, starting in 2000. In May 2000, FamilyTreeDNA launched our first mtDNA test which only covered hypervariable region 1 (HVR1). FamilyTreeDNA quickly added the mtPlus test, covering both HVR1 and HVR2 by 2002.

Other companies offering early testing were Oxford Ancestors, which offered the HVR1 test, GeneTree, which offered HVR1, HVR2, and HVR3 before being sold to Sorenson’s SMGF and eventually Ancestry. Ancestry destroyed their mtDNA database in 2014 and Oxford Ancestors theirs in 2018.

In 2005, National Geographic launched the Genographic Project in partnership with FamilyTreeDNA. The first phase of the Genographic Project covered HVR1, which could be transferred to FamilyTreeDNA for matching. Later phases of the Genographic Project’s test covered only enough mtDNA to provide a haplogroup, and while still available to transfer to FamilyTreeDNA, did not cover enough to provide matching. The Genographic Project stopped offering their tests in 2019 and deleted their database in 2021.

In 2006, FamilyTreeDNA began offering the mtFull Sequence test, covering the entire mitochondria–HVR1, HVR2, HVR3, and the Coding Region. Because the mtFull Sequence covers the entire mitochondria, this test can provide the most matches, the most relevant matches, and your most refined haplogroup.

By the end of 2019, FamilyTreeDNA had discontinued our lower-level mtDNA tests, the mtDNA and the mtPlus, and currently only offers the mtFull Sequence for purchase. Customers with the lower-level tests can upgrade to the mtFull Sequence as well.

Because multiple companies offered mtDNA testing early on, sites where mtDNA data could be transferred for matching were also created. FamilyTreeDNA offered one of these, MitoSearch, from May 2004 until May 2018. The third-party, nonprofit was launched in 2017 and remains an active place for testers to transfer today.

mtDNA mutations help to trace maternal lineages

However, there are several types of mtDNA mutations, or changes, that can happen: transitions, transversions, reversions, insertions, deletions, and heteroplasmies.

Transition mutations show complementary changes

Transitions are where a purine has mutated to the complementary purine (A <-> G) or where a pyrimidine has mutated to the complementary pyrimidine (C <-> T). Transitions are shown by giving the original value capitalized before the location and the mutated value capitalized after the location. For example, a transition of a C nucleotide at position 146 to a T is shown as C146T.

Transition Mutations - mtDNA Mutations Help to Trace Maternal Lineages

Transversion mutations show base switches

Transversions are where a purine has mutated to a pyrimidine or where a pyrimidine has mutated to a purine (C <-> G, C <-> A, T <-> G, or T<-> A). Transversions are shown by giving the original value capitalized before the location and the mutated value uncapitalized after the location. For example, a transversion of an A nucleotide at position 825 to a t is shown as A825t.

Transversion Mutations - mtDNA Mutations Help to Trace Maternal Lineages

Reversions mutations show a nucleotide has changed back

Reversions occur when a mutation has changed back to its ancestral state, and this is labeled with an exclamation mark. For example, T152C! would mean that for position 152, the original reference nucleotide is a C, there was a mutation to a T, and then another mutation back to C.

It is possible to have multiple reversions at the same location, and these will be denoted with multiple exclamation marks.

A mutation that appears with a decimal point is referred to as an insertion. For this particular location, an extra nucleotide, or in some cases more than one extra nucleotide, was wedged between this position and the next.

Reversion Mutations mtDNA Mutations Help to Trace Maternal Lineages

Deletion mutations show the absence of a nucleotide sequence

Deletions occur when your DNA mutates and no longer exists. A deletion cannot revert back to its ancestral position or regenerate itself; a deleted position is removed from your DNA and that of your maternal line forever.

Deletions are indicated without the reference nucleotide in front of the position and instead will only have the position followed by either a lowercase d or a dash. For example, a deletion at position 522 is shown as either 522d or 522-.

Deletions, like other types of mutations, are typically normal. Deletions at locations 522 and 523 are present in nearly every haplogroup.

Deletion Mutations - mtDNA Mutations Help to Trace Maternal Lineages

Heteroplasmy mutations show a change currently happening

Heteroplasmies are mutations that are in progress. Sometimes for a specific location, there are two or more nucleotides present in your DNA sequence.

A heteroplasmy will only be reported if it is detected in 20% or more of the reads of your DNA for that location. The way it is reported depends on which nucleotides are present in those reads.

If you see a letter next to a location for one or more of your mutations that is not one of the main nucleotides (A, C, T, G), and it is not a deletion, then it is likely a heteroplasmy.

Reading Heteroplasmies - mtDNA Mutations Help to Trace Maternal Lineages

All of these differences in our mitochondrial DNA are what make it useful for genealogy. If not for the occasional change or mutation, then everyone would match every tester, and we could not use mtDNA for tracing our matrilineal ancestors.

Take an mtDNA test and find your place on the mtDNA Tree of Humankind

Mitochondrial DNA is a guiding light in the vast landscape of genetic exploration, offering valuable clues about our maternal lineage. From its humble beginnings in DNA testing to its essential role in genealogical research today, mtDNA continues to reveal the intricate stories of our family histories. As we delve into genetic genealogy, let’s embrace the power of mtDNA testing to uncover the mysteries of our maternal ancestors and find our place in the mtDNA Tree of Humankind.

Headshot of Katy Rowe-Schurwanz - Product Manager at FamilyTreeDNA

About the Author

Katy Rowe-Schurwanz

Product Manager at FamilyTreeDNA

Katy Rowe-Schurwanz has always been interested in genealogy, inspired by her maternal grandparents, who told her stories about their family and family history when she was little. After studying anthropology and history in college, she joined FamilyTreeDNA in 2015 and became the Trainer for Customer Support. Katy created and improved training processes and was fundamental in the creation of the Big Y Specialist team. In September 2021, she became Product Manager and has focused closely on improving FamilyTreeDNA’s genetic genealogy products.