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Mitochondrial DNA (mtDNA)

Mitochondria are specialized subunits (organelles) within cells. They are responsible for cellular respiration and for producing energy. They evolved into their current state from separate organisms that formed a mutually beneficial (symbiotic) relationship with the larger cell. Because they were once independent, they have their own mitochondrial DNA (mtDNA) genome.

Both men and women have mitochondria and mtDNA in their cells, but only women pass it on to their children. Because of this unique matrilineal inheritance, we can use mtDNA to trace your direct maternal line. Your mtDNA traces your mother, her mother, her mother’s mother, and so forth and offers a clear path from you to a direct maternal ancestor.

Your Direct Maternal Line

Your direct maternal lineage is the line that follows your mother’s maternal ancestry. Fathers do not pass on their mtDNA to their children, so this line consists entirely of women. Your mtDNA can trace your mother, her mother, her mother’s mother, and so forth. It offers a clear path from you to a known or likely direct maternal ancestor.

For genealogists, this clear line means that they can trace two or more descendants of a single woman many generations back and compare their mtDNA results with the expectation of a match. For those interested in deeper ancestry, tracing the modern geographic origins of exact matches means that they can discover the anthropological origins of their own line. 


Parts of mtDNA

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, G is almost always paired with C, and A is almost always paired with T, and vice versa. Only in certain mutations called transversions do these pairings differ in mtDNA.

Rather than having multiple chromosomes, mitochondria have a single circular chromosome. DNA is made of two major parts, the control region and the coding region.

  • Control Region - The control region is often called the hypervariable region (HVR). There are three human hypervariable regions: HVR1, HVR2 and HVR3. For testing purposes, we combine HVR2 and HVR3. Hypervariable means fast changing and these regions have a faster change (mutation) rate than the coding part of the mitochondrial genome. They do not contain genes and therefore they can mutate more readily without affecting the function of the cell.
  • Coding Region - The coding region (CR) is the part of your mitochondrial genome that contains genes. Because it does contain some genes, the coding region tends to be slower mutating than the control region.


Just as with other types of DNA, over time, copy errors occur. These small copy errors are called mutations. Sometimes when new cells are created, one base pair may be substituted for another. For example, in a particular base pair, adenine (A) might be inadvertently substituted for guanine (G). To track these changes, we use a universal reference sequence. This reference sequence serves as a standard to which all mutations are compared. In a reference sequence, each base pair is assigned a location number and a reference value for that location, such as A or G. If a person has a value other than the reference value, we consider this an alternate value.

You can read more about mutations here.

mtDNA Reference Sequences

There are two reference sequences to which scientists compare changes in mtDNA: the revised Cambridge Reference Sequence (rCRS) and the Reconstructed Sapiens Reference Sequence (RSRS).

By comparing your mtDNA mutations to each sequence, we can distinguish the differences in your DNA from the original values in both the RSRS and the rCRS. FamilyTreeDNA provides a separate list of each of these differences along with your other results when you take an mtDNA test.


The revised Cambridge Reference Sequence is a revision of the very first mitochondrial genome sequenced at Cambridge University in 1981. This was based on an anonymous individual of European descent. In the rCRS system, each nucleotide base is assigned a position along with the value (A, C, T, or G) that was discovered in this anonymous individual. Your rCRS values are reported by listing the location followed by your derived value. For example, if you differ from rCRS at position 263 with a value of G, this will be reported as 263G.

As global testing became more prevalent, we began to find that the rCRS sequence, although common among Europeans, was not ancestral for the wider global human population. In order to address this, a group of scientists published the Reconstructed Sapiens Reference Sequence (RSRS) in 2012.


The Reconstructed Sapiens Reference Sequence was designed to be representative of “Mitochondrial Eve.” This is not the first woman who lived, but rather the woman from whom all modern humans descend in a direct maternal line. The RSRS is a reconstruction of this ancestral mitochondrial sequence. Just like the rCRS, each nucleotide is assigned a position and an ancestral value. RSRS values are reported using a system that lists the ancestral value, the position, then your mutation. For example, if at location 769, the ancestral value is adenine (A), and you have a mutation of guanine (G), then this mutation will be reported as A769G.

The RSRS also contains Extra Mutations and Missing Mutations. Extra Mutations are those that are present in your mtDNA but are not usually found within your haplogroup. Missing mutations are mutations usually found in your haplogroup that you do not have.

If you look at your results and see a value other than A, C, T, or G, this reflects a heteroplasmy. You can read more about heteroplasmy here.

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