What is a mitochondrial DNA test?

Written by Ellen Hinkley
December 22, 2016

There are three main types of ancestry DNA test and they each report on different aspects of your genetic heritage. Broadly speaking, they can be categorized into autosomal, maternal and paternal ancestry tests, and it’s the maternal tests that are conducted using mitochondrial DNA (aka mtDNA).

Though these options may seem a little confusing at first, once you understand a bit more about each type, you’ll be in a better position to pick the test (or combination of tests) that’ll help you research the aspects of your ancestry that you’re interested in.

Mitochondrial DNA is passed on directly from mother to child and is part of your DNA heritage. It can be analyzed to give you ancestral information about your mother, your mother’s mother, your mother’s mother’s mother, and so on. In fact, mitochondrial DNA tests are known to be effective for tracing your maternal lineage up to 52 generations ago! Unlike Y DNA tests, both men and women have mitochondrial DNA and so anyone can take a mitochondrial DNA test.

If you’d like to learn more about the types of mitochondrial DNA test that are on offer, you can visit our genetic ancestry listings, click the ‘Compare Tests’ button next to the genetic ancestry testing companies we’ve listed, and check out the ‘Maternal Analysis’ or ‘Maternal Analysis & Family Finder’ tests.

What is mitochondrial DNA?

Mitochondrial DNA is found in mitochondria; tiny structures that sit within each of our cells. These structures produce energy for our cells, and are involved in several other processes such as signalling and replication. Mitochondrial DNA is separate from the rest of our DNA which is kept in the nuclei of our cells.

There are only 37 genes in mitochondrial DNA compared to approximately 30,000 genes in the rest of our DNA. Because mitochondrial DNA is circular (like bacterial DNA and unlike the rest of human DNA) this has led scientists to theorize that billions of years ago, these structures may once have been separate organisms. As life evolved on our planet, it’s thought that mitochondria may have become incorporated into our cells, and that despite no longer being able to sustain themselves without us, they continue to maintain their DNA separately.

Mitochondrial DNA changes less than the rest of our DNA from generation to generation. This is because the 23 pairs of chromosomes that we inherit from our parents go through a process of recombination shortly after we’re conceived. As mitochondria do not undergo this process, mitochondrial DNA remains unchanged from mother to child.

How mitochondrial DNA testing works

The practical part of taking a mitochondrial DNA test is the same as for most other types of DNA test. After ordering you’ll receive a testing kit in the post which contains a cheek swab or saliva collection tube. Once you’ve rubbed the swab against the inside of your cheek or produced a saliva sample, you simply return the swab or tube to the laboratory and your mitochondrial DNA can be analyzed.

When it comes to analysing your mitochondrial DNA there are two main methods. The first is to put it into solution and run it across specialized computer chips which reveal the specific ‘genetic variants’ or ‘markers’ that are present. The second is to run it through a sequencing machine so that every single base is recorded, producing your ‘mitochondrial sequence’. This record can then be compared to a mitochondrial reference sequence so that all the genetic variants present can be identified.

Although all types of DNA can be run through sequencing machines, it’s a lot more cost-effective to do it for mitochondrial DNA because it only contains around 16,500 bases, whereas the rest of our DNA contains around 2.8 billion bases. Therefore, tests that combine a mitochondrial analysis with autosomal and paternal analyzes tend to use the first method, and standalone mitochondrial DNA tests tend to use the second.

The companies offering mitochondrial DNA tests often include a ‘Family Finder’ feature in their results, in order to help with DNA genealogy. This means that once your results have been processed, you’ll be able to see a list of the ‘living relatives’ who share your maternal lineage (aka ‘matches’ or ‘connections’) who you’ll be able to contact. For this reason, it can be useful to take a mitochondrial DNA test if you’ve hit a roadblock with traditional genealogy research.

Mitochondrial DNA regions
Mitochondrial DNA can be divided into three main regions: HVR1, HVR2 and the coding region (sometimes known as HVR3). Before mitochondrial sequencing became cost-effective, genetic ancestry companies would analyze just the HVR1 region, or both the HVR1 and HVR2 regions, seeking to identify the genetic variants present.

HVR1 and HVR2 stand for hypervariable regions one and two, and they contain the DNA that controls the genes in the coding region. Together, the HVR1 and HVR2 regions account for less than 7% of mitochondrial DNA. Consequently, analysing the HVR1 and HVR2 regions only means that your ability to trace your ancestry on your maternal line is limited.

HVR1 tests
Sometimes referred to as the ‘low resolution’ option, HVR1 tests are a good choice if you’re taking a mitochondrial DNA test to rule out sharing a ‘recent’ maternal ancestor with someone within the last 52 generations. Both you and the person in question would need to take the test with Family Tree DNA (as only Family Tree DNA hold a ‘matching database’ for mitochondrial DNA, discussed later), and if you don’t share a high percentage of DNA in the HVR1 region, you’re unlikely to share a recent maternal ancestor. However, these tests are less useful for confirming that you do share a recent maternal ancestor – your HVR1 regions may match exactly but without examining the other regions, you can only be 50% certain that you share a recent maternal ancestor.

A HVR1 analysis can also provide you with your maternal ‘haplogroup’, which is a code describing the group of people with whom you share a recent maternal ancestor. However, due to the relatively small size of the HVR1 region, your maternal haplogroup can only be identified with a low level of probability.

In the past, HVR1 tests were much cheaper than HVR1 + HVR2 tests, however, as the cost of tests that analyze all three mitochondrial DNA regions continues to drop, it’s likely that HVR1 tests will decrease in popularity and eventually become obsolete.

HVR1 + HVR2 tests
By having both the HVR1 and HVR2 regions of your mitochondrial DNA analyzed, you’ll be able to rule out whether you share a recent maternal ancestor with someone with much more certainty. You’ll also be able to identify individuals with whom you share a recent maternal ancestor with more certainty, but even if your HVR1 and HVR2 regions match exactly, it still doesn’t mean that the likelihood of your sharing a recent maternal ancestor is 100%.

As you would expect, HVR1 + HVR2 tests can identify your maternal haplogroup with a higher level of probability than a HVR1 test, but you still can’t be sure that it’s a definitive result.

Mitochondrial sequencing
Mitochondrial sequencing is the highest resolution mitochondrial DNA test available, it will identify every genetic variant present in the HVR1, HVR2 and coding regions. It will allow you to rule in or rule out sharing a recent maternal ancestor with someone to the highest level of certainty, and it can be used to confidently determine your maternal haplogroup. This is unsurprisingly the most expensive type of mitochondrial DNA test, and it will set you back around $199.

Reference sequences

In order to identify the genetic variants present in your mitochondrial sequence, genetic ancestry companies need to compare your record to a reference sequence. The most commonly used is the revised Cambridge Reference Sequence (rCRS) which is a corrected version of the original Cambridge Reference Sequence (CRS). The CRS was produced in 1981 when the first mitochondrial genome was sequenced, sparking the initiation of the Human Genome Project. However, as more mitochondria were sequenced, it became clear that the original reference sequence would need to be revised, leading to the publication of the rCRS in 1999.

Another sequence that is sometimes used is the Reconstructed Sapiens Reference Sample (RSRS). This is based on the most recent maternal ancestor of all living humans known as ‘Mitochondrial Eve’. Many genetic ancestry companies will use the RSRS in conjunction with the rCRS, as this is believed to be the best method of determining your maternal haplogroup.

Haplogroups

As discussed, mitochondrial sequencing (and HVR1 + HVR2 tests to a lesser extent) can help you identify your maternal haplogroup. These groups have been established by analysing mitochondrial mutations in living population groups and archaeological remains. It’s these mutations which have allowed experts to infer how groups of our maternal ancestors have diverged and migrated since leaving Africa approximately 200,000 years ago, back in the time of Mitochondrial Eve.

This research has been used to develop ‘phylogenetic trees’ for mitochondria (also known as mtDNA haplotrees) which visually represent all maternal haplogroups and subgroups. Each branch represents a mutation(s) in mitochondrial DNA where a divergent population was created. Using various statistical techniques, the geographical location of the divergence can be estimated along with the date to within tens of thousands of years.

This means that by taking a mitochondrial DNA test, not only will you receive your maternal haplogroup, but the company providing it can give you the migratory path of your maternal ancestors over time. Many companies do this by providing colourful and interactive maps with descriptions of your maternal ancestors’ migratory journey.

You can also conduct your own research by identifying your maternal haplogroup on a phylogenetic tree, and following the branches to discover other groups to whom you’re related (albeit less closely than your own group). There are many online resources and ancestry forums to help you do this should you wish.

The difference between those in your haplogroup and your relatives

Although maternal haplogroups can be used to identify those with whom you share your maternal lineage, this doesn’t mean that you’ll be closely related to them. Family Tree DNA currently offer mitochondrial DNA tests that come with a Family Finder feature, which allow you to identify those in your maternal haplogroup (or a closely linked maternal haplogroup), providing they’ve also taken a mitochondrial DNA test with Family Tree DNA. Many of these living relatives will be 4th cousins or more distant. Technically speaking, you’ll share a female ancestor with these living relatives, but it is rare for a provider to hold any details about that shared ancestor – only in the case of a 3rd cousin or closer might you discover when or where that shared ancestor lived.

Do all mitochondrial DNA testing companies offer a Family Finder feature?

Although many companies offer a Family Finder feature, only Family Tree DNA holds matching databases for Y DNA, mtDNA and autosomal DNA. This means that if you’re hoping to find living relatives on your maternal line, you’ll only be able to do this with a Family Tree DNA mitochondrial DNA test.

All other companies with a Family Finder feature (e.g. AncestryDNA) only hold matching databases for autosomal DNA, even though some of these companies may test your mitochondrial DNA to produce your maternal haplogroup (e.g. 23andMe). In these cases, the living relatives they identify will be matched according to your autosomal DNA, not your mitochondrial DNA. This means you will share ancestors with these relatives, but you’ll be unable to tell if they share your maternal lineage.

Don’t forget, when it comes finding living relatives, companies with a Family Finder feature will only be able to compare like with like to identify matches, for example: Your Y-DNA results to their Y-DNA database, your mtDNA results to their mtDNA database, or your autosomal DNA results to their autosomal DNA database. If you want to maximize the number of living relatives you find using DNA testing, we recommend you test all three types of DNA, and that you take Y DNA tests and mitochondrial DNA tests with Family Tree DNA.

How is a mitochondrial DNA test different to an autosomal DNA test or a Y DNA test?

The most common type of ancestry DNA test analyzes your autosomal DNA – our autosomes are the chromosomes we inherit from our parents that do not determine our biological gender. These tests are best for reporting on your ethnic breakdown, by revealing the population groups (e.g. Celtic, Western European, Scandinavian) with whom you share a proportion of your autosomal DNA. You can read our autosomal DNA testing article for more info. An autosomal DNA test (aka an ethnicity test) is known to be most effective for investigating your ancestry from both parents within the past five generations.

A Y DNA test is conducted by analysing your Y DNA (aka your Y chromosome) and is best for researching your paternal lineage (the lineage of your father’s father’s father etc.). The results normally include your paternal haplogroup and a map showing these ancestors’ migratory path after leaving Africa 200,000 years ago. You can read our Y DNA test article for more info.

Autosomal DNA tests and Y DNA tests can also be used to help you find living relatives, providing the company you purchase the test from offers a Family Finder feature.