Interpreting mtDNA Test Results

By: Katy Rowe-Schurwanz

Learn about the significance of mtDNA haplogroups and how your mtDNA test results can help you trace your maternal ancestry back to Mitochondrial Eve.

Editor’s Note: This is part three 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:

• Part 1: What is mtDNA?
• Part 2: Exploring the Full Mitochondrial Genome: Understanding the Inheritance of Mitochondria
• Part 4: Using mtDNA for Genealogical Research

Understanding mtDNA haplogroups

Mitochondrial Eve and migration patterns

Eventually, if you trace everyone’s mothers back as far as you can go, there is one woman who is the most recent common ancestor of all matrilineal lineages. This woman has been dubbed “Mitochondrial Eve.”

Mitochondrial Eve lived in Africa over 150,000 years ago. She was not necessarily the only woman alive at the time, or the only one who had descendants, but is the only one with tested matrilineal descendants still alive today.

This does not necessarily mean that there are no other potential mtDNA lineages, just that if there are, they have not yet been discovered. The same holds true for the age of Mitochondrial Eve. Through additional research and testing of modern and ancient DNA, different and/or older lineages may be discovered in the future.

Mitochondrial Eve was the founder of mtDNA haplogroup L, the haplogroup from which all other branches on the mtDNA Tree of Humankind descend today.

A haplogroup can be considered like an ancestor on your family tree. Each haplogroup forms a branch on that family tree. Depending on the age of the haplogroup (when it formed), you may have the name of that ancestor, or the ancestor may have lived so long ago that their name has been lost to time.

Each haplogroup formed at a specific time and in a specific location. Testing of modern peoples and ancient DNA informs us of those locations and phylogenetic experts are able to build not just a tree of humankind, but also migration paths that those haplogroups took across and out of Africa and to the other continents. Those migration paths have been mapped, and you receive a copy of that map with your mtDNA results.

rCSRs versus RSRS

To keep track of the mutations or changes in mtDNA, when these changes occurred, and how one sequence differs from another, researchers created 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. This is called the ancestral value. If a person has a value other than the ancestral value, we call that mutation a derived value.

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).

The revised Cambridge Reference Sequence is a revision of the very first mitochondrial genome sequenced at Cambridge University in 1981. This was based on a group of anonymous individuals 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 representative of 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. The RSRS is a reconstruction of this ancestral mitochondrial sequence, so it traces the mutations directly from Mitochondrial Eve to you. 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.

Partial versus full haplogroups

Depending on what type of test you have taken, you may have a partial haplogroup or a full haplogroup.

Some autosomal DNA tests are able to provide you with a partial mtDNA haplogroup. This is provided with autosomal results from 23andMe, Living DNA, was provided with the Genographic Project 2.0 and 2.0 Next Generation tests, and soon will also be provided with FamilyTreeDNA’s Family Finder.

These autosomal tests are performed on customized microarray chips. The goal of these tests is to provide autosomal results (like close matches on all any ancestral lines and ancestral population percentages), so the majority of the SNPs on these chips are from chromosomes 1-22 and the X chromosome. However, some companies have also added enough SNPs from the Y chromosome and the mtDNA to be able to provide a partial haplogroup.

FamilyTreeDNA’s discontinued earlier mtDNA tests like the mtDNA and the mtPlus only looked at part of the mitochondria (specifically either only HVR 1 or only HVR1 and HVR2), and so they will also only provide a partial haplogroup.

FamilyTreeDNA’s mtFull Sequence test looks at the entire mitochondria, so we are able to provide you with your full mtDNA haplogroup with these results.

Why does this matter?

The more of your mtDNA that’s tested, the more specific your mtDNA haplogroup will be. A partial haplogroup can give you the beginning of your mother’s story, the part from Mitochondrial Eve to your matrilineal ancestors in the Stone Age or Metal Age. A full haplogroup will give you your mother’s full story, from Mitochondrial Eve to you.

Think of your haplogroup like an address. You have the root of the haplogroup which is a letter like (H, V, U, J, L, etc.). This tells you what country the address is in. With an autosomal DNA test, that might be as specific as you get—and it’s unlikely that a root alone will actually point to a country—it’s more likely to just be a continent.

Past the root, haplogroups are divided into branches notated by alternating numbers and letters. With a mtFull Sequence test, your haplogroup won’t be just a root, like H, but instead, it could be H2a1a1. That’s a mouthful, but it gives you so much more information on your maternal story!

Let’s think about the address again. If H is the country, then 2 is the state. The first A is the county, the first 1 is the city, the next A is the street, and the last 1 is the house number. While your haplogroup migration path won’t be as specific as a street or house number, your full haplogroup can tell you the regions your matrilineal ancestors migrated from and to, if they were Native American, Jewish, or part of another cultural group, and by comparing with the self-reported earliest known maternal ancestor locations of other testers and the improvements to mtDNA reporting coming out later this year, the country, county, or town your ancestors may be from, depending on how well tested your haplogroup is.

mtDNA Tree of Humankind

All haplogroups have been added to the mtDNA Haplotree, or mtDNA Tree of Humankind, a giant family tree of all matrilineal lineages going back to Mitochondrial Eve.

The current mtDNA Tree of Humankind is based on the Phylotree, and FamilyTreeDNA is working to create a new, updated mtDNA Tree of Humankind called the Mitotree.

The Phylotree is an academically built mtDNA Tree of Humankind that was last updated in 2016. It was built with only a little over 24,000 mtDNA results, many of which were only partial results. There is no plan to update the Phylotree again.

Most, if not all, of the haplogroups and branches from the Phylotree are very old—the time to most recent common ancestor for the branch is estimated at thousands of years ago. Just matching someone with the same haplogroup as you is not helpful for determining when your genealogical common ancestor with that match lived or who they were.

Through the Million Mito Project, FamilyTreeDNA is building the new Mitotree with 20 times more data from full sequences than the Phylotree used with both full and partial sequences. That data will create new branches, and most importantly younger branches.

The more refined branching on the new Mitotree will be able to provide you with a better age estimate for that common ancestor with your mtDNA matches, with many estimated within a genealogical timeframe.

Like with Y-DNA, more mtFull Sequence testers will add more data to the Mitotree and allow for more branching and younger branching. Before the Big Y-700 test, many Y-DNA haplogroups were estimated to be several thousand years old. With tens of thousands of new Big Y testers, we’ve added tens of thousands of new branches and haplogroups to the Y-DNA Tree of Humankind and today half of all testers have a Y-DNA haplogroup within a genealogical timeframe, making it easier to discover the common ancestor with your matches.

The same will hold true for the Mitotree—more testers means more branches and younger haplogroups. More connections can be made and more brick walls can be broken.

mtDNA matching

The major benefit of mtDNA testing is that you receive matches you share a common ancestor with on your direct maternal line.

Your mtDNA matches are determined based on how much of your mtDNA and another tester’s mtDNA is the same. The more of your mtDNA that’s the same, the more recently in time you shared a common ancestor.

With the mtFull Sequence, you’ll receive three levels of matches: HVR 1, HVR 2, and the Coding Region.

HVR1 and HVR2 matching

At the HVR1 and HVR2 levels, you’ll need to be an exact match—meaning that there are no differences in your mtDNA and your matches’ mtDNA. Matching only at these levels can mean your common ancestor may have lived before genealogical times.

However, you shouldn’t discount these matches fully—there may be some matches that have only done the discontinued lower-level mtDNA tests and that’s why they don’t match you at the Coding Region level.

Coding Region matching
The Coding Region match level allows you to have up to a genetic distance of 3 with your matches, meaning there are only up to three differences between your mtDNA and that other tester’s mtDNA. These matches may share a common ancestor with you within a genealogical timeframe.

Interpretation of mtFull Sequence results and its comprehensive coverage

Matches

You probably aren’t going to recognize the names of your mtDNA matches, but that’s to be expected. Surnames typically aren’t passed down by maternal lineages—usually, the woman’s surname will change each generation with marriage.

Rather than looking at the names of your matches, you’re going to want to look at the names and locations of their earliest known direct maternal ancestors and the names and locations of their direct maternal line in their shared family trees.

On your mtDNA matches list, there’s an earliest known ancestor column that tells you the information your matches have entered—you may be able to recognize names here. However, your matches’ may be able to trace back farther than you have, or potentially not as far back as you have, so you’ll also want to look at their family trees.

To the right of your matches’ names there are up to three icons—an envelope for emailing your match, an icon that lets you take notes about your match, and if they have shared their family tree, a third icon will show that lets you view that tree.

Because we know an mtDNA match is on your direct maternal line, it’s best to start with the pedigree view. At the bottom will be their direct maternal ancestors, and you may find a name or location here that fits what you know.

Start with the matches whose mtDNA is the closest to your mtDNA. This means start with your Coding Region matches that are a genetic distance of 0 first, then 1, then 2, then 3. Next, look at your matches at the HVR 1 and HVR 2 level, and last look at the matches at only the HVR 1 level.

For any matches that have not provided earliest known direct maternal ancestor information or have not shared a family tree, you can use the envelope icon next to their name to reach out to them and ask for more information.

Keep in mind that the information in the earliest known ancestor column is self-reported by your matches in the genealogy section of account settings. The name, country, and location of their ancestor may be based on family legend, rather than something confirmed through either DNA testing or records.

This information may also be from later than your most recent common ancestor with your match lived. For example, you may have a match that has traced their ancestors to say, Kentucky in the 1800s, but you were born in Australia and everyone you have researched on your line was also born in Australia. That doesn’t mean your ancestors are from the United States, but instead that you have a common ancestor where one member of the line immigrated to the United States/American Colonies and another immigrated to Australia.

Matches Map

Often, the locations of your matches’ direct maternal ancestors are going to be more helpful for finding a connection than the names of their ancestors. Matches who have provided a specific location for their earliest known direct maternal ancestor will show up on the Matches Map with a pin in that location. You can click the pin to view the match’s name, their earliest known ancestor’s name and birth/death dates, where the specific location is, and your match’s email address.

You’re able to filter the list by the different match levels so that you can view your closest matches or your most distant matches.

You’re able to find matches that share ancestor locations with you. For mtDNA, this is especially important because records can be so difficult to find and tracing one particular surname won’t work. While you may not have your brick wall ancestor’s birth surname, you probably know where she lived. You can use the Matches Map to find matches whose ancestor also lived in that same location, which might be the connection that allows you to break your brick wall.

You’ll want to examine the dates your matches’ ancestors were in that location and continue to look for traditional records to prove the connection—many families followed the same migration patterns, especially in the US. Just because your brick wall ancestor migrated from say South Carolina to Kentucky in the early 1800s and a match’s ancestors did the same, it doesn’t mean your common ancestor with that match is from the same time period—with mtDNA it could be, or it could be a few hundred years before and it’s just a coincidence that both ended up following the same migration path around the same time.

Ancestral Origins

The Ancestral Origins section provides an aggregated list of the self-reported countries of origin for your matches’ maternal earliest known ancestors, compared to the self-reported database totals, broken down by test level and genetic distance.

The column headers provide the following information:

• Country: The self-reported country of origin for a match’s maternal earliest known ancestor.
• Match Total: The number of matches who reported their maternal Earliest Known Ancestor is from this country.
• Country Total: The number of mtDNA testers in the FamilyTreeDNA database who reported their maternal earliest known ancestor is from this country.
• Percentage: Match Total divided by Country Total; The percentage of the database that you match who have reported that their maternal earliest known ancestor is from this country.
• Comments: Additional information about a match’s maternal earliest known ancestor location, such as an ethnic group within a country or a more specific region.

While the Matches Map requires the location portion to be filled out in order for a match’s EKA to display on the map, this report depends only on the Country of Origin section. Some matches may have entered a Country of Origin, but not a specific location, and so they may show up here but not on the Matches Map, but they will show up in the Ancestral Origins report.

This report is broken down by match level and genetic distance. It’ll list the Countries of Origin provided by your matches, how many matches listed those countries, as well as any additional comments they may have made, such as an ethnic group or more specific region within that country.

There are a couple of things to keep in mind for this report:

1. This information is all self-reported. Your match may have based their answer on a family legend and not proven fact. For example, you may see matches that have said their Earliest Known Direct Maternal Ancestor is Native American, but your haplogroup is not one that migrated into the Americas in pre-Columbian times.
2. Your common ancestor with your matches may be before or after their earliest known direct maternal ancestor was in a specific country or part of a specific ethnic or cultural group. This report does not provide a guarantee that your matrilineal ancestors were from a specific location or part of a specific culture, but instead, provides hints to where they might be from based on where your matches’ matrilineal ancestors are from. For example, In my Ancestral Origins, I have matches at the lower levels of mtDNA testing that list their ancestors as Ashkenazi Jewish. There is a subclade of my mtDNA haplogroup that is well represented with Ashkenazi testers, however, I am not part of that subclade and these Ashkenazi matches do not match me at the mtFull Sequence level. That means my common ancestor with these testers is further back in time—potentially even before they were Jewish.

Haplogroup Origins

Similar to the Ancestral Origins report, the Haplogroup Origins report provides an aggregated list of the self-reported countries of origin for your matches’ maternal earliest known ancestors, compared to the self-reported database totals, broken down by test level, genetic distance, and haplogroup.

If you match any academic or ancient samples that have been added to the FamilyTreeDNA database, these will be included here as well, unlike on the Ancestral Origins page.

This list is sorted by current haplogroup assignment and can provide hints to later migrations of your haplogroup, past what is displayed on the migration map.

The column headers provide the following information:

• Haplogroup: This is your match’s haplogroup predicted by their mtDNA or mtPlus testing or confirmed by their mtDNA Full Sequence test results.
• Country: The self-reported country of origin for a match’s maternal earliest known ancestor.
• Comments: Additional information about a match’s maternal earliest known ancestor location, such as an ethnic group within a country or a more specific region.
• Match Total: The number of matches who reported their maternal earliest known ancestor is from this country.

There are three things you’ll want to keep in mind when viewing this report:

1. This information is all self-reported. Your match may have based their answer on a family legend and not proven fact. For example, you may see matches that have said their earliest known direct maternal ancestor is Native American, but your haplogroup is not one that migrated into the Americas in pre-Columbian times.
2. The age of the haplogroup may not match up to when your match’s earliest known direct maternal ancestor lived. For example, if the haplogroup was formed 4,000 years before the present but your match’s earliest known direct maternal ancestor was born in 1750 C.E., it’s possible that the haplogroup formed in a different location from where the earliest known direct maternal ancestor was born. Updates to the mtDNA Tree of Humankind, specifically the creation of younger branches and placement of testers on those younger branches, will allow for the locations listed in the Haplogroup Origins report to more accurately reflect the origin of the haplogroup.
3. Your most recent common ancestor with a match on a specific branch of the mtDNA Tree of Humankind may be before or after their self-reported earliest known direct maternal ancestor lived. This report does not mean your ancestors are from a specific location, but instead provides hints to where they might be from, based on your connection to your matches.

Migration Map

The Migration Map shows a reconstructed ancestral journey of your direct maternal line, starting from Mitochondrial DNA Eve to your intermediate haplogroup. All humans today can trace our matrilineal ancestry back to a single maternal ancestor that has been nicknamed “Mitochondrial DNA Eve,” who lived in Africa over 150,000 years ago.

Your mtDNA haplogroup is determined based on your mitochondrial DNA mutations or SNPs. Each mutation occurred at a specific location and point in time, which we know based on archaeological evidence and mtDNA Full Sequence testing.

You can also explore this ancestral journey more with the mtDNA Journey video that you can create from your mtDNA results section.

This part of your results isn’t likely to help break a brick wall, but it can tell you more about where your matrilineal ancestors were from long, long ago.

Coming soon: Mito Discover™ features

With the release of the new Mitotree, FamilyTreeDNA will also release new mtDNA tools to help you discover more of your mother’s story.

We released the Y-DNA Discover haplogroup reports in 2022, and we will soon release the same tools for mitochondrial DNA.

Mito Discover will include tools to help you determine which of your mtDNA matches shares a common ancestor with you more recently in time than your other matches, when that common ancestor lived, and where they were from.

You’ll also be able to match with ancient DNA from archaeological sites around the world and notable historic and modern individuals.

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.