One of the questions I often receive about mitochondrial DNA matching at FamilyTreeDNA is which mutations are included, which are excluded, from what type of matching, and why.

There are three types of matching for full sequence (mtFull) testers.

1. Match page matching
2. Haplotype matching
3. Haplogroup-only matching

Each match type is different and provides something unique and beneficial.

People who have not upgraded to the mtFull, full sequence test, meaning they have only taken the older HVR1 or HVR1+HVR2 level test, don’t have full haplogroups, because only about 1000 of the 16,569 locations were tested with the earlier partial tests. You can easily upgrade to receive your full sequence results.

Navigate Using Your Dashboard

Aftersigning in to your account, you access the following information from your dashboard:

• Your matches
• Information about your matches, as maps showing where their earliest known ancestor (EKA) lived
• mtDNA Discover

Match Types and Discover

Two types of matches show on your matches page, and one type is displayed only on Discover.

Match types are:

1. Matches on your mtDNA Matches page under Genetic Distance – which means you match with less than three mutations difference, shown as a, “1 step”, “2 step” or “3 step” mutation. Locations 309 and 315 are EXCLUDED from the mismatch calculation because they are very unreliable and mutate often.
2. Haplotype matching and clusters – Your haplotype is your exact DNA sequence and is assigned an F number. If you match someone whose F number is checked (in blue), it means you are an exact match with them and everyone in the same Haplotype Cluster, INCLUDING locations 309 and 315. Exact haplotype matches always show on your Matches page. If you have any mismatch, including 309 and 315, you will NOT share the same haplotype. A haplotype match is indicated by a little check mark beside the F number of your match, which means you and anyone else with that same haplotype number form a haplotype cluster.
3. Haplogroup-only matching – which means you don’t match on your Matches page, because you have more than three mutations difference, but you do match at the haplogroup level, which you can see on Discover.

Since people who form a haplotype cluster match exactly on all markers, INCLUDING 309 and 315, you cannot be a haplotype cluster match with someone you don’t match exactly under Genetic Distance on your Matches page. You will always share the same haplogroup, too.

Now let’s look at the variations you might encounter.

Genetic Distance = Exact Match, But Different Haplotype Cluster

You can match someone exactly under Genetic Distance on your matches page, since that calculation excludes locations 309 and 315, but have a different haplotype because you don’t match that person on either 309 or 315, or both.

In this example, the tester and their match don’t share a haplotype, so the box isn’t checked. If the box was checked, it would indicate that their haplotypes match exactly, including 309 and 315. The box isn’t checked, so they aren’t a member of the same haplotype cluster.

In some cases, locations 309 and 315 can be genealogically useful, and in others, they are not. It’s up to you to do the genealogical research work and make that determination.

A Match, But Different a Haplotype and Haplogroup

You may match someone in a different haplogroup with less than three mutations difference, meaning a Genetic Distance of three steps or less. Even though you are members of a different, but closely related haplogroup, they are still shown on your match list because you share less than three mutations difference.

You and your match may share an identifiable common ancestor if at least one of the haplogroups formed more recently in time.

Discounting locations 309 and 315, this match has a Genetic Distance of “1 step”, meaning that there is one mutation difference, and that mutation forms the new haplogroup of J1c2f3. Their legacy haplogroup, before Mitotree, was J1c2f, the same as mine.

You may think that a different haplogroup means a match far different in time, but that’s not necessarily true.

In this example, it’s easy to see that people who are members of three different haplogroups trace back to the same common ancestor a few generations earlier. So even though these testers have different haplogroups, it doesn’t necessarily mean that their common ancestors are far back in time. Don’t summarily dismiss different but closely related haplogroup matches.

The same goes for haplotypes and haplotype clusters, so don’t ignore matches with different haplotypes that may be very genealogically useful.

Haplogroup-Only Matches

You won’t see haplogroup-only matches on your Match list if you mismatch on more than three locations. You’ll only see them in mtDNA Discover.

While three mismatches probably indicates a match before the adoption of surnames, that’s not necessarily the case, especially if the tester(s) have a heteroplasmy. I wrote about heteroplasmies, here.

Haplogroup-only matches can still be quite useful because all haplogroup members share a common ancestor at a specific point in time. Every haplogroup member shares common ancestors between the haplogroup’s formation date and the present-day testers. The most recent common ancestor (MRCA) with any one person or group of people can be anytime between the haplogroup formation date and your own generation.

Remember that the haplogroup name, such as J1c2f or V216a2, was a real living person. We just don’t know her name, and in many cases, never will. She’s still contributing valuable information about our ancestors, though, and perhaps about traceable genealogy..

You CAN see haplogroup-only matches on Discover. If you are a member of a Haplotype Cluster, you’ll match everyone in that cluster. However, on your Matches page, you may not match everyone else that shares your haplogroup.

As you can see on the Time Tree, above, there are two people in haplogroup V216a2 that are not members of haplotype cluster F9712482.

How do you know if you match everyone in your haplogroup, or if there are some people in your haplogroup that you don’t match?

The easiest way is to compare the Time Tree, which shows everyone in your haplogroup, and nearby haplogroups, to your Match Time Tree, above, which displays only the people you match overlayed onto the Time Tree with their name and their earliest known ancestor, if they entered that information.

As you can see, this tester is a member of the haplotype cluster F9712482 and matches one other person who is a member of haplogroup V216a1. They don’t match the second V216a2 person shown on the Time Tree, but who is missing here on the Match Time Tree when compared to the Time Tree.

How might this information be useful? For starters, your haplogroup-only match may include a country location of interest. Suppose there are several people that you don’t match. Their combined location information may be very useful for you when determining the history of your ancestral haplogroup and where your ancestors may have come from.

In my case, in haplogroup J1c2f, my oldest known ancestor is found in the church records in Wirbenz, Germany, marrying in 1647, but nearly all of my matches, including haplogroup-only matches, are from Scandinavia – Norway and Sweden primarily, with a few scattered elsewhere, which was a HUGE surprise to me. I expected Germany, but that’s not the history of my ancestors prior to 1647.

History beyond written records is invaluable history – and only available to us through non-recombinant DNA, such as Y-DNA (for males only) and mitochondrial DNA for everyone. Both maintain their direct line back through history because neither are ever combined with the DNA of the other parent, so they are never divided like autosomal DNA during recombination.

Cheat Sheet

I’ve created this handy dandy cheat sheet as a memory aid to recall which kinds of mutations are included in what type of matching, and why.

Memory Aid

• Haplotype Clusters are your closest match buddies – exactly – clustered together. However, genealogically, you might be equally as close to people with other haplotypes. Remember that mutations 309 and 315 are jokers and may throw a monkey-wrench into matching!
• Matches on your matches page are “serious,” because they ignore those jokers. No 309 and 315 jokers allowed here.
• Haplogroup-Only Matches can still provide important hints. You need to “Discover” them in mtDNA Discover

To See More

To step through your results using all of the mitochondrial DNA tools, including Discover reports, please refer to my article, Mitochondrial DNA A-Z: A Step-by-Step Guide to Matches, Mitotree and mtDNA Discover.

Thanks for coming to my TED talk😊

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