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Haplogroup Matching: What It Does (and Doesn’t) Mean

Roberta Estes

“Our haplogroups (sort of) match, so that means we’re related, right?”

Well, maybe.

It depends.

Great Question

This is an oft-asked great question. Of course, the answer varies depending on the context of the question and what is meant by “related.” A haplogroup match may or may not be a valid match for genealogy. A “match” or a “not match” can mean different things.

The questions people often ask include:

These questions often arise in relation to DNA testing at Family Tree DNA, sometimes when people are trying to compare results to people who have haplogroup estimates, either at FamilyTreeDNA or from testing elsewhere.

In other words, if one person is haplogroup J and someone else is J1, either at the same vendor or at another, what does that tell us? This question pertains to both Y DNA and mitochondrial DNA tests no matter where you’ve tested.

Family Tree DNA offers different levels of Y DNA testing. Interpreting those match results can sometimes be confusing. The same is true for mitochondrial DNA, especially if your matches have not taken the full mitochondrial sequence (mtFull) test.

You might be comparing apples and oranges, or you might be comparing a whole orange (detailed test) with a few slices (haplogroup estimate.) How can you know, and how can you make sense of the results?

If you’re comparing a haplogroup between sources, such as a partial haplogroup determined by testing through a company like 23andMe or LivingDNA to complete tests taken at FamilyTreeDNA, the answer can be less than straightforward.

I discussed the difference between autosomal-based haplogroup assignments and actual testing of both Y DNA and mitochondrial DNA which result in haplogroup assignments, here. In a nutshell, both LivingDNA and 23andMe provide a high-level (base) haplogroup estimates based on a few specific probes when you purchase an autosomal test, but that’s not the same as deeper testing of the Y chromosome or mitochondrial DNA.

The answer to whether your haplogroup has to match is both “yes”, and “no.” Don’t you hate it when this happens?

Let’s look at different situations. But to begin with, there is at least one common answer.

Yes, Your Base Haplogroup Must Match

To even begin to look further for a common ancestor on either your Y DNA line (direct patrilineal) or direct mitochondrial matrilineal line (your mother’s mother’s mother’s line on up the tree), your base haplogroup much match.

In other words, you and your matches must all be in the same base haplogroup. Haplogroups are defined by the presence of specific combinations of mutations which are called SNPs (single nucleotide polymorphisms) in the Y DNA.

Click to enlarge images

All of these men on the Y DNA matches page are a branch of haplogroup R as shown under the Y-DNA Haplogroup column. There are more matches on down the page (not shown here) with more and different haplogroups. However, you’ll notice that all matches are a subset of haplogroup R, the base haplogroup.

The same is true for mitochondrial DNA haplogroups. You can see in this example that people who have not tested at the FMS (full mitochondrial sequence) level have a less specific haplogroup. The entire mitochondria must be tested in order to obtain a full haplogroup, such as J1c2f, as opposed to haplogroup J.

The Y DNA Terminal SNP Might Not Match

For Y DNA testers, when looking at your matches, even to close relatives, you may not have the same exact haplogroup because:

In other words, haplogroups, testing level, and known genealogy all need to be considered, especially when the haplogroups are “close to each other” on the tree.

For Y DNA, FamilyTreeDNA:

That’s why the answer is “no,” your haplogroup does not have to match exactly for you to actually be a match to each other.

A father and son could test, with one having an estimated haplogroup of R-M269 and the other taking the Big Y-700 resulting in a very different Terminal SNP, quite distant on the tree. Conversely, both men could take the Big Y and the son could have a different terminal SNP than the father because a mutation occurred between them. An autosomal DNA test would confirm that they are in fact, father and son.

However, a father and son who test and are placed in different base haplogroups – one in haplogroup I, and the other in haplogroup R, for example, has a very different situation. Their autosomal test would likely confirm that they are not father and son.

Having said this about paternity, especially if haplogroups are estimated and specific Y DNA SNP testing has not been done, don’t have a premature freak-out moment. Look at autosomal DNA, assuming you DO want to know. Y DNA alone should never be used to infer paternity without autosomal testing.

Let’s look at some examples.

Matches and Haplogroups

In the example shown above, you can see that several people have taken the Big Y test, so their SNP will be shown on further down the haplotree than those testers who have not. These are a leaf, not a branch.

You can see by looking at the Terminal SNP column, at far right, that people who have either taken the Big Y, or had any positive SNP test will have a value in the Terminal SNP column.

Anyone who has NOT taken the Big Y or taken a SNP test will have their base haplogroup estimated based on their STR tests. In this case, that estimate is R-M269. People with estimated haplogroups will not show anything in the Terminal SNP column.

It’s possible that if all of these men took the Big Y test that at least some would share the same Terminal SNP, and others might be closely related, only a branch or so different on the tree.

These men in this example are all descendants of Robert Estes born in England in 1555. All have Estes surnames, except for one man who is seeking the identity of his paternal line.

Let’s Look at the Tree

Our tester in the screenshot is haplogroup R-ZS3700 and matches men in the following haplogroups:

There are a few additional haplogroups not shown because they are further down on his match list, so let’s just work with these for now.

After determining that these men are on the same branch of the Y tree, haplogroup R, the real question is how closely they are related and how close or far distant their terminal SNPs are located. More distance means the common ancestor is further back in time.

However, looks can be deceiving, especially if not everyone has tested to the same level.

The haplogroup furthest up in the tree, meaning the oldest, is R-M269, followed by the man who took the single SNP test for R-L21. Notice that R-M269 has more than 15,000 branches, so while this haplogroup could be used to rule out a match, R-M269 alone isn’t useful to determine genealogical matching.

There are a lot of branches between R-L21 and the next haplogroup on the tree.

Finally, here we go. Our tester is haplogroup R-ZS3700 that has one descendant branch. R-ZS3700 is a branch of R-BY490 that has 2 branches.

R-BY154784 is the last SNP on this branch of the tree. Our tester matches this man too.

Another way of viewing these matches is on the Block Tree provided for Big Y testers.

In this view, you can see that the Estes men all match back to about 18 “SNP generations” ago according to the legend at left, but they don’t match men further back in time who have taken the Big Y test.

Notice the up-arrow where haplogroups R-L21 and R-M269 are shown across the top of the display.

If you click on R-L21, you’ll see that that it appears about 61 SNP generations back in time.

Haplogroup R-M269 appears even further back in time, about 174 SNP generations.

The only reason you will match someone at either the R-L21 or R-M269 level is because you both descend from a common long-ago ancestral branch, hundreds to thousands of years in the past. You and they would both need to take either the Big Y-700 test for Y DNA, or the full sequence mitochondrial DNA test in order to determine your full haplogroup and see your list of matches based on those full sequences.

Public Trees

You can view FamilyTreeDNA‘s extensive public Y DNA tree by haplogroup, here.

You can view their public mitochondrial DNA tree by haplogroup, here.

And the Answer Is…

As you can see, there is no single answer to the question of haplogroup relationships. The answer is also partly defined by the context in which the question is asked.

  1. For two men to be “related” on the Y DNA patrilineal line, yes, minimally, the base haplogroup does have to match. Base haplogroups are defined by the leading letter, like “R” in the examples above.
  2. “Related” based on base haplogroup only can be hundreds or thousands of years back in time, but additional testing can resolve that question.
  3. “Related” can mean before the advent of surnames. However, a match to a man with the same surname suggests a common ancestor with that surname in the past several hundred years. That match could, however, be much closer in time.
  4. For two men to be closely related, assuming they have taken the same version of Big Y test, their haplogroup branches need to be fairly closely adjacent on the haplotree. FamilyTreeDNA will be introducing haplogroup aging soon, meaning SNP/haplogroup branch dates on their haplotree. At that time, the “distance” between men will be easier to understand.
  5. You can exclude a genealogical relationship on the direct paternal line if the two men involved have a different base haplogroup. This question often occurs when people are trying to understand if they “might match” with someone whose haplogroup has been estimated.
  6. This holds true as well for mitochondrial DNA haplogroups and matching.

And there you have it, six answers about what haplogroup matching does and does not mean.

The bottom line is that haplogroups can be a great starting point and you can sometimes eliminate people as potential matches.

However, to confirm genealogical matches, you’ll always need more granular testing that includes actual Y DNA or mitochondrial DNA matching based on marker mutation results, not just haplogroups.

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