A new feature called Haplotype Clusters was released with the new Mitotree and mtDNA Discover.

MtDNA Discover includes a dozen new reports for EVERY haplogroup. You can use the public version of Discover with any haplogroup.

However, there are additional included features for mtFull testers, and other information provided will be much more detailed and robust because the mtFull test is much more specific than any partial haplogroup.

If you have only taken the older partial-coverage HVR1 or HVR1/HVR2 tests at FamilyTreeDNA, you can sign in and upgrade, or if you have received a partial haplogroup from another source, you can take the mtFull test at FamilyTreeDNA.

OK, I’ve Taken the mtFull Test, So How Do I Access My Discover Reports?

Sign in to your FamilyTreeDNA account, then from your mtDNA dashboard, click through to Discover to access your Discover reports.

Discover reports are in addition to the tools in the mtDNA Results and Tools section of your dashboard on FamilyTreeDNA.

Definitions

Let’s start with some basic definitions.

• Haplotype – Your individual DNA results at specific adjacent locations that are generally inherited together.

Other people may have the same haplotype as you. If they have mutations that you don’t have, or vice versa, then you have different haplotypes. People with the same haplotypes match exactly on whatever type of DNA is being discussed, such as Y-DNA or mitochondrial DNA, with no mutations or differences. Multiple people who match exactly are considered a Haplotype Cluster.

• Haplogroup – A group of specific mutations that identify people who share a common genetic clan. Haplogroups, based on a series of mutations, can be traced forward and backward in time.

A haplogroup is a grouping of haplotypes with the same foundation mutations. You will share those mutations with other people in your haplogroup, but you may have other, different mutations that form your haplotype.

• Other people will have the same haplogroup as you, because a group implies two or more.
• You may or may not share a haplotype with other people. If you share the exact same haplotype with at least one other person, the two (or more) of you form a Haplotype Cluster

What is a Haplotype Cluster?

Haplotype Clusters are new and have been added to provide additional granularity to the new Mitotree, making results more genealogically useful.

In addition to your mitochondrial DNA haplogroup, you may also have a Haplotype Cluster if you took a full sequence mitochondrial DNA test, called the mtFull.

A mitochondrial DNA haplogroup, such as J1c2f for example, means that everyone within that haplogroup has the same foundation grouping of mutations. You may have additional mutations, or even some missing mutations, based on the older Phylotree Build 17, which was last updated in 2016.

To see your Extra and Missing Mutations in the Classic, or Phylotree build, on the FamilyTreeDNA mtDNA dashboard, click on “See More,” then on Mutations.

In the recently released Mitotree, which reconstructs the tree of humanity with more than 35,000 new branches, or haplogroups, many of those “extra” or “missing” mutations have been used in the definition of new haplogroups.

At FamilyTreeDNA, on your matches page, you’ll see your matches, like always. Matching has not changed.

You’ll notice that some are exact matches, and some may be “1 step” or more distant. That means they have one qualifying genetic mutation difference from you.

Some mutations have always been excluded from matching because they are unreliable. In my case, location 315.1C is one of those. You can read more about matching here. Matching has NOT been rerun with the release of the new Mitotree, but may be in the future.

The new Haplotype Clusters designate other people who you literally match exactly, with no differences – and no excluded marker locations.

So, let’s compare how I match people and what it means:

• Haplogroup match – I match these people at the haplogroup level, which can reach back hundreds or even thousands of years ago. In addition, I may match them on both other relevant, reliable mutations, and/or unreliable mutations. On the current matching page, the mtDNA Haplogroup is the PhyloTree Build 17 haplogroup. Before Mitotree, matches to any other haplogroup were not displayed. Now, new haplogroups of my J1c2f matches, if they received a new haplogroup, are shown in the Mitotree Haplogroup column. My common ancestor with a match can have occurred anytime between when the haplogroup was formed and today.

Some people receive partial haplogroup level matches from other testing companies that also don’t include matching. A haplogroup match alone isn’t particularly useful except when it can eliminate a connection.

That’s why we need matching on the Matches page.

• FamilyTreeDNA Matches Page Match – On the Matches page, I match these people at the haplogroup level as calculated based on Phylotree Build 17, as shown in the mtDNA Haplogroup Column at the Genetic Distance displayed. This means that I match them on the haplogroup markers PLUS possibly other markers.

My first match with Per, above, is listed as an exact match. Before Haplotype Clusters were introduced, I had no way of knowing if I matched him on all of my mutation locations, or just the ones that are NOT excluded from matching. But now I do.

My Haplotype Cluster number is F1752176. I know this because the little circle is checked and blue – meaning this person and I share both a haplogroup in the new Mitotree, and a Haplotype Cluster.

Ronald, above, is a match with a “1 step” Genetic Difference. I know for sure that I match him on the haplogroup markers. I also know that we don’t match on one non-excluded marker – but I have no idea which one. We may also match, or not, on some of the excluded markers. But we are not members of the same Haplotype Cluster. The blue circle is not checked.

You cannot be a member of more than one Haplotype Cluster, because everyone in a Haplotype Cluster must match exactly.

• Haplotype Cluster – A Haplotype Cluster, if you have one, is a random F number assigned to people whose mitochondrial DNA matches exactly – and by exactly, I mean without excluding unstable or unreliable mutations.

You can see my Haplotype Cluster number, above, in the Mitotree Haplogroup column, in addition to my new Mitotree haplogroup – which is still J1c2f and did not change from the earlier version. In Mitotree, some people will receive new haplogroups, and some will not – based on your and other people’s mutations.

My match with Ronald is one step difference. Our haplogroup is the same, so that circle is checked, but Ronald belongs to a different Haplotype Cluster, so that circle is not checked, and he has a different F number. I can’t see his mutations that are different from mine, but I know he matches everyone else in his Haplotype Cluster exactly.

Let’s look at another example.

Looking at my match list, I can see that beneath my matches’ haplogroup, which is the same as mine, F1752176 is checked and the checked circle is blue, which means that I share that Haplotype Cluster with those people. Everyone in that cluster has all of the same mutations in addition to the haplogroup-defining mutations, which is why both the haplogroup and haplotype circles are checked. I match both.

If I look at my Matches page, or the mtDNA Discover Time Tree, or Matches Time Tree, I can see that I have many exact haplotype matches, which means:

• We all share haplogroup-defining mutations and
• We match exactly on all other mutations as well

Before Haplotype Clusters were introduced, I had no way of knowing which of these people I matched exactly if no mutations were excluded.

To summarize, a Haplotype Cluster is a group of people who all match each other exactly within a haplogroup. People in Haplotype Clusters always match exactly, which INCLUDES mutations that are EXCLUDED from haplogroup formation and matching.

If you don’t match someone exactly, you’re not in the same Haplotype Cluster. You can either be in a different cluster, or no cluster at all if no one matches you exactly.

Everyone has a Haplotyupe Cluster number, but you will only be a member of a Haplotype Cluster if you have an exact match to at least one other person.

Don’t Ignore Other Clusters

The F number itself isn’t important. What is important is that Haplotype Clusters serve to focus your genealogy on that cluster first. However, understand that because the Haplotype Cluster does include unreliable or fast-mutating markers, it’s possible for you to share a more recent ancestor with people in a different cluster. It depends on the marker and the mutation, so don’t discount that possibility.

Who Can See Haplotype Cluster Mutations?

The only people who know the exact mutations of the people in a specific Haplotype Cluster are the members of that cluster – because they all match exactly.

If you scroll down your match list, you’ll notice that people, like Anastasia, who have a genetic distance of 1 step or greater have a different F Haplotype Cluster number, which is expected.

You may also notice that someone who is an “exact match” with you on the match list is assigned to a different Haplotype Cluster, such as Rose and Per. Rose is not in my Haplotype Cluster, but Per is, even though they are both “exact matches.”

Remember, “matching exactly” on the match list excludes unreliable mutation locations. Haplotype Clusters always match exactly and include all mutations. So, this tells me that I match Per on all mutation locations, regardless of their stability, and I match Rose on all stable locations, and we mismatch on at least one location that was excluded from matching.

However, the only people who know the exactly mutations of any other person are me and Per, because we both share a Haplotype Cluster. People in other clusters, or without a cluster, don’t know and can’t identify the mutations in clusters not their own.

• The only thing I can tell about my match with Rose is that we don’t share one of the unreliable markers, because we are an “exact match” on the match list which excludes unstable markers. I have no idea whether I carry that unstable marker, or she does, or which marker it is.
• The only thing I can tell about my match with Anastasia is that we don’t share at least one stable marker, because we are a “1-step” genetic distance, and we could also not share some of the unstable markers. I have no way of identifying those markers.
• I know that I match Per exactly on all markers, including unstable or unreliable markers.

Included Versus Excluded Markers

Sometimes people who are listed as exact matches on your Matches page are assigned to different Haplotype Clusters. This is because mutations such as 309 and several others are included in Haplotype Clusters, but excluded from matching and haplogroup formation. The reason they are excluded is because they are sometimes unreliable – but they may be useful to your research. They aren’t always unreliable, but it varies on a case-by-case basis, including when the mutation occurred.

Location	Haplogroup Formation	Matching on Matches Page	Haplotype Cluster
309	Excluded	Excluded	Included

Here’s an example using location 309. While some locations are excluded from matching, their inclusion in the formation of Haplotype Clusters may be very genealogically relevant to you – or perhaps not. That’s where genealogy research becomes important.

Haplotype Clusters give you the ability to focus your research on a specific group of people that you know do, in fact, match you exactly. Just keep in mind that some people in a different Haplotype Cluster, that don’t have a mutation at 309, for example, could have a closer common ancestor. That’s the nature of 309, 315 and other unstable SNPs, especially heteroplasmies, which tend to “come and go,” which I wrote about here. In other words, don’t ignore other Haplotype Clusters that appear on your match list – just begin with your own and evaluate using genealogy..

The Haplotype Cluster number itself isn’t important. What is important is that they serve to focus your genealogy efforts.

Where Else Can I Find My Haplotype Cluster

You can identify your Haplotype Cluster number by looking at your match list, as we have discussed, or by navigating to the Variants tab on the Scientific Details page.

On the variants tab, your haplogroup is marked with the solid red square, along with other information which I have truncated here.

Immediately above your haplogroup, you’ll see your Haplotype Cluster number, if you have one, along with any remaining private variants, aka mutations, that are haplogroup seeds and qualify to potentially become part of a haplogroup in the future.

In my case, this tells me that either all of my mutations are now included in a haplogroup definition, or they are excluded due to their instability or unreliability. Everyone else in this Haplotype Cluster is in exactly the same situation.

The only person who can see your Haplotype Cluster in Discover is you, if you are signed in to FamilyTreeDNA and you toggle “Show Private Variants” to “on.”

Haplotype Clusters as a Subset of Haplogroups

Haplogroups can and do have mutations “beneath” them, meaning haplogroup members may have different mutations or variants, in addition to the mutations used to form the haplogroup. Think of them as twigs or leaves on the tree.

Using the Classic Mitotree view in mtDNA Discover, you’ll notice that haplogroup J1c2f contains six Haplotype Clusters.

Please note that one of these clusters could be people who match the haplogroup definition exactly, and have no additional mutations of any type. They would form their own cluster.

Additionally, above the clusters, there are individual branches listed that don’t (yet) form clusters. You don’t know from looking at the individuals listed by country, such as Sweden, Germany, Norway, and so forth, if these people have only the exact mutations in haplogroup J1c2f, or if they have additional mutations that are unique and no one else has those exact mutations. What you do know is that so far, no one else matches them exactly, but as other people test, they may develop into a HaploType Cluster.

You may not match all of the people in your haplogroup on your matches page, because they may be over the match threshold and have too many mutations difference from you.

Some testers with unique, stable mutations may form new haplogroups as additional people test.

Using the Time Tree, you can see that there are currently 33 people who are in haplogroup J1c2f but do not match anyone else exactly.

The Discover Time Tree

Now that we’ve looked at examples individually, I took a screenshot of my entire haplogroup on the mtDNA Discover Time Tree to get the big picture.

The Time Tree offers a nice visual summary of all of J1c2f, including my full sequence matches, all in one place, along with Haplotype Clusters.

My haplogroup is shown in the black circle, and downstream haplogroups are shown in red circles.

You can see my Haplotype Cluster, which I can identify by the F#. You can see other Haplotype Clusters within my haplogroup, along with some individuals who don’t have any exact matches, who are shown alone on their line.

The Match Time Tree

When you click on Discover Haplogroup Reports from your dashboard, then on the Match Time Tree, you’ll see your matches’ names on your personal Time Tree, along with their self-reported earliest known matrilineal ancestors, in addition to their ancestor’s country of origin.

Here’s an example of a portion of my Match Time Tree with my matches’ names redacted.

With these new Discover and Mitotree tools, you know where to focus your research most closely. Which matches’ trees to view or build out to identify common ancestors, and who to prioritize for communications.

If you have a new haplogroup – that’s wonderful, but you don’t need one to make headway. The clue you need may well be found in your Haplotype Cluster.

There’s so much new information available for you. What can you discover?

_____________________________________________________________

Share the Love!

You’re always welcome to forward articles or links to friends and share on social media.

If you haven’t already subscribed (it’s free,) you can receive an e-mail whenever I publish by clicking the “follow” button on the main blog page, here.

You Can Help Keep This Blog Free

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase your price but helps me keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

DNA Purchases and Free Uploads

• FamilyTreeDNA – Y, mitochondrial and autosomal DNA testing
• MyHeritage DNA – Autosomal DNA test
• MyHeritage FREE DNA file upload – Upload your DNA file from other vendors free
• AncestryDNA – Autosomal DNA test
• AncestryDNA Plus Traits
• 23andMe Ancestry – Autosomal DNA only, no Health
• 23andMe Ancestry Plus Health

Genealogy Products and Services

• MyHeritage Subscription with Free Trial
• Legacy Family Tree Webinars – Genealogy and DNA classes, subscription-based, some free
• Legacy Family Tree Software – Genealogy software for your computer
• OldNews – Old Newspapers with links to save to MyHeritage trees
• MyHeritage Omni comprehensive “everything included” subscription plan
• Newspapers.com – Search newspapers for your ancestors
• NewspaperArchive – Search different newspapers for your ancestors

My Books

• DNA for Native American Genealogy – by Roberta Estes, for those ordering the e-book from anyplace, or paperback within the United States
• DNA for Native American Genealogy – for those ordering the paperback outside the US
• The Complete Guide to FamilyTreeDNA – Y-DNA, Mitochondrial, Autosomal and X-DNA – for those ordering the e-book from anyplace, or paperback within the United States
• The Complete Guide to FamilyTreeDNA – Y-DNA, Mitochondrial, Autosomal and X-DNA for those ordering the paperback from outside the US

Genealogy Books

• Genealogical.com – Lots of wonderful genealogy research books
• American Ancestors – Wonderful selection of genealogy books

Genealogy Research

• Legacy Tree Genealogists – Professional genealogy research