Category Archives: Haplotype

New Mitotree Haplogroups and How to Utilize Them for Genealogy

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Have you received a new Mitotree haplogroup? Or maybe you didn’t? Are you wondering why you might not have received a new haplogroup? How do the new haplogroups work anyway? And how do you work with them?

Great questions!

Approximately 75% of full sequence testers received a new haplogroup with the Mitotree Beta release, which means that about 25% did not. Keep in mind that new sequences are being added to the database, so the tree will be sprouting new haplogroups with each subsequent release.

Check For Your New Haplogroup

Click on any image to enlarge

Sign in to your account at FamilyTreeDNA and look at the Badges in the bottom right corner of your page.

Your Beta haplogroup is your new Mitotree haplogroup, and your Legacy haplogroup is your old one – prior to Mitotree. They may be the same. My haplogroup, shown above, did not change.

This is a good place to note that the tree is not “done,” yet, nor will it ever be. New samples are added daily as more people test and as academic samples from published papers are added to the database as well. Additionally, FamilyTreeDNA is tweaking the algorithm, so the tree branching structure may change from time to time.

When your haplogroup changes, you’ll receive a notification email.

Some people’s haplogroup will remain the same. There can be several reasons why you might not have received a new haplogroup.

Before we discuss that, I’d like to stress that your haplogroup remaining the same isn’t exactly a bad thing because there is SO MUCH new content for everyone. It’s like receiving a whole new book about your mother’s direct matrilineal line.

mtDNA Discover Offers 13 New Reports for Everyone

MtDNA Discover was released with the new Mitotree, and it includes a dozen new reports for EVERY haplogroup.

Discover is available publicly, and also through your FamilyTreeDNA dashboard which provides a customized experience for mtFull testers with additional information that is not available in the free version.

Think of these Discover reports as chapters in your personal book – all about you and your matrilineal ancestors.

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

There’s something for everyone, even if you don’t have a new haplogroup. There’s certainly new information that will help with your genealogy and with understanding the history and ancestral journey of your mother’s direct line maternal ancestors.

Three Reasons Why You Might Not Receive a New Haplogroup

Ok, so why might you not have received a new haplogroup?

The first reason that you might not have received a new haplogroup assignment is the simplest. The new tree is only updated periodically.

After your results are returned, and before the next Mitotree version is available, your Mitotree haplogroup Badge will show as “Analyzing.”

If one of your matches is waiting for a new haplogroup, their Mitotree Haplogroup will show as “Pending Analysis.”

There is no published tree-update schedule, but you’ll receive your new haplogroup soon.

However, you can probably determine your new haplogroup quite easily. If you have any exact matches on your mtDNA Match page, their haplogroup will be your haplogroup as well, so check your full sequence mtDNA Matches on your dashboard for a hint.

For, example, here’s one of my exact matches with their haplogroup.

The second reason you might not have a new haplogroup assignment is that you may not have taken the full sequence mitochondrial DNA test – mtFull.

Only testers with full sequence test results can receive an updated haplogroup, because the full mitochondria needs to be tested. The older HVR1/HVR2 Plus tests only tested a fraction of the full sequence – around 1000 locations of the 16,569 locations tested in the full sequence test.

If you have only taken the HVR1 or HVR1/HVR2 level test, you will only have one badge, and it will say “Predicted.”

The haplogroup for the Plus test is predicted at a high level based on those 1000 locations, while the full sequence test tests the entire mitochondria and uses all locations to confirm your most granular and detailed haplogroup possible.

On your dashboard, if both the Plus and Full icons are pink, you have taken the mtFull test. If the “Full” is grey, you have not. You can click on that grey button to upgrade.

You can also navigating to on Add Ons and Upgrades in the top bar to upgrade to the full sequence test.

The third reason why someone might not have received a new haplogroup assignment is if they didn’t match with anyone else who has the same mutations, or variants, for a particular haplogroup.

In other words, if my mitochondrial DNA has had a mutation or two since my assigned haplogroup was formed and no one else has tested that has those exact same mutations, there’s no one else to form a new haplogroup with, but there might be in the future as additional people test and the tree continues to grow.

Think of those additional mutations, called Private Variants, as foundation blocks, or haplogroup seeds since they are still private to you, and not yet used for a haplogroup.

It’s easy to see if you have any Private Variants by clicking on Discover on your mitochondrial dashboard.

Scientific Details – Private Variants, Building Blocks, Haplogroup Seeds

If you have taken the full sequence test, click through to mtDNA Discover from your dashboard. If you aren’t signed in and click through from your dashboard, you won’t be able to see your variants or other information customized for you.

Navigate to Scientific Details, then click on the Variants tab.

Click on image to enlarge

Be sure that “Show private variants” is toggled to “on,” which is blue with a checkmark.

At the very top, you’ll see two things:

  1. Your haplogroup, which is indicated by the solid pink square.
  2. An F number followed by your private variants, if any, and if so, which ones.

I have no private variants or haplogroup seeds available to form a new haplogroup, so I have no ability to receive a more refined haplogroup.

Haplotype Clusters

However, I’m NOT out of luck, because I have something else – a Haplotype Cluster, indicated by having an F#. My Haplotype Cluster is F1752176 and is indicated by the pink outlined box.

I wrote about haplotype clusters in the article, Mitochondrial DNA: What is a Haplotype Cluster and How Do I Find and Use Mine?.

In a nutshell, haplogroups are only formed around reliable, relatively stable mutations, meaning those that are reliable and don’t tend to randomly mutate back and forth.

You may match exactly with a group of other people who share the same haplogroup, PLUS the same unstable mutations that don’t qualify to become haplogroup-defining.

Those groups of two or more people who match exactly on all mutations are members of the same  Haplotype Cluster – and Haplotype Clusters can be INCREDIBLY genealogically useful. In fact, let me go out on a limb here and say that I think they are even more genealogical useful than haplogroups, although both have their strengths. Let’s look at a good example.

Using Haplogroups and Haplotype Clusters Together

My family member, Jim, had a surprise waiting for him in his mitochondrial DNA. When he received his new haplogroup, I took a look to see what new information might be forthcoming.

His legacy haplogroup was V, and his new Mitotree haplogroup is V216a2 which is significantly more refined.

Before Mitotree and Haplotype Clusters, there wasn’t much to differentiate him from his other matches.

Let’s take a look at JUST his genetic information before adding genealogy.

If I click on the Time Tree for haplogroup V216a2, I see two testers with no cluster, meaning no one matches them exactly, and Jim’s cluster number F9712482.

Keep in mind that Jim might not match everyone in his haplogroup – only people at or beneath the matching threshold.

Jim’s new haplogroup, V216a2 was formed about 1056 CE, or about 975 years ago. Note that as the tree changes and becomes more refined, haplogroup formation dates change too. A haplogroup’s birth date is an approximate year when the mutations occurred that define that haplogroup, based on surrounding mutations and mutation rates.

Many people look at a haplogroup, especially one with a birth date of, say, 1056 CE, which is long before the formation of surnames, shrug their shoulders, and give up.

Don’t. Do. That.

So, let me say this as loudly as possible.

A haplogroup’s most recent common ancestor is NOT the EKA (earliest known ancestor) with any individual match. It’s the approximate date when ALL of the people with this haplogroup share a common ancestor.

When looking at haplogroups, don’t let locations thrown you. Keep in mind that country boundaries are fluid. What was at one time Hungary could be Germany or Romania or something else just a few years earlier or later. So don’t discount that information either. Think regions and take into consideration that people move around – and some people enter incorrect genealogy/location information.

Your common ancestor with the people, individually, who share your haplogroup,  is sometime between the haplogroup formation date and today. Everything else is a clue. 

Think about it this way. You share a haplogroup with your mother, and while you are both descended from the woman who lived when your haplogroup was formed – your most recent ancestor with that haplogroup is your mother – not the woman 975 years ago. Your most recent common ancestor (MRCA) with your mother and her sister is your grandmother – a lot closer in time than 1056 CE. 1056 CE the most recent common ancestor (MRCA) date for everyone in the haplogroup, not between you and any one person in particular. The MRCA date for you plus another person is sometime between now and 1056 CE.

So, let’s take a look at Jim’s results.

Finding Jim’s Gold Nugget

Jim has 27 coding region matches, of which six share both his new haplogroup, V216a2, AND Haplotype Cluster F9712482. His other matches are split between three related haplogroups, and multiple haplotype clusters.

Most of his family, meaning three of his grandparents, were from eastern Europe, meaning Germany, Hungary or the Austro-Hungarian empire as it was recorded in American records. Many genealogical records no longer exist in that region, or if they do, you have to know exactly where to look.

We were brick-walled with Jim’s matrilineal great-grandmother, Sophia Smith, who was born about 1877 and seemed to appear out of thin air.

Thanks to the new haplogroups, combined with Haplogroup Clusters, I knew to focus on his matches in this order:

  • Same haplogroup plus same Haplotype Cluster
  • Same haplogroup plus different Haplotype Cluster, because clusters are built around identical but less reliable mutations
  • Related haplogroup – this is unlikely to yield direct genealogical results, but can be very useful in terms of origins

Of Jim’s exact matches with the same Haplotype Cluster, three showed an earliest known ancestor (EKA) and three did not. Three provided a tree, and three did not. Of the trees, one was private and the other two provided no useful insight.

Of the people who provided EKA information, one EKA matches their tree information, one conflicts with their tree. After viewing their tree, it appears that they did not understand that the mitochondrial EKA is the most distant ancestor in your mother’s direct maternal line. They listed someone in their grandmother’s paternal line.

I find this easiest to deal with if I organize the research in a chart for each match.

Match # Earliest Known Ancestor EKA Location Tree Comment
#1 No No No
#2 No No No
#3 No No Yes – Private
#4 Yes – only one name “Egan” with brith and death dates Ireland Yes – Egan is surname of their grandmother EKA person listed tracks up wrong line in tree
#5 Yes Hungary No Elizabeth Schmidt Hornung b1888 d 1930
#6 Yes No Yes – matches EKA Ancestor born NC in 1811, no common names or location

Match #5 provided an EKA, but no tree, showed a country of origin as Hungary, and the identity of her EKA as “Elizabeth Schmidt Hornung b.1888 and d.1930.”

Hmmm…three things of interest here:

  • The location of Hungary, even though the oral history in Jim’s family said his great-grandmother was a Smith from the US, maybe New York. Jim’s family, including Sophia’s husband, was Eastern European. Remember, I couldn’t find any early records for Sophia Smith.
  • Smith is the anglicized version of Schmidt.
  • Hornung may be a married name.

I’m a genealogist, and Jim’s match had provided enough information that I was able to identify her ancestor, Elizabeth Schmidt, and find additional information.

Sure enough, Elizabeth Schmidt immigrated as an adult by herself, married Karl Hornung in Richland County, Ohio, the same location where Jim’s family was living. That information led me to another record, identifying a brother whose marriage license application provided their parents. Elizabeth’s parents were Ignatius Schmidt and Catherine Schlowe, and her sister was Sophia Schmidt, Jim’s great-grandmother. Deeper digging suggests that Ignatius and Catherine were from Timisoara in what is now Romania. I have been unable to confirm with birth, death or marriage records, but that part of Romania was part of the Austro-Hungarian Empire during that timeframe.

Immigration of siblings, alone, at different times after the 1910 census, without their parents, made this particularly difficult, as did cultural and language barriers – but mitochondrial DNA, and Jim’s Haplotype Cluster in particular, provided the key I needed.

Jim’s common ancestor with his Schmidt match is the birth date of Catherine Schlowe, which was probably about 1850 – NOT 1056 CE, which is the haplogroup formation date.

Don’t get discouraged by misinterpreting haplogroup origin information or missing genealogy information. All you need is that one good match. That gold nugget. Don’t forget that you can email your matches and ask for more information.

The Match Time Tree makes all of this easier.

Match Time Tree

The Match Time Tree shows match, haplogroup, location and Haplotype Cluster information all in one place.

It’s easy to use the Match Time Tree to view how all of your matches are grouped, along with their EKA, displayed together in one place.

Here are all of Jim’s matches. They were all originally haplogroup V, but now his matches have been divided into V216, V216a, V216a1, and V216a2 (Jim’s haplogroup).

I’ve obfuscated the names of his matches, but the EKA, when provided, is there. Each person is grouped into their haplotype cluster of exact matches, and the user-provided country of origin for their ancestor is shown by their profile photo.

Jim’s match with the descendant of Elizabeth Schmidt is indicated in the red boxes, and Jim has updated his own EKA and her country of origin.

Who is waiting for you in your match list?

Will extending and building out trees help?

Have you emailed your matches to see what additional information they can provide?

Female ancestors are sometimes the MOST difficult to find, often due to name changes  – so be sure to mine every possible avenue and don’t become discouraged if you don’t immediately see something “familiar.”

Every generation in a female lineage will probably carry a different surname and the match you need may not have researched as far back as your ancestor, or vice versa.

Don’t forget that autosomal matching can play an important role in confirming relationships.

But wait – there’s STILL more about Jim’s ancestors…

There’s Even More to Discover

There’s more to discover about Jim’s ancestors.

Jim’s Discover Ancient Connections tells me that 5200 years ago, Jim shared a common mitochondrial DNA ancestor with two Hungarian and a Slovakian Yamnaya cultural burial whose remains date to about 2800 BCE, or about 4800 years ago.

To be clear, the common haplogroup between Jim and all three burials dates to 5200 years ago, when their common haplogroup was formed, but the remains themselves are from about 4800 years ago – so only about 400 years difference between the haplogroup birth date and when those people lived, died and were buried.

How close are the remains to the location of Jim’s ancestor in Timisoara?

Using Google Maps, I placed the three Yamnaya burial locations (blue pins), plus Timisoara.

The two most distant points, Timisoara to Lesne, Slovakia, walking, is 393 km or 245 miles. The closest burial to Timisoara, located in Sárrétudvari, Hungary, is 157 km  or 119 miles.

So Jim’s ancestors remained in the same general area for someplace between 4,800 and 5,200 years. And, his great-grandmother was born not far from those burials. That alone is an INCREDIBLE find!

So, what happened to the people of the Yamnaya culture? I think we might have gained some insight into that question.

So, there’s even more to discover using Discover.

You don’t know what you don’t know about your matrilineal ancestors, so test your mitochondrial DNA at FamilyTreeDNA and break through those brick walls. I’ve already solved multiple long-standing mysteries and added generations to my own tree.

Plus, I really, REALLY want to know where every single ancestor “came from,” what culture they were a part of, and when. History is part of genealogy – and a part of our ancestral journey that we can’t reach any other way.

Fortunately, your matches, Scientific Details, Time Tree, Match Time Tree, and Ancient Connections help you visualize all of these various situations and aspects of your ancestor’s history, and evaluate your results.

Both haplogroups and Haplotype Clusters provide very fine degrees of granularity that were not previously available. MtDNA Discover adds a dozen new reports, and Ancient Connections allow you to time travel.

Let me know what you discover!

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Mitochondrial DNA: What is a Haplotype Cluster and How Do I Find and Use Mine?

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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.

Click to enlarge any image

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.

Click on any image to enlarge

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?

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Mitotree is Born

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Mitotree is born and I can hardly contain my excitement.

The Million Mito R&D team members, along with many others at FamilyTreeDNA, are proud to introduce the new Mitotree and mtDNA Discover, which were brought to life thanks to one pivotal entrepreneurial figure, Bennett Greenspan, whose support and vision set the ball in motion and made Mitotree possible.

Left to right, the Million Mito science team is:

  • Goran Runfeldt, Head of R&D at FamilyTreeDNA
  • Dr. Paul Maier, Senior Population Geneticist at FamilyTreeDNA
  • Roberta Estes, DNAexplain, scientist, blogger, author, genetic genealogist, and Genographic Affiliate Researcher
  • Dr. Miguel Vilar, Genetic Anthropologist, Lead Scientist with the Genographic Project, and Professor at the University of Maryland
  • Bennett Greenspan, President Emeritus of FamilyTreeDNA, and avid genealogist
  • John Detsikas, Front End Developer who is responsible for the user interface for both Y-DNA Discover and now mtDNA Discover

The Million Mito Project Inception

The Million Mito Project was launched at RootsTech 2020 and encouraged people to test their mitochondrial DNA, both for their genealogy and to help build the database. More than a million samples were candidates, but only high-quality, full sequence results were used. In the process of building the tree, additional samples were incorporated from other public sources for tree construction.

Drum Roll – The Mitotree

A beta version of the Mitotree is being released today, and boy, is this a big deal.

Before we discuss the rest of what’s coming, I need to mention that the Mitotree is now evergreen, meaning that the tree will be updated periodically, as will mtDNA Discover. This lifetime value is included with the cost of your test, so there’s nothing more to purchase.

Haplogroups will change from time to time, as the tree does, so don’t fall in love with yours, and definitely, no tattoos😊

I’m going to be speaking in terms of “we,” meaning the Million Mito team who built the Mitotree and mtDNA Discover, plus an amazing team of FamilyTreeDNA folks who were absolutely essential in getting this out the door and to you.

The Mitotree is new from the ground up, and yes, haplogroup naming consistency with PhyloTree has been maintained where possible.

One of the unanticipated challenges we encountered was that the 2016 PhyloTree had to be recreated, essentially reverse engineered, to determine the rules they used regarding mutations for haplogroup creation. In other words, which mutations were valid and reliable, which weren’t, determining their relative importance, and so forth.

After the existing 2016 tree was recreated, the next hurdle to overcome was that none of the existing phylogenetic software used in academia would scale from 24,000 samples and 5500 subclades to more than a quarter million samples and 40,000 haplogroups, so that software had to be designed and written by R&D team members.

More information about this process will be forthcoming shortly, and a paper will be published with our methodology, but for right now, let’s look at the user experience and what’s being released now.

Here’s what’s coming today and over the next few days.

The beta Mitotree includes:

  • Over 40,000 branches
  • Over 250,000 mtFull Sequences from FTDNA
  • Over 10,000 third-party full sequences from GenBank, 1000 Genomes, etc.
  • Over 1000 Ancient Connections
  • Over 100 Notable Connections

More is on the way.

The new Mitotree is the tree provided in several formats within mtDNA Discover. You can view the public version of the tree, here, or sign on to your FamilyTreeDNA account and click through from your dashboard to see more.

Today’s Releases

The Mitotree doesn’t exist in a vacuum, so several updates and new features will be rolling out today.

  • mtDNA Discover, which includes the new Mitotree
  • New customer haplogroups for those who have taken mtFull sequence tests
  • New mtDNA matches page

New Haplogroups

New haplogroups have been calculated for FamilyTreeDNA customers who have taken the full sequence test. Those who have taken only the HVR1 or HVR1/HVR2 tests are encouraged to upgrade to the full sequence test.

Not everyone will receive a new Mitotree haplogroup that is different from their classic haplogroup, but most people will. Your original haplogroup is displayed with the classic tag, and the new Mitotree haplogroup with the beta tag.

If your classic and Mitotree haplogroups are the same, it means that either you have no more private variants (mutations) available to form a new haplogroup, or no one else from your lineage has tested yet.

New mtDNA Matches Page

If you click on your mtDNA matches, you’ll notice that the page has been redesigned to look and function like the other FamilyTreeDNA match pages.

If you click to view your matches, you’ll be able to view both the “old” classic haplogroup, and your matches’ new Mitotree haplogroup, plus a new haplotype if they have one. We will talk about haplotypes in a minute.

The people you match are the same as before, but matches may be recalculated in the future.

If you click through to the new mtDNA Discover from your dashboard, you’ll be able to view the public portion of mtDNA Discover, plus the additional customized information provided to FamilyTreeDNA mtFull sequence customers.

mtDNA Discover

If you have taken a full sequence test, sign on to your account to view your new haplogroup, then click on the new mtDNA Discover icon on your dashboard.

If you haven’t taken the mtFull sequence test, but the partial HVR1 or HVR2 versions, you can still view mtDNA Discover on your dashboard, but without the mtFull customization.

Customization that occurs exclusively for FamilyTreeDNA mtFull sequence customers includes:

  • Most detailed placement of your branch on Mitotree
  • Haplotype clusters
  • Additional Ancient Connections
  • Additional Notable Connections
  • The Match Time Tree
  • Globetrekker™ (coming soon)
  • The Group Time Tree (coming soon)

mtDNA Discover is similar to Y-DNA Discover.

You’ll be able to view a dozen new reports about your haplogroup in addition to the tools provided on your dashboard.

The new Mitotree can be viewed in several formats, each with its unique benefit.

  1. Time Tree – a genetic tree that shows when each haplogroup was formed, plus a country flag for where present-day testers report as the location of their earliest known ancestor (EKA)
  2. Classic Tree – a more traditional view of a phylogenetic tree, including the number of testers on each branch, the variants, or mutations that define the haplogroup, the era and approximate date of formation, and other details about the tree topology
  3. Scientific Details Variants Tab – shows the variants that differ in each haplogroup as you reach back in time
  4. Ancestral Path for the selected haplogroup – outlines your path back to early humans, including Denisovans.
  5. Match Time Tree for you and your matches (must be signed in to your account and click on mtDNA Discover icon)
  6. Group Time Tree (coming soon) for those who have joined projects

Match Time Tree

The Match Time Tree is extremely useful because it overlays your matches, plus their earliest known ancestors (EKA), on a genetic Time Tree, by haplogroup and haplotype, so you can see how you may be related, and when.

You can also see your matches that have now fallen into neighboring haplogroups, which suggests that they probably aren’t as genealogically close as people in your haplogroup. However, that’s not always the case, because mutations can occur at any time.

Haplotype Clusters

A haplotype cluster is a new concept introduced specifically for genealogists with the new Mitotree. Haplotypes are identified by numbered “F” groups. Three are shown, below.

There may be groups of people within a haplogroup that have exactly the same mutations, or genetic signature, and no additional mutations. Still, they may not form a new haplogroup. There could be several reasons for not forming a new haplogroup, including known SNP locations where mutations occur that are known to be unstable, such as location  315, which tends to accumulate random insertions and is ignored because of its known instability.

When multiple people share an exactly identical signature, meaning all of the same mutations, they are shown within a haplotype “F” cluster to provide additional specificity to the tree.

The haplotype has been designed to provide additional granularity to the tree and genealogically relevant information. The haplotype “Fxxxxxx” numbers are randomly generated and have no special meaning.

A word of caution here. While the haplotype sequences are identical, it is still possible that another tester from outside the cluster could be a closer relative. For example, they could have accumulated a fast mutating SNP in the last few generations, which would give them a different signature.

Someone who is actually genealogically close to you may be in a different haplotype, or no haplotype at all because no one matches them exactly. For example, if your aunt or sister has a heteroplasmy, they are a close relative and will be in your haplogroup, but won’t be in your haplotype cluster because of the heteroplasmy. So don’t ignore matches who aren’t in your haplotype.

In the above example, under haplogroup V71b, there is one group of three people of unknown origin, meaning they didn’t enter any location for their earliest known ancestor, plus haplotype F9712482 – all of whom are identical matches to each other, but don’t form a new haplogroup.

Beneath V71b is haplogroup V71b1 with nine people, plus two haplotype clusters. F1965416 consists of two people, and F8189900 consists of 16 people.

You can also see haplotype clusters bracketed on any of the Time Trees in mtDNA Discover as well.

More to Come

There’s more information to come in the next few days and weeks, and at RootsTech. I’ll be writing articles when I get back.

For now, take a look to see if you have a new haplogroup. The new haplogroup rollout is being staggered, and you should receive an email when yours has been posted. But there’s no need to wait. Go ahead, sign in and check now, check out mtDNA Discover, and have fun.

Guaranteed, you’ll learn something new, and you may discover the key to a new ancestor!

Resources

Here are additional resources about the new Mitotree, mtDNA Discover, and the associated updates:

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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

Genealogy Products and Services

My Books

Genealogy Books

Genealogy Research