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Haplogroup Comparisons Between Family Tree DNA and 23andMe

Roberta Estes

Recently, I’ve received a number of questions about comparing people and haplogroups between 23andMe and Family Tree DNA.  I can tell by the questions that a significant amount of confusion exists about the two, so I’d like to talk about both.  In you need a review of “What is a Haplogroup?”, click here.

Haplogroup information and comparisons between Family Tree DNA information and that at 23andMe is not apples and apples.  In essence, the haplogroups are not calculated in the same way, and the data at Family Tree DNA is much more extensive.  Understanding the differences is key to comparing and understanding results. Unfortunately, I think a lot of misinterpretation is happening due to misunderstanding of the essential elements of what each company offers, and what it means.

There are two basic kinds of tests to establish haplogroups, and a third way to estimate.

Let’s talk about mitochondrial DNA first.

Mitochondrial DNA

You have a very large jar of jellybeans.  This jar is your mitochondrial DNA.

In your jar, there are 16,569 mitochondrial DNA locations, or jellybeans, more or less.  Sometimes the jelly bean counter slips up and adds an extra jellybean when filling the jar, called an insertion, and sometimes they omit one, called a deletion.

Your jellybeans come in 4 colors/flavors, coincidentally, the same colors as the 4 DNA nucleotides that make up our double helix segments.  T for tangerine, A for apricot, C for chocolate and G for grape.

Each of the 16,569 jellybeans has its own location in the jar.  So, in the position of address 1, an apricot jellybean is always found there.  If the jellybean jar filler makes a mistake, and puts a grape jellybean there instead, that is called a mutation.  Mistakes do happen – and so do mutations.  In fact, we count on them.  Without mutations, genetic genealogy would be impossible because we would all be exactly the same.

When you purchase a mitochondrial DNA test from Family Tree DNA, you have in the past been able to purchase one of three mitochondrial testing levels.  Today, on the website, I see only the full sequence test for $199, which is a great value.

However, regardless of whether you purchase the full mitochondrial sequence test today, which tests all of your 16,569 locations, or the earlier HVR1 or HVR1+HVR2 tests, which tested a subset of about 10% of those locations called the HyperVariable Region, Family Tree DNA looks at each individual location and sees what kind of a jellybean is lodged there.  In position 1, if they find the normal apricot jellybean, they move on to position 2.  If they find any other kind of jellybean in position 1, other than apricot, which is supposed to be there, they record it as a mutation and record whether the mutation is a T,C or G.  So, Family Tree DNA reads every one of your mitochondrial DNA addresses individually.

Because they do read them individually, they can also discover insertions, where extra DNA is inserted, deletions, where some DNA dropped out of line, and an unusual conditions called a heteroplasmy which is a mutation in process where you carry some of two kinds of jellybean in that location – kind of a half and half 2 flavor jellybean.  We’ll talk about heteroplasmic mutations another time.

So, at Family Tree DNA, the results you see are actually what you carry at each of your individual 16,569 mitochondrial addresses.  Your results, an example shown below, are the mutations that were found.  “Normal” is not shown.  The letter following the location number, 16069T, for example, is the mutation found in that location.  In this case, normal is C.  In the RSRS model of showing mitochondrial DNA mutations, this location/mutation combination would be written as C16069T so that you can immediately see what is normal and then the mutated state.  You can click on the images to enlarge.

Family Tree DNA gives you the option to see your results either in the traditional CRS (Cambridge Reference Sequence) model, above, or the more current Reconstructed Sapiens Reference Sequence (RSRS) model.  I am showing the CRS version because that is the version utilized by 23andMe and I want to compare apples and apples.  You can read about the difference between the two versions here.

Defining Haplogroups

Haplogroups are defined by specific mutations at certain addresses.

For example, the following mutations, cumulatively, define haplogroup J1c2f.  Each branch is defined by its own mutation(s).

Haplogroup Required Mutations  
J C295T, T489C, A10398G!,   A12612G, G13708A, C16069T
J1 C462T, G3010A
J1c G185A, G228A,   T14798C
J1c2 A188G
J1c2f G9055A

You can see, below, that these results, shown above, do carry these mutations, which is how this individual was assigned to haplogroup J1c2f. You can read about how haplogroups are defined here.

At 23andMe, they use chip based technology that scans only specifically programmed locations for specific values.  So, they would look at only the locations that would be haplogroup producing, and only those locations.  Better yet if there is one location that is utilized in haplogroup J1c2f that is predictive of ONLY J1c2f, they would select and use that location.

This same individual at 23andMe is classified as haplogroup J1c2, not J1c2f.  This could be a function of two things.  First, the probes might not cover that final location, 9055, and second, 23andMe may not be utilizing the same version of the mitochondrial haplotree as Family Tree DNA.

By clicking on the 23andMe option for “Ancestry Tools,” then “Haplogroup Tree Mutation Mapper,” you can see which mutations were tested with the probes to determine a haplogroup assignment.  23andMe information for this haplogroup is shown below.  This is not personal information, meaning it is not specific to you, except that you know you have mutations at these locations based on the fact that they have assigned you to the specific haplogroup defined by these mutations.  What 23andMe is showing in their chart is the ancestral value, which is the value you DON’T have.  So your jelly bean is not chocolate at location 295, it’s tangerine, apricot or grape.

Notice that 23andMe does not test for J1c2f.  In addition, 23andMe cannot pick up on insertions, deletions or heteroplasmies.  Normally, since they aren’t reading each one of your locations and providing you with that report, missing insertions and deletions doesn’t affect anything, BUT, if a deletion or insertion is haplogroup defining, they will miss this call.  Haplogroup K comes to mind.

23andMe never looks at any locations in the jelly bean jar other than the ones to assign a haplogroup, in this case,17 locations.  Family Tree DNA reads every jelly bean in the jelly bean jar, all 16,569.  Different technology, different results.  You also receive your haplogroup at 23andMe as part of a $99 package, but of course the individual reading of your mitochondrial DNA at Family Tree DNA is more accurate.  Which is best for you depends on your personal testing goals, so long as you accurately understand the differences and therefore how to interpret results.  A haplogroup match does not mean you’re a genealogy match.  More than one person has told me that they are haplogroup J1c, for example, at Family Tree DNA and they match someone at 23andMe on the same haplogroup, so they KNOW they have a common ancestor in the past few generations.  That’s an incorrect interpretation.  Let’s take a look at why.

Matches Between the Two

23andMe provides the tester with a list of the people who match them at the haplogroup level.  Most people don’t actually find this information, because it is buried on the “My Results,” then “Maternal Line” page, then scrolling down until your haplogroup is displayed on the right hand side with a box around it.

Those who do find this are confused because they interpret this to mean they are a match, as in a genealogical match, like at Family Tree DNA, or like when you match someone at either company autosomally.  This is NOT the case.

For example, other than known family members, this individual matches two other people classified as haplogroup J1c2.  How close of a match is this really?  How long ago do they share a common ancestor?

Taking a look at Doron Behar’s paper, “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root,” in the supplemental material we find that haplogroup J1c2 was born about 9762 years ago with a variance of plus or minus about 2010 years, so sometime between 7,752 and 11,772 years ago.  This means that these people are related sometime in the past, roughly, 10,000 years – maybe as little as 7000 years ago.  This is absolutely NOT the same as matching your individual 16,569 markers at Family Tree DNA.  Haplogroup matching only means you share a common ancestor many thousands of years ago.

For people who match each other on their individual mitochondrial DNA location markers, their haplotype, Family Tree DNA provides the following information in their FAQ:

I actually think these numbers are a bit generous, especially on the full sequence.  We all know that obtaining mitochondrial DNA matches that we can trace are more difficult than with the Y chromosome matches.  Of course, the surname changing in mitochondrial lines every generation doesn’t help one bit and often causes us to “lose” maternal lines before we “lose” paternal lines.

Autosomal and Haplogroups, Together

As long as we’re mythbusting here – I want to make one other point.  I have heard people say, more than once, that an autosomal match isn’t valid “because the haplogroups don’t match.”  Of course, this tells me immediately that someone doesn’t understand either autosomal matching, which covers all of your ancestral lines, or haplogroups, which cover ONLY either your matrilineal, meaning mitochondrial, or patrilineal, meaning Y DNA, line.  Now, if you match autosomally AND share a common haplogroup as well, at 23andMe, that might be a hint of where to look for a common ancestor.  But it’s only a hint.

At Family Tree DNA, it’s more than a hint.  You can tell for sure by selecting the “Advanced Matching” option under Y-DNA, mtDNA or Family Finder and selecting the options for both Family Finder (autosomal) and the other type of DNA you are inquiring about.  The results of this query tell you if your markers for both of these tests (or whatever tests are selected) match with any individuals on your match list.

Hint – for mitochondrial DNA, I never select “full sequence” or “all mtDNA” because I don’t want to miss someone who has only tested at the HVR1 level and also matches me autosomally.  I tend to try several combinations to make sure I cover every possibility, especially given that you may match someone at the full sequence level, which allows for mutations, that you don’t match at the HVR1 level.  Same situation for Y DNA as well.  Also note that you need to answer “yes” to “Show only people I match on all selected tests.”

Y-DNA at 23andMe

Y-DNA works pretty much the same at 23andMe as mitochondrial meaning they probe certain haplogroup-defining locations.  They do utilize a different Y tree than Family Tree DNA, so the haplogroup names may be somewhat different, but will still be in the same base haplogroup.  Like mitochondrial DNA, by utilizing the haplogroup mapper, you can see which probes are utilized to determine the haplogroup.  The normal SNP name is given directly after the rs number.  The rs number is the address of the DNA on the chromosome.  Y mutations are a bit different than the display for mitochondrial DNA.  While mitochondrial DNA at 23andMe shows you only the normal value, for Y DNA, they show you both the normal, or ancestral, value and the derived, or current, value as well.  So at SNP P44, grape is normal and you have apricot if you’ve been assigned to haplogroup C3.

As we are all aware, many new haplogroups have been defined in the past several months, and continue to be discovered via the results of the Big Y and Full Y test results which are being returned on a daily basis.  Because 23andMe does not have the ability to change their probes without burning an entirely new chip, updates will not happen often.  In fact, their new V4 chip just introduced in December actually reduced the number of probes from 967,000 to 602,000, although CeCe Moore reported that the number of mtDNA and Y probes increased.

By way of comparison, the ISOGG tree is shown below.  Very recently C3 was renamed to C2, which isn’t really the point here.  You can see just how many haplogroups really exist below C3/C2 defined by SNP M217.  And if you think this is a lot, you should see haplogroup R – it goes on for days and days!

How long ago do you share a common ancestor with that other person at 23andMe who is also assigned to haplogroup C3?  Well, we don’t have a handy dandy reference chart for Y DNA like we do for mitochondrial – partly because it’s a constantly moving target, but haplogroup C3 is about 12,000 years old, plus or minus about 5,000 years, and is found on both sides of the Bering Strait.  It is found in indigenous Native American populations along with Siberians and in some frequency, throughout all of Asia and in low frequencies, into Europe.

How do you find out more about your haplogroup, or if you really do match that other person who is C3?  Test at Family Tree DNA.  23andMe is not in the business of testing individual markers.  Their business focus is autosomal DNA and it’s various applications, medical and genealogical, and that’s it.

Y-DNA at Family Tree DNA

At Family Tree DNA, you can test STR markers at 12, 25, 37, 67 and 111 marker levels.  Most people, today, begin with either 37 or 67 markers.

Of course, you receive your results in several ways at Family Tree DNA, Haplogroup Origins, Ancestral Origins, Matches Maps and Migration Maps, but what most people are most interested in are the individual matches to other people.  These STR markers are great for genealogical matching.  You can read about the difference between STR and SNP markers here.

When you take the Y test, Family Tree DNA also provides you with an estimated haplogroup.  That estimate has proven to be very accurate over the years.  They only estimate your haplogroup if you have a proven match to someone who has been SNP tested. Of course it’s not a deep haplogroup – in haplogroup R1b it will be something like R1b1a2.  So, while it’s not deep, it’s free and it’s accurate.  If they can’t predict your haplogroup using that criteria, they will test you for free.  It’s called their SNP assurance program and it has been in place for many years.  This is normally only necessary for unusual DNA, but, as a project administrator, I still see backbone tests being performed from time to time.

If you want to purchase SNP tests, in various formats, you can confirm your haplogroup and order deeper testing.

You can order individual SNP markers for about $39 each and do selective testing.  On the screen below you can see the SNPs available to purchase for haplogroup C3 a la carte.

You can order the Geno 2.0 test for $199 and obtain a large number of SNPs tested, over 12,000, for the all-inclusive price.  New SNPs discovered since the release of their chip in July of 2012 won’t be included either, but you can then order those a la carte if you wish.

Or you can go all out and order the new Big Y for $695 where all of your Y jellybeans, all 13.5 million of them in your Y DNA jar are individually looked at and evaluated.  People who choose this new test are compared against a data base of more than 36,000 known SNPs and each person receives a list of “novel variants” which means individual SNPs never before discovered and not documented in the SNP data base of 36,000.

Don’t know which path to take?  I would suggest that you talk to the haplogroup project administrator for the haplogroup you fall into.  Need to know how to determine which project to join, and how to join? Click here.  Haplogroup project administrators are generally very knowledgeable and helpful.  Many of them are spearheading research into their haplogroup of interest and their knowledge of that haplogroup exceeds that of anyone else.  Of course you can also contact Family Tree DNA and ask for assistance, you can purchase a Quick Consult from me, and you can read this article about comparing your options.

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