Updates to 23andMe Paternal Haplogroup Assignments

With the holiday season upon us, 23andMe is sprucing up its paternal haplogroup tree! With 23andMe population geneticist and Y-chromosome expert David Poznik at the lead, we’ve updated our Haplogroups paternal-haplo-001Report to reflect significant developments in the field over the past few years. We’re also excited to introduce yHaplo, our new open-source software for researchers.

Major Refinements to the Y-Chromosome Tree
Each generation, fathers pass down copies of their Y chromosomes to their sons. Small variations arise over time and accumulate in patterns that uniquely mark individual paternal lineages. To trace the evolutionary history of these lineages, scientists study DNA sequence differences between and among modern populations and have built a “tree” that shows how global Y chromosomes relate to one another.

However, our understanding of the Y-chromosome tree had, for many years, been limited by our incomplete knowledge of Y-chromosome diversity. Because paternal haplogroup names reflected the structure of the tree, each new insight required renaming haplogroups, and this made it difficult to interpret paternal haplogroup assignments from one year to the next.

Recent research, including a study published in Nature Genetics, has drastically refined the structure of the tree. For that work, David and an international team of 42 scientists used complete Y-chromosome sequences from around the world to carry out the largest-ever study of genetic variation within the human Y chromosome (Poznik et al.). This research identified more than 65,000 Y-chromosome genetic variants, vastly increasing our understanding of the tree and setting a new standard for tracing male lineages through migrations that have occurred over the millennia of human history.

 

What’s Changing
Male customers on the new 23andMe website experience can expect a couple of changes to their paternal haplogroup assignment with this update, and female customers may see changes to the paternal haplogroup assignments of male relatives and friends in other parts of the website.

First, we have substantially updated our Y-chromosome tree to reflect the work of the International Society of Genetic Genealogy (as of January 4, 2016). In most cases, the updated haplogroup assignments are equivalent to previous assignments or differ only slightly. However, since much more is now known about the tree, we can provide more information about an individual haplogroup’s history and how it relates to others.

The second major update is a change to the naming system we use to report paternal haplogroups. Until recently, the convention was to use an often lengthy series of letters and numbers indicating the path of branches from the most recent common ancestor of all men to each haplogroup. The problem is that these names changed from year-to-year as the tree was refined, making it difficult to know from the name alone which haplogroup male customers actually carry.

To reduce confusion, we have moved to a system of shorter and more stable names. Each name uses a letter to identify the major branch of the tree and the name of a genetic marker unique to a specific haplogroup. For example, if we previously reported your paternal haplogroup as “Q1a3a,” we now report it as “Q-M3,” indicating that your Y-chromosome lineage belongs to a subgroup of haplogroup Q that bears the M3 marker. Because this new representation focuses on a specific informative marker associated with your haplogroup, it will be much more stable over time.

small-paternal-2-001

A small section of the updated Y-chromosome tree illustrating the marker-based haplogroup naming convention. The structure of the tree was aggregated from the literature by the International Society of Genetic Genealogy.

For more information on the changes coming to the haplogroups report, visit 23andMe’s customer care page, here.

yHaplo, a New Open-Source Research Tool
The paternal haplogroup update doesn’t end with the tree. As a member of the research team at 23andMe, Poznik has developed a new algorithm to rapidly and robustly identify Y-chromosome haplogroups in very large samples, and he has implemented the algorithm as the yHaplo software package. This software is very flexible; it runs on full Y-chromosome sequences and on smaller sets of genotyped markers. Furthermore, it is easy to incorporate updates as researchers around the world continue to gather data and learn more about the Y-chromosome tree.

At 23andMe, we’re using this software to provide paternal haplogroup assignments to our customers. As we believe the yHaplo software package can be an extremely useful tool to help drive research, we have made it available under a custom open-source software license for non-commercial research use. To learn more about yHaplo, read our white paper or head to the code repository!






  • Reinhold

    Show some dignity…

  • Richie Wolf Bauer

    Howdy. Did 23andMe a few years ago and my Y Haplogroup was originally ‘F’ (Middle East area) for sometime, then with the update, it changed to ‘S M230’ (Papua New Guinea). Any explanation for the drastic change of geographic regions? Just curious…I also am finding that on 23andMe that less than 1% of males have the S M230 lineage, I’m assuming this is something new? Is there any more info on Y Haplogroup S? I am ethnically mixed of European, South East Asian, Polynesian, with some African and Native American.

    • 23blog

      Hi Richie,
      Actually F I think is centered on South East Asia. As for more information on the Y Haplogroup S, although it is common in Papua New Guinea, it is also common in other parts of Oceania and South East Asia. In addition S also is a branch of the Haplogroup GHIJK, which in turn is a major branch of Haplogroup F.

  • maryyamada

    I agree, chatoyante. I used my father’s son’s son’s spit test to link myself up in here a few years ago, and then last year, they took the test results away from me.

  • TheFamilyThalamus

    My brother and I (female) have been tested. I am frustrated that my paternal haplogroup cannot be included in my profile. I would like to see an update that allows this information ( we are sharing) on my profile, for my benefit for direct comparison with DNA relatives on my father’s side.

  • TheFamilyThalamus

    Gah! I just posted the same gripe. Sorry I didn’t scroll down.

  • Straski

    When are you going to combine with Ancestry,.com. The genetics that is.

    • 23blog

      Straski,
      We have no plans to combine with another business. As for whether we might allow customers to upload genetic data from other companies, we are looking at that possibility. But there are some issues with that, namely around accuracy and validity of other tests. This is particularly an issue with our health related reports.

      • clc530

        I know you do DNA for Ancestry why can I not upload my results to Ancestry? Is it because Ancestry wants me to pay for the same results.

  • Daniel DiFondi

    I agree with Straski. We should be able to share our DNA information here with other similar endeavors like Ancestry com.

  • Michelle King

    As a female, when can my paternal haplo get updated with that of my brother?… we share the same father.

    • Carrie Fuller

      I have the same issue. My brother and I both used the full Health kit and yet I do not have paternal haplogroup added to my file. The whole reason I bought him a kit was to get this extra information. I have been an active user of 23 and me, answering all the health questions for years now.

      • Mary

        So true!

    • Mary

      Good question!

    • YES>
      Your brother, father, father’s brothers and their male children all have the same y chromosome from your grandfather.

  • Barbara Heaton Kirsch

    I have a 2nd male cousin on here. His father and my father were cousins. Would I have the same paternal haplogroup as my second cousin?

    • Jared Olar

      Your father and your second cousin will have the same paternal haplogroup IF your father’s father was the brother of your second cousin’s paternal grandfather. But if the cousin relationship goes back to two sisters, or to a brother and a sister, then your father and your second cousin would belong to different paternal haplogroups.

      On the other hand, if the two sisters married brothers, or married men who were male-line cousins, then your father and your second cousin would belong to the same paternal haplogroup.

  • Monica Vaughan

    I used to be able to see the history associated with my son’s paternal haplogroup. Now it is no longer a hot link and I can’t access it even though we are sharing ancestry and health. How do I look up his group on your site and find out more about its migration patterns. BTW–your site has become overall much less user friendly and it is much harder now to compare and share info with those of us who have chosen to share, and harder to just find stuff I used to be able to access readily. I am very disappointed.

    • 23blog

      Hi Monica,
      I’m sorry to hear that. I’ll share your comments with our product team. They are continuing to make changes to help improve the customer experience.

    • connie williams

      I have to agree. the information sent is valuable, but contacting relatives listed is about impossible…even when sharing with them. I have never figured out how to do that.
      Secondly, I have had my paternal haplogroup tested, and it’s I1. I would like to be able to post that on my results.

      • 23blog

        Hi Connie,
        It should not be impossible to contact relatives. I believe the big issue is that not everyone responds to messages or they simply do not wish to share.

        • connie williams

          they can’t reply to something I haven’t sent! I am saying…”how does one send a message to a listed relative?”

        • gwc

          The current setup does make it impossible without knowing the other person’s email address since that is the only way we are able to send an invite. Since 23andMe has every members contact info the requests should be forwarded through the company, much like ebay auctions and dating websites.

    • maryyamada

      I totally agree with you!!

    • Busymom Melissa

      I completely agree. I feel like I have to learn how to use everything all over again.

  • Ruby Lee Thigpen-Whitehurst

    It is awful that we can no longer see the paternal halpogroup of our male relatives.

    • Mary

      Agreed.

    • maryyamada

      I hate it, too. If it works, why break it.

  • Ruby Lee Thigpen-Whitehurst

    I agree with Monica Vaughan. I can no longer encourage people to use your kits.

    • Mary

      Indeed!

  • liz hagen

    My mother Sophia and I are Ashkenazi Jews with ancestry in Eastern Europe I remember 23andMe reporting us as being almost 100% Ashkenazi- which makes sense. But our top cousins were Catholic -whos grandparents had immigrated from the same Sicilian family – which was so confusing. Now there appears to be a change – my mother appears to be 38% Italian with 48% Ashkenazi. The Italian DNA is recent 23andme says within a couple of generations. Her top “Sicilian” cousin shares over 4%. WOW. How did this happen? Could this be due to this new update in Paternal Haplogroup assignments? How can I find out how our families intermingled? Hope someone has answers.

    • 23blog

      Hi Liz,
      This is confusing to me as well. There is nothing in updates that we’ve made that would have so drastically changed your ancestry composition. The paternal haplogroup assignment changes were not changes to the way we estimate ancestry. They were really changes in how we named and assigned paternal haplgroups. As for the percent shared between your mother and her cousins, that of course is in line with what you’d expect for a cousin, but the description of getting an estimate that so drastically changed does not make sense. I’m forwarding your comment to our Customer Care to help you with your questions.

  • Nancy Walling

    Two questions; is it possible for memto manually enter my nephews haplogroup (my brother´s son) on my 23 and me? My nephew’s haplogroup (my biological father’s line) is R1b
    And I see dna relatives that are under paternal haplogroup and don’t seem to be connected to my maternal side with E-M(132 or other number). Is this a connected haplogroup to the R1b or an entirely different group?

    • 23blog

      Nancy,
      At the moment you can’t do that. We’re working on adding back this function.

      • Sheila Renee

        I am seeking to do this exact same thing. I mean… if we pay to have our male lines DNA’d. and then we cannot even attach it, it is starting to seem useless to add relatives in such a case.

        • Mary

          Same problem here. I had my male first cousin join 23andMe for this reason and the system doesn’t even show him as a distant relative.

  • Fern

    I am shown as sharing 9.78% DNA with a “1st cousin”, The name of this person, male, is not familiar at all, and I have a very small family, with only two first cousins. This is very confusing to both my mother and myself. Could this be a mistake?

  • Ember1

    So, my father’s brother’s son recently got his results. There is no way I’ve found for me to mark him as a cousin in the sharing section (though it shows as such on DNA Relatives). Is there anyway to link the paternal haplotype from his results, or even just read the report, seeing as that should also reflect my male lineage?

  • Eugene Rhue

    To contact a relative Connie Williams, you just click on their name and a box will come up for you to write and send your message.

  • This new change has deprived us of valuable genetic info that was once available. For example; Previously, there was a section that showed our DNA as relates to famous people who used 23andme to trace their family tree, now that page no longer exist. I have ask why was it removed? I have yet to get a proper reply. If people are to trace their roots, we should not limited. All information is helpful. My paternal DNA revealed that I share common DNA with 8 of the Presidents of the United States.

    • 23blog

      Sorry you feel that way. There is still some information on famous people with whom you share a haplogroup. You can find it in the summary section of your maternal haplogroup report. Both the maternal and paternal haplogroup reports also now have quite a bit more detail on that can give you context and history as well as explain how your haplogroup branched from others.

  • clc530

    My brother is R.L51 and I’m R P311 and y line cousin is R.l51 so what is up why the difference

    • 23blog

      Hi clc530,
      There are cases when an individual’s haplogroup assignment might not exactly match a sibling. In your case, all three of your are in the paternal haplogroup R but have different subclades. Those slight differences can arise when more data are available for one member of the family than for another. It could be that you tested on different chips — 23andMe has used four different chip platforms over the years and preparing a fifth — or that in some cases the SNPs used to make a more detailed subclade prediction for one sample couldn’t be called for the other. There’s more detail here: https://customercare.23andme.com/hc/en-us/articles/212879967-Why-is-my-haplogroup-different-from-a-family-member-s-

      • mark zero

        As you’re already preparing a fifth chip, does that mean people on v3 should disregard the statements made elsewhere that we’ll eventually be able to upgrade from v3 to v4, that you’ve only “paused” for the website transition? Are we to be stranded on v3, or will we be offered a chance to upgrade to v5?

        • 23blog

          Hi Mark,
          We are on the cusp of transitioning to v5, but it’s not yet available. We expect that to happen a little later this summer. As for upgrading, you should direct that question to our customer care. They can better answer based on your account information: https://customercare.23andme.com/hc/en-us/requests/new

      • Troy Smith

        ..what about if a brother is actually a half brother..

        • 23blog

          If you share the same father, you should share the same paternal haplogroup. If you share the same mother, you should share the same maternal haplogroup. (With we’ve noted.)

  • Laura Jennings Rish

    I used to be able to view my hereditary diseases that are inherited. i no longer can nor can i view my family’s blood type. i need that info, where is it now? also, i signed my aunt up under my email by accident and she wants her own account but for some reason they can not fix it. It has been over 1 year that i have been asking. Laura J Rish

  • Deanie Winter

    Thank you, for finally making it possible to see a list of those who share my DNA. OMG, there are over a thousand people on my list.

  • Mary

    What’s up with that?

  • 1bestdog

    what does it mean when you share dna on the x chromosone?

  • Baldwin

    It’a a few more precize but why my daughter can’t see anymore my haplogroup on her profile?
    Anyway, if we want more precision about ethnicity, FTDNA is still better.

  • Andre Viau

    Well, I am kind of disapointed with the haplogroup updates proposed by 23andme. They use to put me in the R1b-L2 haplogroup and now they retrograded me to R1b-U152, this is not progress at all. I mean, I’ve tested my y-DNA genetics at Genebase, Full Genome Corp, FTDNA, Geno 2.0 and all say that i am am R1b-L2. In fact, I have been at this for a few years now and through many more tests, I can confirm that I am R1b-U152-L2-DF90-FGC14641 et al.,- FGC29470, So i really hope that 23andme revise my haplogroup determination to at least R1b-L2 based on their haplotree. A. Viau, co-admin for FTDNA-U152 research project.

  • Ti Li

    I can see how common my Maternal Haplogroup is (1 out of 8 hundred plus) but for some reason my Paternal Haplogroup just says its rare with no specific number. Why can’t I see that data? Is it unavailable? I’m greatly interested in finding out. Thank you!

  • Tracy Young

    I had my 2nd cousin on my male side tested and want to know how to add our shared paternal group to my ancestry?

  • maryyamada

    So did I…I paid for his admittance to 23andMe for that same reason….and it was working beautifully….until 23andMe yanked it away.

  • Princess2Power

    So I feel a little confused and embarrased as everyone here seems to understand all this haplogroup info. Can 1) only men see the paternal haplogroup? 2) How do I connect as a female with my dad’s family tree? I ask because he is adopted and I’d like to find possible relatives on his side. Thank you.

    • 23blog

      Hi Princess2Power,
      I’ll start with your second question first. You results reflect contributions from both your mother and your father. All of your results reflect the contributions you get from both parents. That includes seeing all of your DNA relatives who come from your mother’s side and all who come from your father’s side. What we can’t do for women is assign what is called a Paternal Haplogroup. That is because women do not inherit a Y chromosome (the male sex chromosome). That can make it harder to discern which of your DNA relatives come from your paternal side, that said, you will still see DNA relatives on all branches of your tree. Here’s a good link to more information about haplogroups: https://customercare.23andme.com/hc/en-us/articles/235201447-Getting-Started-with-the-Haplogroups-report

      • Princess2Power

        That makes sense. Thank you for such a quick response

  • Peter

    I agree it is a good question!!

  • 23blog

    Yes.

  • Adele White

    What male relatives can I submit DNA sample to reveal my paternal heritage? My father and brother are both deceased as are all father’s brothers.

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