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.

  • 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?”

  • Ruby Lee Thigpen-Whitehurst

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

  • Ruby Lee Thigpen-Whitehurst

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

  • 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.

  • 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.

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