Haplogroups Explained

Many 23andMe customers that contact Customer Care are confused by their haplogroup assignments and what they actually mean.

But knowing your haplogroup, and how you can use it, can give you much more clarity about your own ancestry. So in the interest of helping you out, we will walk through an example of a maternal and paternal haplogroup assignment, and explain how knowing your haplogroups can place you in the human family tree and connect you to your ancestry.Migration_map4

In this case we’re using someone who is Asian, who has roots  in Southeast Asia. But his maternal haplogroup – B4’5 and more specifically subgroup B5a1a – is most commonly found among Native Americans of the U.S. Southwest and northern Mexico.

Migration

So why is that?

What connects him to Native Americans?

This is where understanding a little bit about haplogroups is helpful in placing you and your ancestry in the broader context of human history. Each haplogroup describes individual branches – or closely related groups of branches – on the genetic family tree of all humans. All members of a haplogroup trace their ancestry back to a single individual.In this case, the individual shares his maternal haplogroup with many Native Americans because 12,000 years ago people migrated from Asia to Alaska, when sea levels were lower.

Or another way of looking at it is that descendants of his ancient maternal ancestor – a common ancestor he shares with many Native Americans – had crossed the Bering Land Bridge to populate the Americas.Looking deeper into his results his maternal haplogroup is a subgroup of B4’5, specifically B5a1a. It has its own history where it broke off from B4’5 in Southeast Asia.

Recent migration patterns have altered the global distribution of this haplogroup, but that ancient history is written in his DNA and being able to read that and identify his maternal haplogroup connects him to that history.The ability to trace back a person’s maternal haplogroup back so far – more than 50,000 years in the case of B4’5 – has to do with how it is passed down to each of us from our mother, and her mother, and her mother’s mother, and so on back in time.

Maternal Haplogroups

Maternal haplogroups are determined by defining variants in your mitochondrial DNA. Everyone  inherits  their mitochondria from their mothers. Unlike your other pieces of DNA, your mitochondrial DNA is the only type of DNA that is found outside of the nucleus. For this reason, your mitochondrial DNA does not recombine with other types of DNA. Because your mitochondria is inherited directly from you mother and undergoes very little recombination, you will share the same maternal haplogroup with any relative you share a direct maternal line with. For example, you, your mother, your brother, your sister, your maternal aunt, your maternal grandmother, etc. would all share the same maternal haplogroup as you. And that maternal haplogroup traces back through the generations to a single mutation at a specific place and time.

In the case we’re looking at, his maternal haplogroup is one that is shared by many people, not only of Han Chinese ancestry, but also with many Polynesians, Native Americans, and Southeast Asians.

Paternal Haplogroups

Now that we’ve looked at maternal haplogroups, we can turn our attention to paternal haplogroup assignments. In this case the person’s paternal haplogroup assignment is O3a3c1*.

It traces to East Asia and is also common among Han Chinese, Koreans, Filipinos and Malaysians. The paternal haplogroup assignment is  determined by defining variants in your Y Chromosome. The Y chromosome is the sex-determining chromosome for males, which men inherit from their fathers. Therefore, unless you inherited a Y chromosome from your father, you will not have a paternal haplogroup assignment. (You can find out more about this here.) This is why women will see this page is unavailable to them within their 23andMe account, but in a moment we’ll explain how women can determine their paternal haplogroup. 

First understanding a little bit more about the the Y chromosome is helpful. The Y chromosome does undergo recombination with the X chromosome, but only does so at the ends. So about 95 percent of the Y chromosome remains relatively intact across generations. For this reason, the Y chromosome is a reflection of your ancient paternal ancestry. You would therefore share a paternal haplogroup assignment with any male relative that you shared a direct paternal line with.

A woman can infer her paternal haplogroup if a male relative on her paternal line has been genotyped by 23andMe.Because both the Y chromosome and mitochondrial DNA change so little over generations, they are very informative about your ancient ancestry. But that is not to say that they do not change at all. In fact,  each letter and number that you see within your haplogroup corresponds to a set of defining mutations in your mitochondrial DNA or your  Y chromosome. This marks a period in time when your haplogroup branched off into a distinct line. So, for example, it may mark when a population first migrated out of Africa, or when another group became geographically isolated.

Assigning Haplogroups

23andMe is  able to trace your ancestry based on these mutations, because they occurred in distinct geographical locations during specific periods of time. Haplogroup assignments can even be traced back to specific languages.That DNA evidence is often corroborated by the fossil record. Our oldest fossils date back 200,000 years  and were found in Omo Kibish in Ethiopia. According to genetic and paleontological records, Homo sapiens only began migrating out of Africa 60,000-70,000 years ago moving into the Eurasian continent.

Some of these migrants moved along the Indian coast reaching first Southeast Asia and then Australia around 50,000 years ago. Since then, different migratory events have spread our species across the continents along different routes and paths.We are able to trace migratory patterns based on defining mutations in mitochondrial DNA and Y chromosome DNA.

In the case of the individual we’re looking at in this post, ancient ancestors who were part of his maternal haplogroup were among a group of individuals who were in Southeast Asia, and that some of those individuals eventually migrated across the Bering land bridge to populate the Americas. Some stayed around East Asia and developed some new defining mutations in their mitochondrial DNA making them B5a1a.It is important to keep in mind that your mitochondrial DNA and Y chromosome account for very small portion of your DNA and a small portion of your overall ancestry.

As most haplogroups arose over tens of thousands of years ago, these pieces of DNA generally reflect your very ancient ancestry. Therefore, it is possible for two people to share the same haplogroup assignment but no recent ancestry. So for example, while you may share a paternal haplogroup with Stephen Colbert, you probably don’t share any recent common ancestors.

A large portion of our DNA is found within your autosomal DNA, which undergoes recombination with each successive generation. Your results analyzing your autosomal DNA therefore generally reflect your ancestry from within the past five to ten  generations. Therefore, it is not uncommon for the ancestry found within your haplogroup to differ from your own understanding of your ancestry and the ancestry found in the features analyzing your autosomal DNA, such as Ancestry Composition. This does not mean that any of these pieces are incorrect; they are each simply describing a different part of your rich and unique ancestry.

  • Mr. Gregg

    So, how do I find out what my Haplogroup is?

  • 23blog

    Gregg,
    If you’ve tested there are several places to go to see your haplogroup. The easiest is to go to the Ancestry Overview. Once there you’ll see a box that says “Father’s Line” and another that says “Mother’s Line.” Click on the “More” button and you’ll see your haplogroup with some details about how old it is, the geography it’s associated with and what groups its most associated with.

  • Linda

    I know that was supposed to make things more clear, but I’m still lost. The fact that this blogger has a degree in genetics doesn’t help in making what he said clear! Can someone “translate” this industry-speak into language someone not familiar with genetics at all can understand? I’m sorry. but I’m still not understanding what this tells me. 🙁

    • 23blog

      Hi Linda,
      Sorry that this posts doesn’t address your questions about haplogroups.

      There is additional information when you look at your 23andMe results, specifically your maternal or paternal line results. In there you’ll find information that is specific to your haplogroup. And it will give you some information about what is informative about your haplogroup.

      If your question is a general one about haplogroups and what they are, I’ll try and give explaining it one more shot.

      One way to look at haplogroups is as a branch of the human family tree. As humans migrated out of Africa, they branched out in a different directions. Some populations migrated to Asia, some to Europe some to the Middle East, and some remained in Africa.

      We might think of different haplogroups as those different branches of the human family tree. This is helpful because it can inform you about your ancestry.

      So if your maternal haplogroup is H, you would see that H is concentrated in Europe. If you then find out that you are find out that you are in the subgroup H1 and H3 you’d learn that that is concentrated in the Iberian Peninsula, along the Atlantic coast and into central and northern Europe.

  • walcyrn@yahoo.com

    My haplogroup is X2b, but my daughters is T. I contacted 23 and me when we got these results, and they acted as this was normal. I am still a bit confused, and would appreciate an explanation. Thanks, Cindy 🙂

  • 23blog

    Hi Cindy,
    I did forward your question to our Customer Care team, and my apologies if you did not get your questions answered when you contacted them.

    It isn’t unusual for relatives to have different haplogroups, but what you are describing is unusual. You and your daughter should share the same maternal haplogroup. If the haplogroups were just different subgroups that would be more likely but in this case these two are different.
    I will work to get an answer for you and post it in the comments section when I do.

  • 23blog

    Hi Cindy,
    I’m just adding an additional comment. I should have asked you whether both you and your daughter tested with 23andMe? If you tested with different companies that could explain the different assignment.

    While neither X2b or T are subgroups of the other, they both are subgroups of N. It’s also possible that one or the other of your samples did not have a “call” in a key defining SNP, and that led to the different assignments.

    A little more information could help us figure this out.
    Thanks.

    • walcyrn@yahoo.com

      Hi, Yes we both tested with 23 and me at about the same time. I questioned if we could re-test, so that both would have the same haplogroup. It has been very disturbing, since they identify her as my daughter, and me as her mother on 23 and me, but we have totally different maternal haplogroups. Thanks Again.

      • 23blog

        Cindy,
        Thanks for the added information. In looking at this with one of our ancestry scientists it appears the best explanation is that you or your daughter’s sample, or possibly both samples, had a “no call” on one or more SNP that was important for making the assignment.

        The two assignments are consistent in that they are both subgroups of N, but it looks like your daughters assignment X2b is at a higher resolution. This is probably because a one SNP did not yield a call in your sample.

        Following the rules of genetics, you would learn from her child’s assignment that you both share the X2b haplogroup. In other words, her assignment is more exact than the one given to you.

        I am forwarding your request to our Customer Care team and they will be in contact with you.

        Thanks for your patience.

  • Gerald Alexander Lopez Castell

    Why hasn’t 23andme updated to the latest phylotree, 23andme is still in the 2008 revision, so this means some haplogroups are wrongfully assigned or not specific as they should be given the current tree. There has been many new mtdnas since 2008 guys…

    • Gerald Alexander Lopez Castell

      23andme, any news on updating to the latest phylotree, the one on the site is deprectated and old, please respond.

  • Timothy A. Do

    I am O2a1 and B5a1a.

  • 23blog

    Hi Gerald,
    Thanks for the note and the question. Yes we do have plans to update the phylotree, but won’t likely happen until next year.
    Just a note in addition, these trees actually change quite frequently as scientists reconfigure them based on new information. So it’s hard to maintain an updated map. We try to keep it consistent with how we make assignments.
    Hope this addresses your question.

    • Gerald Alexander Lopez Castell

      It does! I really love this communication, the feedback i get from my friends in the 23andme community is the lack of updates on your product roadmap, we’d love to hear as much as possible. If it won’t happen until next year thats fine as long as we are aware that you guys have it in sight it makes us happy to know it is an action item. Thank you = )

      • 23blog

        The only thing I can add right now is that we will be making some important announcement before the end of the year. These will have a much greater positive impact for users than making changes to the Haplogroup tree.

        • Gerald Alexander Lopez Castell

          Im really hoping these changes are Ancestry/Autosomal/Genealogy based as this is still your largest customer base. There are thousands of us who are active daily users that use 23andme for its Ancestry breakdown, relative finder, and countries of ancestry. If none of these are improved by end of year and only health we will be pretty dissapointed, given that we are probably some of the most avid referers of 23andme. I aplaud these comign changes! I just hope that the ancestry portion of 23andme hasn’t been forgotten, it feels like big changes on the Ancestry side happened a few years back and now have been completely abandoned.

  • Michael Roseman

    Not being sure where to direct the questions I have, I found your haplogroup article and several posts with questions, and I’m adding my questions with the hope that you can help me get started. My paternal haplogroup is listed by 23andme as being I2B1. I’m pretty much a beginner at understanding human genetics and I want to learn as much as I can of my genetic heritage. I am of Ashkenazi Jewish descent on my father’s side. Searching outside 23andme I can’t find I2B1 listed as a known paternal Ashkenazi haplogroup. Is that a possible hint that at some point I had a non-Jewish paternal ancestor, or is my admittedly skimpy research incomplete? Where can I go to read more about human genetic geneological research? And finally, has the I2B1 name been changed, as some web searches seem to indicate? If I’m searching outside of 23andme, what naming convention should I follow?
    I really appreciate any help you can provide.
    Michael

    • 23blog

      First off there are some estimates that say about 5 percent of people with Ashkenazi Jewish ancestry are part of Haplogroup I. As for haplogroup names, this has been a moving target over the last several years. Sometimes research leads to the discovery of mutations that link several of the different prominent haplogroups. When that happens the lineages get a new name. 23andMe has periodically updated our haplogroup trees to account for some of these changes, but we do not change our own designations as often. You can look at the haplogroup tree mapper to see where your haplogroup aligns. Here’s more information on it: https://customercare.23andme.com/hc/en-us/articles/202906900-More-about-Haplogroups

      • Michael Roseman

        Thanks for your fast follow up! Can you suggest where I can find more about paternal haplogroup distributions in Ashkenazi Jews?

  • My name is Adrian Yohanes Purnomo, an Indonesians with Chinese and Austronesia descendant. My Geno 2,0 results: Y Hg O-CTS5492 or O3a3c-M134, mtDNA Hg B4c2. 1,2% Neandherthal 0,6% Denisovan. I am 65% NE Asian and 35% SE Asian. So, my Autosomal Regional DNA are more similar with a Chinese – Kinh Vietnamese. Both my Parental line share a common ancestor with a majority of Eurasians people: Y Hg K2-M526 and mtDNA Hg R – R11 – B4c.

  • Jacob Bower

    Hi. I haven’t taken 23andme but my paternal uncle has and it said his/our Y-Haplogroup is C3e. Could you give me some info on this Haplogroup please? Thanks!

    • 23blog

      Here’s some information we provide regarding this Haplogroup assignment:
      C3e is a subgroup of C3, which branches from C.
      Haplogroup: C3
      Age: less than 50,000 years
      Region: Central Asia, Eastern Asia, Americas

      Haplogroup C3 Migration

      Origin: Haplogroup C originated soon after humans began to expand outside of Africa. Different sub-groups of C colonized different continents. C3 succeeded in expanding across much of Siberia and central Asia, where it is one of the major haplogroups today. C3 can also be found in many Native Americans, an indication that men carried the haplogroup across the land bridge that connected Siberia and Alaska at the end of the Ice Age.

      Highlight: Haplogroup C3 spread into Mongolia across the Silk Road to eastern Europe roughly 1,000 years ago, at the same time as the expansion of the Mongol empire under Genghis Khan. It is likely that this lineage came from Khan himself.

      Example Populations: Oroqen, Mongolians, Sioux

  • B Cohen

    Hi, I’m looking for an explanation for why my maternal haplogroup would be different from my son’s maternal haplogroup. Not very different – I’m Hb3 and he is Hb, but he happens to match his father’s maternal haplogroup instead of mine, his mother’s. Why is this? Thanks.

  • 23blog

    Adrian,
    Just a note to let you know that we are planning to update our haplogroup assignments in the not too distant future. This will add more refinement to the assignments.

  • Kerry Ann

    Hi, my daughters haplogroup is H and mine is H3. My mom’s is also H3, I am a little confused as to why my daughter has a different haplogroup than myself and my mother.