Sunday, November 4, 2012

Understanding Mitochondrial DNA Testing


     Good Day Everyone. In this document, I am going to provide an introduction to the basis of a mitochondrial DNA test. This document should remove any confusion people may have concerning the test. As it stands right now, Family Tree DNA is the premier company that peforms mtDNA testing. The company known as 23andME currently does NOT perform a mtDNA test. 23andME only provides a haplogroup assignment which is an added and extra piece of information to the test. Let's begin with two important and basic principals that DNA tests are built on.


Basic Principals
     The first principal is that when two or more people share or match segments (regions) of DNA, they share a common ancestor in their past. It is from that ancestor that the shared DNA segments are inherited. In this case, the common ancestor was a woman.

   The second principal is that the more DNA you share with someone, the more closer you are to that person. This means your shared common ancestor lived in a more recent time. As we are going to see, this principal is extremely important when considering mtDNA given its slow rate of change.

Now let's look at the mtDNA basics. 

Short Science Part - mtDNA Basics
     The mitochondrian is a structure that sits inside the human cell. It's job is to provide energy to the cell. There are multiple copies of it that lay outside the nucleus. Inside the mitochondrian is a round piece of DNA called mtDNA. mtDNA is circular and has 16,569 DNA base pairs. The mtDNA is composed of three DNA regions - HVR1, HVR2, and CR (Coding Region that has genes). FTDNA has three mtDNA tests based on these three regions.
  1. Low resolution (HVR1) test
  2. High resolution (HVR1 + HVR2) test
  3. Full Genome Sequence test (HVR1 + HVR2 + CR) which looks at the entire mtDNA.
Three important points
  1. Only women pass along their mtDNA to a son and daughter. Men cannot pass along their mtDNA. This means that the inheritance of the mtDNA is child -> mother -> mother's mother -> mother's mother's mother -> etc. In other words, a mtDNA test look at the strict maternal side. 
  2. The word "match" in this context means having an identical mtDNA region (HVR1, HVR2, or CR) as someone else. NOT one base pair should be different. For example, the HVR1 region contains 400 DNA base pairs.  An HVR1 low resolution match means you and someone both share the exact and entire 400 base pairs. A single base mismatch can mean a difference of say 1000 years between you and someone else.
  3. The mtDNA changes very very slowly over time. Because of this, the mtDNA test is mainly used for deep distant ancestry. For example, if you have a HVR1 match, you are very distantly related to that person. In other words - your last common maternal ancestor could have lived over thousands of years ago. The more mtDNA regions you match with someone (there is only 3 regions) - the closer you are related to that person. Ideally and from a practical perspective, you really want to match someone in all three mtDNA regions such as between a mother and daughter. This means your last common maternal ancestor lived recently - say within the last 6 to 8 generations - which is approximately within the last 125 years. 
An mtDNA test also provides a separate piece of information known as a haplogroup. Let's take a look.

Short Science Part - Haplogroups
       A haplogroup is a population of people who are all descendants of a single man or woman who lived in the distant past. In this case - we are talking about mtDNA haplogroups. Each mtDNA haplogroup has a unique set of mtDNA markers that define that haplogroup. Every member of a single haplogroup bears a unique set of mtDNA markers that sets them apart from being a member in a different haplogroup. 

     There are currently 26 known mtDNA haplogroups. All 7 billion humans that currently live on the planet fall into a mtDNA haplogroup. Letters of the alphabet are assigned to a mtDNA haplogroup. An example of a mtDNA haplogroup is L3e. Essentially L3e represents a single woman that lived in the very very distant past. As science studies more populations, more mtDNA haplogroups will be added.

    IMPORTANT: Your haplogroup maternal common ancestor (L3e for example) and your last common maternal ancestor are two completely different women. Let's now look at how to get an estimate of when your last common maternal ancestor lived.

 Statistics
  Unfortunately DNA doesn't have a sign on it that tells you exactly in time when your last common maternal ancestor lived. Because of this, we have to use statistics to get a probability of when your last common maternal ancestor lived. Family Tree DNA currently uses the following accepted criteria to determine a time period.  
  1.   Matching on HVR1 (low resolution match) means that you have a 50% chance of sharing a common maternal ancestor within the last fifty-two generations. That is about 1,300 years.
  2.   Matching on HVR1 and HVR2 (high resolution match) means that you have a 50% chance of sharing a common maternal ancestor within the last twenty-eight generations. That is about 700 years.
  3.   Matching on the Mitochondrial DNA Full Genomic Sequence test (full resolution match) brings your matches into more recent times. It means that you have a 50% chance of sharing a common maternal ancestor within the last 5 generations. That is about 125 years.
      As you can see, these time ranges can be quite large. Remember these are probabilites that are based on an ancestor which could have lived within one of two intervals of a time range. For example, an HVR1 match means that your last common maternal ancestor may have lived within the last 1300 years. This also means that there is still a 50 percent chance that the maternal ancestor could have lived beyond 1300 years ago!!!!

   As you can see, from a practical standpoint, you really want to match someone at the Full Genomic Matching level. In other words, if you take a mtDNA test, you should probably order the FGS test and hopefully match to someone at that level. At the FGS level, your last common maternal ancestor is likely to have lived within the last 5 generations which is a genealogical time frame of about 125 years.

     Well that's it!!!  In short, mtDNA testing involves finding matches that reveal a shared common maternal ancestor. As you can see, the mtDNA changes very slowly which means it's mainly used distant ancestry, but it can be used for recent ancestry as well.

Hope that helps. Please let me know if you have questions. As always, it's a pleasure!!!!

Thanks
Steve Handy

13 comments:

  1. Steve, thanks for de-mystifying the mtDNA testing. Could you comment on "genetic distance" in relation to mtDNA full sequence testing? I can find many references to Y-DNA but not mtDNA. For example, if a genetic distance of 0 means an exact match (no mismatches) then what is the significance of a genetic distance of 1 in a mtDNA full sequence test? I have 2 matches (thru FTDNA full sequence testing) both with a genetic distance of 1. How does this affect the percentages you speak of ("50 % chance of sharing a common ancestor in thee last 5 generations"). Thanks

    ReplyDelete
  2. Anonymous #1, that is a very good question, and one that I would like to know the answer to also. Thanks

    ReplyDelete
  3. Thanks, Steve, this was very helpful. Per the two anonymous posters above, if anybody has or could create a table indicating the probability percentages for genetic distances of 0,1,2 and 3, it would be very helpful to me and my matches. This seems like a resource which probably already exists but is surprisingly difficult to find.

    ReplyDelete
  4. I have been trying to figure out this as well. I do hope someone responds.

    ReplyDelete
  5. I am awaiting my Grandmothers mtDNA HVR-1 results but I have already received her mtDNA HVR-2 results. It is far too complex for me to comprehend. How does one decipher it please??? Can someone help please. CM

    ReplyDelete
  6. I hope someone responds. I also have a full sequence match with a genetic distance of 1. Curious what this means.

    ReplyDelete
  7. Same here, I have 3 matches one genetic distance 2 and another genetic distance 3.

    ReplyDelete
  8. I tested in early 2014 and I have only 2 "matches" both with a genetic distance of 1. An FTDNA support person responded to my similar question about genetic distances for the mtDNA test. I was told that there is no scientific data currently available to accurately predict distances for mismatches of 1 or greater for the mtDNA test. Very disappointing to say the least.

    ReplyDelete
  9. I have a mtdna genetic distance of 0 with a match ...how close is he related ...my mom is adopted we do not know her dad's side

    ReplyDelete
  10. Have each of you done the autosomal test? I've read that it is accurate up to 4th cousins. Would that help determine how closely you are related? A question to ask administrators were you had your test done.

    ReplyDelete
  11. Steve, thank you. I am still trying to demystify all this information. Is it correct that the mtdna only pertains to my mother and her mother etc.? If that is correct, then my mother's family, which came to the USA from Ireland in 1894 is the ONLY line I can concern myself. Is that correct? Then the BIG mystery is "why do I have T2f1a matches In HVR1 and HVR2 that are Native American?" My mother's family has been well documented and no Native Americans. Another thing, many T2f1a's are in Iceland. We don't have any known family in Iceland. Some research shows that a Native American woman may have mated with a "Viking" man. But that is only a theory from a university professor which I read about on line. My father's family has many branches which came in 1607. There are some lines I can trace to possible Native American Eastern tribes. No one in my family has ever discussed this possibility. Is this where my Native American matches come from? through my father? Or can matches only come from my mother's family? I guess I sound like I am upset, but the truth is that I am pretty excited about the whole thing. Just confused. Could you please answer and tell me how my results are possible? Thanks.

    ReplyDelete
  12. Is this last the Elizabeth Warren story?

    ReplyDelete
    Replies
    1. Doubtful as no one knows what Chokeahontas really is besides a typical opportunistic female politician riding it for all it's worth.

      Delete