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Citation: Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup

Citation: Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup

A new paper in The American Journal of Human Genetics, Estimates of Continental Ancestry Vary Widely among Individuals with the Same mtDNA Haplogroup, tells you something which should be obvious:one marker tells you only so much about individual ancestry. In other words, the history of one gene can only tell you so much about the whole genome. Because mtDNA and Y chromosome* does not recombine you can treat it as one long genetic marker. On the coarse grain they can tell us a great deal. Both mtDNA and Y confirmed that it seems the modern human populations seem to be diverged from a group with an African origin. Genomics, even using the whole genome, has confirmed this. Additionally, non-recombining regions of the genome are more tractable for a coalescent framework. They are actually trees.

But Richard Lewontin’s insight that a great deal of human genetic variation is not partitioned across populations, but within them, applies to mtDNA and the Y chromosomes as well. Where Lewontin’s insight misleads is that using just a few more markers one can obtain relatively robust phylogenetic trees which reflect well the population structure and history of a given species. One can see this when one considers mtDNA and Y chromosomal lineages jointly. If someone tells you that their Y chromosomal lineage is R1a1a you can infer that their ancestry is anywhere from Central Europe all the way to South Asia. But if they add that their mtDNA is U2b you can be confident that they are South Asian. U2b spans South Asia, as well as parts of the Middle East. But in the latter zones R1a1a is very rare.

Though the phylogeographic import of mtDNA for a given individual is often questionable, that’s true of any marker. Because mtDNA is amenable to phylogenetic modelling it is still quite useful, especially when making very geographically coarse inferences. But the paper’s argument that the geographic inferences of DTC tests is questionable based on the fact autosomal SNP-chips are the same framework used within the paper to test the informativeness of mtDNA.**

* The NRY

** Disclosure, I have done consulting for Family Tree DNA on their autosomal tests.

• Category: Science • Tags: Personal Genomics 
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  1. These authors don’t seem to have much knowledge of the genetic genealogy market. They say: “Overall, our results question the validity of making anything but fairly crude inferences of continental ancestry on the basis of most mtDNA lineage tests.” However, they’ve only looked at HVR1 for the purposes of their analysis. That was the only mtDNA test available 15 years ago but the times have changed. It is now becoming almost routine to test the full mitochondrial sequence. Family Tree DNA, who are the market leaders for mtDNA testing, don’t even sell an HVR1 test any more. When the mitogenome is sequenced you get a much more refined haplogroup assignment and much better geographical resolution with some subclades confined almost exclusively to specific populations (there are, for example, Jewish subclades of haplogroup K).

    However, knowing the haplogroup is only one part of the analysis. The value comes from going into a matching database and having the chance to compare genealogical information with the people you match. There are, of course, limitations with mtDNA testing and even with the full sequence test you do find people with an exact match who have ancestry from different countries. However, the mtDNA test is not normally used on its own but in combination with an autosomal DNA test. People are not generally taking autosomal DNA tests to get ethnicity percentages but to find matches with genetic cousins. It’s the genealogical information from your matches that yields the most useful information about your ancestry.

    There are other companies and organisations that sell mtDNA tests but which don’t have a matching database. They mostly offer microarray tests covering several thousand mtDNA SNPs and which provide a detailed haplogroup assignment. However, these tests also include autosomal and, if applicable, Y-chromosome SNPs to give a more rounded picture of one’s ancestry. See the mtDNA testing comparison chart in the ISOGG Wiki:

  2. I married internationally. I hope that one day there will be a commercially available ancestry test that will tell us how many generations back we shared a common ancestor, or common ancestral population, and who & where it was.

  3. Anonymous • Disclaimer says: • Website


    I’d always dismissed mt and Y chromosome ancestry studies because they only detect a single lineage (for example, my father’s father’s (…) father) to the exclusion of, for example, my father’s mother’s father’s (…) father).

    Ancestry is exponential, not linear! Haplogroups only detect a single branch out of a very large number of branches.

    Assuming a generation time of 20 years, 500 years ago (=25 generations) I could have had 33 million great […] grandparents! But then I realized that the population of Europe (I have European ancestry) was only around 60 million in A.D. 1500 (Jan de Vries, compilation of estimates). Assuming no interbreeding of ancestors in the last 500 years, I would have to be related to everyone with European ancestry a little over 25 generations ago. Clearly there must have been some interbreeding, which would imply that I did NOT have 33 million great […] grandparents.

    I think the key question is…*How many great […] grandparents did I have?* THAT would tell us how informative mtDNA or Y-chromosome haplogroups are. If I had more grandparents then these tests are less informative. If I had fewer grandparents they could be quite informative.

    I’d be curious just to know ballpark figures. Did I have 10 million or 10,000 great […] grandparents in A.D. 1500?

    Is there any published work that has delved into these questions?

  4. There is a collection of articles on the subject of how many ancestors we have here:

    The people buying ancestry tests are primarily interested in using DNA testing as an aid to genealogical research, and so the focus is generally within the last 500 years. They are not buying these tests to find out their haplogroup. Y-DNA testing is particularly useful because of the correlation with surnames. You can test other people with the relevant surnames in your tree so that you cover not just your own patriline but other surname lines as well.

  5. “using just a few more markers one can obtain relatively robust phylogenetic trees which reflect well the population structure and history of a given species. One can see this when one considers mtDNA and Y chromosomal lineages jointly.”

    Of course, this can break down for individuals with ancestry from different populations, which is becoming more common with increased travel and migration in recent centuries, so that just knowing the mt and y haplogroup becomes less informative. My Y haplogroup is r1b but my mt is L3 (23andme says my haplogroup is most commonly found in Mozambique), yet autosomal DNA indicates I’m just 1.5% African, 4.5% indigenous American, and the rest is European (with a little North African/ME).

  6. Sorry, submitted previous comment too soon.

    My mother is Brazilian (mostly Portuguese ancestry, with some south american indian and African), while my ancestry on my father’s side is mostly English. Just knowing the y and mt haplogroups doesn’t tell you enough to get close to figuring this out.

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