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General Introduction to mtDNA Haplogroups

This page was compiled to keep track of my own research/education into the structure of mtDNA Haplogroups, sub-groups, revisions, etc. (Much of which applies to the documentation of Y-DNA Haplogroups as well.) The discussion focuses on the J1c2 mtDNA Haplogroup but general concepts apply more broadly.

J1c2 is the Haplogroup identified through testing(1) for Janet Elizabeth Curry Riehle (JECR). J1c2 is both a broad sub-grouping of the J1c(2) Haplogroup and a base level grouping in itself. To provide context for this, the FamilyTree DNA testing population includes several thousand individuals in the broader J1c2 Haplogroup, including those identified as J1c2a, J1c2b, etc. but less than 800 that are just J1c2 (sometimes shown as J1c2*).

The broad grouping for J1c2 is defined as those with the HVR2 variant A188G. By way of example, the sub-group J1c2a has this variant plus its defining variant T6293C, which J1c2* does not have.

Yet JECR has additional variants not definitional to J1c2 or to any of its sub-groups. In other words, individuals identified as J1c2* do not all have identical mtDNA.

Again to give this some context, we said above that FamilyTree DNA has thousands of individuals in the broad J1c2 category but less than 800 of the J1a2* Haplogroup. Yet JECR has no fully identical matches (see discussion of Heteroplasmy below} that have done FamilyTree DNA testing and only 4 that have just 1 differing variant. In total, she has only 193 matches using a threshold of 3 or fewer variants to her on a full mtDNA testing analysis (referred to as a genetic distance or GD of 3). These still do not constitute all tested individuals within the J1c2* Haplogroup; GD 3 just happens to be the threshold at which FamilyTree DNA cuts off their listing of matches.

To describe JECR’s true and complete haplogroup group we would identify her J1c2* Haplogroup plus provide the 8 specific mutations not typically seen in the J1c2* group plus 1 missing mutation which is normally found in the J1c2* group (Related Details).

This description would not be unique to JECR. Her sons, daughter, sister, mother, maternal grandmother, maternal aunts and uncles and many other relatives might all have identical mitochondria. However, the more generations separating her from another such individual, even one along an all-female lineage, the more likely that genetic distancing will occur, which is to say the mitochondria would show a mutation.

The timing between mutations is quite random but one estimate suggests they occur about every five generations or 125 years along a given lineage (after five generations at least one mutation is 50% likely; after 22 generations, at least one mutation is 95% likely). A DNA match with the most recent common ancestor born 5 generations previously might then have two different mutations, with one 50% likely along each lineage from that common ancestor.

In the case of JECR’s genome, a new variant appears to be ambiguous. The private (“extra”) mutations T16093Y is a Heteroplasmy which makes it unlike that there will be any close (genetic distance 0) matches found and even close relatives may not match if this is a new variant with this individual and if it resolves its ambiguity in the next generation.

And someday the authorities who manage all this may decide there are enough people identified with J1c2* variants to further refine it into new Haplogroups. Ignoring specific digits, but assuming they characterize each of the 8 additional and one missing variants with an additional digit, JECR’s particular haplogroup might look something like J1c2t1b2a1b1a. One or more of the variants may only ever occur in test subjects in the presence of another variant, in which case those variants might be combined to define a single level of sub-grouping, such that the descriptor would be shorter.

As many of us have murmured to ourselves when first exposed to mtDNA and Y-DNA Haplogroups, why does it has to be so complicated? Oh well, evolution is messy and as more people are tested more variants are found and the process of identifying haplogroup information gets messier!


  1. JECR information is based on a FamilyTree DNA Full mtDNA test
  2. See the defining mutations for all J Haplogroup sub-groupings

Private Link re. JECR’s Full Detail mtDNA

Private Link re. JECR mtDNA Lineage

Not to be shared without permission

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