DNA Basics: Mitochondrial DNA

The first post of this series ended with a reference to different “types” of DNA. In truth, DNA is DNA, and every living organism, from the tiniest bacterium to the largest blue whale, has the same four nucleotides—A, C, G, and T—at its core.

The four “types” of DNA in genetic genealogy do not differ in chemical structure but in inheritance patterns. And inheritance patterns are critical to how we apply DNA data to genetic genealogy. Those four types are: mitochondrial DNA, the Y chromosome, the X chromosome, and autosomal DNA.

Mitochondrial DNA (abbreviated mtDNA) is the least useful type of DNA for genealogical purposes, but it’s the easiest to understand. For that reason, I will describe it first.  Some of the concepts explained here will come up again when we discuss the X and Y chromosomes and autosomal DNA later on.

 

Mitochondrial DNA

Hands down, mtDNA is is the weirdest kind of DNA we have. The rest of our DNA comes in massive, linear molecules (called chromosomes) that are stored in a central part of our cells called the “nucleus”. mtDNA, on the other hand, is small, circular, and stored in multiple compartments throughout the cell called mitochondria. (The singular is mitochondrion).  Any given cell can have dozens or even thousands of mitochondria, each with its own little stash of DNA. (Oddly, red blood cells have no mitochondria at all.)

 

 

“Small” in this case means that the entire mtDNA unit is only 16,569 bases long. Some people may have a few extra bases due to an event called an “insertion”, or fewer due to a “deletion”, but we all have roughly the same size mitochondrial genomes. (Insertions and deletions together are called indels.) That may seem like a lot until you consider that the nuclear genome has 3 billion bases!

Mitochondria are the powerhouses of the cell.  Their main job is to convert the energy stored in sugars into a form the cell can use quickly. It’s basically a controlled burn from the moment the mitochondrion comes into existence until it dies.

Up close and personal, a mitochondrion looks something like this.  All those extra squiggles in the inner bit create extra surface area for burning energy. The small rings are the DNA. Note that each mitochondrion can have multiple copies of the DNA ring, and each cell can have dozens or thousands of mitochondria.

The fact that mitochondria have their own DNA is fascinating. They’re the only compartment in animal cells aside from the nucleus to have DNA. (Plants have three compartments with DNA: the nucleus, mitochondria, and chloroplasts. Plants are cool.) What’s more, mtDNA is more similar to bacterial DNA than to our nuclear DNA. There’s a very good reason for that: mitochondria were once free-living bacteria that established a long-term partnership with larger host cells. The mitochondria process energy for the cell, and the host protects the mitochondria. This bargain has worked so well for nearly 2 billion years that neither partner can survive alone.

 

Inheritance of Mitochondrial DNA

Mitochondrial inheritance is simple: we get it from our moms. And our moms got it from their moms, who got it from their moms, and so on, and so on, and so on, all the way back to a theoretical woman called Mitochondrial Eve, who lived about 160,000 years ago, give or take. Every human alive carries mtDNA that ultimately came from Mitochondrial Eve.

Men have mitochondria, too—if they didn’t, they’d be dead—but they don’t pass them on to their children. Why is a question scientists have yet to fully explain. Current thinking is that the swim-fast-die-young lifestyle of sperm causes so much genetic damage that the mitochondria self destruct during fertilization to avoid passing on mutations to the offspring.

Don’t forget to thank Mom for your mitochondria on Mother’s Day!

 

Ch-Ch-Changes and Haplogroups

Each of us inherited our mtDNA in an unbroken line of women that traces back to Mitochondrial Eve. But we don’t all have identical mitochondria. How is that?

Mitochondria reproduce by duplicating their DNA then splitting in half. Nothing fancy: copy and split, copy and split, copy and split. Over and over. In theory, each “daughter” mitochondrion should get an identical copy of the original DNA, but you know the saying: $#!☨ happens.  In this case, the “$#!☨” is mutations, rare genetic typos that occur during the copying process. For example, an ‘A’ might get copied incorrectly as a ‘G’ (a type of mutation called a SNP), or an indel could occur that changes the length of the mtDNA ring.

Many mutations are harmful and will kill the mitochondrion, but some are benign and can be passed on to a woman’s offspring. Over thousands of years, those changes build up, causing people from different maternal lineages to have different suites of unique mtDNA mutations. And the more time since the shared matrilineal ancestor, the more differences there are likely to be.

 

You might have the exact same mtDNA sequence (or haplotype) as a total stranger, a difference or two, or many differences. But chances are a stranger with the exact same haplotype shares a more recent matrilineal ancestor with you than someone with a few (or more) differences.

Similar haplotypes can be lumped together into haplogroups, the idea being that people with identical haplotypes are descended from a common matrilineal ancestor, while people with similar haplotypes are descended from a shared matrilineal ancestor a bit further back in time.

The main haplogroups are given simple letter, letter–number, or letter–letter names, e.g., “L”, “N1”, or “JT”. Just as we are all descended from Mitochondrial Eve (who is assigned haplotype L), everyone in the same haplogroup traces back to the same matrilineal ancestor (more recent than Eve, still quite ancient). What’s more, haplogroups can be nested within one another. N1 is a subgroup of N, which is a subgroup of L3, which in turn is descended from L. Any haplogroup can be subdivided even further, until you get to clusters of people with identical haplotypes.

Of course, we can’t sequence the haplotype of Mitochondrial Eve, nor of those ancestral women at the branch points in the tree. Instead, we reverse-engineer the evolutionary branching pattern using the sequences of modern-day people and analysis methods developed in the discipline of phylogenetics.

You can see an overview of the current mtDNA haplotree here. The tree will become more defined, and some branching patterns may change slightly, as more data from more people are included.

 

Why Do mtDNA Testing?

I said at the beginning of this post that mtDNA isn’t particularly useful for genealogy. That’s true. There are two main reasons.  First, surnames tend to be inherited from the father. Genealogists must contend with surname changes every generation when tracing their matrilines, and many brick walls hit up against a woman whose maiden name is unknown.

Second, mtDNA changes too slowly to tell us much. For example, at Family Tree DNA, I have 14 exact haplotype matches to my full mtDNA sequence, including two who list their most distant known ancestor as Michelle Aucoin (abt 1621–1706), the sister of my 10th great grandmother, Jeanne Aucoin (1630–1718). In the 12 generations between Jeanne and me, and the 12 or so generations between Michelle and my matches, not a single mutation occurred. I also have exact matches that trace their matrilines to Bulgaria, Serbia, and Germany. The mtDNA data can’t tell me whether I’m descended from Jeanne, Michelle, or some more distant ancestor from the Balkans.

While mtDNA isn’t great bait for “cousin fishing”, it can be a valuable tool for testing specific hypotheses on a matriline. For example, if your 5th great grandfather had two wives, and you’re not sure which was the mother of your 4th great grandmother, you could use targeted mtDNA testing to tell. You would test yourself, one matrilineal descendant of the first wife, and one of the second wife to see which you matched.

mtDNA can also often address an ancestral woman’s continental origins. Was she of African descent? Native American? European? Determining her haplogroup by testing a matrilineal descendant might answer the question.

Finally, for the geeks among us, there’s the neato factor. You can trace your matriline through time and space from Mitochondrial Eve to present day. The map below shows mine. Solid lines are ancient migration patterns inferred by mtDNA scientists, and the dashed lines are historical movements based on my family tree.

We’ve come so far!

 

Ancient DNA Studies

One last use of mtDNA is in archaic studies. Because the mtDNA ring is small, and because each cell has so many copies, mtDNA is more likely to survive intact over long periods of time than other forms of DNA. A portion of Neanderthal mtDNA was extracted from fossils in 1997, a full decade before advanced techniques allowed the nuclear genome to be sequenced. mtDNA was a key piece of evidence in identifying the remains of King Richard III of England. It’s currently being used to put a name to the unknown Australian sailor whose body was the only one found from the sunken HMAS Sydney.

 

Which mtDNA Test Is Best?

There are two approaches to mtDNA testing. One is to do an autosomal DNA test with 23andMe (normally $99) or Living DNA (normally $159). These two companies test enough mitochondrial SNPs to assign a haplogroup, but they don’t match you to others based on mtDNA data. These results are often sufficient to address the “which wife” or “continental origins” scenarios. Plus, you get autosomal DNA results rolled into the price.

The gold standard, though, is having all or part of your mitochondrial genome sequenced at Family Tree DNA. They offer two levels of testing: mtDNA Plus and mtFull Sequence. Both levels will match you to others in their database of nearly 300,000 mtDNA testers. mtDNA-based matching can identify matrilineal relatives who are too distant to share autosomal DNA. The 23andMe and Living DNA tests wouldn’t find these connections.

The mtDNA Plus test (normally $89) at Family Tree DNA sequences a small portion of the mtDNA ring that changes faster than the rest of the mitochondrial genome. In fact, that section is called the hypervariable region, hence the terms HVR1 and HVR2 that you’ll see in the reported results. This test is a cost-effective approach to “which wife” or “continental origins” questions. An exact match at this level might still differ from you elsewhere in the mtDNA genome.

The mtFull Sequence (normally $199) is exactly that. It analyzes every base pair in your mtDNA genome, and an exact match with this test is truly an exact match. This test will address all of the research scenarios I described above, including deep ancestry. Your results can also help to advance science by contributing new samples to the mtDNA haplogroup tree.

 

Updates to This Post

30 December 2018—minor edits to improve clarity

 

Other Posts in This Series

• DNA Basics: What Is DNA?
• DNA Basics: Mitochondrial DNA
• DNA Basics: Mutations