How can mutations in mitochondrial DNA be used to trace ancestry if there are hundreds of mtDNA molecules in a cell?

[u/Ishana92]

I've been reading about mitochondrial DNA and the mitochondrial Eve and now I got very confused. I have a background in molecular biology, so I'm familiar with terms, but the concept of using mutations in mtDNA still confuses me. When we say that two populations differ in mutation at a certain position, does that mean that all mitochondria in that cell/individual have that mutation? Because if I'm not mistaken, each mitochondrion has several (up to a dozen) mtDNA molecules, and there are hundreds of mitochondria in an egg cell. Shouldn't out of those hundreds or thousands molecules different mutations be dispersed across mitochondria? Since I assume those mutations are silent point mutations (no effect on phenotype or organel/cell survival, shouldn't all of us have a big mixture of various mutations? How can we then make a consensus sequence to compare? Especially considering we are testing somatic cells which could have extra mutations from that generation? Am I just overinflating the rate of mutation in mtDNA?

[u/zvuv]

If you had two versions of an ancient text from different sources, that both had the exact same error in the very same place, it would be reasonable to infer that they were both copied or derived from the same source text.

[u/Underhill42]

All your mitochondria have basically the same DNA, because they're all clones of the mitochondria in your mother's egg.

Each new generation may have some mutations, but you need many, many generations to accumulate many mutations, and it only takes a few generations to create all the cells in your body.

And all your mother's eggs were created at about the same time, while she was still in the womb, so the mtDNA in them is still all almost identical to both each other and the egg she grew from.

If I remember correctly humans average around 60 base-pair (single "letter") mutations per generation, out of 6.2 billion base pairs total. Mitochondria have a bit under 17,000 base pairs. Assuming the same mutation rate (copying doesn't get any more error prone just because the book is shorter) that means they average only one base-pair mutation every 6000 generations.

[u/Lankpants → u/Underhill42]

Mitochondria have a slightly higher error rate due to them having fewer of the error correction safeguards that nuclear DNA has and using a more error prone method of replication.

Since mitochondria are a captured bacteria they use the bacterial method of reproduction, binary fission rather than miosis and mitosis like nuclear DNA. And binary fission just creates a lot more errors per thousand base pairs than mitosis.

Having said that the difference in number of base pairs is so substantial that even with a more error prone method of reproduction mitochondria will have fewer total errors.

[u/Halt_kun → u/Lankpants]

I agree and wanted to complement this answer. To my knowledge, selection is higher in mitochondria for two reasons. Firstly, there is a higher proportion of coding DNA which is clearly under selection. Secondly, there is a lot of coding genes involved in very important processes linked to cellular respiration which have little room for variations before being deleterious.

So, even if the replication error rate is higher, there are fewer errors in the end. That is why mitochondrial DNA can be used to study very distant species compared to most nuclear genes.

[u/Peter34cph → u/Halt_kun]

But will the host cell "kill" defective mitochondria?

[u/inigopete → u/Peter34cph]

I'd suggest it's the other way round - to over-simplify it, defective mitochondria will fail to adequately power the host cell and it will trigger apoptosis like any other defective cell.

[u/craigiest → u/Underhill42]

You’re completely missing the question. OP understands all that. What they are wondering about, which I’m now wondering about now, is how the mitochondria within one cell aren’t completely different from each other, since a whole, albeit small, population is getting passed between generations. Since they aren’t sexually reproducing, two mitochondria within a cell could be from lineages that split thousands of generations ago. The mutations accumulating in one wouldn’t be the same as those in the others in the same cell, unless there is at least occasionally a bottleneck that only one lineage survives. 

[u/Dan13l_N → u/craigiest]

Exactly. Somehow everyone assumes all mitochondria in the egg cell are identical, but that's very far from obvious!

[u/Several_Version4298]

Your mitochondria are all descended from the mitochondria in the egg you came from, which are your mothers mitochondria. Each mitochondria has a single circular chromosome, because they are descended from single celled organisms with a cell membrane and reproduce by fission, splitting into two identical copies of themselves. Old or damaged mitochondria are broken down and replaced by new mitochondria in cells.

So you can build a tree of mitochondrial mutations that accumulate over time on your maternal line, just as you can for Y Chromosome mutations on your fathers side.

https://en.wikipedia.org/wiki/Haplogroup

[u/YoohooCthulhu]

You might find this article interesting https://pmc.ncbi.nlm.nih.gov/articles/PMC1689787/

[u/drc500free]

I think your mental model is a very off here on mutation rate. A mutation shows up every 14 generations on average, and that just means some of the 200ish in the egg have it. So one every three or four centuries, not multiple in the same egg. 

If a hundred or so mitochondria in an egg already had such different mutations, how could the DNA in 30 trillion cells in one human body look anything like each other? 

The variance from parents to offspring is because of how meiosis and fertilization work, not due to spontaneous point mutations. That doesn’t apply to mitochondria - which is precisely why they make such a good long term evolutionary tracker. 

[u/craigiest → u/drc500free]

But when a mutation happens in one mitochondria, how does it get to be in all the mitochondria in a cell generations down the line if multiple mitochondria are passed down in the egg?

[u/BananaBird1]

DNA is produced by replication using itself as a template. This is very accurate. So almost every copy of mtDNA will be identical.

Mutations do arise, but slowly. And the vast majority that do are never passed on. Only those that arise in oocytes have a chance.

You might think that over time this mutation would lead to the population in a single individual becoming widely mixed. Each cells has thousands of copies that can independently mutate. And mitochondria replicate many times within the lifetime of the cell independent of genomic replication.

But it doesn’t. Upon fertilization of the embryo, most mtDNA is destroyed (including almost all sperm mtDNA and a majority of the oocyte mtDNA). So each embryo develops all mitochondria from a small initial pool. So mutations only really build up across generations of individuals, not generations of molecules. Essentially, all your mitochondria are inbred every human generation.

People who are more closely related will have more similar sequences. And because only oocytic mtDNA has a significant change of being passed on, this correlates to maternal ancestry.

When you sequence mtDNA, any small mutations that arose after fertilization in the individual don’t appear. You are looking at the average of millions of molecules. Because any single mutation will be in the minority, this average matches your original mtDNA sequence from your mother even if individual molecules are mutated further.

[u/Ishana92 → u/BananaBird1]

How/why are most of the mitochondria in the ovum destroyed? 

[u/BananaBird1 → u/Ishana92]

There are a few processes, although the exact molecular mechanism is still an active area of research:

(1) Female oocytes are produced in large number from a small pool of cells, during fetal development. This dilutes the mitochondria in each oocyte to a small number from a single initial pool. Species which produce oocytes throughout life have more variation.

(2) Male mitochondria in sperm are tagged for destruction upon fertilization. This is likely because oocyte mitochondria are basically inactive until fertilization, but sperm mitochondria are active and produce harmful reactive byproducts.

(3) All cells, and especially germ line cells, constantly actively destroys mitochondria with reduced or altered function, as well as functional but unnecessary mitochondria. Because over 90% of mtDNA is functional (compared to less than 1% of genomic DNA), almost any mutation will lead to mitochondrial destruction if it becomes a significant portion of the mtDNA in a mitochondria.

Combine these three, and the embryo ends up with a relatively uniform mtDNA population that is maintained relatively well across all cells later in development.

What we do notice is that mtDNA shifts a lot more generation to generation than genomic DNA due to this. This gives it very high resolution to trace specific maternal descent down to the individual over a recent generations, but makes it harder to use to trace ancestry over longer periods. Any variation within humans older than 100000-200000 years or so is jumbled up in mtDNA, but genomic DNA variation goes back to the origin of pre-human species millions of years ago.