I’ve written in the past on the topic of the rate of mutation of mtDNA, in an attempt to calculate the age of mankind. It turns out, there really isn’t a good single answer to the rate at which human mtDNA mutates, and as a result, you really can’t come to any clear answer using mtDNA alone. And in fact, I realized the other day, that it seems to vary by maternal line. Specifically, some modern humans carry archaic mtDNA, in particular Heidelbergensis, Denisovan, and Neanderthal mtDNA. Other modern humans carry  mtDNA that is basically identical to ancient mtDNA (e.g., 4,000 years old), but not archaic mtDNA (e.g., 100,000 years old). In particular, many modern humans globally carry Ancient Egyptian mtDNA, from about 4,000 years ago.

You can get an idea of the rate of mutation, by taking e.g., a modern human that has Denisovan mtDNA, and comparing that to a bona fide archaic Denisovan genome, count the number of changed bases, and then divide by the number of years since the archaic sample lived, which will produce a measure of the number of changed bases per year. This can of course be expressed as a percentage of the total genome size, which is what I’ve done below.

We can be a bit fancier about it, by comparing a given genome to many others, producing a distribution of the number of changed bases per year. The code below does exactly this, producing the average total percentage change, minimum total change, maximum total change, and standard deviation over all total changes. The comparison was made only to modern genomes, and so we can take the known (and plainly approximate) date of the archaic / ancient genome, and divide by the number of years to the present. This will produce a rate of change per year, which I’ve expressed as a rate of change per 1,000 years.

The results are as follows:

Again, note that Denisovan, Neanderthal, and Heidelbergensis are all archaic humans. In contrast, the Ancient Egyptians are of course ancient, but not archaic. The dataset contains 664 rows, 76 of which are archaic or ancient, which leaves 588 rows for the comparisons produced above. As a result, even though the table above was produced using only 4 input genomes, the results were generated comparing each of the 4 input genomes to all 588 complete, modern human mtDNA genomes in the dataset. The plain implication is that modern human mtDNA is evolving faster than archaic human mtDNA, since, e.g., the Ancient Egyptian genome has an average total rate of change equal to that of the Neanderthals, despite having only 4,000 years to achieve this total change, in contrast to the roughly 120,000 years that have passed since the Neanderthal genome. Technically, we should only be testing genomes we believe to be descended from the archaic / ancient genomes, since e.g., it is theoretically possible that a modern person has mtDNA that predates the Ancient Egyptian genome, since mtDNA is so stable. That said, the bottom line is that this is a measure of the variability of a particular maternal line, and the amount of mutation cannot exceed that variability. For this and other reasons, more studies are required, but this is an interesting observation.

The code is below, the balance of the code can be found in my paper, A New Model of Computational Genomics.