Genetic change since Mitochondrial Eve

What mechanisms have (theoretically) led to genetic changes since Mitochondrial Eve, especially other than mutations? According to the Wikipedia article on ME mutations occur in mtDNA approximately every 3500 years. My advisor calls this “random noise.” However, I’m also aware of a study which found that lactase persistence through adulthood may have emerged within the last 5-10k years, which would apparently be inconsistent with the random noise hypothesis, indicating other mechanisms for adaptation may be at work.

This question is asked purely out of curiosity. To pique yours I will ask, according to modern theories of selection what is the timescale that brain evolution has occurred on? Have brains been the same for the last 50-100k years, with differences in culture being the only change relevant to intelligence, or were changes to neural architecture needed over and above learning based on the environment encountered? To get even more concrete, is it possible that Neanderthals weren’t as smart as Homo Sapiens, and even further, that Homo Sapiens Sapiens are even smarter than Homo Sapiens? Here, “smart” is controlling for culture, i.e., if you were to transplant a newborn Neanderthal into modern culture, is it possible, based on modern theories of selection, that they would have been seen as less intelligent than us?

IANAGenetisist, but for starters, mutation has several causes. Random errors, radiation, selection, etc. if a species is going to evolve, mutation itself is a foundational factor. Right?

So, there is no “other than mutation,” but rather what the cause of the mutation is, and how likely it is to occur for a species at a given time and environment.

IAA Genetisist, and find the phrasing of the question odd.

Mitochondrial DNA is only inherited matrilineally. As there is no sexual recombination of mtDNA the only changes from generation to generation are mutations.

There are lots of types of mutations - point substitutions, frame shifting insertions or deletions, non-frame shifting insertions or deletions, translocations, inversions, and so on… but they are all mutations.

mtDNA is a pretty small scrap with few genes. The genes governeing lactose persistence are autosomal and not in the mtDNA.

Lactase persistance is controlled by regulatory sections of DNA that control the expression of the LCT gene located on Chromosome 2. The commonly expressed variant is a point mutation.

You could imagine that a mutation allowing someone to digest milk into adulthood could help such a person survive by providing access to an alternate food source. If this mutation arose in a relatively small community the selective advantage could spread that dominant mutation into a large segment on that population rather quickly. Seelctive pressure might be stronger in a population that was already herding animals and might have been quite weak in a hunter gatherer culture.
Brain evolution is a much more complex issue with multiple genes involved. Any one gene mutation may have provided an advantage which spread throughout the population but there were likely many such events in multiple genes during the evolution of the human brain.

As mentioned, mitochondrial DNA is it’s own thing, completely separate from the much much bigger mass of ‘regular’ nuclear DNA. Because mtDNA doesn’t recombine, is a small tightly focused segment, has been doing the same function for so long, and is so critical to a cell’s functioning, there’s good reason to assume that any change to mtDNA is either going to kill the cell be neutral in effect (e.g. ‘random noise’). Which means mutations that survive end up accumulating more-or-less regularly through time, and can be used as a very rough clock.

On the other hand, the nuclear DNA has a lot more chances to possibly change for the better-- the mutation that allows adults to digest milk is one good example. Which means that there’s an opportunity for selection. For timing, you might note that the gene hasn’t yet spread completely throughout the human population.

So the short answer to OP is that there’s a helluva lot more genetic material in the chromosomes than in the mitochrondrial DNA. So a chance of one mutation per 3500 years per X pairs of GATC means once every 3500 years for the mitochrondrial and once every few minutes or so for chromosomes with millions more pairs?

Let me address this part. I’m not going to use the term H. sapiens sapiens only because I’m more of a lumper than a splitter, but that doesn’t much matter.

Current thinking is that our line splint with the Neanderthal line about 600k years ago. +/-. Our species and the Neanderthals arose about the same time-- maybe 200k years ago.

But the funny thing about us is that our tools didn’t differ much from the Neanderthal tool kit for the first 100k years or so. Then, there seemed to be an explosion of new tools, new materials being used from tools, and evidence of symbolic thought (mainly art and body decorations like strings of beaded shells). So, biologists talk about “anatomically modern humans” as those guys before this creative explosion. They looked like us, but didn’t seem to quite act like us. Then you have “fully modern humans” after that creative explosion. Some biologist think (although we can’t prove this) that our ancestors didn’t have fully articulate speech as we know it until about 100k years ago.

Now, there is some evidence that Neanderthals shared some advanced tool making and maybe even some artistic tendencies, but we don’t know if those arose separately, or were copied from us once we invaded Europe.

But generally speaking, it’s thought that Neanderthals weren’t as “smart” as we are, and that our ancestors didn’t get “fully smart” until about 100k years ago. However, it’s not generally thought that any people living today are any more or less smart, as a group, than any others.