Re: rates of change of mitochondrial DNA

Stephen Montgomery-Smith wrote:

> John Harshman wrote:
>
>
>>Are we now clear on what "fixation" means, by the way? It
>>just means "spreads throughout the population to the point where all
>>other alleles are eliminated".
>
>
> I now think that I'm not clear on this. I had assumed that fixation
> meant something "the mutation takes" that is, the mutation appears
> sufficiently often in the population that it doesn't disappear anytime
> soon. I would guess that most mutations simply disappear after one
> generation.

No, I wouldn't say "most". If they're neutral, in a diploid they would
have around a 25% chance of disappearing in one generation (assuming a
stable population in which every individual has 2 expected offspring).
For a mitochondrial mutation, the calculations would be different, since
the probability would depend on the variance in number of offspring
between individuals.

> So, for example, I did spend quite a bit of time thinking about
> mitochondrial DNA (albeit from a state of relative ignorance), and it
> wasn't at all clear to me why there shouldn't be many variants
> co-existing in a single species (say human beings) at the same time.

Yes, there could be. But additional variation won't affect the fixation,
at least from a historical perspective. We still end up with a set of
alleles all descended from one ancestral allele, with the other alleles
that were present at the time the ancestral allele arose having been all
lost. But new mutations will maintain genetic variability even as
fixation reduces it.

> Indeed the only reason I could think of why there wouldn't even be many
> variants in a single human being is because every few years or so there
> is a bottleneck effect when the next offspring happens in a single
> cell. Well that is if the egg cell only carries a single mitochondria.
> (I did ask some knowledgable friends how many mitochondria a typical
> cell contains, and the answer I mostly got was - its hard to know.)

Eggs typically contain lots and lots of mitochondria. But in the process
of cell replication there are frequent mitochondrial bottlenecks.

> I was also wondering about when the egg cells are actually produced -
> are they produced in the human being when they are very young, or when
> the emale is relatively mature? If the former, this gives a really
> rather short time for any kind of mutation to happen in the
> mitochondria if it is to get passed to the next generation.

Eggs are all produced fairly early in a human being's life. But the
mitochondria in the egg cells don't just sit there. They keep on
replicating and mutating throughout the life of the individual.

>>>>>So is there some data that could be used to check my hypothesis:
>>>>>
>>>>>"If one looks at how bases in the protein coding part of mitochondrial
>>>>>DNA change, is it then a Poisson process?"
>>>>>
>>>>>I think that would provide at least some circumstancial evidence for
>>>>>your notion that the sites are independent. (I mentioned in an earlier
>>>>>post that I might try to prove this from the data you pointed me to,
>>>>>but having thought about it, I cannot see how to do this.)
>>>>
>>>>There's plenty of data on GenBank if you really wanted to try this.
>>>
>>>
>>>Do you have recommendations for papers where people have already done
>>>this kind of research? It would be nice to see what other people did
>>>before trying to figure it out myself.
>>
>>I don't pay a lot of attention to the literature on this, because it's
>>peripheral to what I'm interested in, but here's an entry: Takahata, N.
>>1987. On the overdispersed molecular clock. Genetics 116:169-179. I'm
>>afraid it's old, but it's what I have. And here's a book which I found
>>quite difficult, largely because of the math, and you may find difficult
>>because of the biology: Gillespie, J. H. 1991. The causes of molecular
>>evolution. Oxford, New York.
>
>
> Thanks - I'll check them out shortly and see what I can understand.

There are probably many better, more recent references that I haven't
looked at.

.

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