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From: "Ian Logan" <>
Subject: Re: [DNA] News item: neutral evolution and numts
Date: Wed, 11 Jul 2007 21:05:27 +0100
References: <cbc.14d479fb.33c63e7a@aol.com><001501c7c3d1$44c6d110$4001a8c0@IanLogan><a81622ac0707111153t54958dd9j630c65d7bf796de5@mail.gmail.com>


> Just because, to quote from the paper,
> 'their (NUMTs) rate of aquisition spikes dramatically around population bottlenecks'
> it does not follow that the acquisition of a NUMT is a path to the way out of a bottleneck.
> I suggest the formation of a NUMT is a random event and as long as the cell survives,
> there is no benefit to the organism.
.........
Joe replied:
But aren't the authors specifically saying that the mutation has no
benefit & that the population bottleneck just increases its chance of
survival by genetic drift? Any mutation--even a selectively neutral
one--will survive longer, on average, if it arises in a smaller
population. So even junk DNA benefits from bottlenecks, no?
.........

Joe,

Thank you for your comment.

Yes, you are correct in saying that a 'mutation' in a small population will survive
as that population grows; and this surely applies to NUMTs after a 'bottleneck'.
So is this survival the benefit ?

But, the authors say:
'We begin by assuming that prior to 54 mya, the effective population size of the primate ancestor
was relatively large, leading to a insertion/deletion/selection equilibrium with NUMT count
being few and held stable at that low level'.

What might they think holds NUMTs 'few and stable' ?

So all this does not make good sense to me as we are not dealing with a population
but a single line of inheritance; and the size of a population in the past does not affect the
number of NUMTs in our modern human genome.

As a parallel example, I think of the 50 or so 'mutations' in the mtDNA that have occurred
in everyone in the last 200,000 years since 'Mitochondrial Eve'. I suggest that these mutations
have arisen and 'survived' after a very severe 'bottleneck' (just down to 'Eve' herself, so it
couldn't have been more severe).
And this suggests that 1 mutation occurs every few thousand years - in everybody's
line of inheritance. We are all survivors from the 'bottleneck'.

But this does not mean that in the period before 'Mitochondrial Eve' mutations
were not occurring at about the same rate in the single line of descent that survived.
Indeed looking at NUMTs show which mutations are likely to have been the
ones that occurred before 'Eve' - and there were plenty !

Another point: I mentioned in the first posting about the 'degradation' of NUMTs,
despite DNA repair mechanisms, as being a reason for not finding 'older NUMTs.
But let me just mention another problem - related to function.
A new NUMT is a copy of a functioning mtDNA - at the time of its formation
But the mtDNA has to keep functioning and in its coding areas it cannot keep
'mutating' and 'diverging' - there will also be 'mutation' back to a previous
functional state. I suggest the authors ignored this 'horizon' effect which tends
to make a 'mutation' rate appear lower as one goes further back.

And, a final point - the Macaque (rhesus) monkey has lots of NUMTs.
So I suggest the number of NUMTs found in most species depends on the
'data available' and on 'how' one looks at the data.

Ian

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