Re: Why don't mitochondria have junk DNA?


John Harshman wrote:
> rev.goetz wrote:
>
> > John Harshman wrote:
> >
> >>rev.goetz wrote:
> >>
> >>
> >>>John Harshman wrote:
> >>>
> >>>
> >>>>rev.goetz wrote:
> >>>>
> >>>>
> >>>>
> >>>>>John Harshman wrote:
> >>>>>
> >>>>>
> >>>>>
> >>>>>>rev.goetz wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>>John Harshman wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>>Selection for fast replication? That's the usual idea for bacteria, but
> >>>>>>>>do mitochondria have to replicate that often compared to the nucleus of
> >>>>>>>>the same cell? That would depend on the lifetime of a mitochondrion and
> >>>>>>>>its standing population in the cell. I'll have to look that up.
> >>>>>>>>
> >>>>>>>>If not that, then what?
> >>>>>>>>
> >>>>>>>>There are mitochondria with junk. In fact the control region has been
> >>>>>>>>duplicated several times in different groups of birds, and one of the
> >>>>>>>>copies is clearly non-functional. So it does happen. But why so rarely?
> >>>>>>>
> >>>>>>>
> >>>>>>>Junk DNA is an extavagant byproduct of evolutionary processes because
> >>>>>>>the rate of neutral mutational insertions from various types of
> >>>>>>>repeated sequences appears to be significantly more frequent than the
> >>>>>>>fixation rate of all mutational deletions. And I recall that only
> >>>>>>>diploid cells have the mechanisms that generate various types of
> >>>>>>>repeated sequences. (I do not have the time to look up the reasons for
> >>>>>>>this.)
> >>>>>>
> >>>>>>You would seem to be talking about unequal crossing over. That's only
> >>>>>>one of a host of processes that generate new sequences.
> >>>>>
> >>>>>Unequal crossing over is only one of a few mechanisms that help to
> >>>>>generate non-coding DNA in eukaryotes.
> >>>>
> >>>>It's the only one I know of that relies on diploidy.
> >>>>
> >>>>
> >>>>
> >>>>>>>Concerning some junk DNA in mitochondria, this could have occurred by
> >>>>>>>DNA transfer from the nuclear genome to the mitochondrial genome. I am
> >>>>>>>not sure if I have heard of cases of DNA transfer from the nuclear
> >>>>>>>genome to the mitochondrial genome, but I know that I heard of several
> >>>>>>>examples of gene transfer from the mitochondrial genome to the the
> >>>>>>>nuclear genome. So I would not be surprised to see if the reverse ever
> >>>>>>>happened.
> >>>>>>
> >>>>>>I don't know of any such case. Like I said, the only mt junk I know of
> >>>>>>involves a duplication of a mitochondrial region.
> >>>>>
> >>>>>I missed that you said it was a duplication of a mitochondrial region,
> >>>>>so scratch what I said about DNA transfer from the nuclear genome to
> >>>>>the mitochondrial genome.
> >>>>>
> >>>>>In general, mutational insertions/duplications are more likely to occur
> >>>>>in eukaryotes compared to prokaryotes. And as someone said earlier in
> >>>>>this topic, many eukaryotes are not harmed by an accumulation of DNA in
> >>>>>the genome. So many insertions/duplications are neutral in terms of
> >>>>>fitness in many eukaryotes, but in many prokaryotes a large increase in
> >>>>>genome size causes a decrease in fitness. So natural selection prevents
> >>>>>a large increase of "useless DNA"in many prokaryotes.
> >>>>
> >>>>As I theorized at the outset. But can this possibly apply to
> >>>>mitochondria? Larry's mechanism obviously can't, since mt genomes are
> >>>>tiny by comparison with bacterial genomes. The other suggested
> >>>>mechanism, selection for speedy replication, also would seem not to be
> >>>>that strong in mitochondria, though that would depend on their
> >>>>population genetics. I really have to dig this up and read it again:
> >>>>Birky, C. W., Jr. 1991. Evolution and population genetics of organelle
> >>>>genes: Mechanisms and models. Pages 112-134 In R. K. Selander, A. G.
> >>>>Clark and T. S. Whittam (eds), Evolution at the Molecular Level. Sinauer
> >>>>Assoc., Sunderland, MA.
> >>>
> >>>
> >>>Even though mitochondria has a small genome size compared to
> >>>prokaryotes, natural selection favoring a compact genome could still be
> >>>the primary force that keeps it compact. For example, we know by theory
> >>>that mitochondria ancestors once had a complete prokaryote genome when
> >>>they were prokaryotes. And I conjecture that natural selection favoring
> >>>compactness helped to reduce the mitochondrial genomes to their current
> >>>sizes. And I see no reason why anything else but natural selection
> >>>favoring compactness would be needed to keep the mitochondrial genomes
> >>>near their current sizes.
> >>>
> >>>On the otherhand, I know nothing about "selection for speedy
> >>>replication" so I cannot comment about that.
> >>
> >>It's a form of selection for compactness. Unless you can suggest a
> >>reason why compactness would be selected, all you are saying is that
> >>selection produces whatever you happen to see, i.e. you are falling
> >>victim to the panglossian paradigm. I'm saying that I have trouble
> >>figuring out a reason why compactness (one or two orders of magnitude
> >>more compactness than in a bacterium) should be selected here.
> >>
> >>No selection is required in order for mt genes to be transferred to the
> >>nucleus, by the way. Just 1) transfer of a functional copy of a mt gene
> >>into the nucleus followed by 2) decay of the mt copy, no longer
> >>maintained by selection.
> >
> >
> > Yes, no natural selection is required. Neutral theory helps to explain
> > this. On the other hand, the hierarchal transfer of ribosomal protein
> > small unit (_rps_) genes from mitochondrial genomes to nuclear genomes
> > most likely resulted from natural selection because the hierarchy
> > relates to the importance on the functional importance of respective
> > the _rps_ genes.
> >
> Words missing or added here? It doesn't parse. Not sure what you mean by
> "hierarchal transfer" either. At any rate, plase explain why rps
> transfer to the nucleus is any less potentially the result of neutral
> processes than, say, cytochrome c transfer.

I do not know enough about cytochrome c to make the comparison, but I
will try to explain the hierarchy and the relationship to natural
selection. Buratovich (2005) notes an approximate hierarchy in the
transfer of rps genes from the mitochondrial genome to the nuclear
genome based on a comparison of 14 species. The approximate hierarchy
follows: rps1, rps10, rps11, rps2, rps7, rps8, rps4, rps19, rps19,
rps13, rps14, rps12, and rps3.

The genes that encode the proteins that are more vital for ribosomal
function are more likely to be transferred and preserved according to
the probabilities of natural selection. Likewise, the genes that encode
proteins that are less important to ribosomal function are less likely
to be transferred and preserved according to the probabilities of
natural selection.

Buratovich (June 2005) _Perspectives on Science and Christian Faith_.
Table 2, p.107.

.

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