Re: New Cytochrome C evidence

On Aug 10, 9:46 am, r norman <r_s_norman@xxxxxxxxxxxx> wrote:
On Sun, 10 Aug 2008 06:44:43 -0700 (PDT), Ron O <rokim...@xxxxxxx>
wrote:





On Aug 9, 3:14 pm, r norman <r_s_norman@xxxxxxxxxxxx> wrote:
On Sat, 9 Aug 2008 12:07:04 -0700 (PDT), _Arthur

<Arth...@xxxxxxxxxxxx> wrote:
Complete Neanderthal Mitochondrial Genome Sequenced From 38,000-year-
old Bone
http://www.sciencedaily.com/releases/2008/08/080807130824.htm

"Analysis of the new sequence confirms that the mitochondria of
Neanderthals falls outside the variation found in humans today,
offering no evidence of admixture between the two lineages although it
remains a possibility. It also shows that the last common ancestor of
Neanderthals and humans lived about 660,000 years ago, give or take
140,000 years.

Of the 13 proteins encoded in the mitochondrial DNA, they found that
one, known as subunit 2 of cytochrome c oxidase of the mitochondrial
electron transport chain or COX2, had experienced a surprising number
of amino acid substitutions in humans since the separation from
Neanderthals. While the finding is intriguing, Green said, it's not
yet clear what it means."

-------------------

Let's see how Sean Pitman spins this one.  Of course, no "1000 aa"
changes were involved, so it falls under the Pitman Treshold.

The paper is

A Complete Neandertal Mitochondrial Genome Sequence
   Determined by High-Throughput Sequencing
Richard E Green (and 24 co-authors)
Cell 134(3): 416-426( 8 August 2008)

"A complete mitochondrial (mt) genome sequence was reconstructed from
a 38,000 year-old Neandertal individual with 8341 mtDNA sequences
identified among 4.8 Gb of DNA generated from 0.3 g of bone. Analysis
of the assembled sequence unequivocally establishes that the
Neandertal mtDNA falls outside the variation of extant human mtDNAs,
and allows an estimate of the divergence date between the two mtDNA
lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the
mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron
transport chain has experienced the largest number of amino acid
substitutions in human ancestors since the separation from
Neandertals. There is evidence that purifying selection in the
Neandertal mtDNA was reduced compared with other primate lineages,
suggesting that the effective population size of Neandertals was
small."

The "surprising number of amino acid substitutions" is four.  I don't
think Pitman will be too impressed.  As to the significance of these
four changes, the authors state: "However, all these substitutions are
in regions of the protein that, based on the crystal structure, do not
have any obvious function, and they are variable among primates.
Hence, they may represent either minor adaptive advantages, perhaps of
regulatory relevance, or have no significant functional consequences
for mitochondrial function."-

I recall that other researchers in the past have pointed out that
humans and their close relatives seem to have a rapidly evolving COXII
gene compared to other mammals.  One explanation is that we inherited
a defective COXII system from our monkey like ancestor.  Either a
mutation in the COXII gene or another protein that COXII interacts
with cause a portion of the COXII gene to become more selectively
neutral (lost function).  Either the higher number of substitutions
don't matter any more or they are selected for because they might be
"fixing" the problem or at least making the situation a little
better.  Either way we might have inherited some defect that we and
our ancestors have had to live with for millions of years, but most
other species have no such problem.

Based on the chimp and gorilla sequence did the substitutions occur in
the human lineage or Neandertal lineage?

In the human line, if I recall correctly.

Maybe we got lucky with one of the substitutions.

We spend a lot of calories on maintaining our brains. If there is an
inefficiency in our oxidative phosphorylation chain it would be a big
deal.

It is sort of counter intuitive that the primate lineage may have
selected for larger brains to run a race to collect enough calories to
survive.

If primates are less efficient at producing ATP oxidatively they would
have to evolve a way to insure that they could collect more calories
than their competition. You have to wonder if larger brains be would
be a hindrance or a positive?

Ron Okimoto


Google "COX II mutation" to see more about this interesting gene.   It
seems to be a mutation target for some oncogenes and is implicated in
colorectal cancer.  - Hide quoted text -

- Show quoted text -


.

Relevant Pages

  • New Scientist: Seafood gave us the edge on the Neanderthals
    ... visit the Food and Drink and Human ... Chemical signatures locked into bone suggest the Neanderthals got the ... "It seems modern humans had a much broader diet, ...
    (sci.anthropology.paleo)
  • Re: New Cytochrome C evidence
    ... Neanderthals and humans lived about 660,000 years ago, give or take ... Neandertal mtDNA falls outside the variation of extant human mtDNAs, ... Neandertal mtDNA was reduced compared with other primate lineages, ...
    (talk.origins)
  • Close correspondence between quantitative- and molecular-genetic divergence times for Neande
    ... 2008 -- Neanderthals and humans once shared a common ... Now that scientists have a better idea on when Neanderthals split from ... *Department of Anthropology, University of California, One Shields ... cranial differences between Neandertals and modern humans. ...
    (sci.archaeology)
  • Re: New Cytochrome C evidence
    ... Neanderthals and humans lived about 660,000 years ago, give or take ... Neandertal mtDNA falls outside the variation of extant human mtDNAs, ... Neandertal mtDNA was reduced compared with other primate lineages, ...
    (talk.origins)
  • Re: New Cytochrome C evidence
    ... Neanderthals and humans lived about 660,000 years ago, give or take ... Neandertal mtDNA falls outside the variation of extant human mtDNAs, ... That is a far too simplistic look on cytochrome oxidase mutations. ...
    (talk.origins)