Re: Thermophiles and Selection Pressure Model

From: IRR (iotarhorho_at_REMOV3hotmail.com)
Date: 03/14/05 

Date: Mon, 14 Mar 2005 01:07:38 -0500 (EST)

> Dr. Felsenstein,
>
> I was moderately well read in the sequence literature as of 1990 or
> so, but have not kept up since. In particular, I have not read your
> book, so if my questions are answered there, just say so, and I will
> buy the book! My questions are:

So I'm also most interested in hearing from an expert but was tempted to
throw in a few brief comments.

> 1. Do thermophiles and hyperthermophiles tend to have CG/AT ratios
> higher than other microorganisms?
>
> 2. Can sequence data distinguish selection for CG/AT (for reasons
> of thermal stability of RNA stems, say) from the results of CG/AT
> mutation pressure?

There is no correlation between GC skew and optimum growth temperature,
illustrated by a number of post-genomic analyses. High temperature
organisms almost certainly have ways to maintain DNA duplex stability, but
GC bias "ain't it".

> 3. In constructing trees, is there an accepted methodology for
> "correcting for" CG/AT differences between taxa?

Yes there are indeed models used in inferring phylogenies that
incorporate/attempt to correct for e.g. GC skew, codon usage bias, and
transition/transversion ratios. Buy Felsenstein's book :).

> 4. I seem to recall a controversy between Lake and Olson regarding
> archaea (Lake wanted to split up the archaea, grouping some of them
> with the eukariotes and others with the bacteria.) What ever came of
> this idea?

The archaeal monophyly is intact despite some continued efforts at
deconvolution (I think even Lake accepts this; though see e.g. RS Gupta
papers for dissention).

> 6. What cautions would you urge in drawing inferences regarding the
> lifestyle of the MRCA from evidence that some taxa have apparently
> experienced greater sequence change than others.

I think you're driving at the correct mark that such inferences -- based
predominantly on a single gene (rRNA) that has nothing to do with
metabolism/'lifestyle' in organisms (early branching thermophiles) notorious
for a slow rate of evolutionary change -- are overstated. Things get more
interesting and at least worth considering when other evidence is
incorporated, such as the predominance of iron reduction and sufur/sulfide
oxidation in early branching organisms, coupled with geological data
suggesting a large reservoir of ferrous iron in the oceans until circa 1.8
billion years ago.

None of these findings are convincing by themselves, but start to paint an
interesting and not inconsistent picture when taken together.

Relevant Pages

  • Undersea Microbes Active But Living on the Slow Side (Forwarded)
    ... tenth of Earth's living biomass, but little is known about the organisms, ... The populations of interest are two groups of Archaea -- tiny ... The researchers looked for 16S rRNA in the sediment samples and found the ... carbon to grow, repair and reproduce. ...
    (sci.space.news)
  • Undersea Microbes Active But Living on the Slow Side (Forwarded)
    ... -- Deeply buried ocean sediments may house populations of tiny organisms that have extremely low maintenance energy needs and population turnover rates of anywhere from 200 to 2,000 years, according to an international team of researchers. ... The populations of interest are two groups of Archaea -- tiny bacteria-like organisms that are often found in extreme environments such as deep-sea hot vents, inside cows or termites or in deep sediments. ... The researchers looked for 16S rRNA in the sediment samples and found the transition zones dominated by two groups -- Marine Benthic Group B and Miscellaneous Crenarchaeotal Group. ... Many organisms living in environments with methane use the methane for energy and use the methane's carbon to grow, ...
    (sci.astro)