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From: chi9@quads.uchicago.edu (Lucius Chiaraviglio)
Newsgroups: sci.bio
Subject: Re: Rates of Evolution
Message-ID: <1990Nov11.061807.25156@midway.uchicago.edu>
Date: 11 Nov 90 06:18:07 GMT
References: <1990Nov8.160656.24748@gpu.utcs.utoronto.ca>
Sender: news@midway.uchicago.edu (News Administrator)
Organization: Department of Biology at the University of Chicago
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In article <1990Nov8.160656.24748@gpu.utcs.utoronto.ca>
lamoran@gpu.utcs.utoronto.ca (L.A. Moran) writes:
>                     [. . .] But I do not believe that it is correct to 
>state that eukaryotes have evolved faster than eubacteria (Bacteria). 
>
>The data on 5S RNA sequences does not suggest this (Hein, 1990) nor does
>analysis of translation factors and ATPases (Iwabe et al. 1989). The ATPases
>have also been looked at by Gogarthen et al. (1989) and your statement is
>not supported by their data either.

	Wait a minute -- I got the impression from the 1990 Woese papers and
the 1989 Iwabe et al paper that the COMBINATION of the ATPase, translation
factor, and 16S rRNA sequences put the root of the overall tree approximately
midway between the Bacteria (Eubacteria) and the Archaea (Archaebacteria),
which leaves the Eucarya (Eukaryotes) hanging way out on their limb.

>In my quick search of the literature the only evidence for a rapid rate
>of evolution in eukaryotes is based on analysis of ribosomal RNA sequences
>(eg. Lake (1988); Gouy and Li (1989)). However, there are others such as 
>Sogin et al. (1989), Lynn and Sogin (1988) and Cedergren et al. (1988) 
>whose dendrograms based on ribosomal RNAs do not suggest a difference in
>evolutionary rate. The figure in Woese et al. (1990) is also based on 
>ribosomal RNAs and it does suggest that eukaryotes have evolved at a faster 
>rate but the data is from Woese (1987) and more recent analyses give a 
>different result in terms of the length of the branches.

	The dendrograms, and for that matter the other unrooted trees, do not
suggest a faster rate of evolution for the Eukaryotes because the authors did
not know the position of the root of the overall tree, and so they printed
their trees so as not to imply a position for it.  Woese, using the data of
Iwabe et al, claims in his 1990 paper that the root is somewhere near to
midway between the Bacteria (Eubacteria) and the Archaea (Archaebacteria).
Unless you alter the relationship of these two groups to the Eukaryotes, this
gives the Eukaryotes a lot more evolutionary mileage than the other two
groups.  Actually, I slightly misremembered Woese's latest tree in my last
article -- the evolutionary mileage that the Eukaryotes have is more like 1.5
times that of the other two groups, rather than 2 times.  However, my basic
interpretation of Woese's article is correct.  Now, what Woese figured from
his data and the data of Iwabe et al may be the wrong conclusion, but that is
another matter.

>Lucius Chiaraviglio has also said that;
>
>     "...microsporidia and Giardia and its relatives evolve very rapidly;"
>
>The only references that I could find were Sogin et al. (1989) and Vossbrinck
>et al. (1987) and their data does not suggest that the rate of molecular 
>evolution in Giardia is faster than the rate in bacteria (based on ribosomal
>RNA sequences). [. . .]

	The trees in Woese's 1987 and 1990 papers suggest this.  Also, if you
root the tree of Sogin et al the way Woese did in his 1990 paper, Sogin's tree
does support this contention.

>I conclude that it is misleading to state in Sci.bio that eukaryotes have 
>evolved faster than other groups of organisms, particularly bacteria.
>My own preliminary analysis of the sequences of the major heat shock gene 
>also suggests that the rates of evolution in Bacteria and Eucarya (eukaryotes)
>are similar (see Nicholson et al. 1990). If Lucius would supply references 
>to support his contention I would be happy to look them up and read them. 

	Done above.  I have also added the references you printed below (not
reposted here) to my stack of umpteen zillion things that I need to read, and
intend to get to them eventually (except for a subset of those that I have
already read).  However, if you could supply me with information suggesting
that Woese's interpretation of the molecular phylogenetic data is not correct,
or if you could tell me which particular ones of your references address this,
I will certainly give higher priority to these.

>I am particularly interested in evidence that eukaryotes are evolving at about
>TWICE the rate of Bacteria and Archaea, I doubt that this is true.

	Okay, ONE-AND-A-HALF times as fast.  I will admit to a little spatial
distortion of the tree in my memory.

>With respect to the archaebacteria (Archaea) the data is less reliable. A 
>survey of the literature suggests that the rate of change in archaebacterial
>ribosomal RNA sequences is slower than that in the other two groups (bacterai
>and eukaryotes). However, when other genes are examined this difference is
>often not seen.

	Rooting the various trees that I have seen according to Woese's 1990
paper does not show this either, but instead shows both Archaea and Bacteria
evolving on the average at about 0.7 times the rate of the Eukaryotes.

>                The methodology for constructing dendrograms from distantly
>related sequences is still being developed and there is controversy over
>the validity of measured distances (hence evolutionary rates). Some of the
>problems are reviewed in Felsenstein 1988). In addition, little attention has
>been paid to the accuracy of published sequences and this could be a 
>significant factor when only a small number of sequences are available for 
>certain taxa.

	These are certainly valid points.

>              I think that it is unwise to spend too much time constructing 
>theories that depend on archebacteria evolving more slowly than other 
>organisms.

	Aarrgghh!  Get this straight:  I did not say that the archaebacteria
evolve more slowly than everybody else.  Did I say something earlier which was
particularly misinterpretable?

>Incidently, I fully agree with those who object to the term "living fossil".
>There is no such thing.

	Agreed.  We don't need to beat this over the head any more.

--
|   Lucius Chiaraviglio    |    Internet:  chi9@midway.uchicago.edu