Newsgroups: sci.bio
Path: utzoo!utgpu!lamoran
From: lamoran@gpu.utcs.utoronto.ca (L.A. Moran)
Subject: Rates of Evolution
Message-ID: <1990Nov8.160656.24748@gpu.utcs.utoronto.ca>
Organization: UTCS Public Access
Date: Thu, 8 Nov 90 16:06:56 GMT



Lucius Chiaraviglio has recently written;

     "...it has become fairly obvious from doing molecular phylogeny 
      that not all organisms evolve at the same rate. The high thermophiles
      (so far all archaebacteria and eubacteria) have been evolving 
      slowly; ... all of the known eukaryotes evolve rapidly;..."

 and earlier he stated;

     "However, the Eukaryotes really do seem to be evolving at about 
      twice the rate of the other two lineages -- see Carl Woese's 
      article ...."

I do not dispute the idea that some groups of organisms may show evidence
of a faster rate of fixation of alleles than others; or even that the rate
of mutation in some lines may be different than in others. Certainly the
rate of molecular evolution will be influenced by the generation time of
organisms and the size of the evolving population and these will be
different in different taxa. 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. There is some hint of faster evolution
in eukaryotes when dehydrogenase sequences are compared (Iwabe et al. 1989;
Smith 1989) but the effect is not remarkable. In the case of the three 
comparisons by Iwabe et al. (1989) the root of the phylogenetic tree has 
been defined so that comparisons between the three major kingdoms (or 
domains) are valid.

Sidow and Wilson (1990) have specifically addressed the question of deep
phylogenetic relationships between the major taxa. Using the data from
RNA polymerase sequences they do not find significnat differences in the 
rates of evolution of bacteria and eukaryotes.

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.

Wilson's group is particularly interested in molecular clocks and they have
investigated the question of evolutionary rates. They have concluded that
the absolute rate of evolution in bacteria is very similar to that in
mammals (Wilson et al. 1987).

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). But, the brief review by Cavalier-Smith (1989) does suggest 
that one species of microsporidia shows more changes than lines leading to 
bacteria and other eukaryotes based on analysis on one species of 
microsporidia as described in Vossbrinck et al. 1987.

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. 
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.

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

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

Cavalier-Smith, T. (1989) Nature 339, 100-101.
Felsenstein, J. (1988) Ann. Rev. Genet. 22, 521-565
Gogarten, J.P. et al. (1989) PNAS 86, 6661-6665.
Hein, J. (1990) Meth. in Enzymol. 183, 626-645.
Iwabe, N. et al. (1989) PNAS 86, 9355-9359.
Lake, J.A. (1988) Nature 331, 184-186.
Lynn, D.H. and Sogin, M.L. (1988) BioSystems 21, 249-254.
Nicholson, R.C. et al. (1990) PNAS 86, 1159-1163.
Sidow, A. and Wilson, A.C. (1990) J. Mol. Evol. 31, 51-68.
Smith, T.L. (1989) PNAS 86, 7063-7066.
Sogin, M.L. et al. (1989) Sci. 243, 75-77.
Wilson, A.C. et al. (1987) Trends in Genetics 3, 241-247.
Woese, C.R. et al. (1990) PNAS 87, 4576-4579.
Woese, C.R. (1987) Microbiol. Rev. 51, 221-271.
Vossbrinck, C.R. et al. (1987) Nature 326, 411-414.

-Larry Moran
Dept. of Biochemistry