lamoran@gpu.utcs.utoronto.ca (L.A. Moran) (11/09/90)
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 Biochemistrychi9@quads.uchicago.edu (Lucius Chiaraviglio) (11/11/90)
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