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genetic code & mutation rates

Doug Eernisse DEernisse at fullerton.edu
Thu Jul 27 11:51:56 EST 1995

In article <3v7ujo$1m8 at decaxp.harvard.edu>, robison at lipid.harvard.edu
(Keith Robison) wrote:

> HPYockey (hpyockey at aol.com) wrote:
> : Chapter 7 of my book Information theory and molecular Biology discusses
> : the evolution of the standard triplet genetic code from a primitive
> : doublet code. The mathematical background needed to understand the
> : argument is in Part I of this book. 
> : Chapter 7 shows that if the primeval genetic code had a vocabulary of
> : fewer than 20 amino acids, for example perhaps 8, then there should have
> : evolved about 10 separate codes. These are the mitochondrial genetic codes
> : usually regarded as minor differences from the standard genetic code. 
> : When you read Chapter 7 please e-mail me any comment or questions. 
> Disclaimer: I haven't read your book (time to go to library :-)
> The main problem with this hypothesis is that the phylogenetic 
> distribution of non-standard genetic codes doesn't support this
> very well -- the non-standard codes show up all over the tree,
> and not just in mitochondria.  I think Thomas Jukes and coworkers
> have made a pretty strong argument that the non-standard codes
> are a recent, derived phenomenon rather than an ancient relic.

I agree with Keith, except that all the non-standard codes I know about are
restricted to mitochondrial DNAs. If the following information requires
updating, I would greatly appreciate some references. For
example, fluke (flatworm), protostome (arthropods, molluscs) (? +
nematode), echinoderm, and chordate mtDNAs all have different codes from
each other and
from the standard code. Outside of metazoan mtDNAs, I know of only the
following departures from the standard code: 

Saccharomyces cerevisiae (yeast) mtDNA (Hudspeth et al., 1982, Sibler et
al., 1986), Paramecium aurelia (a ciliate) mtDNA (Pritchard et al., 1986),
Chlamydomonas reinhardtii (green alga) mtDNA (Boer & Gray, 1988),
Land plant mtDNAs use the standard code except CGG = tryptophan, but RNA 
editing C -> U restores the normal coding. Some other even more extreme
departures are likewise restored to the standard code by RNA editing.

Are there non-mtDNA examples that I am missing, or are any of the
above deviations no longer accepted?

Keith's point is still valid, especially if these mtDNAs all had a common 
origin from a eukaryotic ancestral mtDNA that had standard coding
(references on early diverging eukaryotic lineages whose mtDNAs have
standard coding would also be appreciated).

Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Science MH282
California State University
Fullerton, CA 92634

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