genetic code & mutation rates

Keith Robison robison at mito.harvard.edu
Fri Jul 28 09:04:43 EST 1995

Doug Eernisse (DEernisse at fullerton.edu) wrote:
: 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. 

Other examples (from memory; don't have my copies of cites handy)
	Cilliate nuclear DNA
	Some mycoplasmas (bacteria)

Very new reference on cilliate nuclear code deviations
	Genetic code deviations in the ciliates:  evidence for multiple and
	independent  events
	EMBO-J.   1995 JULY 3.   14(13).   P 3262-3267.

Good reference, though getting old
	Recent evidence for evolution of the genetic code.
	Osawa S; Jukes; TH; Watanabe K; Muto A
	Microbiol Rev 56: 229-264 (1992) 

: 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).

Well, I think the phylogenetic evidence pretty clearly places the
mitochondria in the purple bacteria, which all use the standard code.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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