Thorsten Burmester wrote:
>> Dear evolutionists,
>> Is there any paper on the frequencies of the phases (relative to the
> reading frame of the exon) in which the introns are inserted.
There are a number of papers that address this topic. Probably
the first to document an asymmetry in phase distribution was
Hickey, et al., 1989. J. Theor. Biol. 137:41
Since then there have been several more comprehensive and
quantitative surveys of data. For animal and plant genes
(which are most of the intron-containing genes in databases),
40-55% of introns are phase 0, 30-40% are phase 1, and about
20% are phase 2. See:
Federov, et al., 1992. Nucl. Acids Res. 20: 2553
Gelfand, 1992. J. Mol. Evol. 35:239
Fichant, 1992. Human Mol. Genet. 1:259.
Gelfand's paper uses an unusual sample of genes with a
larger fraction of phase 1 introns.
Quite probably, the assymetric distribution is due to
addition of introns to target sequences (something like
AG^G) that are themselves non-randomly distributed with
respect to phase. In particular, Federov et al (Tab. 2),
Gelfand (p. 248) and Long, et al:
Long, et al. 1998. Proc. Natl. Acad. Sci. 95:219.
(Tab. 3) all show that phase 0 introns are expected to be
the most common if introns are added non-randomly at a
sequence like AG^G, due to the distribution of AGG in
There have also been several papers on the subject of intron
phase autocorrelation, that is, the tendency for neighboring
introns to have the same phase:
Long, et al., 1995. Proc. Natl. Acad. Sci. 92:12495
Tomita, et al., 1996. Mol. Biol. Evol. 13:1219.
Federov, et al., 1998. J. Mol. Evol. 46:263.
The causes of this pattern, and whether it is an ancient
(as opposed to eukaryote-specific) phenomenon, are topics
presently under study by these research groups. All three
groups tend to believe that the autocorrelation is due
to exon shuffling, and it is clearly partly due to exon
shuffling, though there is a good deal of room for
interpretations about additional causes. Hope this helps.
Arlin Stoltzfus, Ph.D. (arlin at is.dal.ca)
Department of Biochemistry, Dalhousie University
Halifax, Nova Scotia B3H 4H7 CANADA
phone: 902-494-2968 fax: 902-494-1355