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* California Institute of Technology, 101 Dahlia Avenue, Corona del
Mar, CA 92625; and Contributed by Roy J. Britten, February 15, 2003
It was recently shown that indels are responsible for more than
twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is
Evolution
Majority of divergence between closely related DNA samples is
due to indels
,
, Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The ratio
(Ru) of unpaired nucleotides
attributable to indels to those attributable to substitutions is 3.0 for this 2 million-nt chimp DNA sample compared with human. There is
similar evidence of a large value of Ru for sea
urchins from the polymorphism of a sample of Strongylocentrotus
purpuratus DNA (Ru = 3-4). Other
work indicates that similarly, per nucleotide affected, large
differences are seen for indels in the DNA polymorphism of the plant
Arabidopsis thaliana (Ru = 51). For the insect Drosophila melanogaster a high value of
Ru (4.5) has been determined. For the nematode
Caenorhabditis elegans the polymorphism
data are incomplete but high values of Ru are
likely. Comparison of two strains of Escherichia coli
O157:H7 shows a preponderance of indels. Because these six examples are from very distant systematic groups the implication is that in general,
for alignments of closely related DNA, indels are responsible for many
more unmatched nucleotides than are base substitutions. Human genetic
evidence suggests that indels are a major source of gene defects,
indicating that indels are a significant source of evolutionary change.
To whom correspondence should be addressed. E-mail:
rbritten{at}caltech.edu.
www.pnas.org/cgi/doi/10.1073/pnas.0330964100
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