Genetics. Published Articles Ahead of Print: December 18, 2008, Copyright © 2008
doi:10.1534/genetics.108.097535


A more recent version of this article appeared on February 1, 2009.
Originally published as Genetics Published Articles Ahead of Print on December 15, 2008.

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Polymorphism Due to Multiple Amino Acid Substitutions at a Codon Site Within Ciona savignyi

Nilgun Donmez 1, Georgii Bazykin 2, Michael Brudno 1* and Alexey S. Kondrashov 3

1 University of Toronto
2 Institute of Information Transmission Problems
3 University of Michigan

* To whom correspondence should be addressed. E-mail: brudno{at}cs.toronto.edu.

Submitted on October 15, 2008
Revised on December 8, 2008
Accepted on 8 December 2008


Abstract

We compared two haploid genotypes of one Ciona savignyi individual and identified codons at which these genotypes differ by two non-synonymous substitutions. Using the Ciona intestinalis genome as an outgroup, we showed that both substitutions tend to occur in the same genotype. Only in 53 (34.4%) of 154 codons, one substitution occurred in each of the two genotypes, although 77 (50%) of such codons are to be expected if substitutions were independent. We considered two feasible evolutionary causes for the observed pattern: substitutions driven by positive selection and compensatory substitutions, as well as several potential biases. However, none of these explanations is fully compelling, and data on multiple genotypes of C. savignyi would help to elucidate the causes of this pattern.

Key Words: Ciona savignyi, non-synonymous substitutions, polymorphism, two-substitution codons