Originally published as Genetics Published Articles Ahead of Print on December 15, 2008.

Genetics, Vol. 181, 685-690, February 2009, Copyright © 2009
doi:10.1534/genetics.108.097535

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

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

^* Department of Computer Science and Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3G4, Canada, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia and Life Sciences Institute and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109-2216

² Corresponding author: University of Toronto, 6 King's College Rd., Pratt Bldg., Room 283, Toronto, ON M5S 3G4, Canada.
E-mail: brudno{at}cs.toronto.edu

We compared two haploid genotypes of one Ciona savignyi individual and identified codons at which these genotypes differ by two nonsynonymous substitutions. Using the C. 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.

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