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MBE Advance Access published online on November 24, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj067
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 14, 2005

Research Article

Patterns of Protein Evolution in Tetrahymena thermophila: Implications for Estimates of Effective Population Size

Laura A. Katz 1 *, Oona Snoeyenbos-West 2, and F. Paul Doerder 3

1 Department of Biological Sciences, Smith College, Northampton, MA 01063, USA; Program in Organismic & Evolutionary Biology, Univ. Mass. Amherst, Amherst MA 01003, USA
2 Department of Biological Sciences, Smith College, Northampton, MA 01063, USA
3 Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland OH 44115, USA

* To whom correspondence should be addressed.
Laura A. Katz, E-mail: LKatz{at}Smith.edu


  Abstract

High levels of synonymous substitutions among alleles of the surface antigen SerH led to the hypothesis that Tetrahymena thermophila has a tremendously large effective population size, one that is greater than estimated for many prokaryotes (Lynch, M. & Conery, J. S. (2003) Science 302, 1401-1404.). Here we show that SerH is unusual as there are substantially lower levels of synonymous variation at five additional loci (four nuclear and one mitochondrial) characterized from T. thermophila populations. Hence, the effective population size of T. thermophila, a model single celled eukaryote, is lower and more consistent with estimates from other microbial eukaryotes. Moreover, reanalysis of SerH polymorphism data indicates that this protein evolves through a combination of vertical transmission of alleles and concerted evolution of repeat units within alleles. SerH may be under balancing selection due to a mechanism analogous to the maintenance of antigenic variation in vertebrate immune systems. Finally, the dual nature of ciliate genomes, and particularly the amitotic divisions of processed macronuclear genomes, may make it difficult to estimate accurately effective population size from synonymous polymorphisms. This is because selection and drift operate on processed chromosomes in macronuclei, where assortment of alleles, disruption of linkage groups and recombination can alter the genetic landscape relative to more canonical eukaryotic genomes.

Keywords: genome evolution; effective population size; ciliates; protein evolution; Tetrahymena thermophila.
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