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MBE Advance Access originally published online on April 4, 2008
Molecular Biology and Evolution 2008 25(7):1375-1383; doi:10.1093/molbev/msn079
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© The Author 2008. 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

Research Articles

Selection on Amino Acid Substitutions in Arabidopsis

John Paul Foxe*, Vaqaar-un-Nisa Dar*, Honggang Zheng{dagger}, Magnus Nordborg{dagger}, Brandon S. Gaut{ddagger} and Stephen I. Wright*

* Department of Biology, York University, Toronto, Ontario, Canada
{dagger} Molecular and Computational Biology, University of Southern California
{ddagger} Department of Ecology and Evolutionary Biology, University of California, Irvine

E-mail: stephenw{at}yorku.ca.

Accepted for publication March 31, 2008.

Studies of nucleotide diversity have found an excess of low-frequency amino acid polymorphisms segregating in Arabidopsis thaliana, suggesting a predominance of weak purifying selection acting on amino acid polymorphism in this inbreeding species. Here, we investigate levels of diversity and divergence at synonymous and nonsynonymous sites in 6 circumpolar populations of the outbreeding Arabidopsis lyrata and compare these results with A. thaliana, to test for differences in mutation and selection parameters across genes, populations, and species. We find that A. lyrata shows an excess of low-frequency nonsynonymous polymorphisms both within populations and species wide, consistent with weak purifying selection similar to the patterns observed in A. thaliana. Furthermore, nonsynonymous polymorphisms tend to be more restricted in their population distribution in A. lyrata, consistent with purifying selection preventing their geographic spread. Highly expressed genes show a reduced ratio of amino acid to synonymous change for both polymorphism and fixed differences, suggesting a general pattern of stronger purifying selection on high-expression proteins.

Key Words: McDonald–Kreitman test • site-frequency spectrum • Arabidopsis • inbreeding • nonsynonymous • synonymous

Michael Nachman, Associate Editor


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