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MBE Advance Access published online on April 4, 2008
Molecular Biology and Evolution, 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 Article

Selection on amino acid substitutions in Arabidopsis

John Paul Foxe1, Vaqaar-un-Nisa Dar1, Honggang Zheng2, Magnus Nordborg2, Brandon S. Gaut3 and Stephen I. Wright1

1 Department of Biology, York University
2 Molecular and Computational Biology, University of Southern California
3 Department of Ecology and Evolutionary Biology, University of California Irvine

Author for correspondence: Stephen I. Wright, Department of Biology, York University, Toronto, ON, Canada, M3J 1P3, E-mail: stephenw{at}yorku.ca

Received for publication November 16, 2007. Revision received March 26, 2008. 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 six circumpolar populations of the outbreeding A. 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


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