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MBE Advance Access published online on January 6, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp001
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© The Author 2009. 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

Possible diversifying selection in the imprinted gene, MEDEA, in Arabidopsis

Takashi Miyake, Naoki Takebayashi and Diana E. Wolf

University of Alaska Fairbanks, Institute of Arctic Biology, Fairbanks, AK 99775

Corresponding Author: Diana E. Wolf, Phone: 907-474-5538, FAX: 907-474-5712, email: diana.wolf{at}uaf.edu

Received for publication September 12, 2008. Revision received December 7, 2008. Accepted for publication December 7, 2008.

Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that influences seed growth. Disagreement exists regarding the type of selection acting on this gene. We present new data and analyses of sequence diversity of MEA in self-fertilizing and outcrossing Arabidopsis and its relatives, to help clarify the form of selection acting on this gene. Codon-based branch analysis among taxa (PAML) suggests that selection on the coding region is changing over time, and nonsynonymous substitution is elevated in at least one outcrossing branch. Codon-based analysis of diversity within outcrossing A. lyrata ssp. petraea (OmegaMap) suggests that diversifying selection is acting on a portion of the gene, to cause elevated nonsynonymous polymorphism. Providing further support for balancing selection in A. lyrata, HKA analysis indicates that diversity/divergence at silent sites in the MEA promoter and genic region is elevated relative to reference genes, and there are deviations from the neutral frequency spectrum. This combination of positive selection as well as balancing and diversifying selection in outcrossing lineages is consistent with other genes influence by evolutionary conflict, such as disease resistance genes. Consistent with predictions that conflict would be eliminated in self-fertilizing taxa, we found no evidence of positive, balancing or diversifying selection in A. thaliana promoter or genic region.

Key Words: genomic imprinting • Arabidopsis • MEDEA • diversifying selection • antagonistic coevolution


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