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MBE Advance Access originally published online on July 3, 2009
Molecular Biology and Evolution 2009 26(10):2229-2244; doi:10.1093/molbev/msp129
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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 Articles

Evolution of Plant MADS Box Transcription Factors: Evidence for Shifts in Selection Associated with Early Angiosperm Diversification and Concerted Gene Duplications

Hongyan Shan*,{dagger}, Laura Zahn{ddagger},1, Stephane Guindon§,||, P. Kerr Wall{ddagger}, Hongzhi Kong*, Hong Ma{ddagger}, Claude W. dePamphilis{ddagger} and Jim Leebens-Mack{dagger}

* State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Xiangshan, Beijing, People's Republic of China
{dagger} Department of Plant Biology, University of Georgia, Athens
{ddagger} Department of Biology and the Huck Institutes of the Life Sciences, The Pennsylvania State University
§ Méthodes et Algorithmes pour la Bioinformatique (MAB), LIRMM, CNRS—Université Montpellier II, France
|| Department of Statistics, University of Auckland, Auckland, New Zealand

E-mail: jleebensmack{at}plantbio.uga.edu.

Accepted for publication June 24, 2009.

Phylogenomic analyses show that gene and genome duplication events have led to the diversification of transcription factor gene families throughout the evolutionary history of land plants and that gene duplications have played an important role in shaping regulatory networks influencing key phenotypic characters including floral development and flowering time. A molecular evolutionary investigation of the mode and tempo of selection acting on the angiosperm MADS box AP1/SQUA, AP3/PI, AG/AGL11, and SEP gene subfamilies revealed site-specific patterns of shifting evolutionary constraint throughout angiosperm history. Specific positions in the four canonical MADS box gene regions, especially K domains and C-terminal regions of all four of these MADS box gene subfamilies exhibited clade-specific shifts in selective constraint following concerted duplication events. Moreover, the frequency of site-specific shifts in constraint was correlated with gene duplications and early angiosperm diversification. We hypothesize that coevolution among interacting MADS box proteins may be responsible for simultaneous increases in the ratio of nonsynonymous to synonymous substitutions (dN/dS = {omega}) early in angiosperm history and following concerted duplication events.

Key Words: MADS box genes • angiosperms • gene duplication • molecular evolution

1 Present address: The American Association for the Advancement of Science (AAAS), NW, Washington, DC.

Kenneth Wolfe, Associate Editor


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