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MBE Advance Access published online on September 15, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh261
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted September 1, 2004

Research Article

Molecular Population Genetics of Redundant Floral Regulatory Genes in Arabidopsis thalianana

Richard C. Moore 1*, Sarah R. Grant 2, and Michael D. Purugganan 1

1 Department of Genetics. North Carolina State University, Raleigh, NC 27695
2 Department of Biology. University of North Carolina, Chapel Hill, NC 27695

* To whom correspondence should be addressed. E-mail: rcmoore{at}unity.ncsu.edu.


  Abstract

Functional redundancy between duplicated genes is predicted to be transitory, as one gene either loses its function, gains a new function, or both genes accrue degenerative, yet complimentary mutations. Yet there are many examples where functional redundancy has been maintained between gene duplicates. In order to determine whether selection is acting on functionally redundant gene duplicates, we performed molecular evolution and population genetic analyses between two pairs of functionally redundant MADS-box genes from the model plant Arabidopsis thaliana: SEPALLATA1 (SEP1) and SEPALLATA2 (SEP2), involved in floral organ identity; and SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2), involved in seed shattering. We found evidence for purifying selection acting to constrain functional divergence between paralogous genes. The protein evolution of both pairs of duplicate genes is functionally constrained, as evidenced by Ka/Ks ratios of 0.16 between paralogs. This functional constraint is stronger in the highly conserved DNA- and protein-binding MIK region than in the C-terminal region. We also assayed the evolutionary forces acting between orthologs of the SEP and SHP genes in A. thaliana and the closely related species, Arabidopsis lyrata. Heterogeneity analyses of the polymorphism-to-divergence ratio indicate selective sweeps have occurred within the transcriptional unit of SHP1 and the promoter of SHP2 in the A. thaliana lineage. Similar analyses identified a significant reduction in polymorphism within the SEP1 locus, spanning the 3' region of intron 1 to exon 3, and may represent an intragenic sweep within the SEP1 locus. We discuss whether the evolutionary forces acting on SEP1 and SEP2 versus SHP1 and SHP2 vary according to their position in the floral developmental pathway, as found with other floral regulatory genes.

Keywords: SEPALLATA; SHATTERPROOF; paralogs; functional redundancy; floral development.
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