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MBE Advance Access published online on December 5, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh022
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted September 22, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Heterogeneous Selection on LEGCYC Paralogs in Relation to Flower Morphology and the Phylogeny of Lupinus (Leguminosae)

Richard H. Ree 1, Hélène L. Citerne 1, Matt Lavin 1, and Quentin C. B. Cronk 1*

1 University of British Columbia, Botanical Garden and Centre for Plant Research, 6804 SW Marine Drive, Vancouver, British Columbia, Canada, V6T 1Z4

* To whom correspondence should be addressed. E-mail: quentin.cronk{at}ubc.ca.


  Abstract

An analysis of the molecular evolution of two LEGCYC paralogs in Lupinus (Genisteae: Leguminosae) reveals a varied history of site- and lineage-specific evolutionary rates and selection both within and between loci. LEGCYC genes are homologous to regulatory loci known to control floral symmetry and adaxial flower organ identity in Antirrhinum and its relatives. Within Lupinus, L. densiflorus is unusual in having flowers with a proportionally smaller standard (fused adaxial petals) and larger wings (lateral petals) than other lupin species. Phylogenetic estimates of the nonsynonymous/synonymous substitution rate ratio, {omega}, suggest that along the L. densiflorus lineage, positive selection ({omega} > 1) acted at some codon sites of one paralog, LEGCYC1B, and greater purifying selection ({omega} < 1) acted at some sites of the other paralog, LEGCYC1A. Overall, LEGCYC1A appears to be evolving faster than LEGCYC1B, and both paralogs are evolving faster than ITS. The predominant historical pattern inferred is a highly heterogeneous "selectional mosaic" which we suggest may be typical of the TCP class of transcriptional activators, and possibly other genes. Codon models that do not account for both siteand lineage-specific variation in {omega} do not detect positive selection at these loci. We suggest a modification of existing branch-site models involving an additional {omega} parameter along the foreground branch, to account for the effects of both greater positive selection and greater purifying selection at different codon sites along a particular branch. The higher rates of evolution and congruent phylogenetic signal of both LEGCYC paralogs show promise for the use of these genes as markers for phylogeny reconstruction at low taxonomic levels in Genisteae.

Key Words: nonsynonymous/synonymous rate ratio, flower morphology, LEGCYC, CYCLOIDEA, Papilionoideae, Lupinus


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