Resolving the green branch of life: Current progress and future challenges
Des Marais, David L. .
A Phylogenetic Approach to Interpreting Patterns of Functional Divergence and Regulation of Duplicated Genes.
Green plant genome sequencing projects have revealed the ubiquity of gene duplications, which often appear to be quite long-lived. While gene duplications present a significant problem to systematists interested in reconstructing evolutionary histories using nuclear markers, duplicates afford the student of molecular evolution rich insights into functional divergence. Three general fates have been identified concerning the fate of duplicate genes: (i) maintenance of both copies via epigenetic regulation, subfunctionalization, or concerted evolution, (ii) loss of one copy via pseudogenization, and (iii) maintenance of both copies via gain of novel function in one copy. One of these, subfunctionalization, has received considerable attention over the past 5 years but the evidence necessary to document such change has not been critically evaluated. I argue that we cannot distinguish between neofunctionalization and subfunctionalization without knowing the role of duplicate genes’ single-copy ancestor. I present a novel method for studying the evolution of duplicate genes using gene trees embedded in species trees to reconstruct ancestral expression patterns and enzyme function. Gene expression and function information can be combined with analysis of sequence evolution to unambiguously decide among the fates presented above. By combining such comparative expression data with sequence bioinformatics, the methods presented herein may also prove fruitful in identifying cis-elements involved in regulation of duplicated genes. While no suitable dataset currently exists for such an analysis, I discuss the prospects for analyzing data arising from microarray analyses, MPSS, and quantitative PCR and present preliminary results from my own work reconstructing the functional divergence of a small family of anthocyanin genes in Ipomoea (Convolvulaceae).
1 - Duke University, Department of Biology, 139 Biological Sciences Building, PO Box 90338, Durham, North Carolina, 27708-0338, USA
gene tree/species tree.
Presentation Type: Symposium
Location: Ballroom 3 (Cliff Lodge)
Date: Wednesday, August 4th, 2004
Time: 9:30 AM