Plant Molecular Evolution and Evolutionary Genomics
Adaptive evolution, the product of natural selection, underlies much of all biological diversity. My research seeks to understand the genetic basis of adaptation, as well as the population and genomic context in which adaptive evolution occurs. To this effect, research interests in the lab span a range of disciplines, including population genetics, molecular evolution, evolutionary ecology, phylogeography, and evolutionary genomics. We focus on the study of loci contributing to traits of evolutionary or ecological importance and the processes governing diversification within and between closely related plant species. Among the questions we address are: Which are the genes underlying adaptive traits? How is variation at these genes distributed at the population level? What evolutionary forces act on these genes and what are their molecular signatures? What role does the genomic context play in the evolution of ecologically important genes?
Our research makes use of model organisms (e.g. Arabidopsis thaliana), wild relatives of crop species (e.g. Solanum spp., Oryza spp.), and domesticated plant species (e.g. cultivated rice, O. sativa). The process of domestication, in particular, can provide insight into rapid evolution and adaptive responses under strong selection. By comparing domesticated species with their wild and weedy relatives we can learn about the genetic/genomic changes that accompany domestication, and those leading to adaptation in agricultural environments. Understanding of selective processes in the wild can also be gained by studying the wild relatives of domesticated plants; the genetic and genomic resources available for many crop species can inform the search for ecologically relevant genes and the characterization of genomic variation. Current projects in the lab include the molecular evolution of genes associated with weedy phenotypes in red rice (a weedy form of O. sativa) and the identification of genes contributing to diversification and stress tolerance in the wild tomato relative, S. cheesmaniae.
Reagon, M., C.S. Thurber, K.M. Olsen, Y. Jia, A.L. Caicedo. 2011. The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice. Molecular Ecology, 20: 3743-3756.
Thurber, C.S., M. Reagon, B.L. Gross, K.M. Olsen, Y. Jia, and A.L. Caicedo. 2010. Molecular evolution of shattering loci in U.S. weedy rice. Molecular Ecology, 19: 3271-3284.
Reagon, M., C.S. Thurber, B.L. Gross, K.M. Olsen, Y. Jia, and A.L Caicedo. 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology, 10: 180.
Caicedo, A.L., C. Richards, I.M. Ehrenreich, and M.D. Purugganan. 2009. Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster. Molecular Biology and Evolution, 26: 699 - 711.
Caicedo, A.L.*, S.H. Williamson*, R.D. Hernandez, A. Boyko, A. Fledel-Alon, T.L. York, N. Polato, Bustamante, and M.D. Purugganan. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics, 3: 1745-1756. *shared authorship.
Olsen, K.M., A.L. Caicedo, N. Polato, A. McClung, S. McCouch, M.D. Purugganan. 2006. Selection under domestication: Evidence for a sweep in the rice Waxy genomic region. Genetics, 173: 975-983.
Caicedo, A.L. and B.A. Schaal, 2004. Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium. Proc. Natl. Acad. Sci. U.S.A., 101: 17444-17449.
Caicedo, A.L., J.R. Stinchcombe, K.M. Olsen, J. Schmitt and M.D. Purugganan, 2004. Epistatic interaction between the Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. Proc. Natl. Acad. Sci. U.S.A., 101: 15670-15675.
Caicedo, A.L., B.A. Schaal, and B.N. Kunkel, 1999. Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 96: 302-306.