Ana L. Caicedo

Assistant Professor of Biology, University of Massachusetts

A. Caicedo Biology Department Web Site
A. Caicedo Lab Homepage

Ph.D.: Washington University, St. Louis
Postdoctoral Training: North Carolina State University

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.

Representative publications:

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.

Kover, P.X. and A.L. Caicedo, 2001. The genetic architecture of disease resistance in plants and the maintenance of recombination by parasites. Molecular Ecology, 10: 1-16.

Caicedo, A.L. and B.A. Schaal, 2004. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology, 13: 1871-1882.

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.

Shimizu, K.K., J.M. Cork, A.L. Caicedo, C.A. Mays, R.C. Moore, K.M. Olsen, S. Ruzsa, G. Coop, C.D. Bustamante, P. Awadalla, and M.D. Purugganan, 2004. Darwinian selection on a selfing locus. Science, 306: 2081-2084.

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. and M.D. Purugganan. 2005. Comparative plant genomics: frontiers and prospects. Plant Physiology, 138: 545-547.

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.