Journal Papers


Huang, Z., J.A. Rodriguez, R. Matsuo, L. Caicedo. Assessing physiological and genetic evidence for weedy rice competitiveness traits at the vegetative growth stage. Frontiers in Agronomy. 3:31. link

Pereira L., M. Sapkota, M. Alonge, Y. Zheng, Y. Zhang, H. Razifard, N.K. Taitano, M.C. Schatz, A.R. Fernie, Y. Wang, Z. Fei, A.L. Caicedo, D.M. Tieman and E. van der Knaap. 2021. Natural Genetic Diversity in Tomato Flavor Genes. Frontiers in Plant Science 12:642828. link

Marden, E, R.J. Abbott, F. Austerlitz,  et al. 2021. Sharing and reporting benefits from biodiversity researchMolecular Ecology 30:11031107. link


 Alonge, M., X. Wang, M. Benoit, S. Soyk, L. Pereira, L. Zhang, H. Suresh, S. Ramakrishnan, F. Maumus, D. Ciren, Y. Levy, T. H. Harel, G. Shalev-Schlosser, Z. Amsellem, H. Razifard, A.L. Caicedo, D.M. Tieman, H. Klee, M. Kirsche, S. Aganezov, T.R. Ranallo-Benavidez, Z.H. Lemmon, J. Kim, G. Robitaille, M. Kramer, S. Goodwin, W.R. McCombie, S. Hutton, J. Van Eck, J. Gillis, Y. Eshed, F.J. Sedlazeck, E. van der Knaap, M.C. Schatz, Z.B. Lippman. 2020. Major impacts of widespread structural variation on gene expression and crop improvement in tomato. Cell 182: 145-161. e23. link

Goad, D.M., Y. Jia, A. Gibbons, Y. Liu, D. Gealy, A.L. Caicedo, K.M. Olsen. 2020. Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations. Rice. 13, 1-10. link

 Hoyos, V., G. Plaza, X. Li, A.L. Caicedo. 2020. Something old, something new: Evolution of Colombian weedy rice (Oryza spp.) through de novo dedomestication, exotic gene flow, and hybridization. Evolutionary Applications. link

Razifard, H., A. Ramos, A.L. Della Valle, C. Bodary, E. Goetz, E.J. Manser, X. Li, L. Zhang, S. Visa, D. Tieman, E. van der Knaap, and A.L. Caicedo. 2020. Genomic evidence for complex domestication history of the cultivated tomato in Latin America. Molecular Biology and Evolution, 37: 1118-1132. link

Check out the press coverage this paper received at The Boston Globe, El País, Der Taggesspiegel, Cosmos Magazine, The Conversation, and many others.


Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J. et al. One thousand plant transcriptomes and the phylogenomics of green plants. 2019. Nature 574, 679–685. doi:10.1038/s41586-019-1693-2 link

Bagavathiannan, M., S. Graham, Z. Ma, J. Barney, S. Coutts, A.L. Caicedo, R. De Clerck-Floate, N. West, L. Blank, A. Metcalf, M. Lacoste, C. Moreno, J. Evans, I. Burke, and H. Beckie. 2019. Considering Weed Management as a Social Dilemma Bridges Individual and Collective Interests. Nature Plants, 5: 343-351link

Hoyos, V., G. Plaza, A.L. Caicedo. 2019. Characterization of the phenotypic variability in Colombian weedy rice (Oryza spp.). Weed Science, 67(4), 441-452. doi:10.1017/wsc.2019.18 link


Huang, Z., S. Kelly, R. Matsuo, L.F. Li, Y. Li, K.M. Olsen, Y. Jia, and A.L. Caicedo. 2018. The role of standing variation in the evolution of weediness traits in South Asian weedy rice (Oryza spp.). G3: Genes, Genomes, Genetics, 8: 3679-3690.

Vigueira, C.C., X. Qi, B.-K. Song, L.-F. Li, A.L. Caicedo, Y. Jia, K.M. Olsen. 2018. Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications 00:1–12.


Gordon, S.P., B. Contreras-Moreira, D.P. Woods, D.L. Des Marais, D. Burgess, S. Shu, C. Stritt, A.C. Roulin, W. Schackwitz, L. Tyler, J. Martin, A. Lipzen, N. Dochy, J. Phillips, K. Barry, K. Geuten, H. Budak, T.E. Juenger, R. Amasino, A.L. Caicedo, D. Goodstein, P. Davidson, L.A.J. Mur, M. Figueroa, M. Freeling, P. Catalan, J.P. Vogel. 2017. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications, 8: 2184.

Huang, Z. N.D. Young, M. Reagon, K.E. Hyma, K.M. Olsen, Y. Jia, and A. L. Caicedo. 2017. All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian OryzaMolecular Ecology. 26: 3151-3167.

Li, L-F., Y.-L. Li, Y. Jia, A.L. Caicedo*, and K.M. Olsen*. 2017. Signatures of adaptation in the weedy rice genome. Nature Genetics 49:811-814. *co-corresponding authors


Tyler, L., S.J. Lee, N.D. Young, G.A. DeIulio, E. Benavente, M. Reagon, J. Sysopha, R.M. Baldini, A. Troìa, S.P. Hazen, and A.L. Caicedo. 2016. Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. Plant Genome, 9. doi: 10.3835/plantgenome2015.08.0074

Cui, Y., B.K. Song, L.F. Li, Y.L. Li, Z. Huang, A.L. Caicedo, Y. Jia, K.M. Olsen. 2016. Little white lies: pericarp color provides insights into the origins and evolution of Southeast Asian weedy rice. G3, 6: 4105-4114.

Singh, V., N.R. Burgos, S. Singh, D.R. Gealy, E.E. Gbur, A.L. Caicedo. 2016. Impact of volunteer rice infestation on yield and grain quality of rice. Pest Management Science. Doi: 10.1002/ps.4343

Liu, Y., Y. Jia, D. Gealy, D.M. Goad, A.L. Caicedo, K.M. Olsen. 2016. Marker development for rice blast resistance gene Pi66(t) and application in the USDA rice mini-core collection. Crop Science. 56: 1-8.


López-Alvarez, D., Manzaneda, A.J., Rey, P.J., Giraldo, P., Benavente, E., Allainguillaume, J., Mur, L., Caicedo, A.L., Hazen, S.P., Breiman, A., Ezrati, S., Catalán, P. (2015) Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range. American Journal of Botany,102: 1–16.

Qi, X.-S., Y. Liu, C.C. Vigueira, N.D. Young, A.L. Caicedo, Y. Jia, D.R. Gealy, and K.M. Olsen. 2015. More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms. Molecular Ecology, 24: 3329–3344.

Liu, Y., X. Qi, D.R. Gealy, K.M. Olsen, A.L. Caicedo, and Y. Jia. 2015. QTLs analysis for resistance to blast disease in US weedy rice. Molecular Plant-Microbe Interactions, 28: 834-844.

Ziska, L.H., D.R. Gealy, N.R. Burgos, A.L. Caicedo, J. Gressel, A.L. Lawton-Rauh, L.A. Avila, G. Theisen, J. Norsworthy, A. Ferrero, F. Vidotto, D.E. Johnson, F.G. Ferreira, E. Marchesan, V. Menezes, M.A. Cohn, S. Linscombe, L. Carmona, R. Tang and A. Merotto, Jr. 2015. Weedy (Red) Rice: An Emerging Constraint to Global Rice Production. Advances in Agronomy, 129: 181-228.

Liu, Y., X. Qi, N.D. Young, K.M. Olsen, A.L. Caicedo, and Y. Jia.2015. Characterization of resistance genes to rice blast fungus Magnaporthe Oryzae in a “Green revolution” rice variety. Molecular Breeding. 35: 52.


Burgos, N.R., V. Singh, T.M. Tseng, H. Black, N. D. Young, Z. Huang, K.E. Hyma, D. R. Gealy, and A.L. Caicedo. 2014. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of U.S. weedy rice. Plant Physiology. 166: 1208-1220.

Thurber, C.S., M. Reagon, K.M. Olsen, Y. Jia, and A.L. Caicedo. 2014. The evolution of flowering strategies in US weedy rice. American Journal of Botany, 101:1737-1747.

Craig, S., M. Reagon, L. Resnick and A.L. Caicedo. 2014. Allele distributions at hybrid incompatibility loci facilitate the potential for gene flow between cultivated and weedy rice in the US. PLOS One. 9(1): e86647.


Vigueira, C.C., K.M. Olsen, and A.L. Caicedo. 2013. The red queen in the corn: Agricultural weeds as models of rapid adaptive evolution. Heredity, 110: 301-311.

Thurber, C.S., M.H. Jia, Y. Jia, and A.L. Caicedo. 2013. Similar traits, different genes? Examining convergent evolution in related weedy rice populations. Molecular Ecology, 22: 685–698.


Lee, S., Y. Jia, M. Jia, D.R. Gealy, K.M. Olsen, and A.L. Caicedo. 2011. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA. PLos ONE, 6: e26260.

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.

Hyma, K.E. and A.L. Caicedo. 2011. Shedding light on the evolution of plasticity in natural populations. Molecular Ecology, 20: 3491-3493.

Brkljacic J., Grotewold E., Scholl R., Mockler T., Garvin D.F., Vain .P, Brutnell T., Sibout R., Bevan M., Budak H., Caicedo A.L., Gao C., Gu Y., Hazen S.P., Holt III B.F., Hong S-Y, Jordan M., Manzaneda A.J., Mitchell-Olds T., Mochida K., Mur L.A.J., Park C-M, Sedbrook J., Watt M., Zheng S.J., Vogel J.P. 2011. Brachypodium as a model for the grasses: Today and the future. Plant Physiology, 157: 3-13.

Thurber, C.S., P.K. Hepler, and A.L. Caicedo. 2011. Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice. BMC Plant Biology, 11: 14.


Mather, K.A., J. Molina, J.M. Flowers, S. Rubinstein, B.L. Rauh, A. Lawton-Rauh, A.L. Caicedo, K.L. McNally, and M.D. Purugganan. 2010. Migration, isolation and hybridization in island populations: The case of Madagascar rice. Molecular Ecology, 19: 4892-4905.

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.

Gross, B.L., M. Reagon, S.C. Hsu, A.L. Caicedo, Y. Jia, and K.M. Olsen. 2010. Seeing red: the origin of grain pigmentation in US weedy rice. Molecular Ecology, 19: 3380-3393.

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.


Lee, S, S. Costanzo, Y. Jia, K.M. Olsen, and A.L. Caicedo. 2009. Evolutionary dynamics of the genomic region around the blast resistance gene Pi-ta in AA genome Oryza species. Genetics, 183. 1315-1325.

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. 2008. Geographic diversity cline of R gene homologs in wild populations of Solanum pimpinellifolium (Solanaceae). American Journal of Botany, 95: 393-398.


Mather, K.A., A.L. Caicedo, N.R. Polato, K.M. Olsen, S. McCouch and M.D. Purugganan. 2007. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics. 177: 2223–2232.

Caicedo, A.L.*, S.H. Williamson*, R.D. Hernandez, A. Boyko, A. Fledel-Alon, T.L. York, N. Polato, K.M. Olsen, R. Nielsen, S. McCouch, C.D. Bustamante, and M.D. Purugganan. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics 3: e163. *shared authorship

Olsen, K.M., A.L. Caicedo, and Y. Jia. 2007. Evolutionary genomics of weedy rice in the U.S.A. Journal of Integrative Plant Biology 49, 811-816.

Korves, T.M., K.J. Schmid, A.L. Caicedo, C. Mays, J.R. Stinchcombe, M.D. Purugganan, and J. Schmitt. 2007. Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. American Naturalist 169, E141-E157.


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.


Stinchcombe, J.R., A.L. Caicedo, R. Hopkins, C. Mays, M.D. Purugganan, and J. Schmitt. 2005. Vernalization sensitivity in Arabidopsis thaliana: the effects of latitude and FLC variation. American Journal of Botany 92: 1701-1707.

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


Caicedo, A.L. and B.A. Schaal, 2004. Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifoliumProceedings of the National Academy of Sciences USA 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. Proceedings of the National Academy of Sciences USA 101: 15670-15675.

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.

1999 – 2003

Schaal, B.A., J.F. Gaskin, and A.L. Caicedo, 2003. Phylogeography, haplotype trees, and invasive plant species. Journal of Heredity 94: 197-204.

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., B.A. Schaal, and B.N. Kunkel, 1999. Diversity and molecular evolution of the RPS2 resistance gene in Arabidopsis thalianaProceedings of the National Academy of Sciences USA 96: 302-306.

Caicedo, A.L., E. Gaitan, M.C. Duque, O.Toro, D.G. Debouck, J.Tohme, 1999. AFLP fingerprinting of Phaseolus lunatus L. and related wild species from South America. Crop Science 39: 1497-1507.

Book Chapters

Labate, J.A., S. Grandillo, T. Fulton, S. Muños, A.L. Caicedo, I. Peralta, Y. Ji, R.T. Chetelat, et al. (39 authors in total). 2007. Tomato. p.1-125. In C. Kole (ed.) Genome mapping and molecular breeding in plants: Volume 5 Vegetables. Springer Publishing Co., NY.

Caicedo, A.L. and I. Peralta. 2012. Basic information on the plant. In B. Liedl, J. Labate, J. Stommel, A. Slade, S. Hurst (ed.) Tomato (Genomics of Fruit and Vegetable Crops series), Science Publishers, NH.