Journal Papers
2023
Barnett, J. R. , Tieman, D. M., and Caicedo, A. L. 2023. Variation in ripe fruit volatiles across the tomato clade: An evolutionary framework for studying fruit scent diversity in a crop wild relative. American Journal of Botany 110(9): e16223. link
Li, X., Zhang, S., Lowey, D., Hissam, C., Clevenger, J., Perera, S., Jia, Y., & Caicedo, A. L. 2023. A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs. Molecular Ecology, 32,5971–5985. link
, , ,,,,,,,,,,,,,,,,, Tillería, S., Ureta, S. Warschefsky, E., and 2023. Building a feral future: Open questions in crop ferality. Plants, People, Planet,1–15. link
, , , , , & (2023). Evidence of fruit syndromes in the recently diverged wild tomato clade opens new possibilities for the study of fleshy fruit evolution. Plants, People, Planet, 1– 15. link
2022
Li, X., Zhang, S., Amaro-Blanco, I., Perera, S., Khandekar*, N. S., Lowey*, D., Osuna, M. D., & Caicedo, A. L. 2022. Multiple compensatory mutations contribute to the de-domestication of Iberian weedy rice. Plants, People, Planet, 4(5), 499–510. link
Jia, Y., Singh, V., Gealy, D., Liu, Y., Ma, J., Thurber, C., Roma-Burgos, N., Olsen, K.M., & Caicedo, A.L. Registration of two rice mapping populations using weedy rice ecotypes as a novel germplasm resource.Journal of Plant Registrations. 16: 162–175. link
2021
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
2020
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 de‐domestication, 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.
2019
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: 343-351. link
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
2018
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. https://doi.org/10.1111/eva.12581
2017
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 Oryza. Molecular 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
2016
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.
2015
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.
2014
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.
2013
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.
2011
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.
2010
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.
2009
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.
2008
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.
2007
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.
2006
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.
2005
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.
2004
Caicedo, A.L. and B.A. Schaal, 2004. Heterogeneous evolutionary processes affect R gene diversity in natural populations of Solanum pimpinellifolium. Proceedings 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 thaliana. Proceedings 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.