Selected Publications

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Goad, D.M., I. Baxter, E.A. Kellogg, and K.M. Olsen (2020). Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum).  Molecular Ecology, in press.
Vigueira, C.C., P.A. Vigueira, K.M. Olsen, CR Wagner, and ZB Chittick (2020). Weedy rice from South Korea arose from two distinct de-domestication events. Frontiers in Agronomy, 2: 602612. DOI:10.3389/fagro.2020.602612  
Brock, J.R., T. Scott, A.Y. Lee, S.L. Mosyakin, and K.M. Olsen (2020). Interactions between genetics and environment shape Camelina seed oil composition. BMC Plant Biology, 20:423.  DOI:10.1186/s12870-020-02641-8
Waselkov, K.E., N.D. Regenold, R.C. Lum, and K.M. Olsen (2020). Agricultural adaptation of the native North American weed waterhemp, Amaranthus tuberculatus (Amaranthaceae).  PLoS One 15(9): e0238861
Ye, C.-Y, D. Wu, L.-F. Mao, L. Jia, J. Qiu, S. Lao, M. Chen, B. Jiang, W. Tang, Q. Peng, L. Pan, L. Wang, X. Feng, L. Guo, C. Zhang, E.A. Kellogg, K.M. Olsen, L. Bai, and L. Fan  (2020). The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation.  Molecular Plant, 13:1-13.  DOI: 10.1016/j.molp.2020.07.001
Qiu, J., L. Jia, D. Wu, X. Weng, L. Chen, J. Sun, M. Chen, L. Mao, B. Jiang, C. Ye, G. Turra, L. Guo, G. Ye, Q.-H. Zhu, T. Imaizumi, B.-K. Song, L. Scarabel, A. Merotto Jr, K.M. Olsen, and L. Fan (2020). Diverse genetic mechanisms underlie worldwide convergent rice feralization.  Genome Biology 21: 70.  PDF   DOI : 10.1186/s13059-020-01980-x
Li, L.-F. and K.M. Olsen (2020).  Population Genomics of Weedy Crop Relatives: Insights from Weedy Rice.  In: Population Genomics: Crop PlantsOm P. Rajora (ed.). Springer Nature Switzerland AG.   PDF  DOI: 10.1007/13836_2020_77
Goad, D.M., Y. Jia, A. Gibbons, Y. Liu, D.R. Gealy, A.L. Caicedo, and K.M. Olsen (2020).  Identification of novel QTL conferring sheath blight resistance in two weedy rice mapping populations.  Rice 13:21. PDF
Xie, H., Y. Han, X. Li, W. Dai, X. Song, K.M. Olsen, and S. Qiang (2020). Climate-dependent variation in cold tolerance of weedy rice and rice mediated by OsICE1 promoter methylation.  Molecular Ecology 29: 121-137. PDF


Zheng, X.-M., J. Chen, H. Pang, S. Liu, J. Wang , W. Qiao, H. Wang, J. Liu, K. M. Olsen, and Q.Yang (2019). Genome-wide analyses reveal the role of non-coding variation in complex traits during rice domestication. Science Advances 5:eaax3619. DOI: 10.1126/sciadv.aax3619
Ye, C. , W. Tang, D. Wu, L. Jia, J. Qiu, M. Chen, L. Mao, F. Lin, H. Xu, X. Yu, Y. Lu, Y. Wang, K.M. Olsen, M. Timko, and L. Fan (2019). Genomic evidence of human selection on Vavilovian mimicry.  Nature Ecology & Evolution 3: 1474-1482.  PDF
Wedger, M.J., T. Pusadee, A.Wongtamee, and K.M. Olsen (2019). Discordant patterns of introgression suggest historical gene flow into Thai weedy rice from domesticated and wild relatives.  Journal of Heredity 110: 601–609. PDF      
Neik, T.-X., J.-Y. Chai, S.-Y. Tan, M. Sudo, Y. Cui, J. Jayaraj, S.-S. Teo, K.M. Olsen and B.K. Song (2019). When West meets East: the origins and spread of weedy rice between continental and island Southeast Asia.  G3 9: 2941-2950. PDF
Wedger, M.J., C.N. Topp, and K.M. Olsen (2019). Convergent evolution of root system architecture in two independently evolved lineages of weedy rice.  New Phytologist 223: 1031–1042.  PDF
Pusadee, T., A. Wongtamee, B. Rerkasem, K.M. Olsen, and S. Jamjod (2019).  Farmers drive genetic diversity of Thai purple rice (Oryza sativa L.) landraces. Economic Botany 73: 76-85.  PDF
Vigueira, C.C., X.-S. Qi, , B.-K. Song, L.-F. Li, A.L. Caicedo, Y. Jia, and K.M. Olsen (2019). Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evolutionary Applications 12: 93–104. PDF


Guo, L., J. Qiu, L.-F. Li, B. Lu, K. M. Olsen, and L. Fan (2018).  Genomic clues for crop-weed interactions and evolution.  Trends in Plant Science 12:1102-1115.  PDF.
Kooyers, N.J., B.H. Bakken, M.C. Ungerer, and K.M. Olsen (2018). Freeze-induced cyanide toxicity does not maintain the cyanogenesis polymorphism in white clover (Trifolium repens L.).  American Journal of Botany 105: 1-8. PDF
Huang, Z., S. Kelly, R. Matsuo, L.-F. Li , Y. Li , K. M. Olsen, Y. Jia, A.L. Caicedo (2018).  The role of standing variation in the evolution of weediness traits in South Asian weedy rice (Oryza spp.).  G3 8: 3679-3690. PDF
Brock, J.R., A.A. Dӧnmez, M.A. Beilstein, and K.M. Olsen (2018). Phylogenetics of Camelina Crantz. (Brassicaceae) and insights on the origin of gold-of-pleasure (Camelina sativa). Molecular Phylogenetics and Evolution 127: 834-842.  PDF
Olsen, K.M. and L.L. Small (2018). Micro- and macroevolutionary adaptation through repeated loss of a complete metabolic pathway.  New Phytologist 219: 757-766.  PDF
Wedger, M.J. and K.M. Olsen (2018).  Evolving insights on weedy rice. Ecological Genetics and Genomics 7-8: 23-26. PDF
Waselkov, K.E., A. Boleda, and K.M. Olsen (2018).  A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions.  Systematic Botany 43: 439-458.  PDF
Khumto, S., T. Pusadee, K.M. Olsen, and S. Jamjod (2018). Genetic relationships between anther and stigma traits revealed by QTL analysis in two rice advanced-generation backcross populations.  Euphytica 214: 5. PDF
Olsen, K.M. and L.-F. Li (2018). Rooting for new sources of natural rubber. National Science Review 5: 89. PDF 


Zheng, X.-M., T. Gong, H.-L. Ou, D. Xue, W. Qiao, J. Wang, S. Liu, Q. Yang, and K.M. Olsen (2017). Genome-wide association study of rice grain width variation.  Genome 8: 1-8. PDF
Wright, S.J., D. Cui Zhou, A. Kuhle, and K.M. Olsen (2017).  Continent-wide climatic variation drives local adaptation in North American white clover.  Journal of Heredity 109: 78-89.  PDF
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. PDF
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. PDF


Cui, Y., B.K. Song, L.-F. Li, Y.-L. Li, Z. Huang, A.L. Caicedo, Y. Jia, and 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.  PDF
Vigueira, C.C., L.L. Small, and K.M. Olsen (2016). Long-term balancing selection at the Phosphorus Starvation Tolerance 1 (PSTOL1) locus in wild, domesticated, and weedy rice (Oryza).  BMC Plant Biology 16:101. PDF
Muto C., R. Ishikawa, K.M. Olsen, K. Kawano, C. Bounphanousay, T. Matoh, and Y-I. Sato (2016). Genetic diversity of the wx flanking region in rice landraces in northern Laos. Breeding Science, 66: 580-590. PDF
Sudianto, E., T.-X. Neik, S.M. Tam, T. Chuah,  A.A. Idris, K.M. Olsen, and B.K. Song. (2016). Morphological diversity of Malaysian weedy rice (Oryza sativa) and its implications for weed management. Weed Science 64:501–512. PDF
Hokanson, K.E., N.C. Ellstrand, A.G.O. Nixon, H.P. Kulembeka, K.M. Olsen, and A. Raybould (2016). Risk assessment of gene flow from genetically engineered virus resistant cassava to wild relatives in Africa: An expert panel report.  Transgenic Research 25: 71-81. PDF
Li, L.F. and K.M. Olsen (2016). To have and to hold: selection for seed and fruit retention during crop domestication.  Current Topics in Developmental Biology 119: 63-109. PDF
Liu, Y., Y. Jia, D.R. Gealy, D.M. Goad, A.L. Caicedo, and 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: 1001-1008. PDF


Liu, Y., X. Qi, D.R. Gealy, K.M. Olsen, A.L. Caicedo, and Y. Jia (2015). QTL analysis for resistance to blast disease in US weedy rice. Molecular Plant-Microbe Interactions 28: 834-844. PDF
Cervantes-Alcayde, M.A., M.E. Olson, K.M. Olsen, and L.E. Eguiarte (2015). Apparent similarity, underlying homoplasy: morphology and molecular phylogeny of the North American clade of Manihot (Euphorbiaceae).  American Journal of Botany 102: 520-32. PDF
Li, L.F., B. Liu, K.M. Olsen, and J.F. Wendel (2015). Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex.  New Phytologist 208: 11-12. PDF
Li, L.F., B. Liu, K.M. Olsen, and J.F. Wendel (2015). A reevaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D-subgenome.  New Phytologist 208: 4-8. PDF
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. PDF
Liu, Y., X.S. Qi, N.D. Young, K.M. Olsen, A.L. Caicedo, and Y.L. Jia (2015). Characterization of resistance genes to rice blast fungus Magnaporthe oryzae in a "Green Revolution" rice variety.  Molecular Breeding 35: 52. PDF
Olsen, K.M.  Cassava.  In: The Archaeology of Food: An Encyclopedia. (2015). Mary C. Beaudry and Karen Bescherer Metheny, eds. New York: AltaMira/Rowman & Littlefield. 


Olsen, K.M., N.J. Kooyers, and L.L. Small (2014). Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genus Trifolium (Fabaceae).  Philosophical Transactions of the Royal Society B 369: 1648. PDF
Khan, M.A., K.M. Olsen, V. Sovero, M.M. Kushad, and S.S. Korban (2014). Fruit quality traits have played critical roles in domestication of the apple.  Plant Genome, 7: 1-18 PDF.
Kooyers, N.J. and K.M. Olsen (2014). Adaptive cyanogenesis clines evolve recurrently through geographical sorting of existing gene deletions. Journal of Evolutionary Biology 27: 2554–2558. PDF
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 PDF
Waselkov, K.E. and K.M. Olsen (2014). Population genetics and origin of the native North American agricultural weed waterhemp (Amaranthus tuberculatus). American Journal of Botany 101:1726-1737. PDF
Song, B.-K., T.-S. Chuah, S.M. Tam, and K.M. Olsen (2014).  Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia.  Molecular Ecology 23: 5003-5017.  PDF
Larson, G., D.R. Piperno, R. Allaby, M. Purugganan, L. Andersson et al. (2014). Current perspectives and the future of domestication studies.   Proceedings of the National Academy of Sciences 111: 6139-6146.  PDF
       (For the complete PNAS special issue, click here.)
Doust, A.N., L. Lukens, K.M. Olsen, M. Mauro-Herrera, A. Meyer, and K. Rogers (2014).  Beyond the single gene: how epistasis and gene-by-environment effects influence crop domestication.  Proceedings of the National Academy of Sciences USA 111: 6178-6183.  (equal contribution)  PDF  
Kooyers, N.J., L.R. Gage, A. Al-Lozi, and K.M. Olsen (2014). Aridity shapes cyanogenesis cline evolution in white clover (Trifolium repens L.).  Molecular Ecology 23: 1053-1070. doi: 10.1111/mec.12666  PDF
Baudouin, L., B.F. Gunn, and K.M. Olsen (2014). The presence of coconut in southern Panama in pre-Columbian times: clearing up the confusion. Annals of Botany 113: 1-5. doi: 10.1093/aob/mct244  PDF
Olsen, K.M.  (2014). The Evidence of Evolution.  In Oxford Bibliographies in Evolutionary Biology. Ed. Jonathan Losos. New York: Oxford University Press.  


Olsen, K.M. and J.F. Wendel (2013). Crop plants as models for understanding plant adaptation and diversification.  Frontiers in Plant Evolution and Development 4: 290. doi: 10.3389/fpls.2013.00290 PDF
Kooyers, N.J. and K.M. Olsen (2013).  Searching for the bull’s-eye: agents and targets of selection vary among geographically disparate cyanogenesis clines in white clover (Trifolium repens L.). Heredity 111: 495–504. doi: 10.1038/hdy.2013.71 PDF
Vigueira, C.C., W. Li, and K.M. Olsen (2013). The role of Bh4 in parallel evolution of hull color in domesticated and weedy rice. Journal of Evolutionary Biology 26: 1738-49. doi: 10.1111/jeb.12171 PDF
Olsen, K.M. and J.F. Wendel (2013). A bountiful harvest: genomic insights into crop domestication phenotypes.  Annual Review of Plant Biology 64: 47–70. PDF

Olsen, K.M., N.J. Kooyers, and L.L. Small (2013). Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.). Molecular Ecology 22: 724-738. PDF

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: 303-311. PDF


Trejo, L., P. Feria, K.M. Olsen, L.E. Eguiarte, B. Arroyo, J.A. Gruhn, and M.E. Olson (2012). Poinsettia's wild ancestor in the Mexican dry tropics: historical, genetic, and environmental evidence. American Journal of Botany 99: 1146-1157. PDF

Olsen, K.M. (2012). One gene's shattering effects. Nature Genetics 44: 616-617. PDF

Kooyers, N.J. and K.M. Olsen (2012). Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.). Molecular Ecology 21: 2455-2468. PDF


Lee, S., Y. Jia, D.R. Gealy, M. Jia, 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. PDF

Reagon, M., C.S. Thurber, K.M. Olsen, Y. Jia, and 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. PDF

Gunn, B.F., L. Baudouin, and K.M. Olsen (2011). Independent origins of cultivated coconut (Cocos nucifera L.) in the Old World Tropics. PLoS ONE 6: e21143. PDF

Yu, G., K.M. Olsen, and B.A. Schaal (2011). Association between nonsynonymous mutations of Starch Synthase IIa and starch quality in rice (Oryza sativa). New Phytologist 189: 593-601. PDF

Yu, G., K.M. Olsen, and B.A. Schaal (2011). Molecular evolution of endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. Molecular Biology and Evolution 28: 659-671. PDF


Gross, B.L., and K.M. Olsen (2010). Genetic perspectives on crop domestication. Trends in Plant Science 15: 529-537. PDF

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. PDF

Thurber, C., M. Reagon, B.L. Gross, K.M. Olsen, Y. Jia, and A.L. Caicedo (2010). Molecular evolution of shattering loci in US weedy rice. Molecular Ecology 19: 3271-3284. PDF

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. PDF

Gross, B.L., F.T. Steffen, and K.M. Olsen (2010). Molecular basis of white pericarps in African domesticated rice: Novel mutations at the Rc gene. Journal of Evolutionary Biology 23: 2747-2753. PDF


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. PDF

Gross, B.L., K.J. Skare, and K.M. Olsen (2009). Novel Phr1 mutations and the evolution of phenol reaction variation in US weedy rice (Oryza sativa L.). New Phytologist 184: 842-850. PDF


Olsen, K.M. and M.C. Ungerer (2008). Freezing tolerance and cyanogenesis in white clover (Trifolium repens L., Fabaceae). International Journal of Plant Sciences 169: 1141-1147. PDF

Olsen, K.M. and B.L. Gross (2008). Detecting multiple origins of domesticated crops. Proceedings of the National Academy of Sciences USA 105: 13701-13702. PDF

Olsen, K.M., S.-C. Hsu, and L.L. Small (2008). Evidence on the molecular basis of the Ac/ac adaptive cyanogenesis polymorphism in white clover (Trifolium repens L.). Genetics 179: 517-526. PDF

Halsey, M. E., K.M. Olsen, N.J.Taylor and P. Chavarriaga-Aguirre (2008). Reproductive biology of cassava (Manihot esculenta Crantz) and isolation of experimental field trials. Crop Science 48: 49-58. PDF

Hurtado, P., K.M. Olsen, C. Buitrago, C. Ospina, J. Marin, M. Duque, C. de Vicente, P. Wongtiem, P. Wenzel, A. Killian, and M. Fregene (2008). Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz). Plant Genetic Resources 6: 208-214. PDF


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

Caicedo, A.L., S.H. Williamson, 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 (1745-1756). PDF

Olsen, K.M., B.L. Sutherland and L.L. Small (2007). Molecular evolution of the Li/li chemical defence polymorphism in white clover (Trifolium repens L.). Molecular Ecology 16: 4180-4193. PDF

Olsen, K.M. and B.A. Schaal (2007). Insights on the evolution of a vegetatively propagated crop species. Molecular Ecology 16 (14): 2838-2840. PDF

Olsen, K.M., A.L. Caicedo and Y. Jia (2007). Evolutionary genomics of weedy red rice in the USA. Journal of Integrative Plant Biology 49 (6): 811-816. PDF

Narasimhamoorthy, B., J.H. Bouton. K.M. Olsen and M.K. Sledge (2007). Quantitative trait loci and candidate gene mapping of aluminum tolerance in diploid alfalfa. Theoretical and Applied Genetics 114: 901-913. PDF