Publications

Gupta, S., Groen, S.C., Zaidem, M.L, Sajise, A.G.C., Calic, I., Natividad, M.A., McNally, K.L, Vergara, G.V., Satija, R., Franks, S.J, Singh, R.K., Joly-Lopez, Z., and Purugganan, M.D. (2024) Systems genomics of salinity stress response in rice. Elife. Doi.10.1101/2024.05.31.596807.

Alam, O. and Purugganan, M.D. (2024) Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. The Plant Cell. Doi.10.1093/plcell/koae013.

Hamann, Groen, E.S.C, Ćalić, I., Cochran, C., Konshok, R., Purugganan, M.D., and Franks, S.J. (2024) Fitness costs and benefits of gene expression plasticity in rice under drought. Molecular Ecology. Doi.10.1101/2021.03.16.435597.

Gutaker, R.M. and Purugganan, M.D. (2023). Adaptation and the Geographic Spread of Crop Species. Annual Review of Plant Biology. Doi.org.10.1146/annurev-arplant-060223-030954. Download

He Q., Tang S., Zhi H., Chen J., Zhang J., Liang H., Alam O., Li H., Zhang H., Xing L., Li X., Zhang W., Wang H., Shi J., Du H., Wu H., Wang L., Yang P., Xing L., Yan H., Song Z., Liu J., Wang H., Tian X., Qiao Z., Feng G., Guo R., Zhu W., Ren Y., Hao H., Li M., Zhang A., Guo E., an F., Li Q., Liu Y., Tian B., Zhao X., Jia R., Feng B., Zhang J., Wei J., Lai J., Jia G., Purugganan, M.D. & Diao X. (2023). A graph-based genome and pan-genome variation of the model plant Setaria. Nature Genetics. Doi.org/10.1038/s41588-023-01423-w. Download

Castanera, R., Morales-Díaz, N., Gupta, S., Purugganan, M.D., Casacuberta, J.M. (2023). Transposons are a major contributor to gene expression variability under selection in rice populations. eLife. Doi .org/10.7554/eLife.86324. Download

Molina, J., Wicaksono A., Michael T.P., Kwak S.H., Pedales R.D., Joly-Lopez Z., Petrus S., Mamerto A., Tomek B., Ahmed S., Maddu V., Yakubova K., Tandang D., Morin J.W., Park S.Y., Lee H.O., McLaughlin W., Wallick K., Adams J., Novy A., Pell, S., Purugganan M.D. (2023). The seed transcriptome of Rafflesia reveals horizontal gene transfer and convergent evolution: Implications for conserving the world's largest flower. Plants, People, Planet. 1-19. Doi.org/10.1002/ppp3.10370. Download

Lye Z., Choi, J.Y., Purugganan M.D. (2022). Deleterious Mutations and the Rare Allele Burden on Rice Gene Expression. Molecular Biology and Evolution. 39 (9). Doi.org/10.1093/molbev/msac193 Download

Gros-Balthazard, M., Battesti, V., Flowers, J. M., Ferrand, S., Breil, M., Ivorra, S., Terral, J.-F., Purugganan, M. D., Wing, R. A., Mohammed, N., and Bourgeois, Y. (2022). What lies behind a fruit crop variety name? A case study of the barnī date palm from al-‘Ulā oasis, Saudi Arabia. Plants, People, Planet. 1-16. Doi.org/10.1002/ppp3.10326 Download

Sudalaimuthuasari, N., Ali, R., Kottackal, M., Rafi, M., Al Nuaimi, M., Kundu, B., Al-Maskari, R. S., Wang, X., Mishra, A. K., Balan, J., Chaluvadi, S. R., Al Ansari, F., Bennetzen, J. L., Purugganan, M. D., Hazzouri, K. M., Amiri, K. M. A. (2022). The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree. Int J Mol Sci. 23(15):8503 Doi.org/10.3390/ijms23158503 Download

Hazzouri, M. K., Sudalaimuthuasari, N., Saeed, E. E., Kundu, B., Al-Maskari, S. R., Nelson, D., AlShehhi, A. A., Aldhuhoori, A. M., Almutawa, S. D., Alshehhi, R. F., Balan, J., Mundra, S., Alam, M., Salehi-Ashtiani, K., Purugganan, M. D. and Amiri, K. (2022). Salt flat microbial diversity and dynamics across salinity gradient. Scientific Reports 12, 11293 Doi.org/10.1038/s41598-022-15347-8 Download

Andersson, L. and Purugganan, M. (2022). Molecular genetic variation of animals and plants under domestication. PNAS 119 (30) e2122150119 Doi.org/10.1073/pnas.2122150119 Download

Ćalić, I., Groen, S.C., Choi, J.Y, Joly-Lopez, Z., Hamann, E., Natividad, M.A., Dorph, K., Cabral, C.L.U., Torres, R.O., Vergara, G.V., Henry, A., Purugganan, M.D. and Franks, S.J. (2022). The influence of genetic architecture on responses to selection under drought in rice. Evolutionary Applications 00:1–21 Doi.org/10.1111/eva.13419 Download

Purugganan, M. D. (2022). What is domestication? Trends in Ecology and Evolution 2996 Doi.org/10.1016/j.tree.2022.04.006 Download

Flowers, J.M., Hazzouri, K. M., Lemansour, A., Capote, T., Gros-Balthazard, M., Ferrand, S., Lebrun, M., Amiri, K. M. A. and Purugganan, M. D. (2022). Patterns of volatile diversity yield insights into the genetics and biochemistry of the date palm fruit volatilome. Frontiers Plant Sci 13:853651 Doi.org/10.3389/fpls.2022.853651 Download

Groen, S.C., Joly-Lopez, Z., Platts, A. E., Natividad, M., Fresquez, Z., Mauck, W. M., Quintana, M., Cabral, C. L. U., Torres, R. O., Satija, R., Purugganan, M. D., and Henry, A. (2022). Evolutionary systems biology reveals polygenic patterns of rice adaptation to drought-prone agro-ecosystems. Plant Cell 34: 759–783 Doi.org/10.1093/plcell/koab275 Download

Purugganan, M. (2022). Vavilov’s law and phenotypes across species. Nature Reviews Genetics Doi.org/10.1038/s41576-022-00464-x Download

Kurbidaeva, A., Purugganan, M. (2021). Insulators in plants: progress and open questions. Genes 12 (9): 1422 Doi.org/10.3390/genes12091422 Download

Choi, J.Y., Dai, X., Alam, O., Peng, J.Z., Rughani, P., Hickey, S., Harrington, E., Juul, S., Ayroles, J.F., Purugganan, M., Stacy, E.A. (2021). Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands. Proc. Natl. Acad. Sci. USA 118 (37): e2023801118 Doi.org/10.1073/pnas.2023801118 Download

Alam, O., Gutaker, R., Wu, C., Hicks, K., Bocinsky, K., Castillo, C., Acabado, S., Fuller, D., Guedes, J., Hsing, Y., Purugganan, M. (2021). Genome analysis traces regional dispersal of rice in Taiwan and Southeast Asia. Molecular Biology and Evolution Doi.org/10.1093/molbev/msab209 Download

Gros-Balthazard, M., Flowers, J. (2021). A brief history of the origin of domesticated date palms. The Date Palm Genome. Compendium of Plant Genomes 1: 55-74 Download

Pérez-Escobar, O., Bellot, S., Przelomska, N., Flowers, J., Nesbitt, M., Ryan, P., Gutaker, R., Gros-Balthazard, M., Wells, T., Kuhnhäuser, B., Schley, R., Bogarín, D., Dodsworth, S., Diaz, R., Lehmann, M., Petoe, P., Eiserhardt, W., Preick, M., Hofreiter, M., Hajdas, I., Purugganan, M., Antonelli, A., Gravendeel, B., Leitch, I., Jimenez, M.F., Papadopulos, A., Chomicki, G., Renner, S., Baker, W. (2021). Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Molecular Biology and Evolution Doi.org/10.1093/molbev/msab188 Download

Gros-Balthazard, M., Flowers, J. M., Hazzouri, K. M., Ferrand, S., Aberlenc, F., Sallon S., and M. D. Purugganan (2021). The genomes of ancient date palms germinated from 2,000 y old seeds. Proc. Natl. Acad. Sci. USA 118 (19): e2025337118 Doi.org/10.1073/pnas.2025337118 Download

Purugganan, M.D. and S. A. Jackson (2021). Advancing crop genomics from lab to field. Nature Genetics 53: 595-601 Doi.org/10.1038/s41588-021-00866-3 Download

Choi, J.Y., L. R Abdulkina, J. Yin, I. B. Chastukhina, J. T. Lovell, I. A. Agabekian, P. G. Young, S. Razzaque, D. E. Shippen, T. E. Juenger, E. V. Shakirov and M. D. Purugganan (2021). Natural variation in plant telomere length is associated with flowering time. Plant Cell 0: 1–17 Doi.org/10.1093/plcell/koab022 Download

Capote, T. C., J. M. Flowers, K. M. Hazzouri, M.D. Purugganan and K.A. Amiri (2021). The genomics of date palms: current perspectives. Annual Plant Reviews Online 4: 57-86 Doi.org/10.1002/9781119312994.apr0748 Download

Hamann, E., C. S. Pauli, Z. Joly-Lopez, S. C. Groen, J. S. Rest, N. C. Kane, M. D. Purugganan and S. J. Frank (2020). Rapid evolutionary changes in gene expression in response to climate fluctuations. Mol. Ecol. 30(1): 193-206 Doi.org/10.1111/mec.15583 Download

Hinojosa-Alvarez, S., S. Arias, S. Ferrand, M. D. Purugganan, J. Rozas, U. Rosas and Ana Wegier (2020). The chloroplast genome of the pincushion cactus Mammilllaria haageana subsp. san-angelensis, a Mexican endangered species. Mitochondrial DNA B 5: 2038-2039 Download

Gutaker, R.M. S. C. Groen, E. S. Bellis, J. Y. Choi, I. S. Pires, R. K. Bocinsky, E. R. Slayton, O. Wilkins, C. C. Castillo, S. Negrao, M. M. Oliveira, D. Q. Fuller, J. A. d’Alpoim Guedes, J. R. Lasky, M. D. Purugganan (2020). Genomic history and ecology of the geographic spread of rice. Nature Plants 6: 492–502 Download

Shin, D., S. Lee, T.-H. Kim, J.-H. Lee, J. Park, J. Lee, J. Y. Lee, L.-H. Cho, J. Y. Choi, W. Lee, J.-H. Park, D.-W. Lee., H. Ito, D. H. Kim, A. Tanaka, J.-H. Cho, Y.-C. Song, D. Hwang, M. D. Purugganan, J.-S. Jeon, G. An and H. G. Nam (2020). Natural variation at the Stay-Green gene promoter control lifespan and yield in rice cultivars. Nature Communications 11: 2819 Download

Choi, J.Y., Z. N. Lye, S. C. Groen, X. Dai, P. Rughani, S. Zaaijer, E. D. Harrington, S. Juul and M. D. Purugganan (2020). Nanopore-based genome assembly and the evolutionary genomics of circum-basmati rice. Genome Biol. 21: 21 Download

Read, A.C., M. J. Moscou, G. Pertea, A. V. Zimin, R. S. Meyer, M. D. Purugganan, L. R. Triplett, S. L. Salzberg, and A. J. Bogdanove (2020). Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with nanopore sequencing. PLoS Genetics 16: e1008571 Download

Choi, J.Y., M.D. Purugganan and E. A. Stacy (2020). Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii Island. Mol. Biol. Evol. 37: 695–710 Download

Joly-Lopez, Z., A. E. Platts, B. Gulko, J. Y. Choi, S. C. Groen, X. Zhong, A. Siepel and M. D. Purugganan (2020). An inferred fitness consequence map of the rice genome. Nature Plants 6: 119–130 Download

Groen, S.C., I. Ćalić, Z. Joly-Lopez, A. Platts, M. Aquino, K. Dorph, W. M. Mauck, B. Bracken, C. L. Cabral, J. Y. Choi, A. Kumar, R. O. Torres, R. Satija, G. Vergara, A. Henry, S. J. Franks and M. D. Purugganan (2020). The strength and pattern of natural selection on gene expression in rice. Nature 578: 572–576 Download

Hazzouri, K.M., M. Gros-Balthazard, J. M. Flowers, D. Copetti, A. Lemansour, M. Lebrun, K. Masmoudi, S. Ferrand, M. I. Dhar, Z. Fresquez, U. Rosas, J. Zhang, J. Talag, S. Lee, D. Kudrna, R. Powell, I. Leitch, R. Krueger, R. Wing, K. M. Amiri and M. D. Purugganan (2019). Genome-wide association mapping of date palm fruit traits. Nature Communications 10: 4680 Download

VanBuren, R., Paris, M., Wai, J., Zhang, J., Huang, L., Zhou, H., Wang, H., Hwa, T., Kao, S., Choi, J., Liao, Z., Lin, Z., Wang, L., Zhang, X., Yue, J., Sharma, A., Singh, R., Song, J., Yim, W., Cushman, J., Paull, R., Matsumoto, T., Qin, Y., Wu, Q., Wang, J., Yu, Q., Wu, J., Zhang, S., Boches, P., Tung, C., d’Eeckenbrugge, G., Sanewski, G., Purugganan, M.D., Bennetzen, J., Lexer, C., Ming, R. (2019). The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics 51: 1549-1558 Download

Purugganan, M.D. (2019). Evolutionary insights into the nature of plant domestication. Current Biology 29: R705-R714 Download

Choi, J.Y., M. Zaidem, K. Dorph, R. Gutaker, R.K. Singh and M.D. Purugganan (2019). The complex geography of domestication of the African rice Oryza glaberrima. PLoS Genetics 15(3): e1007414 Doi.org/10.1371/journal.pgen.1007414 Download

Lye, Z.N. and M.D. Purugganan (2019). Copy number variation in domestication. Trends Plant Sci. 24: 352-365 Download

Flowers, J.M., K. M. Hazzouri, M. Gros-Balthazard, Z. Mo, K. Koutroumpa, A. Perrakis, S. Ferrand, H. Khierallah, D. Q. Fuller, F. Aberlenc, C. Fournaraki and M. D. Purugganan (2019). Cross-species hybridization and the origin of North African date palms. Proc. Natl. Acad. Sci. USA. 116: 1651-1658 Download

Zaidem, M., S. C. Groen and M.D. Purugganan (2019). Evolutionary and ecological functional genomics, from lab to the wild. The Plant Journal 97: 40-55 Download

Wing, R.A., M.D. Purugganan and Q. Zhang (2018). Rice genome revolution: from an ancient grain to green super rice. Nature Reviews Genetics 19: 505-517 Download

Hazzouri, K., D. Pauli, D., T. Blake, M. Shahid, B. Khraiwesh, K. Salehi-Ashtiani, K. Amiri, M. Purugganan and K. Masmoudi (2018). Mapping of HKT1;5 gene in barley using GWAS approach and its implication in salt tolerance mechanism. Frontiers Plant Sci. 9: 156 Download

Choi, J.Y. and M.D. Purugganan (2018). Multiple origin but single domestication led to Oryza sativa. G3 8: 797-803 Download

Choi, J.Y. and M.D. Purugganan (2018). Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice. Mol. Biol. Evol. 35: 365-382 Download

Choi, J. Y., A. Platts, D.Q. Fuller, Y.-L. Hsing, R. Wing and M.D. Purugganan (2017). The rice paradox: Multiple origins but single domestication in Asian rice. Mol. Biol. Evol . 34: 969–979 Download

Groen, S.C. and M.D. Purugganan (2016). Systems genetics of plant adaptation to environmental stresses. Amer. J. Botany 103: 2019-2021 Download

van Andel, T.R., R. S. Meyer, S. A. Aflitos, J. A. Carney, M. A. Veltman, D. Copetti, J. M. Flowers, R. M. Havinga, H. Maat, M. D. Purugganan, R. A. Wing, M. E. Schranz (2016). Tracing ancestor rice of Suriname Maroons back to its African origin. Nature Plants 2: 16149 Doi:10.1038/nplants. 2016.149 Download

Wilkins, O., C. Hafemeister, A. Plessis, M. Holloway-Phillips, G. Pham, A. B. Nicotra, G. B. Gregorio, S.V. K. Jagadish, E. M. Septiningsih, R. Bonneau, and M.D. Purugganan (2016). EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments. Plant Cell 28: 2365-2384 Download

Yuan, W. J. Flowers, D. Sahraie, and M. D. Purugganan (2016). Cryptic genetic variation for Arabidopsis thaliana seed germination speed in a novel salt stress environment. G3 6(10): 3129–3138 Doi: 10.1534/g3.116.033944 Download

Meyer, R. J.Y. Choi, J.Y., M. Sanches, A. Plessis, J. M. Flowers, J. Amas, K. Dorph, A. Barretto, B. Gross, D. Q. Fuller, I. K. Bimpong, M. Ndjiondjop, K.M. Hazzouri, G. Gregorio and M. D. Purugganan (2016). Domestication history and geographic adaptation inferred from a SNP map of African rice. Nature Genetics 48: 1083–1088 Download

Yuan, W. J. Flowers, D. Sahraie, I. Ehrenreich and M. D. Purugganan (2016). Extreme QTL mapping of germination speed in Arabidopsis thaliana. Mol. Ecol. 25: 4177–4196 Download

Casacuberta, J.M., S. Jackson, O. Panaud, M.D. Purugganan and J. Wendel (2016). Evolution of plant phenotypes, from genomes to traits. G3 6: 775-778 Download

Joly-Lopez, Z., Flowers, J.M. and M.D. Purugganan (2016). Developing maps of fitness consequences for plant genomes. Curr. Opinion Plant Biol 30: 101-107 Download

Rest, J., Wilkins, O., Yuan, W., Purugganan, M. and Gurevitch, J. (2016). Meta-regression of transcriptomic response to water stress in Arabidopsis. Plant Journal 85: 548-560 Download

Plessis, A., O. Wilkins, C. Hafemeister, Z. Gonzaga, R. Meyer, I. Pires, C. Muller, G. Gregorio, E. Septiningsih, R. Bonneau, M. D. Purugganan (2015). Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions. ELife 4: e08411 Download

Hazzouri, K.M., J.M. Flowers, J. Visser, H.S.M. Khierallah, U. Rosas, Z. Fresquez, G.M. Pham, R.S. Meyer, G.S. Markhand, N. Haider, N. Kadri, Y. Idaghdhour, J. Malek, D. Thirkhill, R. Kruegger, A.W. Zayed and M.D. Purugganan (2015). Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nature Communications 6: 8824 Doi: 10.1038/ncomms9824 Download

Pires, I., S. Negrao, M.M.Oliveira, M.D. Purugganan (2015). Comprehensive phenotypic analysis of rice (Oryza sativa L.) response to salinity stress. Physiologia Plantarum 155: 43-54 Download

Flowers, J.M., K.M. Hazzouri, G.M. Pham, U. Rosas, T. Bahmani, B. Khraiwesh, E. Harris, P. Lefebvre, E. Hom, K. Salehi-Ashtiani and M.D. Purugganan (2015). Whole genome re-sequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. Plant Cell 27: 2353-2369 Download

Li, S.I., N. Buttery, C. Thompson, M.D. Purugganan (2014). Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum. BMC Genomics 15: 616 Doi: 10.1186/1471-2164-15-616 Download

Gerbault, P., R. Allaby, N. Boivin, A. Rudzinski, I. Grimaldi, J. C. Pires, C. C. Vigueira, K. Dobney, K. J. Gremillion, L. Barton, M. Arroyo-Kalin, M. Purugganan, R. Rubio de Casas, R. Bollongino, J. Burger, D. Q. Fuller, D. G. Bradley, D. J. Balding, P. Richerson, M. T. P. Gilbert, G. Larson, M. G. Thomas (2014). Story telling and story testing in domestication. Proc. Natl. Acad. Sci. USA 111: 6159-6164 Download

Larson, G., D. Piperno, R. Allaby, M.D. Purugganan, L. Andersson, M. Arroyo-Kalin, C. Climer, T. Denham, K. Dobney, A. Doust, P. Gepts, T. Gilber, K. Gremillion, L. Lucas, L. Lukens, F. Marshall, K. Olsen, J. C. Pires, P. Richerson, R.R. de Casas, O. Sanjur, M. Thomas and M.J. West-Eberhard, D. Q. Fuller (2014). Current perspectives and the future of domestication studies. Proc. Natl. Acad. Sci. USA 111: 6139-6146 Download

Molina, J., K. M. Hazzouri, D. Nickrent, M. Geisler, R. Meyer, M. Pentony, J. M. Flowers, P. Pelser, J. Barcelona, S. A. Inovejas, I. Uy, W. Yuan, O. Wilkins, C.I. Michel. S. Locklear, G. P. Concepcion, and M. D. Purugganan (2014). Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae. Mol. Biol. Evol. 31: 798-803 Download

U. Rosas, Y. Mei, Q. Xie, J. Banta, R. Zhou, G. Seufferheld, S. Gerard, L. Chou, N. Bhambra, J.D. Parks, J.M. Flowers, C. Robertson McClung, Y. Hanzawa and M.D. Purugganan (2014). Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS. Nature Comm. 5: 3651 Doi 10.1038/ncomms4651 Download

Fuller, D., T. Denham, M. Arroyo-Kalin, L. Lucas , C. Stevens, L. Qin, R. Allaby, and M. D. Purugganan (2014). Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc. Natl. Acad. Sci. USA 111: 6147-6152 Download

Hazzouri, K.M., J.M. Flowers and M.D. Purugganan (2014). Population genomics of plant species. In: Advances in Botanical Research: Genomics of Herbaceous Land Plants (Editor: A.H. Paterson) Elsevier Download

Meyer, R.M. and M.D. Purugganan (2013). Evolution of crop species: Genetics of domestication and diversification. Nature Reviews Genetics 14: 840–852 Download

Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, Qi XT, Guo XS, Zhang L, He WM, Chang RZ, Liang QS, Guo Y, Ye C, Wang XB, Tao Y, Guan RX, Wang JY, Liu YL, Jin LG, Zhang XQ, Liu ZX, Zhang LJ, Chen J, Wang KJ, Nielsen R, Li RQ, Chen PY, Li WB, Reif JC, Purugganan M, Wang J, Zhang MC, Wang J, Qiu LJ. (2013). Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14: 579 Download

Rosas, U., A. Cibrian-Jaramillo, D. Ristova, J. Banta, M. Gifford, A. Fan, R. W. Zhou, G. Krouk, K. D. Birnbaum, M. D. Purugganan, and G. Coruzzi (2013). Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. Proc. Natl. Acad. Sci. USA 110: 15133-15138 Download

Gifford, M.L., J. Banta, M. S. Katari, J. Hulsmans, L. Chen, D. Ristova, D. Tranchina, M. D. Purugganan, G. M. Coruzzi and K. D. Birnbaum (2013). Plasticity regulators modulate specific root traits in discrete nitrogen environments. Plos Genetics 9: e1003760 Download

Thanawala, S. J. Rister, G. Goldberg, A. Zuskov, E. C. Olesnicky, J. M. Flowers, M. D. Purugganan, E. R. Gavis, C. Desplan and R. Johnston (2013). Regional modulation of a stochastically expressed factor determines ommatidial subtypes in the Drosophila retina. Developmental Cell 25: 93-105 Download

Pires, I., S. Negrao, M.M. Pentony, I.A. Abreu, M.M. Oliveira and M.D. Purugganan (2013). Different evolutionary histories of two cation/proton exchanger gene families in plants. BMC Plant Biol. 13:97 Download

Huang, P., J. Molina, J. M. Flowers, S. A. Jackson, M.D. Purugganan and B. A. Schaal (2012). Phylogeography of Asian wild rice, Oryza rufipogon: A genome-wide view. Mol. Ecol. 21: 4593–4604 Download

Pentony, M, P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau, M.D. Purugganan (2012). The Plant Proteome Folding Project: Structure and positive selection in plant protein families. Genome Biol. Evol. 4: 360–371 Download

Richards, C.L., U. Rosas, J. Banta, N. Bhambhra and M.D. Purugganan (2012). Genome-wide gene expression patterns of Arabidopsis thaliana in nature. PLoS Genetics 8: e1002662 Doi:10.1371/journal.pgen.1002662 Download

Banta, J., S. Gerard-Martinez, L. Chou, I. Ehrenreich, A. Wilczek, J. Schmitt and M.D. Purugganan (2012). Climate envelope modeling reveals intraspecific relationships among flowering phenology, niche breadth, and potential range size in Arabidopsis thaliana. Ecol. Letters 15: 769–777 Download

Samis, K.E. C. J. Murren, O. Bossdorf, K. Donohue, C. B. Fenster, Y. Li, R. L. Malmberg, M. D. Purugganan, J. O. Borevitz, J. R. Stinchcombe (2012). Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana. Ecol. Evolution 2: 1162–1180 Download

Fuller, D.Q., E. Asouti and M.D. Purugganan (2012). Cultivation as slow evolutionary entanglement: Comparative data on rate and sequence of domestication. Vegetation History and Archaeobotany 21: 131–145 Download

Flowers, J.M., J. R. Molina, S.R. Rubenstein, P. Huang, B.A. Schaal and M.D. Purugganan (2012). Natural selection in gene dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol. Biol. Evol. 26: 2475–2486 Download

Molina, J.R., M. Sikora, N. Garud, J.M. Flowers, S. Rubinstein, P. Huang, S. A. Jackson, B. A. Schaal, C.D. Bustamante, A.R. Boyko and M.D. Purugganan (2011). Molecular evidence for a single evolutionary origin of domesticated rice. Proc. Natl. Acad. Sci. USA 108: 8351–8356 Download

Xie, X., J. Molina, R. Hernandez, A. Reynolds, A. Boyko, C. D. Bustamante and M. D. Purugganan (2011). Levels and patterns of nucleotide variation in genomic regions on rice chromosome 3 associated with domestication QTLs suggest lineage-specific selection. PLoS One 6: e20670 Download

Li, S.I. and M.D. Purugganan (2011). The cooperative amoeba: Dictyostelium as a model for social evolution. Trends in Genetics 27: 48–54 Download

Purugganan, M.D. and D. Q. Fuller (2011). Archaeological data reveals slow rates of evolution during plant domestication. Evolution 65: 171-183 Download

Banta, J. and M.D. Purugganan (2011). Loci controlling flowering time variation in plants. In: Mechanisms of Life History Evolution (T. Flatt and A. Heyland, eds). Oxford University Press, Oxford, UK

Nicotra, A., O. Atkin, S. Bonser, A. Davidson, J. Finnegan, R. Furbank, U. Mathesius, P, Poot, M.D. Purugganan, C.L. Richards, F. Valladares and M. van Kleunen (2010). Plant phenotypic plasticity in a changing climate. Trends in Plant Science 15: 684-692 Download

Mather, K.A., J. Molina, S. Rubinstein, J.M. Flowers, B. Rauh, A. Lawton-Rauh, K. McNally and M.D. Purugganan (2010). Migration, isolation and hybridization in island populations: The case of Madagascar rice. Mol. Ecol. 19: 4892–4905 Download

Purugganan, M.D. (2010). The evolution of rice: Molecular vignettes on its origins and spread. Archaeological and Anthropological Sciences 2: 61-68 Download

Flowers, J. M., S. Li, A. Stathos, G. Saxer, E. Ostrowski, D. Queller, J. Strassmann and M. D. Purugganan (2010). Variation, sex and social cooperation: Molecular population genetics of the social amoeba Dictyostelium discoideum. PLOS Genetics 6: e1001013 Download

Purugganan, M.D. (2010). Complexities in genome structure and evolution: Vignettes and challenges. In: The Vienna Series in Theoretical Biology: Extending the Evolutionary Synthesis (G. Muller and M. Pigliucci, eds). MIT Press, Cambridge, MA

Kover, P.X., Valdar, W., Scarcelli, N., Trakalo, J., Durrant, J., Ehrenreich, I.M., Purugganan, M.D. and Mott, R. (2009). A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics 5: e1000551 Download

Flowers, J., Hanzawa, Y., Hall, M., Moore, R.C. and M.D. Purugganan (2009). Population genomics of the Arabidopsis thaliana flowering time genetic network. Mol. Biol. Evol. 26: 2475–2486 Download

Ehrenreich, I., Hanzawa, Y., Chou, L., Roe, J.L., Kover, P.X. and M.D. Purugganan (2009). Candidate gene association mapping of Arabidopsis flowering time. Genetics 183: 325–335 Download

Reininga-Craven, J., D. Nielsen and M.D. Purugganan (2009). Functional and geographic differentiation of candidate balanced polymorphisms in Arabidopsis thaliana . Mol. Ecol. 18: 2844–2855 Download

Caicedo, A., Richards, C. L., Ehrenreich, I. M. and M.D. Purugganan (2009). Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis MAF2-5 flowering time gene cluster. Mol. Biol. Evol. 26: 699–711 Download

Purugganan, M.D. and D. Fuller (2009). The nature of selection during plant domestication. Nature 457: 843–848 Download

Richards, C.L., Hanzawa, Y., Katari, M., Ehrenreich, I., Engelmann, K. and M.D. Purugganan (2009). Perspectives on ecological and evolutionary systems biology. In: Systems Biology, Anuual Plant Reviews vol. 35 (R.A. Gutierrez and G.M. Coruzzi, ed.) Blackwell Publishing, New York Download

Flowers, J. M. and M.D. Purugganan (2008). The evolution of plant genomes – scaling up from a population perspective. Curr. Op. Genetics Dev. 18: 565–570 Download

Boualem, A., Fergany, M., Fernandez, R., Troadec, C., Martin, A., Morin, H., Sari, M.A., Flowers, J.M., Pitrat, M., Purugganan, M. D., Dogimont, C. and Bendahmane, A. (2008). A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons. Science 321: 836–838 Download

Ehrenreich, I. and M.D. Purugganan (2008). Sequence variation of Arabidopsis microRNAs and their binding sites. Plant Physiol. 146: 1974–1982 Download

Shimizu, K., Shimizu, R., Tsuchimatsu, T. and M. D. Purugganan (2008). Independent origins of self-compatibility in A. thaliana. Mol. Ecol. 171: 704–714 Download

Mather, K.A., A. Caicedo, S.R. McCouch and M.D. Purugganan (2007). The extent of linkage disequilibrium in rice. Genetics 177: 2223-2232 Download

Saisho, D. and M.D. Purugganan (2007). Molecular phylogeography of barley traces the spread of agriculture in the Old World. Genetics 177: 1765-1776 Download

Caicedo, A.L., Williamson, S., Fiedel-Alon, A., York, T., Polato, N., Olsen, K.M., Nielsen, R., McCouch, S.R., Bustamante, C.D. and Purugganan, M.D. (2007). Genome-wide patterns of nucleotide variation in domesticated rice. PLOS Genetics. 3: 1745–1756 Download

Lawton-Rauh, A., Robichaux, R.H. and M.D. Purugganan (2007). Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently-derived species of the Hawaiian silversword alliance adaptive radiation (Heliantheae, Asteraceae). Mol. Ecol. 16: 3995-4013 Download

Hall, M.C., I. Dworkin, M.C. Ungerer and M.D. Purugganan (2007). The genetic architecture of micro-environmental canalization in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA. 104: 13717–13722 Download

Ehrenreich, I., Stafford, P. and M.D. Purugganan (2007). The genetic architecture of shoot branching in Arabidopsis thaliana: Comparison of candidate gene associations vs. QTL mapping. Genetics. 176: 1223-1236 Download

Korves, T., Schmid, K.J., Caicedo, A.L., Mays, C., Stinchcombe, J.R., Purugganan, M.D. and J. Schmitt (2007). Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. Amer. Nat. 169: E141–E157 Download

Engelmann, K. and Purugganan, M.D. (2006). The molecular evolutionary ecology of plant development: Flowering time in Arabidopsis thaliana. Adv. Bot. Research 44: 505–524 Download

Tang, T., Lu, J., Huang, J.Z., He, J.H., McCouch, S.R., Shen, Y., Kai, Z.,Purugganan, M.D., Shi, S.H. and Wu, C.I. (2006). Genomic variation in rice: Genesis of highly polymorphic linkage blocks during domestication. PLOS Genetics 2: 1824-1833 Download

Shimizu, K. and M. D. Purugganan (2006). Arabidopsis thaliana as a model system in ecology and evolution. In: Evolutionary Genetics: Concepts and Case Studies (C. Fox and J.B. Wolf, eds.) Oxford University Press, Oxford, UK

Jackson, S., S. Rounsley and M.D. Purugganan (2006). Comparative sequencing of plant genomes: Choices to make. Plant Cell 18: 1100–1104 Download

Olsen, K.M., Caicedo, A.L., Polato, N., McClung, A., McCouch, S.R. and Purugganan, M.D. (2006). Selection under domestication: Evidence for a sweep in the rice Waxy genomic region. Genetics 173: 975–983 Download

Ehrenreich, I. and Purugganan, M.D. (2006). The molecular genetic basis of plant adaptations. Amer. J. Bot. 93: 953-962 Download

Miller, S.R., Purugganan, M.D. and Curtis, S.E. (2006). Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus. Appl. Env. Microbiol. 72: 2793-2800 Download

Stinchcombe, J.R., Caicedo, A.L., Hopkins, R., Mays, C., Boyd, E.W., Purugganan, M.D. and J. Schmitt (2005). Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae): The effects of latitude and FLC variation. Amer. J. Botany 92: 1701–1707 Download

Caicedo, A.L. and Purugganan, M.D. (2005). Comparative plant genomics. Frontiers and Prospects Plant Physiol. 138: 545-547 Download

Shimizu, K. and Purugganan, M.D. (2005). Evolutionary and ecological genomics of Arabidopsis thaliana. Plant Physiol. 138: 578-584 Download

Cork, J. M. and M.D. Purugganan (2005). High-diversity genes in the Arabidopsis genome. Genetics 170: 1897-1911 Download

Robichaux, R.H. and M.D. Purugganan (2005). Adaptive radiation and regulatory gene evolution in the Hawaiian silversword alliance (Asteraceae). Annals Missouri Bot. Garden 92: 28-35 Download

Moore, R.C. and M.D. Purugganan (2005). The evolutionary dynamics of plant duplicate genes. Curr. Opinion Plant Biol. 8: 122-128 Download

Tsompana, M., Abad, J., Purugganan, M. and J. Moyer (2005). The molecular population genetics of the Tomato Spotted Wilt Virus. Mol. Ecol. 14: 53-66 Download

Moore, R.C. and Purugganan, M.D. (2005). Molecular population genetics of redundant floral regulatory genes in Arabidopsis thaliana. Mol. Biol. Evol. 22: 91-103 Download

Caicedo, A.L., J. Stinchcombe, J. Schmitt, M.D. Purugganan (2004). Epistatic interaction between the Arabidopsis FRI and FLC flowering time genes establishes a latitudinal cline in a life history trait. Proc. Natl. Acad. Sci. USA 101: 15670-15675 Download

Fan, C.Z., Purugganan, M.D., Thomas, D.T., Wiegmann, B., Xiang, Q.Y. (2004). Heterogeneous evolution of the myc-like anthocyanin regulatory gene and its phylogenetic utility in Cornus L. Mol. Phylogenetics Evol. 33: 580-594 Download

Friedman, W.E., R.C. Moore and M.D. Purugganan (2004). The evolution of plant development. Amer. J. Botany 91: 1726-1741 Download

Olsen, K.M., Haldorsdottir, S., Stinchcombe, J., Weinig, C., Schmitt, J. and Purugganan, M.D. (2004). Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 157: 1361-1369 Download

Olsen, K.M. and M.D. Purugganan (2004). Plant population genomics, linkage disequilibrium and the genetics of adaptation. In Plant Adaptation: Molecular Genetics and Ecology (Edited by Cronk, Q.C., J. Whitton, R.H. Ree and I.E.P. Taylor), NRC Research Press, Ottawa Download

Cork, J.M. and Purugganan, M.D. (2004). The evolution of molecular genetic pathways and networks. Bioessays. 26: 479-484 Download

Kalisz, S. M. and M.D. Purugganan (2004). Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol. Evol. 19: 309-314 Download

Stinchcombe, J.R., C. Weinig, M. Ungerer, K.M. Olsen, C. Mays, S. Halldorsdottir, M.D. Purugganan and J. Schmitt (2004). A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA. Proc. Natl. Acad. Sci. USA. 101: 4712-4717 Download

Moore, R.C. and Purugganan, M.D. (2003). The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA. 100: 15682-15687 Download

Ungerer, M.C., Halldorsdottir, S., Purugganan, M.D. and Mackay, T.F.C. (2003). Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana. Genetics. 165: 353–365 Download

Xie, J.H., Wehner, T.C., Wollenberg, K., Purugganan, M.D. and Conkling, M.A. (2003). Intron and polypeptide evolution of conserved NPA-to-NPA motif regions in plant aquaporins. J. Amer. Hort. Soc. 128: 591-597 Download

Weinig, C., Dorn, L.A., Kane, N.C., Ungerer, M.C., Halldorsdottir, S., German, Z., Toyonaga, Y., Mackay, T.F.C., Purugganan, M.D. and Johanna Schmitt (2003). Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics 165: 321-329 Download

Lawton-Rauh, A.L., Robichaux, R.H. and Purugganan, M.D. (2003). Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). Mol Ecol. 12: 1301 – 1313 Download

Remington, D.L. and Purugganan, M.D. (2003). Candidate Genes, Quantitative Trait Loci, and Functional Trait Evolution in Plants. Int. J. Plant Sci. 164: S7-S20 Download

Shepard, K.A. and Purugganan, M.D. (2003). Molecular population genetics of the Arabidopsis CLAVATA2 genomic region: The genomic scale of balanced polymorphisms in a selfing species. Genetics 163: 1083-1095 Download

Barrier, M. Bustamante, C. Yu, J. and Purugganan, M.D. (2003). Selection on rapidly-evolving proteins in the Arabidopsis genome. Genetics 163: 723-733 Download

Olsen, K.M., and Purugganan, M.D. (2002). Molecular evidence on the origin and evolution of glutinous rice. Genetics 162: 941-950 Download

Jackson, R., Linder, C.R., Lynch, M., Purugganan, M.D., Sommerville, S. and S. Thayer (2002). Linking molecular insights and ecological research. Trends Ecol. Evol. 17: 409-414 Download

Olsen, K.M., Womack, A., Garret, A.R., Suddith, J.I. and Purugganan, M.D. (2002). Contrasting evolutionary forces in the Arabidopsis floral developmental pathway. Genetics 160: 1641-1650 Download

Bustamante, C., Nielsen, R., Sawyer, S., Olsen, K.M., Purugganan, M.D. and Hartl, D.L. (2002). The cost of inbreeding in Arabidopsis. Nature 416: 531-534 Download

Weinig, C., Ungerer, M., Dorn, L.A., Kane. N.C., Halldorsdottir, S., Mackay, T.F.C., Purugganan, M.D. and Schmitt, J.I (2002). Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments. Genetics 162: 1875-1881 Download

Ungerer, M.C., Halldorsdottir, S., Modliszewski, J., Mackay, T.F.C. and Purugganan, M.D. (2002). Quantitative trait loci for inflorescence development in Arabidopsis thaliana. Genetics 160: 1133-1151 Download

Shepard, K.A. and Purugganan, M.D. (2002). The genetics of plant morphological evolution. Curr. Op. Plant Biol. 5: 49-55 Download

Remington, D.L. and Purugganan, M.D. (2002). GAI Homologues in the Hawaiian Silversword Alliance (Asteraceae-Madiinae): Molecular Evolution of Growth Regulators in a Rapidly Diversifying Plant Lineage. Mol. Biol. Evol. 19: 1563-1574 Download

Barrier, M., Robichaux, R.H. and Purugganan, M.D. (2001). Accelerated regulatory gene evolution in a plant adaptive radiation. Proc. Natl. Acad. Sci. USA. 98: 10208-10213 Download

Remington, D.L., Ungerer, M.C. and Purugganan, M.D. (2001). Map-based cloning of quantitative trait loci: Progress and prospects. Genet. Res. 78: 213-218 Download

Juenger, T.E., Purugganan, M.D. and Mackay, T.F.C. (2000). Quantitative Trait Loci for Floral Morphology in Arabidopsis thaliana. Genetics 156: 1379-1392 Download

Purugganan, M.D. (2000). The molecular population genetics of regulatory genes. Mol. Ecol. 9: 1451–1461 Download

Lawton-Rauh, A.L., Alvarez-Buylla, E.A. and Purugganan, M.D. (2000). Molecular evolution of flower development. Trends Ecol. Evol. 15: 144–149 Download

Barrier, M., Friar, E.A., Robichaux, R.H. and Purugganan, M.D. (2000). Interspecific evolution in plant microsatellite structure. Gene 241: 101-105 Download

Purugganan, M.D., Boyles, A.L. and Suddith, J.I. (2000). Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea. Genetics 155: 855-862 Download

Lowman, A.C. and Purugganan, M.D. (1999). Duplication of the Brassica oleracea APETALA1 floral homeotic gene and the evolution of domesticated cauliflower. J. Heredity 90: 514-520 Download

Barrier, M., Baldwin, B., Robichaux, R.H., and Purugganan, M.D. (1999). Interspecific hybrid ancestry of a plant adaptive radiation: Allopolyploidy of the Hawaiian silversword alliance inferred from duplicated floral homeotic genes. Molecular Biology and Evolution 16: 1105-1113 Download

Purugganan, M.D. and J. I. Suddith (1999). Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana Genetics 151: 839-848 Download

Lawton-Rauh, A., Buckler, E., and Purugganan, M.D. (1999). Patterns of molecular evolution among paralogous floral homeotic genes. Molecular Biology and Evolution 16: 1037-1045 Download

Purugganan, M.D. and Suddith, J.I. (1998). Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: Nonneutral evolution and naturally occurring variation on floral homeotic function. Proc. Natl. Acad. Sci. USA 95: 8130-8134 Download

Purugganan, M.D. (1998). The molecular evolution of development. BioEssays 20: 700-711 Download

Purugganan. M.D. (1998). The Splicing of Transposable Elements:Evolution of a Nuclear Defense AgainstGenomic Invaders? In Horizontal Gene Transfer: Implications and Consequences (Ed. M. Syvanen), Chapman-Hall. Download

Swaffield, J.C. and Purugganan, M.D. (1997). The evolution of the conserved ATPAse domain (CAD): Reconstructing the history of an ancient protein module. J. Mol. Evol. 45: 549-563 Download

Purugganan, M.D. (1997). The MADS-box floral homeotic gene lineages predate the origin of the seed plants: Phylogenetic and molecular clock estimates. J. Mol. Evol. 45: 392-396 Download

Purugganan, M.D., Rounsley, S.D., Schmidt, R.J. and Yanofsky, M.F. (1995). Molecular evolution of flower development: Diversification of the plant MADS-box regulatory gene family. Genetics 140: 345-356 Download

Purugganan, M.D. and Wessler, S.R. (1995). Transposon signatures: Species-specific molecular markers that utilize a class of multiple-copy nuclear DNA. Molecular Ecology 4: 265-269 Download

Purugganan, M.D. and Wessler, S. R. (1994). Molecular evolution of the plant R regulatory gene family. Genetics 138: 849-854 Download

Purugganan, M.D. and Wessler, S.R. (1994). Molecular evolution of Magellan, a maize Ty3/gypsy-like retrotransposon. Proc. Natl. Acad. Sci. USA . 91: 11674-11678 Download

Purugganan, M.D. (1993). Transposable elements as introns: Evolutionary connections. Trends in Ecol. Evol. 8: 239-243 Download

Purugganan, M.D. (1993). Scale-invariant spatial patterns in genome organization. Phys. Lett. A. 175: 252-256 Download

Purugganan, M.D. and Wessler, S.R. (1992). The splicing of transposable elements and its role in intron evolution. Genetica 86: 295-303. Reprinted in Transposable Elements and Evolution (J.F. McDonald, ed.) Dordrecht: Kluwer Publishing, 1993 Download

Purugganan, M.D., Varagona, M.J. and Wessler, S.R. (1992). Alternative splicing induced by insertion of retrotransposons into the maize waxy gene. Plant Cell 4: 811-820 Download

Wessler, S.R., Tarpley, A., Purugganan, M.D., Spell, M. and Okagaki, R.J. (1990). Filler DNA is associated with spontaneous deletions in maize. Proc. Natl. Acad. Sci. USA 87: 8731-8735 Download

Purugganan, M.D. (1989). The fractal nature of RNA secondary structure. Naturwiss 76: 471-473 Download

Purugganan, M.D., Kumar, C.V., Turro, N.J. and Barton, J.K. (1988). Accelerated electron transfer between metal complexes mediated by DNA. Science 241: 1645-1649 Download

Purugganan, M.D. and Casimiro, D.R. (1985). A heuristic algorithm to determine the secondary structure of RNA. Nat. Appl. Sci. Bull. . 37: 125-139

Purugganan, M.D. (1984). A lattice statistical formulation for ligand binding to biological macromolecules. Nat. Appl. Sci. Bull. . 36: 215-218.

Casimiro, D.R. and Purugganan, M.D. (1984). Parameters of hemoglobin cooperativity models from Hill plot binding data. Nat. Appl. Sci. Bull. 36: 207-214