Publications Current Lab Members


2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 1997

2016


Groen S.C. and Purugganan M.D. 2016. Systems genetics of plant adaptation to environmental stresses. Am. J. Botany. http://www.amjbot.org/cgi/doi/10.3732/ajb.1600340

Wilkins O.W., Hafemeister C., Plessis A., Holloway-Phillips M-M., Pham G.M., Nicotra A.B., Gregorio G.B., Septiningsih, E.M., Bonneau R., Purugganan M.D. 2016. EGRINs (Environmental Gene Regulatory Influence Networks ) in Rice that function in the response to water deficity, high temperature, and agricultural environments. Plant Cell. 28: 2365-2384. www.plantcell.org/cgi/doi/10.1105/tpc.16.00158

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

Yuan W., Flowers J.M., Sahraie D.J., Purugganan M.D. 2016. Cryptic genetic variation for Arabidopsis thaliana seed germination speed in a novel salt stress environment. G3. doi: 10.1534/g3.116.033944

Meyer R.S., Choi J.Y., Sanches M., Plessis A., Flowers J.M., Amas J., Dorph K., Barretto A., Gross B., Fuller D.Q., Kofi Bimpong I., Ndjiondjop M-N., Hazzouri K.M., Gregorio G.B., Purugganan M.D. 2016. Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat. Genet. doi:10.1038/ng.3633

Yuan W., Flowers J.M., Sahraie D.J., Ehrenreich I. M., Purugganan M.D. 2016. Extreme QTL mapping of germination speed in Arabidopsis thaliana. Mol. Ecol. doi: 10.1534/g3.116.033944

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

Rest J.S., Wilkins O., Yuan W., Purugganan M.D., Gurevitch J. 2016. Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis. Plant Journal. 85(4):548-560

2015


Plessis A., Hafemeister C., Wilkins O., Gonzaga ZJ, Meyer RS, Pires I et al. 2015. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions. Elife. Nov 26;4. pii: e08411. doi: 10.7554/eLife.08411

Hazzouri K.M., Flowers, J.M., Visser H.J., Khierallah H.S.M., Rosas, U. et al. 2015. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat. Commun. 6:8824 doi:10.1038/ncomms9824

Flowers J.M., Hazzouri K.M., Pham G.M., Rosas U., Bahmani T. et al. 2015. Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii. 2015. Plant Cell. 27:2353-2369. doi:10.1105/tpc.15.00492

Pires, I.S., Negrao S., Oliveira M.M., Purugganan M.D. 2015. Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress. Physiologia Plantarum. 155(1):43-54.

2014


Larson G, Piperno DR, Allaby RG, Purugganan MD, Andersson L, Arroyo-Kalin M, Barton L, Climer Vigueira C, Denham T, Dobney K, Doust AN, Gepts P, Gilbert MT, Gremillion KJ, Lucas L, Lukens L, Marshall FB, Olsen KM, Pires JC, Richerson PJ, Rubio de Casas R, Sanjur OI, Thomas MG, Fuller DQ. (2014). Current perspectives and the future of domestication studies. Proc Natl Acad Sci 111(17):6139-46. doi: 10.1073/pnas.1323964111

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

Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MT, Larson G, Thomas MG. (2014) Storytelling and story testing in domestication. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6159-64

Molina J., Hazzouri K. M., Nickrent D., Geisler M., Meyer R. S., Pentony M. M., Flowers J. M.Pelser P., Barcelona J., Inovejas S. A. Uy I., Yuan W., Wilkins O., Michel C.I., LockLear S.,Concepcion G. P. Purugganan M. D. 2014. Possible Loss of the Chloroplast Genome in the ParasiticFlowering Plant Rafflesia lagascae (Rafflesiaceae). Mol. Biol. Evol. 31:793-803

Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stevens CJ, Qin L, Allaby RG, Purugganan MD. (2014) Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6147-52. doi: 10.1073/pnas.1308937110

Li S.I., Buttery N.J., Thompson C.R.L., Purugganan M.D. 2014. Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum. BMC Genomics. 15, 616.

2013


Meyer RS, Purugganan MD. (2013) Evolution of crop species: genetics of domestication and diversification. Nat Rev Genet. 2013 Dec;14(12):840-52. doi: 10.1038/nrg3605

Rosas U., Cibrian-Jaramillo A., Ristova D., Banta J.A., Gifford M.L., Fan A.H. Zhou R.W., Kim G.J., Krouk G., Birnbaum K.D., Purugganan M.D., Coruzzi G.M. (2013) Proc. Nat. Acad. Sci. USA. 110(37):15133-8

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. doi: 10.1186/1471-2164-14-579.

Thanawala SU, Rister J, Goldberg GW, Zuskov A, Olesnicky EC, Flowers JM, Jukam D, Purugganan MD, Gavis ER, Desplan C, Johnston RJ Jr. (2013) Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina. Dev Cell. 15;25(1):93-105. doi: 10.1016/j.devcel.2013.02.016

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

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

2012


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
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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
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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.
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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.

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.
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Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, Desalle R, Bonneau R, Purugganan MD (2012). The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families. Genome Biol Evol.
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Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD (2012). Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol Feb;29(2):675-87
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2011


Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD (2011). Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection. PLoS One 6(6):e20670
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Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD. Molecular evidence for a single evolutionary origin of domesticated rice.Proceddings of the National Academy of Sciences 2011 May 17;108(20):8351-6
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Li SI, Purugganan MD. The cooperative amoeba: Dictyostelium as a model for social evolution. Trends in Genetics 2011 Feb;27(2):48-54.
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Archaeological data reveal slow rates of evolution during plant domestication. Purugganan MD, Fuller DQ. Evolution 2011 Jan;65(1):171-83.
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2010


Mather KA, Molina J, Flowers JM, Rubinstein S, Rauh BL, Lawton-Rauh A, Caicedo AL, McNally KL, Purugganan MD. Migration, isolation and hybridization in island crop populations: the case of Madagascar rice. Molecular Ecology. 2010 Nov;19(22):4892-905
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Flowers JM, Li SI, Stathos A, Saxer G, Ostrowski EA, Queller DC, Strassmann JE, Purugganan MD. Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum. PLoS Genetics 2010 Jul 1;6(7)
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2009


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.
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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.
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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.
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Reininga-Craven,J., Nielsen,D. and M.D. Purugganan (2009). Functional and geographic differentiation of candidate balanced polymorphisms in Arabidopsis thaliana. Mol. Ecol. 18:2844-2855.
Note: This paper is accompanied by a News and Views article.
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Purugganan,M.D. 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.

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.
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Purugganan, M.D. and D. Fuller (2009). The nature of selection during plant domestication.Nature 457:843-848.
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Richards, C.L., Hanzawa, Y., Katari, M., Ehrenreich, I., Englemann, K. and M.D. Purugganan (2009). Perspectives on ecological and evolutionary systems biology. In : Systems Biology, Annual Plant Reviews vol. 35 (R.A. Gutierrez and G.M. Coruzzi, eds.) Blackwell Publishing, New York.

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2008

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.
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Boualem, A., Fergany, M., Fernandez, R., Troadex, 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.
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Ehrenreich, I. and M.D. Purugganan (2008). Sequence variation of Arabidopsis microRNAs and their binding sites. Plant Physiol. 146:1974-1982.
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Shimizu, K.K., Shimizu-Inatsugi, R., Tsuchimatsu, T., and Purugganan, M.D. (2008) Independent origins of self-compatibility in Arabidopsis thaliana. Molecular Ecology 17:704-714.
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2007

Saisho, D. and Purugganan, M.D. (2007). Molecular phylogeography of domesticated barley traces expansion of agriculture in the old world. Genetics 177: 1765-1776.
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Hall, M.C., Dworkin, I., Ungerer, M.C. and Purugganan, M.D. (2007). Genetics of microenvironmental canalization in Arabidopsis thaliana. Proceedings of the National Academy of Sciences USA 104 (34): 13717-13722.
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Mather, M.A., Caicedo, A.L., Polato, N.R., Olsen, K.M., McCouch, S., and Purugganan, M.D. The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177: 2223-2232.
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Lawton-Rauh, A., Robichaux, R.H., and Purugganan, M.D. (2007). Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae). Molecular Ecology 16 (19):3995-4013.
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Caicedo, A.L., Williamson, S.H., Hernandez, R.D., Boyko, A., Fledel-Alon, A., York, T.L., Polato, N.R., Olsen, K.M., Nielsen, R., McCouch, S.R., Bustamante, C.D., Purugganan, M.D. (2007). Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLOS Genetics 3: 1745-1756.
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Ehrenreich, I.M., Stafford, P.A., and Purugganan, M.D. (2007).The Genetic Architecture of Shoot Branching in Arabidopsis thaliana: A Comparative Assessment of Candidate Gene Associations vs. Quantitative Trait Locus Mapping. Genetics 176: 1223-1236.
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Korves, T.M., Schmid, K.J., Caicedo, A.L., Mays, C., Stinkchcombe, J.R., Purugganan, M.D., and Schmitt, J. (2007). Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field. American Naturalist 169: electronically published.
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2006

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

Ehrenreich, I.M. and Purugganan, M.D. (2006). The molecular genetic basis of plant adaptation. American J. Botany 93: 953-962.
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Olsen, K.M., Caicedo, A.L., Polato, N., McClung, A., McCouch, S., and Purugganan, M.D. (2006). Selection under domestication: Evidence for a sweep in the rice Waxy genomic region. Genetics 173: 975-983.
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Shimizu, K.K. and Purugganan, M.D. (2006). Evolutionary and ecological genomics - Darwinian selection on a selfing locus in Arabidopsis thaliana. Plant and Cell Physiology 47: S13-S13.

Jackson, S., Rounsley, S., and Purugganan, M.D. (2006). Comparative sequencing of plant genomes: Choices to make. Plant Cell 18: 1100-1104.
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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. Environ. Micro. 72: 2793-2800.
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2005

Engelmann, K. E. and Purugganan, M.D. (2005). The molecular evolutionary ecology of plant development: Flowering time in Arabidopsis thaliana. Advances in Botanical Research.

Cork, J.M. and Purugganan, M.D. (2005). High-diversity genes in the Arabidopsis genome. Genetics 170: 1897-1911.
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Shimizu, K.K. and Purugganan, M.D. (2005). Evolutionary and ecological genomics of Arabidopsis. Plant Physiology 138: 578-584.
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Caicedo, A.L. and Purugganan, M.D. (2005). Comparative plant genomics. Frontiers and Prospects. Plant Physiology 138: 545-547.
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Robichaux, R.H. and Purugganan, M.D. (2005). Adaptive radiation and regulatory gene evolution in the Hawaiian silversword alliance (Asteraceae). Annals Missouri Bot. Garden. 92: 28-35.

Moore, R.C., and Purugganan, M.D. (2005). The evolutionary dynamics of plant duplicate genes. Curr. Op. in Plant Biol. 8: 122-128.
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Tsompana, M., Abad, J., Purugganan, M.D., and Moyer, J.W. (2005). The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol. Ecol. 14: 53-66.
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Moore, R.C., Grant, S.R., and Purugganan, M.D. (2005). Molecular Population Genetics of Redundant Floral-Regulatory Genes in Arabidopsis thaliana. Molecular Biology and Evolution 22: 91-103.
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2004

Fan, C.Z., Purugganan, M.D., Thomas, D.T., Wiegmann, B.M., and Xiang, Q.Y. (2004). Heterogeneous Evolution of the Myc-like Anthocyanin Regulatory Gene and its Phylogenetic Utility in Cornus L. (Cornaceae). Molecular Phylogenetics and Evolution 33: 580-594.
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Caicedo, A.L., Stinchcombe, J.R., Olsen, K.M., Schmitt J., and Purugganan, M.D. (2004). Epistatic Interaction Between 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.
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Friedman, W.E., Moore, R.C., and Purugganan, M.D. (2004). The Evolution of Plant Development. American Journal of Botany 91: 1726-1741.
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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 167: 1361-1369.
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Cork, J.M. and Purugganan, M.D. (2004). The evolution of molecular genetic pathways and networks. Bioessays 26: 479-484.
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Kalisz, S. M. and Purugganan, M.D. (2004). Epialleles via methylation - plant population epigenetic consequences. Trends in Ecology and Evolution 19: 309-314
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Stinchcombe, J.R., Weinig, C., Ungerer, M., Olsen, K.M., Mays, C., Halldorsdottir, S., Purugganan, M.D. and Schmitt, J. (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.
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2003

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

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 Schmitt, J. (2003). Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana. Genetics 165: 321-329.
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Lawton-Rauh, A., Robichaux, R.H. and Purugganan, M.D. (2003). Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae). Molecular Ecology. 12: 1301-1313.
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Remington, D.L. and Purugganan, M.D. (2003). The genetics of functional trait evolution. Int. J. Plant Sci. 164: S7-S20.
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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.
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Barrier, M., Bustamante, C., Yu, J. and Purugganan, M.D. (2003). Selection on rapidly-eVolving proteins in the Arabidopsis genome. Genetics 163: 723-733.
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Purugganan, M.D., Remington, D.L. and Robichaux, R.H. (2003). Molecular evolution of regulatory genes in the silversword alliance. In Madiinae (Carlquist, S.H. and Baldwin, B.G., ed.). Missouri Botanical Garden Press.

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2002

Weinig, C., Ungerer, M.C., Dorn, L.A., Kane, N.C., Toyonaga, Y., Halldorsdottir, S.S., Mackay, T.F.C., Purugganan, M.D. and Schmitt, J. (2002). Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments. Genetics 162: 1875-1884.
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Olsen, K.M. and Purugganan, M.D. (2002). Molecular evidence on the origin and evolution of glutinous rice. Genetics 162: 941-950.
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Remington, D.L. and Purugganan, M.D. (2002). GAI homologues in the Hawaiian silversword alliance: Molecular evolution of growth regulators in a rapidly diversifying plant lineage. Mol. Biol. Evol. 19: 1563-1574.
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Jackson, R.B., Linder, C.R., Lynch, M., Purugganan, M., Somerville, S. and Thayer, S.S. (2002). Linking molecular insight and ecological research. Trends in Ecology and Evolution 17: 409-414.
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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.
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Bustamante, C., Nielsen, R., Sawyer, S., Olsen, K.M., Purugganan, M.D. and Hartl, D.L. The cost of inbreeding in Arabidopsis. Nature. 416: 531 - 534.
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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.
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Shepard, K.A. and Purugganan, M.D. (2002). The genetics of plant morphological evolution. Curr. Op. Plant Biol. 5: 49 - 55.
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2001

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.

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.
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2000

Barrier, M., Friar, E.A., Robichaux, R.H. and Purugganan, M.D. (2000). Interspecific evolution in plant microsatellite structure.
Gene 241: 101 - 105.
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Purugganan, M.D. (2000). Molecular population genetics of regulatory genes. Mol. Ecol. 9: 1451 - 1461.
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Lawton-Rauh, A.L., Alvarez-Buylla, E.A. and Purugganan, M.D. (2000). Molecular evolution of flower development. Trends Ecol. Evol. 15: 144 - 149
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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.
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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.
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1999

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.
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Purugganan, M.D. and Suddith, J. I. (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.
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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.
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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.
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1998

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.
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Purugganan, M.D. (1998). The molecular evolution of development. BioEssays 20: 700 - 711.
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Purugganan, M.D. (1998). The splicing of transposable elements: evolution of a nuclear defense against genomic invasions? In Horizontal Gene Transfer (M. Syvanen, C.I. Kado, ed.). Chapman-Hall, London.

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1997

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.
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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.
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