Michael Purugganan

Silver Professor; Professor of Biology; Dean for Science



Evolutionary and ecological genomics of plant adaptations

We study the evolutionary forces that act in plant developmental networks at the species level, and in mapping and isolating genes that underlie natural variation in that are responsible for plant adaptation. We are also interested in exploring the “ecological transciptome” – the dynamic gene networks found in plants in ecological environments. This work combines concepts and techniques in evolutionary and quantitative genomics, developmental biology, evolutionary ecology, and computational biology.

Genetics of Plant Domestication

Crops are plant species that have evolved in a cultural context to provide food and other products for human society. Crop species are fascinating subjects for evolutionary study, since they are examples of species that have undergone rapid diversification under intense selection pressures. They also permit us to understand the dynamic interface between genetics, evolution and human culture. We are studying the evolution of genes in rice (Oryza sativa). By using tools of molecular and evolutionary genomics, these studies provide insights into the processes and mechanisms that accompany cultural selection on plant species during domestication events.

The Evolution of Multicellularity and Social Behaviour

The model protist Dictyostelium discoideum has been a model for the study of social biology as well as the evolution of multicellularity. We are integrating techniques and approaches in population genetics, genomics, systems biology and glycomics to study kin discrimination and recognition in this social microbe.


Work in my laboratory is funded by grants from the NSF Plant Genome Research program and the Population and Evolutionary Processes program.


Carlos Bustamante (Stanford), Barbara Schaal (Washington University), Scott Jackson (University of Georgia), Richard Bonneau (NYU), Kourosh-Salehi Ashtiani (NYU Abu Dhabi), Endang Septiningsih (International Rice Research Institute)


Dr. Michael Purugganan received his B.S. in Chemistry from the University of the Philippines (1985), an M.A. from Columbia University (1986) and a Ph.D. in Botany with a Global Policy minor at the University of Georgia (1993). After obtaining his Ph.D., he did postdoctoral research as an Alfred P. Sloan Molecular Evolution Fellow at the University of California in San Diego, studying the evolution of development (1993-1995). Dr. Purugganan is a leader in the field of evolutionary and ecological genomics and his work focuses on identifying the molecular basis for evolutionary adaptations that occur in nature. Prior to joining the NYU faculty in 2006, he was the William Neal Reynolds Distinguished Professor of Genetics at North Carolina State University, where he also won the Outstanding Faculty Research Award and the Sigma Xi Research Prize. He is the recipient of an Alfred P. Sloan Foundation Young Investigator Award, a Guggenheim Fellowship, is a Kavli Fellow, and in 2005 was elected a Fellow of the American Association for the Advancement of Science. Dr. Purugganan is on the editorial boards of the journals Genome Biology and Evolution, Molecular Ecology, Trends in Plant Science and the Annual Review of Ecology, Evolution and Systematics.

External Affiliations

American Association for the Advancement of Science

Genetics Society of America and Society for Molecular Biology and Evolution



The Rice Paradox: Multiple Origins but Single Domestication in Asian Rice.
Mol Biol Evol (2017 Apr 01) PMC5400379 free full-text archive
Choi JY, Platts AE, Fuller DQ, Hsing YI, Wing RA, Purugganan MD

Systems genetics of plant adaptation to environmental stresses.
Am J Bot (2016 Dec) PMID: 27864265
Groen SC, Purugganan MD

Tracing ancestor rice of Suriname Maroons back to its African origin.
Nat Plants (2016 Oct 03) PMID: 27694825
van Andel TR, Meyer RS, Aflitos SA, Carney JA, Veltman MA, Copetti D, Flowers JM, Havinga RM, Maat H, Purugganan MD, Wing RA, Schranz ME

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.
Plant Cell (2016 Oct) PMC5134975 free full-text archive
Wilkins O, Hafemeister C, Plessis A, Holloway-Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish SV, Septiningsih EM, Bonneau R, Purugganan M

Cryptic Genetic Variation for Arabidopsis thaliana Seed Germination Speed in a Novel Salt Stress Environment.
G3 (Bethesda) (2016 Oct 13) PMC5068935 free full-text archive
Yuan W, Flowers JM, Sahraie DJ, Purugganan MD

Domestication history and geographical adaptation inferred from a SNP map of African rice.
Nat Genet (2016 Sep) PMID: 27500524
Meyer RS, Choi JY, Sanches M, Plessis A, Flowers JM, Amas J, Dorph K, Barretto A, Gross B, Fuller DQ, Bimpong IK, Ndjiondjop MN, Hazzouri KM, Gregorio GB, Purugganan MD

Extreme QTL mapping of germination speed in Arabidopsis thaliana.
Mol Ecol (2016 Sep) PMID: 27454560
Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD

Developing maps of fitness consequences for plant genomes.
Curr Opin Plant Biol (2016 Apr) PMID: 26950251
Joly-Lopez Z, Flowers JM, Purugganan MD

Evolution of Plant Phenotypes, from Genomes to Traits.
G3 (Bethesda) (2016 Feb 11) PMC4825648 free full-text archive
Casacuberta JM, Jackson S, Panaud O, Purugganan M, Wendel J

Meta-analysis and meta-regression of transcriptomic responses to water stress in Arabidopsis.
Plant J (2016 Feb) PMC4815425 free full-text archive
Rest JS, Wilkins O, Yuan W, Purugganan MD, Gurevitch J

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.
Elife (2015 Nov 26) PMC4718725 free full-text archive
Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Muller C, Septiningsih EM, Bonneau R, Purugganan M

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.
Nat Commun (2015 Nov 09) PMC4667612 free full-text archive
Hazzouri KM, Flowers JM, Visser HJ, Khierallah HS, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD

Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii.
Plant Cell (2015 Sep) PMC4815094 free full-text archive
Flowers JM, Hazzouri KM, Pham GM, Rosas U, Bahmani T, Khraiwesh B, Nelson DR, Jijakli K, Abdrabu R, Harris EH, Lefebvre PA, Hom EF, Salehi-Ashtiani K, Purugganan MD

Comprehensive phenotypic analysis of rice (Oryza sativa) response to salinity stress.
Physiol Plant (2015 Sep) PMID: 26082319
Pires IS, Negrao S, Oliveira MM, Purugganan MD

An evolutionary genomic tale of two rice species.
Nat Genet (2014 Sep) PMID: 25162803
Purugganan MD

Sociogenomics of self vs. non-self cooperation during development of Dictyostelium discoideum.
BMC Genomics (2014 Jul 21) PMC4118049 free full-text archive
Li SI, Buttery NJ, Thompson CR, Purugganan MD

Current perspectives and the future of domestication studies.
Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035915 free full-text archive
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

Convergent evolution and parallelism in plant domestication revealed by an expanding archaeological record.
Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035951 free full-text archive
Fuller DQ, Denham T, Arroyo-Kalin M, Lucas L, Stevens CJ, Qin L, Allaby RG, Purugganan MD

Storytelling and story testing in domestication.
Proc Natl Acad Sci U S A (2014 Apr 29) PMC4035932 free full-text archive
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

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS.
Nat Commun (2014 Apr 16) PMC3997802 free full-text archive
Rosas U, Mei Y, Xie Q, Banta JA, Zhou RW, Seufferheld G, Gerard S, Chou L, Bhambhra N, Parks JD, Flowers JM, McClung CR, Hanzawa Y, Purugganan MD

Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).
Mol Biol Evol (2014 Apr) PMC3969568 free full-text archive
Molina J, Hazzouri KM, Nickrent D, Geisler M, Meyer RS, Pentony MM, Flowers JM, Pelser P, Barcelona J, Inovejas SA, Uy I, Yuan W, Wilkins O, Michel CI, Locklear S, Concepcion GP, Purugganan MD

Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms.
Rice (N Y) (2013 Oct 28) PMC3874672 free full-text archive
Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, Flowers JM, Purugganan MD, Nakamura I, Sato Y, Sato T, Crayn D, Simon B, Waters DL, Henry RJ, Ishikawa R

Evolution of crop species: genetics of domestication and diversification.
Nat Rev Genet (2013 Dec) PMID: 24240513
Meyer RS, Purugganan MD

Plasticity regulators modulate specific root traits in discrete nitrogen environments.
PLoS Genet (2013) PMC3764102 free full-text archive
Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
BMC Genomics (2013 Aug 28) PMC3844514 free full-text archive
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

Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
Proc Natl Acad Sci U S A (2013 Sep 10) PMC3773737 free full-text archive
Rosas U, Cibrian-Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM

Different evolutionary histories of two cation/proton exchanger gene families in plants.
BMC Plant Biol (2013 Jul 04) PMC3726471 free full-text archive
Pires IS, Negrao S, Pentony MM, Abreu IA, Oliveira MM, Purugganan MD

Regional modulation of a stochastically expressed factor determines photoreceptor subtypes in the Drosophila retina.
Dev Cell (2013 Apr 15) PMC3660048 free full-text archive
Thanawala SU, Rister J, Goldberg GW, Zuskov A, Olesnicky EC, Flowers JM, Jukam D, Purugganan MD, Gavis ER, Desplan C, Johnston RJ Jr

Longitudinal trends in climate drive flowering time clines in North American Arabidopsis thaliana.
Ecol Evol (2012 Jun) PMC3402192 free full-text archive
Samis KE, Murren CJ, Bossdorf O, Donohue K, Fenster CB, Malmberg RL, Purugganan MD, Stinchcombe JR

Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view.
Mol Ecol (2012 Sep) PMID: 22646149
Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, Purugganan MD, Schaal BA

Climate envelope modelling reveals intraspecific relationships among flowering phenology, niche breadth and potential range size in Arabidopsis thaliana.
Ecol Lett (2012 Aug) PMID: 22583905
Banta JA, Ehrenreich IM, Gerard S, Chou L, Wilczek A, Schmitt J, Kover PX, Purugganan MD

Genome-wide patterns of Arabidopsis gene expression in nature.
PLoS Genet (2012) PMC3330097 free full-text archive
Richards CL, Rosas U, Banta J, Bhambhra N, Purugganan MD

The plant proteome folding project: structure and positive selection in plant protein families.
Genome Biol Evol (2012) PMC3318447 free full-text archive
Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD

Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice.
Mol Biol Evol (2012 Feb) PMID: 21917724
Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD

Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.
PLoS One (2011) PMC3108957 free full-text archive
Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD

Molecular evidence for a single evolutionary origin of domesticated rice.
Proc Natl Acad Sci U S A (2011 May 17) PMC3101000 free full-text archive
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S, Reynolds A, Huang P, Jackson S, Schaal BA, Bustamante CD, Boyko AR, Purugganan MD

The cooperative amoeba: Dictyostelium as a model for social evolution.
Trends Genet (2011 Feb) PMID: 21167620
Li SI, Purugganan MD

Plant phenotypic plasticity in a changing climate.
Trends Plant Sci (2010 Dec) PMID: 20970368
Nicotra AB, Atkin OK, Bonser SP, Davidson AM, Finnegan EJ, Mathesius U, Poot P, Purugganan MD, Richards CL, Valladares F, van Kleunen M

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice.
Mol Ecol (2010 Nov) PMID: 20964753
Mather KA, Molina J, Flowers JM, Rubinstein S, Rauh BL, Lawton-Rauh A, Caicedo AL, McNally KL, Purugganan MD

Laboratory markers of cardiovascular risk in pediatric SLE: the APPLE baseline cohort.
Lupus (2010 Oct) PMC4049625 free full-text archive
Ardoin SP, Schanberg LE, Sandborg C, Yow E, Barnhart HX, Mieszkalski Kl, Ilowite NT, von Scheven E, Eberhard A, Levy DM, Kimura Y, Silverman E, Bowyer SL, Punaro L, Singer NG, Sherry DD, McCurdy D, Klein-Gitelman M, Wallace C, Silver R, Wagner-Weiner L, Higgins GC, Brunner HI, Jung LK, Imundo L, Soep JB, Reed AM

Archaeological data reveal slow rates of evolution during plant domestication.
Evolution (2011 Jan) PMID: 20666839
Purugganan MD, Fuller DQ

Variation, sex, and social cooperation: molecular population genetics of the social amoeba Dictyostelium discoideum.
PLoS Genet (2010 Jul 01) PMC2895654 free full-text archive
Flowers JM, Li SI, Stathos A, Saxer G, Ostrowski EA, Queller DC, Strassmann JE, Purugganan MD

MicroRNAs in plants: Possible contributions to phenotypic diversity.
Plant Signal Behav (2008 Oct) PMC2634387 free full-text archive
Ehrenreich IM, Purugganan M

Population genomics of the Arabidopsis thaliana flowering time gene network.
Mol Biol Evol (2009 Nov) PMID: 19625391
Flowers JM, Hanzawa Y, Hall MC, Moore RC, Purugganan MD

A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana.
PLoS Genet (2009 Jul) PMC2700969 free full-text archive
Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R

Candidate gene association mapping of Arabidopsis flowering time.
Genetics (2009 Sep) PMC2746157 free full-text archive
Ehrenreich IM, Hanzawa Y, Chou L, Roe JL, Kover PX, Purugganan MD

Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana.
Mol Ecol (2009 Jul) PMID: 19457201
Reininga JM, Nielsen D, Purugganan MD

The nature of selection during plant domestication.
Nature (2009 Feb 12) PMID: 19212403
Purugganan MD, Fuller DQ

Complex rearrangements lead to novel chimeric gene fusion polymorphisms at the Arabidopsis thaliana MAF2-5 flowering time gene cluster.
Mol Biol Evol (2009 Mar) PMID: 19139056
Caicedo AL, Richards C, Ehrenreich IM, Purugganan MD

The evolution of plant genomes: scaling up from a population perspective.
Curr Opin Genet Dev (2008 Dec) PMID: 19131240
Flowers JM, Purugganan MD

A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons.
Science (2008 Aug 08) PMID: 18687965
Boualem A, Fergany M, Fernandez R, Troadec C, Martin A, Morin H, Sari MA, Collin F, Flowers JM, Pitrat M, Purugganan MD, Dogimont C, Bendahmane A

Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
Plant Physiol (2008 Apr) PMC2287364 free full-text archive
Ehrenreich IM, Purugganan MD

Independent origins of self-compatibility in Arabidopsis thaliana.
Mol Ecol (2008 Jan) PMID: 18179433
Shimizu KK, Shimizu-Inatsugi R, Tsuchimatsu T, Purugganan MD

Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World.
Genetics (2007 Nov) PMC2147987 free full-text archive
Saisho D, Purugganan MD

The extent of linkage disequilibrium in rice (Oryza sativa L.).
Genetics (2007 Dec) PMC2219496 free full-text archive
Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD

Genome-wide patterns of nucleotide polymorphism in domesticated rice.
PLoS Genet (2007 Sep) PMC1994709 free full-text archive
Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD

Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae).
Mol Ecol (2007 Oct) PMID: 17784920
Lawton-Rauh A, Robichaux RH, Purugganan MD

Genetics of microenvironmental canalization in Arabidopsis thaliana.
Proc Natl Acad Sci U S A (2007 Aug 21) PMC1959448 free full-text archive
Hall MC, Dworkin I, Ungerer MC, Purugganan M

The genetic architecture of shoot branching in Arabidopsis thaliana: a comparative assessment of candidate gene associations vs. quantitative trait locus mapping.
Genetics (2007 Jun) PMC1894586 free full-text archive
Ehrenreich IM, Stafford PA, Purugganan MD

Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field.
Am Nat (2007 May) PMID: 17427127
Korves TM, Schmid KJ, Caicedo AL, Mays C, Stinchcombe JR, Purugganan MD, Schmitt J

Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication.
PLoS Genet (2006 Nov 17) PMC1636696 free full-text archive
Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI

Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae).
Genetica (2007 May) PMID: 16924407
Fan C, Xiang QY, Remington DL, Purugganan MD, Wiegmann BM

The molecular genetic basis of plant adaptation.
Am J Bot (2006 Jul) PMID: 21642159
Ehrenreich IM, Purugganan MD

Epialleles via DNA methylation: consequences for plant evolution.
Trends Ecol Evol (2004 Jun) PMID: 16701276
Kalisz S, Purugganan MD

Comparative sequencing of plant genomes: choices to make.
Plant Cell (2006 May) PMC1456863 free full-text archive
Jackson S, Rounsley S, Purugganan M

Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus.
Appl Environ Microbiol (2006 Apr) PMC1449082 free full-text archive
Miller SR, Purugganan MD, Curtis SE

Selection under domestication: evidence for a sweep in the rice waxy genomic region.
Genetics (2006 Jun) PMC1526538 free full-text archive
Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD

Vernalization sensitivity in Arabidopsis thaliana (Brassicaceae): the effects of latitude and FLC variation.
Am J Bot (2005 Oct) PMID: 21646087
Stinchcombe JR, Caicedo AL, Hopkins R, Mays C, Boyd EW, Purugganan MD, Schmitt J

Evolutionary and ecological genomics of Arabidopsis.
Plant Physiol (2005 Jun) PMC1150378 free full-text archive
Shimizu KK, Purugganan MD

Comparative plant genomics. Frontiers and prospects.
Plant Physiol (2005 Jun) PMC1150366 free full-text archive
Caicedo AL, Purugganan MD

High-diversity genes in the Arabidopsis genome.
Genetics (2005 Aug) PMC1449776 free full-text archive
Cork JM, Purugganan MD

The evolutionary dynamics of plant duplicate genes.
Curr Opin Plant Biol (2005 Apr) PMID: 15752990
Moore RC, Purugganan MD

The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome.
Mol Ecol (2005 Jan) PMID: 15643950
Tsompana M, Abad J, Purugganan M, Moyer JW

Darwinian selection on a selfing locus.
Science (2004 Dec 17) PMID: 15604405
Shimizu KK, Cork JM, Caicedo AL, Mays CA, Moore RC, Olsen KM, Ruzsa S, Coop G, Bustamante CD, Awadalla P, Purugganan MD

Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae).
Mol Phylogenet Evol (2004 Dec) PMID: 15522789
Fan C, Purugganan MD, Thomas DT, Wiegmann BM, Xiang JQ

Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait.
Proc Natl Acad Sci U S A (2004 Nov 02) PMC524852 free full-text archive
Caicedo AL, Stinchcombe JR, Olsen KM, Schmitt J, Purugganan MD

The evolution of plant development.
Am J Bot (2004 Oct) PMID: 21652320
Friedman WE, Moore RC, Purugganan MD

Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana.
Mol Biol Evol (2005 Jan) PMID: 15371526
Moore RC, Grant SR, Purugganan MD

Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles.
Genetics (2004 Jul) PMC1470957 free full-text archive
Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD

The evolution of molecular genetic pathways and networks.
Bioessays (2004 May) PMID: 15112228
Cork JM, Purugganan MD

A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA.
Proc Natl Acad Sci U S A (2004 Mar 30) PMC384812 free full-text archive
Stinchcombe JR, Weinig C, Ungerer M, Olsen KM, Mays C, Halldorsdottir SS, Purugganan MD, Schmitt J

The early stages of duplicate gene evolution.
Proc Natl Acad Sci U S A (2003 Dec 23) PMC307628 free full-text archive
Moore RC, Purugganan MD

Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana.
Genetics (2003 Sep) PMC1462760 free full-text archive
Ungerer MC, Halldorsdottir SS, Purugganan MD, Mackay TF

Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana.
Genetics (2003 Sep) PMC1462755 free full-text archive
Weinig C, Dorn LA, Kane NC, German ZM, Halldorsdottir SS, Ungerer MC, Toyonaga Y, Mackay TF, Purugganan MD, Schmitt J

Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae).
Mol Ecol (2003 May) PMID: 12694292
Lawton-Rauh A, Robichaux RH, Purugganan MD

Merging ecology, molecular evolution, and functional genetics.
Mol Ecol (2003 May) PMID: 12694275
Purugganan M, Gibson G

Molecular population genetics of the Arabidopsis CLAVATA2 region. The genomic scale of variation and selection in a selfing species.
Genetics (2003 Mar) PMC1462473 free full-text archive
Shepard KA, Purugganan MD

Selection on rapidly evolving proteins in the Arabidopsis genome.
Genetics (2003 Feb) PMC1462452 free full-text archive
Barrier M, Bustamante CD, Yu J, Purugganan MD

Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments.
Genetics (2002 Dec) PMC1462365 free full-text archive
Weinig C, Ungerer MC, Dorn LA, Kane NC, Toyonaga Y, Halldorsdottir SS, Mackay TF, Purugganan MD, Schmitt J

Molecular evidence on the origin and evolution of glutinous rice.
Genetics (2002 Oct) PMC1462305 free full-text archive
Olsen KM, Purugganan MD

GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): molecular evolution of growth regulators in a rapidly diversifying plant lineage.
Mol Biol Evol (2002 Sep) PMID: 12200483
Remington DL, Purugganan MD

Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway.
Genetics (2002 Apr) PMC1462059 free full-text archive
Olsen KM, Womack A, Garrett AR, Suddith JI, Purugganan MD

Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase.
Mol Cell Biol (2002 May) PMC133788 free full-text archive
Huye LE, Purugganan MM, Jiang MM, Roth DB

Distinct and opposite diversifying activities of terminal transferase splice variants.
Nat Immunol (2002 May) PMID: 11938351
Thai TH, Purugganan MM, Roth DB, Kearney JF

The cost of inbreeding in Arabidopsis.
Nature (2002 Apr 04) PMID: 11932744
Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL

Quantitative trait loci for inflorescence development in Arabidopsis thaliana.
Genetics (2002 Mar) PMC1462026 free full-text archive
Ungerer MC, Halldorsdottir SS, Modliszewski JL, Mackay TF, Purugganan MD

Map-based cloning of quantitative trait loci: progress and prospects.
Genet Res (2001 Dec) PMID: 11865710
Remington DL, Ungerer MC, Purugganan MD

The genetics of plant morphological evolution.
Curr Opin Plant Biol (2002 Feb) PMID: 11788308
Shepard KA, Purugganan MD

Accelerated regulatory gene evolution in an adaptive radiation.
Proc Natl Acad Sci U S A (2001 Aug 28) PMC56940 free full-text archive
Barrier M, Robichaux RH, Purugganan MD

Ku80 is required for addition of N nucleotides to V(D)J recombination junctions by terminal deoxynucleotidyl transferase.
Nucleic Acids Res (2001 Apr 01) PMC31272 free full-text archive
Purugganan MM, Shah S, Kearney JF, Roth DB

Quantitative trait loci for floral morphology in Arabidopsis thaliana.
Genetics (2000 Nov) PMC1461322 free full-text archive
Juenger T, Purugganan M, Mackay TF

The molecular population genetics of regulatory genes.
Mol Ecol (2000 Oct) PMID: 11050541
Purugganan MD

Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea.
Genetics (2000 Jun) PMC1461124 free full-text archive
Purugganan MD, Boyles AL, Suddith JI

Molecular evolution of flower development.
Trends Ecol Evol (2000 Apr) PMID: 10717683
Lawton-Rauh AL, Alvarez-Buylla ER, Purugganan MD

Interspecific evolution in plant microsatellite structure.
Gene (2000 Jan 04) PMID: 10607903
Barrier M, Friar E, Robichaux R, Purugganan M

Duplication of the Brassica oleracea APETALA1 floral homeotic gene and the evolution of domesticated cauliflower.
J Hered (1999 Sep-Oct) PMID: 10544496
Lowman AC, Purugganan MD

Patterns of molecular evolution among paralogous floral homeotic genes.
Mol Biol Evol (1999 Aug) PMID: 10474900
Lawton-Rauh AL, Buckler ES 4th, Purugganan MD

Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications.
Mol Biol Evol (1999 Aug) PMID: 10474905
Barrier M, Baldwin BG, Robichaux RH, Purugganan MD

Molecular population genetics of floral homeotic loci. Departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana.
Genetics (1999 Feb) PMC1460493 free full-text archive
Purugganan MD, Suddith JI

The molecular evolution of development.
Bioessays (1998 Sep) PMID: 9819559
Purugganan MD

V(D)J recombination intermediates and non-standard products in XRCC4-deficient cells.
Nucleic Acids Res (1998 Aug 15) PMC147771 free full-text archive
Han JO, Erskine LA, Purugganan MM, Stamato TD, Roth DB

Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: nonneutral evolution and naturally occurring variation in floral homeotic function.
Proc Natl Acad Sci U S A (1998 Jul 07) PMC20941 free full-text archive
Purugganan MD, Suddith JI

Cellular localization of Arabidopsis xyloglucan endotransglycosylase-related proteins during development and after wind stimulation.
Plant Physiol (1997 Dec) PMC158597 free full-text archive
Antosiewicz DM, Purugganan MM, Polisensky DH, Braam J

The Arabidopsis TCH4 xyloglucan endotransglycosylase. Substrate specificity, pH optimum, and cold tolerance.
Plant Physiol (1997 Sep) PMC158473 free full-text archive
Purugganan MM, Braam J, Fry SC

The evolution of the conserved ATPase domain (CAD): reconstructing the history of an ancient protein module.
J Mol Evol (1997 Nov) PMID: 9342402
Swaffield JC, Purugganan MD

The MADS-box floral homeotic gene lineages predate the origin of seed plants: phylogenetic and molecular clock estimates.
J Mol Evol (1997 Oct) PMID: 9321418
Purugganan MD

Plant responses to environmental stress: regulation and functions of the Arabidopsis TCH genes.
Planta (1997) PMID: 9299794
Braam J, Sistrunk ML, Polisensky DH, Xu W, Purugganan MM, Antosiewicz DM, Campbell P, Johnson KA

Life in a changing world: TCH gene regulation of expression and responses to environmental signals.
Physiol Plant (1996 Dec) PMID: 11539337
Braam J, Sistrunk ML, Polisensky DH, Xu W, Purugganan MM, Antosiewicz DM, Campbell P, Johnson KA

Evolution of development: molecules, mechanisms and phylogenetics.
Trends Ecol Evol (1996) PMID: 21237741
Purugganan MD

Arabidopsis TCH4, regulated by hormones and the environment, encodes a xyloglucan endotransglycosylase.
Plant Cell (1995 Oct) PMC161010 free full-text archive
Xu W, Purugganan MM, Polisensky DH, Antosiewicz DM, Fry SC, Braam J

Molecular evolution of flower development: diversification of the plant MADS-box regulatory gene family.
Genetics (1995 May) PMC1206560 free full-text archive
Purugganan MD, Rounsley SD, Schmidt RJ, Yanofsky MF

Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA.
Mol Ecol (1995 Apr) PMID: 7735530
Purugganan MD, Wessler SR

Molecular evolution of magellan, a maize Ty3/gypsy-like retrotransposon.
Proc Natl Acad Sci U S A (1994 Nov 22) PMC45294 free full-text archive
Purugganan MD, Wessler SR

Molecular evolution of the plant R regulatory gene family.
Genetics (1994 Nov) PMC1206232 free full-text archive
Purugganan MD, Wessler SR

Arabidopsis TCH3 encodes a novel Ca2+ binding protein and shows environmentally induced and tissue-specific regulation.
Plant Cell (1994 Nov) PMC160543 free full-text archive
Sistrunk ML, Antosiewicz DM, Purugganan MM, Braam J

Transposable elements as introns: evolutionary connections.
Trends Ecol Evol (1993 Jul) PMID: 21236158
Purugganan MD

Alternative splicing induced by insertion of retrotransposons into the maize waxy gene.
Plant Cell (1992 Jul) PMC160176 free full-text archive
Varagona MJ, Purugganan M, Wessler SR

The splicing of transposable elements and its role in intron evolution.
Genetica (1992) PMID: 1334914
Purugganan M, Wessler S

Filler DNA is associated with spontaneous deletions in maize.
Proc Natl Acad Sci U S A (1990 Nov) PMC55033 free full-text archive
Wessler S, Tarpley A, Purugganan M, Spell M, Okagaki R

The fractal nature of RNA secondary structure.
Naturwissenschaften (1989 Oct) PMID: 2479842
Purugganan MD

Accelerated electron transfer between metal complexes mediated by DNA.
Science (1988 Sep 23) PMID: 3420416
Purugganan MD, Kumar CV, Turro NJ, Barton JK