@article{ehrenreich_hanzawa_chou_roe_kover_purugganan_2009, title={Candidate Gene Association Mapping of Arabidopsis Flowering Time}, volume={183}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.109.105189}, abstractNote={Abstract}, number={1}, journal={GENETICS}, author={Ehrenreich, Ian M. and Hanzawa, Yoshie and Chou, Lucy and Roe, Judith L. and Kover, Paula X. and Purugganan, Michael D.}, year={2009}, month={Sep}, pages={325–335} } @article{caicedo_richards_ehrenreich_purugganan_2009, title={Complex Rearrangements Lead to Novel Chimeric Gene Fusion Polymorphisms at the Arabidopsis thaliana MAF2-5 Flowering Time Gene Cluster}, volume={26}, ISSN={["1537-1719"]}, DOI={10.1093/molbev/msn300}, abstractNote={Tandem gene clusters of multigene families are rearrangement hotspots and may be a major source of novel gene formation. Here, we report on a molecular population genetic analysis of the MAF2-5 gene cluster of the model plant species, Arabidopsis thaliana. The MAF2-5 genes are a MADS-box multigene family cluster spanning approximately 24 kbp on chromosome 5. We find heterogeneous evolutionary dynamics among these genes, all of which are closely related to the floral repressor, FLC, and are believed to play a role in the control of flowering time in A. thaliana. Low levels of nonsynonymous single nucleotide polymorphism (SNP) observed for MAF4 and MAF5 suggest purifying selection and conservation of function. In contrast, high levels of nonsynonymous SNPs, insertion-deletion, and rearrangements are observed for MAF2 and MAF3, including novel gene fusions that persist as a moderate-frequency polymorphism in A. thaliana. These fused genes, involving MAF2 and portions of MAF3, are expressed, resulting in the production of chimeric, alternatively spliced transcripts of MAF2. Association studies support a correlation between the described MAF2-MAF3 gene rearrangements and flowering time variation in the species. The finding that complex rearrangements within gene clusters, such as those observed for MAF2, might play a role in the generation of ecologically important phenotypic variation, emphasize the need for emerging high throughput genotyping and sequencing techniques to correctly reconstruct gene chimeras and other complex polymorphisms.}, number={3}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Caicedo, Ana L. and Richards, Christina and Ehrenreich, Ian M. and Purugganan, Michael D.}, year={2009}, month={Mar}, pages={699–711} } @article{reininga_nielsen_purugganan_2009, title={Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana}, volume={18}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2009.04206.x}, abstractNote={Abstract}, number={13}, journal={MOLECULAR ECOLOGY}, author={Reininga, Jennifer M. and Nielsen, Dahlia and Purugganan, Michael D.}, year={2009}, month={Jul}, pages={2844–2855} } @article{shimizu_reininga_caicedo_mays_moore_olsen_ruzsa_coop_bustamante_purugganan_2008, title={Darwinian selection on a selfing locus (vol 306, pg 2081, 2004)}, volume={320}, number={5873}, journal={Science}, author={Shimizu, K. K. and Reininga, J. M. and Caicedo, A. L. and Mays, C. A. and Moore, R. C. and Olsen, K. M. and Ruzsa, S. and Coop, G. and Bustamante, C. D. and Purugganan, M. D.}, year={2008}, pages={176–176} } @article{shimizu_shimizu-inatsugi_tsuchimatsu_purugganan_2008, title={Independent origins of self-compatibility in Arabidopsis thaliana}, volume={17}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2007.03605.x}, abstractNote={Abstract}, number={2}, journal={MOLECULAR ECOLOGY}, author={Shimizu, Kentaro K. and Shimizu-Inatsugi, Rie and Tsuchimatsu, Takashi and Purugganan, Michael D.}, year={2008}, month={Jan}, pages={704–714} } @article{ehrenreich_purugganan_2008, title={Sequence variation of microRNAs and their binding sites in Arabidopsis}, volume={146}, ISSN={["1532-2548"]}, DOI={10.1104/pp.108.116582}, abstractNote={Abstract}, number={4}, journal={PLANT PHYSIOLOGY}, author={Ehrenreich, Ian M. and Purugganan, Michael D.}, year={2008}, month={Apr}, pages={1974–1982} } @article{lawton-rauh_robichaux_purugganan_2007, title={Diversity and divergence patterns in regulatory genes suggest differential gene flow in recently derived species of the Hawaiian silversword alliance adaptive radiation (Asteraceae)}, volume={16}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2007.03445.x}, abstractNote={Abstract}, number={19}, journal={MOLECULAR ECOLOGY}, author={Lawton-Rauh, A. and Robichaux, R. H. and Purugganan, M. D.}, year={2007}, month={Oct}, pages={3995–4013} } @article{fan_xiang_remington_purugganan_wiegmann_2007, title={Evolutionary patterns in the antR-Cor gene in the dwarf dogwood complex (Cornus, Cornaceae)}, volume={130}, ISSN={0016-6707, 1573-6857}, url={http://link.springer.com/10.1007/s10709-006-0016-3}, DOI={10.1007/s10709-006-0016-3}, abstractNote={The evolutionary pattern of the myc-like anthocyanin regulatory gene antR-Cor was examined in the dwarf dogwood species complex (Cornus Subgenus Arctocrania) that contains two diploid species (C. canadensis and C. suecica), their putative hybrids with intermediate phenotypes, and a tetraploid derivative (C. unalaschkensis). Full-length sequences of this gene ( approximately 4 kb) were sequenced and characterized for 47 dwarf dogwood samples representing all taxa categories from 43 sites in the Pacific Northwest. Analysis of nucleotide diversity indicated departures from neutral evolution, due most likely to local population structure. Neighbor-joining and haplotype network analyses show that sequences from the tetraploid and diploid intermediates are much more strongly diverged from C. suecica than from C. canadensis, and that the intermediate phenotypes may represent an ancestral group to C. canadensis rather than interspecific hybrids. Seven amino acid mutations that are potentially linked to myc-like anthocyanin regulatory gene function correlate with petal colors differences that characterize the divergence between two diploid species and the tetraploid species in this complex. The evidence provides a working hypothesis for testing the role of the gene in speciation and its link to the petal coloration. Sequencing and analysis of additional nuclear genes will be necessary to resolve questions about the evolution of the dwarf dogwood complex.}, number={1}, journal={Genetica}, author={Fan, Chuanzhu and Xiang, Qiu-Yun (Jenny) and Remington, David L. and Purugganan, Michael D. and Wiegmann, Brian M.}, year={2007}, month={Apr}, pages={19–34} } @article{korves_schmid_caicedo_mays_stinchcombe_purugganan_schmitt_2007, title={Fitness effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field}, volume={169}, ISSN={["1537-5323"]}, DOI={10.1086/513111}, abstractNote={To date, the effect of natural selection on candidate genes underlying complex traits has rarely been studied experimentally, especially under ecologically realistic conditions. Here we report that the effect of selection on the flowering time gene FRIGIDA (FRI) reverses depending on the season of germination and allelic variation at the interacting gene FLOWERING LOCUS C (FLC). In field studies of 136 European accessions of Arabidopsis thaliana, accessions with putatively functional FRI alleles had higher winter survival in one FLC background in a fall‐germinating cohort, but accessions with deletion null FRI alleles had greater seed production in the other FLC background in a spring‐germinating cohort. Consistent with FRI’s role in flowering, selection analyses suggest that the difference in winter survival can be attributed to time to bolting. However, in the spring cohort, the fitness difference was associated with rosette size. Our analyses also reveal that controlling for population structure with estimates of inferred ancestry and a geographical restriction was essential for detecting fitness associations. Overall, our results suggest that the combined effects of seasonally varying selection and epistasis could explain the maintenance of variation at FRI and, more generally, may be important in the evolution of genes underlying complex traits.}, number={5}, journal={AMERICAN NATURALIST}, author={Korves, Tonia M. and Schmid, Karl J. and Caicedo, Ana L. and Mays, Charlotte and Stinchcombe, John R. and Purugganan, Michael D. and Schmitt, Johanna}, year={2007}, pages={E141–E157} } @article{hall_dworkin_ungerer_purugganan_2007, title={Genetics of microenvironmental canalization in Arabidopsis thaliana}, volume={104}, number={34}, journal={Proceedings of the National Academy of Sciences of the United States of America}, author={Hall, M. C. and Dworkin, I. and Ungerer, M. C. and Purugganan, M.}, year={2007}, pages={13717–13722} } @article{mather_caicedo_polato_olsen_mccouch_purugganan_2007, title={The extent of linkage disequilibrium in rice (Oryza sativa L.)}, volume={177}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.107.079616}, abstractNote={Abstract}, number={4}, journal={GENETICS}, author={Mather, Kristie A. and Caicedo, Ana L. and Polato, Nicholas R. and Olsen, Kenneth M. and McCouch, Susan and Purugganan, Michael D.}, year={2007}, month={Dec}, pages={2223–2232} } @article{ehrenreich_stafford_purugganan_2007, title={The genetic architecture of shoot branching in Arabidopsis thaliana: A comparative assessment of candidate gene associations vs. quantitative trait locus mapping}, volume={176}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.107.071928}, abstractNote={Abstract}, number={2}, journal={GENETICS}, author={Ehrenreich, Ian M. and Stafford, Phillip A. and Purugganan, Michael D.}, year={2007}, month={Jun}, pages={1223–1236} } @article{jackson_rounsley_purugganan_2006, title={Comparative sequencing of plant genomes: Choices to make}, volume={18}, number={5}, journal={Plant Cell}, author={Jackson, S. and Rounsley, S. and Purugganan, M.}, year={2006}, pages={1100–1104} } @article{tang_lu_huang_he_mccouch_shen_kai_purugganan_shi_wu_2006, title={Genomic variation in rice: Genesis of highly polymorphic linkage blocks during domestication}, volume={2}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.0020199}, abstractNote={Genomic regions that are unusually divergent between closely related species or racial groups can be particularly informative about the process of speciation or the operation of natural selection. The two sequenced genomes of cultivated Asian rice, Oryza sativa, reveal that at least 6% of the genomes are unusually divergent. Sequencing of ten unlinked loci from the highly divergent regions consistently identified two highly divergent haplotypes with each locus in nearly complete linkage disequilibrium among 25 O. sativa cultivars and 35 lines from six wild species. The existence of two highly divergent haplotypes in high divergence regions in species from all geographical areas (Africa, Asia, and Oceania) was in contrast to the low polymorphism and low linkage disequilibrium that were observed in other parts of the genome, represented by ten reference loci. While several natural processes are likely to contribute to this pattern of genomic variation, domestication may have greatly exaggerated the trend. In this hypothesis, divergent haplotypes that were adapted to different geographical and ecological environments migrated along with humans during the development of domesticated varieties. If true, these high divergence regions of the genome would be enriched for loci that contribute to the enormous range of phenotypic variation observed among domesticated breeds.}, number={11}, journal={PLOS GENETICS}, author={Tang, Tian and Lu, Jian and Huang, Jianzi and He, Jinghong and McCouch, Susan R. and Shen, Yang and Kai, Zeng and Purugganan, Michael D. and Shi, Suhua and Wu, Chung-I}, year={2006}, month={Nov}, pages={1824–1833} } @article{miller_purugganan_curtis_2006, title={Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.72.4.2793-2800.2006}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Miller, SR and Purugganan, MD and Curtis, SE}, year={2006}, month={Apr}, pages={2793–2800} } @article{olsen_caicedo_polato_mcclung_mccouch_purugganan_2006, title={Selection under domestication: Evidence for a sweep in the rice Waxy genomic region}, volume={173}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.106.056473}, abstractNote={Abstract}, number={2}, journal={GENETICS}, author={Olsen, Kenneth M. and Caicedo, Ana L. and Polato, Nicholas and McClung, Anna and McCouch, Susan and Purugganan, Michael D.}, year={2006}, month={Jun}, pages={975–983} } @misc{ehrenreich_purugganan_2006, title={The molecular genetic basis of plant adaptation}, volume={93}, number={7}, journal={American Journal of Botany}, author={Ehrenreich, I. M. and Purugganan, M. D.}, year={2006}, pages={953–962} } @article{purugganan_robichaux_2005, title={Adaptive radiation and regulatory gene evolution in the Hawaiian silversword alliance (Asteraceae)}, volume={92}, number={1}, journal={Annals of the Missouri Botanical Garden}, author={Purugganan, M. D. and Robichaux, R. H.}, year={2005}, pages={28–35} } @article{caicedo_purugganan_2005, title={Comparative plant genomics. Frontiers and prospects}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.104.900148}, abstractNote={Comparative methods have long been the cornerstone of studies that draw inferences about function and evolution at various levels of biological organization. The availability of whole-genome sequences as well as other genomic resources (e.g. microarray methods, expressed sequence tag [EST] libraries}, number={2}, journal={PLANT PHYSIOLOGY}, author={Caicedo, AL and Purugganan, MD}, year={2005}, month={Jun}, pages={545–547} } @article{shimizu_purugganan_2005, title={Evolutionary and ecological genomics of arabidopsis}, volume={138}, ISSN={["1532-2548"]}, DOI={10.1104/pp.105.061655}, abstractNote={Why are some plants self-pollinating? What determines the timing of flowering and germination? Why do resistant and susceptible alleles of pathogen-resistant genes coexist in populations? These are just a few questions traditionally asked in the domain of ecology and evolutionary biology, and}, number={2}, journal={PLANT PHYSIOLOGY}, author={Shimizu, KK and Purugganan, MD}, year={2005}, month={Jun}, pages={578–584} } @article{cork_purugganan_2005, title={High-diversity genes in the Arabidopsis genome}, volume={170}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.104.036152}, abstractNote={Abstract}, number={4}, journal={GENETICS}, author={Cork, JM and Purugganan, MD}, year={2005}, month={Aug}, pages={1897–1911} } @article{moore_grant_purugganan_2005, title={Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana}, volume={22}, number={1}, journal={Molecular Biology and Evolution}, author={Moore, R. C. and Grant, S. R. and Purugganan, M. D.}, year={2005}, pages={91–103} } @misc{moore_purugganan_2005, title={The evolutionary dynamics of plant duplicate genes}, volume={8}, ISSN={["1879-0356"]}, DOI={10.1016/j.pbi.2004.12.001}, abstractNote={Given the prevalence of duplicate genes and genomes in plant species, the study of their evolutionary dynamics has been a focus of study in plant evolutionary genetics over the past two decades. The past few years have been a particularly exciting time because recent theoretical and experimental investigations have led to a rethinking of the classic paradigm of duplicate gene evolution. By combining recent advances in genomic analysis with a new conceptual framework, researchers are determining the contributions of single-gene and whole-genome duplications to the diversification of plant species. This research provides insights into the roles that gene and genome duplications play in plant evolution.}, number={2}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Moore, RC and Purugganan, MD}, year={2005}, month={Apr}, pages={122–128} } @article{tsompana_abad_purugganan_moyer_2005, title={The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome}, volume={14}, ISSN={["1365-294X"]}, DOI={10.1111/j.1365-294X.2004.02392.x}, abstractNote={Abstract}, number={1}, journal={MOLECULAR ECOLOGY}, author={Tsompana, M and Abad, J and Purugganan, M and Moyer, JW}, year={2005}, month={Jan}, pages={53–66} } @article{stinchcombe_caicedo_hopkins_mays_boyd_purugganan_schmitt_2005, title={Vernalization sensitivity in Arabidopsis thaliana (brassicaceae): The effects of latitude and FLC variation}, volume={92}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.92.10.1701}, abstractNote={Latitudinal variation in climate is predicted to select for latitudinal differentiation in sensitivity to the environmental cues that signal plants to flower at the appropriate time for a given climate. In Arabidopsis thaliana, flowering is promoted by exposure to cold temperatures (vernalization), and several vernalization pathway loci are known. To test whether natural variation in vernalization sensitivity could account for a previously observed latitudinal cline in flowering time in A. thaliana, we exposed 21 European accessions to 0, 10, 20, or 30 d of vernalization and observed leaf number at flowering under short days in a growth chamber. We observed a significant latitudinal cline in vernalization sensitivity: southern accessions were more sensitive to vernalization than northern accessions. In addition, accessions that were late flowering in the absence of vernalization were more sensitive to vernalization cues. Allelic variation at the flowering time regulatory gene FLC was not associated with mean vernalization sensitivity, but one allele class exhibited greater variance in vernalization sensitivity.}, number={10}, journal={AMERICAN JOURNAL OF BOTANY}, author={Stinchcombe, JR and Caicedo, AL and Hopkins, R and Mays, C and Boyd, EW and Purugganan, MD and Schmitt, J}, year={2005}, month={Oct}, pages={1701–1707} } @article{stinchcombe_weinig_ungerer_olsen_mays_halldorsdottir_purugganan_schmitt_2004, title={A latitudinal cline in flowering time in Arabidopsis thaliana modulated by the flowering time gene FRIGIDA}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0306401101}, abstractNote={ A latitudinal cline in flowering time in accessions of Arabidopsis thaliana has been widely predicted because the environmental cues that promote flowering vary systematically with latitude, but evidence for such clines has been lacking. Here, we report evidence of a significant latitudinal cline in flowering time among 70 Northern European and Mediterranean ecotypes when grown under ecologically realistic conditions in a common garden environment. The detected cline, however, is found only in ecotypes with alleles of the flowering time gene FRIGIDA ( FRI ) that lack major deletions that would disrupt protein function, whereas there is no relationship between flowering time and latitude of origin among accessions with FRI alleles containing such deletions. Analysis of climatological data suggests that late flowering in accessions with putatively functional FRI was associated with reduced January precipitation at the site of origin, consistent with previous reports of a positive genetic correlation between water use efficiency and flowering time in Arabidopsis , and the pleiotropic effects of FRI of increasing water use efficiency. In accessions collected from Southern latitudes, we detected that putatively functional FRI alleles were associated with accelerated flowering relative to accessions with nonfunctional FRI under the winter conditions of our experiment. These results suggest that the ecological function of the vernalization requirement conferred by FRI differs across latitudes. More generally, our results indicate that by combining ecological and molecular genetic data, it is possible to understand the forces acting on life history transitions at the level of specific loci. }, number={13}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Stinchcombe, JR and Weinig, C and Ungerer, M and Olsen, KM and Mays, C and Halldorsdottir, SS and Purugganan, MD and Schmitt, J}, year={2004}, month={Mar}, pages={4712–4717} } @article{shimizu_cork_caicedo_mays_moore_olsen_ruzsa_coop_bustamante_awadalla_et al._2004, title={Darwinian selection on a selfing locus (Retracted Article. See vol 320, pg 176, 2008)}, volume={306}, ISSN={["1095-9203"]}, DOI={10.1126/science.1103776}, abstractNote={ The shift to self-pollination is one of the most prevalent evolutionary transitions in flowering plants. In the selfing plant Arabidopsis thaliana , pseudogenes at the SCR and SRK self-incompatibility loci are believed to underlie the evolution of self-fertilization. Positive directional selection has driven the evolutionary fixation of pseudogene alleles of SCR , leading to substantially reduced nucleotide variation. Coalescent simulations indicate that this adaptive event may have occurred very recently and is possibly associated with the post-Pleistocene expansion of A. thaliana from glacial refugia. This suggests that ancillary morphological innovations associated with self-pollination can evolve rapidly after the inactivation of the self-incompatibility response. }, number={5704}, journal={SCIENCE}, author={Shimizu, KK and Cork, JM and Caicedo, AL and Mays, CA and Moore, RC and Olsen, KM and Ruzsa, S and Coop, G and Bustamante, CD and Awadalla, P and et al.}, year={2004}, month={Dec}, pages={2081–2084} } @article{kalisz_purugganan_2004, title={Epialleles via DNA methylation: consequences for plant evolution}, volume={19}, ISSN={["0169-5347"]}, DOI={10.1016/j.tree.2004.03.034}, abstractNote={In plants, naturally occurring methylation of genes can affect the level of gene expression. Variation among individuals in the degree of methylation of a gene, termed epialleles, produces novel phenotypes that are heritable across generations. To date, ecologically important genes with methylated epialleles have been found to affect floral shape, vegetative and seed pigmentation, pathogen resistance and development in plants. Currently, the extent to which epiallelic variation is an important common contributor to phenotypic variation in natural plant populations and its fitness consequences are not known. Because epiallele phenotypes can have identical underlying DNA sequences, response to selection on these phenotypes is likely to differ from expectations based on traditional models of microevolution. Research is needed to understand the role of epialleles in natural plant populations. Recent advances in molecular genetic techniques could enable population biologists to screen for epiallelic variants within plant populations and disentangle epigenetic from more standard genetic sources of phenotypic variance, such as additive genetic variance, dominance variance, epistasis and maternal genetic effects.}, number={6}, journal={TRENDS IN ECOLOGY & EVOLUTION}, author={Kalisz, S and Purugganan, MD}, year={2004}, month={Jun}, pages={309–314} } @article{caicedo_stinchcombe_olsen_schmitt_purugganan_2004, title={Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait}, volume={101}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0406232101}, abstractNote={ Epistatic gene interactions are believed to be a major factor in the genetic architecture of evolutionary diversification. In Arabidopsis thaliana , the FRI and FLC genes mechanistically interact to control flowering time, and here we show that this epistatic interaction also contributes to a latitudinal cline in this life history trait within the species. Two major FLC haplogroups ( FLC A and FLC B ) are associated with flowering time variation in A. thaliana in field conditions, but only in the presence of putatively functional FRI alleles. Significant differences in latitudinal distribution of FLC haplogroups in Eurasia and North Africa also depend on the FRI genotype. There is significant linkage disequilibrium between FRI and FLC despite their location on separate chromosomes. Although no nonsynonymous polymorphisms differentiate FLC A and FLC B , vernalization induces the expression of an alternatively spliced FLC transcript that encodes a variant protein with a radical amino acid replacement associated with the two FLC haplogroups. Numerous polymorphisms differentiating the FLC haplogroups also occur in intronic regions implicated in the regulation of FLC expression. The features of the regulatory gene interaction between FRI and FLC in contributing to the latitudinal cline in A. thaliana flowering time are consistent with the maintenance of this interaction by epistatic selection. These results suggest that developmental genetic pathways and networks provide the molecular basis for epistasis, contributing to ecologically important phenotypic variation in natural populations and to the process of evolutionary diversification. }, number={44}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Caicedo, AL and Stinchcombe, JR and Olsen, KM and Schmitt, J and Purugganan, MD}, year={2004}, month={Nov}, pages={15670–15675} } @article{fan_purugganan_thomas_wiegmann_xiang_2004, title={Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae)}, volume={33}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2004.08.002}, abstractNote={Anthocyanin is a major pigment in vegetative and floral organs of most plants and plays an important role in plant evolution. The anthocyanin regulatory genes are responsible for regulating transcription of genes in the anthocyanin synthetic pathway. To assess evolutionary significance of sequence variation and evaluate the phylogenetic utility of an anthocyanin regulatory gene, we compared nucleotide sequences of the myc-like anthocyanin regulatory gene in the genus of dogwoods (Cornus: Cornaceae). Phylogenetic analyses demonstrate that the myc-like anthocyanin regulatory gene has potential as an informative phylogenetic marker at different taxonomic levels, depending on the data set considered (DNA or protein sequences) and regions applied (exons or introns). Pairwise nonsynonymous and synonymous substitution rate tests and codon-based substitution models were applied to characterize variation and to identify sites under diversifying selection. Mosaic evolution and heterogeneous rates among different domains and sites were detected.}, number={3}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Fan, CZ and Purugganan, MD and Thomas, DT and Wiegmann, BM and Xiang, QY}, year={2004}, month={Dec}, pages={580–594} } @article{olsen_halldorsdottir_stinchcombe_weinig_schmitt_purugganan_2004, title={Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles}, volume={167}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.103.024950}, abstractNote={Abstract}, number={3}, journal={GENETICS}, author={Olsen, KM and Halldorsdottir, SS and Stinchcombe, JR and Weinig, C and Schmitt, J and Purugganan, MD}, year={2004}, month={Jul}, pages={1361–1369} } @misc{cork_purugganan_2004, title={The evolution of molecular genetic pathways and networks}, volume={26}, ISSN={["1521-1878"]}, DOI={10.1002/bies.20026}, abstractNote={Abstract}, number={5}, journal={BIOESSAYS}, author={Cork, JM and Purugganan, MD}, year={2004}, month={May}, pages={479–484} } @misc{friedman_moore_purugganan_2004, title={The evolution of plant development}, volume={91}, ISSN={["1537-2197"]}, DOI={10.3732/ajb.91.10.1726}, abstractNote={The last decade has witnessed a resurgence in the study of the evolution of plant development, combining investigations in systematics, developmental morphology, molecular developmental genetics, and molecular evolution. The integration of phylogenetic studies, structural analyses of fossil and extant taxa, and molecular developmental genetic information allows the formulation of explicit and testable hypotheses for the evolution of morphological characters. These comprehensive approaches provide opportunities to dissect the evolution of major developmental transitions among land plants, including those associated with apical meristems, the origins of the root/shoot dichotomy, diversification of leaves, and origin and subsequent modification of flower structure. The evolution of these major developmental innovations is discussed within both phylogenetic and molecular genetic contexts. We conclude that it is the combination of these approaches that will lead to the greatest understanding of the evolution of plant development.}, number={10}, journal={AMERICAN JOURNAL OF BOTANY}, author={Friedman, WE and Moore, RC and Purugganan, MD}, year={2004}, month={Oct}, pages={1726–1741} } @misc{remington_purugganan_2003, title={Candidate genes, quantitative trait loci, and functional trait evolution in plants}, volume={164}, ISSN={["1058-5893"]}, DOI={10.1086/367812}, abstractNote={Two key characteristics of the neo‐Darwinian synthesis in evolutionary biology have been its emphasis on the importance of mutations of small effect (micromutationism) and the view that studies of individual gene function shed relatively little light on evolutionary processes. Recent advances in molecular biology, however, have broken down many of the barriers between functional and evolutionary inquiry, opening the door to detailed studies of the genetic basis of functional trait evolution in plants. In this article, we review the insights into plant evolution that have been provided by molecular methods and address future research needs. Quantitative trait locus (QTL) mapping in crop and model plants has shown that individual loci often have large effects on trait variation, at variance with the micromutationist perspective. Evidence so far indicates that QTLs with large effects are also important in wild populations, underlying interspecific differences as well as intraspecific variation. Isolation of some of these QTLs, in particular for flowering time variation, has revealed a prominent role for regulatory genes known to function in regulation of flowering and exposed the complexity of regulatory processes. Preliminary evidence indicates that plant growth variation may be directly regulated rather than primarily the indirect result of selection on constituent processes. Future research should expand the number of traits that are intensively studied and make greater use of QTL mapping in wild plant taxa, especially those undergoing adaptive radiations, while continuing to draw on insights from model plants. Promising techniques include testing of candidate gene‐trait associations in wild populations, genetic mapping in hybrid zones, and microarray analyses of gene expression.}, number={3}, journal={INTERNATIONAL JOURNAL OF PLANT SCIENCES}, author={Remington, DL and Purugganan, MD}, year={2003}, month={May}, pages={S7–S20} } @article{ungerer_halldorsdottir_purugganan_mackay_2003, title={Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana}, volume={165}, number={1}, journal={Genetics}, author={Ungerer, M. C. and Halldorsdottir, S. S. and Purugganan, M. D. and Mackay, T. F. C.}, year={2003}, month={Sep}, pages={353–365} } @article{weinig_dorn_kane_german_hahdorsdottir_ungerer_toyonaga_mackay_purugganan_schmitt_2003, title={Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana}, volume={165}, number={1}, journal={Genetics}, author={Weinig, C. and Dorn, L. A. and Kane, N. C. and German, Z. M. and Hahdorsdottir, S. S. and Ungerer, M. C. and Toyonaga, Y. and Mackay, T. F. C. and Purugganan, M. D. and Schmitt, J.}, year={2003}, month={Sep}, pages={321–329} } @article{xie_wehner_wollenberg_purugganan_conkling_2003, title={Intron and polypeptide evolution of conserved NPA to NPA motif regions in plant aquaporins}, volume={128}, number={4}, journal={Journal of the American Society for Horticultural Science}, author={Xie, J. H. and Wehner, T. C. and Wollenberg, K. and Purugganan, M. D. and Conkling, M. A.}, year={2003}, pages={591–597} } @article{purugganan_gibson_2003, title={Merging ecology, molecular evolution, and functional genetics}, volume={12}, ISSN={["0962-1083"]}, DOI={10.1046/j.1365-294X.2003.01851.x}, abstractNote={'This structure has novel features which are of considerable biological interest.' This has to be one of the boldest understatements in all of biology, written 50 years ago in Nature by Francis Crick and Jim Watson in describing their model for the DNA double helix (Watson & Crick 1953). The unveiling of the structure of the molecule that carries the hereditary information of living organisms is rightly hailed as a landmark in the history of science, and we rightly celebrate the golden anniversary of this discovery this year. Understanding the molecular basis of genes has transformed biological research since 1953, and ecologists have participated in the fruits of this revolution. The use of molecular markers, beginning with restriction fragment length polymorphisms (RFLPs) to today's single nucleotide polymorphisms (SNPs), has had a significant impact on our ability to trace parentage and kinship, to measure gene flow and migration patterns and to reconstruct the demographic histories of populations and species. Few will argue that the advent of modern genetic technology has provided an unparalleled ability to examine evolutionary and ecological forces in nature. Yet the full impact of molecular genetics (and today, genomics) has yet to be felt by the discipline of ecology. While the use of molecular markers by ecologists has been fruitful, there is more to the molecules than their current dominant role in ecological research as mere genetic barcodes. We have yet to understand ecological processes at a fundamentally molecular level, and our inability to make this connection from the ecological gene to the ecological organism hampers any dreams we may harbour of creating a unified picture of life. We do not know, to a large extent, the interplay between genes and the ecological processes that dominate life at and above the organ-ismal level. We stand today at a crossroads that provide unprecedented opportunity to make these connections. Molecular biologists have proved adept at unravelling the molecular mechanisms behind many of the physiological, developmental and at times behavioural processes that characterize organismal lives. It is time that ecologists make use of this information in meaningful ways to gain further insights into the nature of organismal ecologies. How do we go about doing this? There is no one single answer to this question. There remains no single coherent program of molecular ecology. But it is the diversity of approaches that make this an interesting enterprise, and in this issue we …}, number={5}, journal={MOLECULAR ECOLOGY}, author={Purugganan, M and Gibson, G}, year={2003}, month={May}, pages={1109–1112} } @article{purugganan_2003, title={Michael Purugganan}, volume={421}, DOI={10.1038/421117a}, number={6919}, journal={Nature}, author={Purugganan, M.}, year={2003}, pages={117} } @article{shepard_purugganan_2003, title={Molecular population genetics of the Arabidopsis CLAVATA2 region: The genomic scale of variation and selection in a selfing species}, volume={163}, number={3}, journal={Genetics}, author={Shepard, K. A. and Purugganan, M. D.}, year={2003}, pages={1083–1095} } @article{lawton-rauh_robichaux_purugganan_2003, title={Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae)}, volume={12}, ISSN={["1365-294X"]}, DOI={10.1046/j.1365-294X.2003.01814.x}, abstractNote={Abstract}, number={5}, journal={MOLECULAR ECOLOGY}, author={Lawton-Rauh, A and Robichaux, RH and Purugganan, MD}, year={2003}, month={May}, pages={1301–1313} } @article{barrier_bustamante_yu_purugganan_2003, title={Selection on rapidly evolving proteins in the Arabidopsis genome}, volume={163}, number={2}, journal={Genetics}, author={Barrier, M. and Bustamante, C. D. and Yu, J. Y. and Purugganan, M. D.}, year={2003}, pages={723–733} } @article{moore_purugganan_2003, title={The early stages of duplicate gene evolution}, volume={100}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.2535513100}, abstractNote={ Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems. Gene duplicates account for 8–20% of the genes in eukaryotic genomes, and the rates of gene duplication are estimated at between 0.2% and 2% per gene per million years. Duplicate genes are believed to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty, yet very little is known about the early stages of the evolution of duplicated gene pairs. It is unclear, for example, to what extent selection, rather than neutral genetic drift, drives the fixation and early evolution of duplicate loci. Analysis of recently duplicated genes in the Arabidopsis thaliana genome reveals significantly reduced species-wide levels of nucleotide polymorphisms in the progenitor and/or duplicate gene copies, suggesting that selective sweeps accompany the initial stages of the evolution of these duplicated gene pairs. Our results support recent theoretical work that indicates that fates of duplicate gene pairs may be determined in the initial phases of duplicate gene evolution and that positive selection plays a prominent role in the evolutionary dynamics of the very early histories of duplicate nuclear genes. }, number={26}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Moore, RC and Purugganan, MD}, year={2003}, month={Dec}, pages={15682–15687} } @article{olsen_womack_garrett_suddith_purugganan_2002, title={Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway}, volume={160}, number={4}, journal={Genetics}, author={Olsen, K. M. and Womack, A. and Garrett, A. R. and Suddith, J. I. and Purugganan, M. D.}, year={2002}, pages={1641–1650} } @article{remington_purugganan_2002, title={GAI homologues in the Hawaiian silversword alliance (Asteraceae-Madiinae): Molecular evolution of growth regulators in a rapidly diversifying plant lineage}, volume={19}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a004218}, abstractNote={Accelerated evolution of regulatory genes has been proposed as an explanation for decoupled rates of morphological and molecular evolution. The Hawaiian silversword alliance (Asteraceae-Madiinae) has evolved drastic differences in growth form, including rosette plants, cushion plants, shrubs, and trees, since its origin approximately 6 MYA. We have isolated genes in the DELLA subfamily of putative growth regulators from 13 taxa of Hawaiian and North American Madiinae. The Hawaiian taxa contain two copies of DaGAI that form separate clades within the Madiinae, consistent with an allotetraploid origin for the silversword alliance. DaGAI retains conserved features that have previously been identified in DELLA genes. Selective constraint in the Hawaiian DaGAI copies remains strong in spite of rapid growth form divergence in the silversword alliance, although the constraint was somewhat relaxed in the Hawaiian copies relative to the North American lineages. We failed to detect evidence for positive selection on individual codons. Notably, selective constraint remained especially strong in the gibberellin-responsive DELLA region for which the gene subfamily is named, which is truncated or deleted in all identified dwarf mutants in GAI homologues in different angiosperm species. In contrast with the coding region, however, approximately 900 bp of the upstream flanking region shows variable rates and patterns of evolution, which might reflect positive selection on regulatory regions.}, number={9}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Remington, DL and Purugganan, MD}, year={2002}, month={Sep}, pages={1563–1574} } @article{jackson_linder_lynch_purugganan_somerville_thayer_2002, title={Linking molecular insight and ecological research}, volume={17}, ISSN={["1872-8383"]}, DOI={10.1016/S0169-5347(02)02571-5}, abstractNote={Significant environmental challenges, including the genetic and physiological effects of environmental pollutants, the rapid spread of diseases and invasive species, the release of transgenic organisms and global climate change, affect our daily lives and the sustainability of ecosystems. Managing these environmental problems will require new approaches that span the biology of genes, organisms, populations, communities and ecosystems. In parallel with these practical concerns is the basic need to study gene functions in their natural context. The Arabidopsis 2010 project, for example, seeks to understand the functions of all 25 000 Arabidopsis genes within a decade but, to do so, we must also understand the role of the environment in determining gene function. A new priority is evident – understanding the interplay of molecular mechanisms with organismal and ecosystem biology. Combining genomic and ecological research perspectives will answer crucial unresolved questions, but will require significant new multidisciplinary resources, infrastructure and training.}, number={9}, journal={TRENDS IN ECOLOGY & EVOLUTION}, author={Jackson, RB and Linder, CR and Lynch, M and Purugganan, M and Somerville, S and Thayer, SS}, year={2002}, month={Sep}, pages={409–414} } @article{olsen_purugganan_2002, title={Molecular evidence on the origin and evolution of glutinous rice}, volume={162}, number={2}, journal={Genetics}, author={Olsen, K. M. and Purugganan, M. D.}, year={2002}, pages={941–950} } @article{weinig_ungerer_dorn_kane_toyonaga_halldorsdottir_mackay_purugganan_schmitt_2002, title={Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments}, volume={162}, number={4}, journal={Genetics}, author={Weinig, C. and Ungerer, M. C. and Dorn, L. A. and Kane, N. C. and Toyonaga, Y. and Halldorsdottir, S. S. and Mackay, T. F. C. and Purugganan, M. D. and Schmitt, J.}, year={2002}, month={Dec}, pages={1875–1884} } @article{ungerer_halldorsdottir_modliszewski_mackay_purugganan_2002, title={Quantitative trait loci for inflorescence development in Arabidopsis thaliana}, volume={160}, number={3}, journal={Genetics}, author={Ungerer, M. C. and Halldorsdottir, S. S. and Modliszewski, J. L. and Mackay, T. F. C. and Purugganan, M. D.}, year={2002}, month={Mar}, pages={1133–1151} } @article{bustamante_nielsen_sawyer_olsen_purugganan_hartl_2002, title={The cost of inbreeding in Arabidopsis}, volume={416}, ISSN={["0028-0836"]}, DOI={10.1038/416531a}, abstractNote={Population geneticists have long sought to estimate the distribution of selection intensities among genes of diverse function across the genome. Only recently have DNA sequencing and analytical techniques converged to make this possible. Important advances have come from comparing genetic variation within species (polymorphism) with fixed differences between species (divergence). These approaches have been used to examine individual genes for evidence of selection. Here we use the fact that the time since species divergence allows combination of data across genes. In a comparison of amino-acid replacements among species of the mustard weed Arabidopsis with those among species of the fruitfly Drosophila, we find evidence for predominantly beneficial gene substitutions in Drosophila but predominantly detrimental substitutions in Arabidopsis. We attribute this difference to the Arabidopsis mating system of partial self-fertilization, which corroborates a prediction of population genetics theory that species with a high frequency of inbreeding are less efficient in eliminating deleterious mutations owing to their reduced effective population size.}, number={6880}, journal={NATURE}, author={Bustamante, CD and Nielsen, R and Sawyer, SA and Olsen, KM and Purugganan, MD and Hartl, DL}, year={2002}, month={Apr}, pages={531–534} } @misc{shepard_purugganan_2002, title={The genetics of plant morphological evolution}, volume={5}, ISSN={["1879-0356"]}, DOI={10.1016/S1369-5266(01)00227-8}, abstractNote={Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations.}, number={1}, journal={CURRENT OPINION IN PLANT BIOLOGY}, author={Shepard, KA and Purugganan, MD}, year={2002}, month={Feb}, pages={49–55} } @article{barrier_robichaux_purugganan_2001, title={Accelerated regulatory gene evolution in an adaptive radiation}, volume={98}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.181257698}, abstractNote={The disparity between rates of morphological and molecular evolution remains a key paradox in evolutionary genetics. A proposed resolution to this paradox has been the conjecture that morphological evolution proceeds via diversification in regulatory loci, and that phenotypic evolution may correlate better with regulatory gene divergence. This conjecture can be tested by examining rates of regulatory gene evolution in species that display rapid morphological diversification within adaptive radiations. We have isolated homologues to theArabidopsis APETALA3(ASAP3/TM6) andAPETALA1(ASAP1) floral regulatory genes and theCHLOROPHYLL A/B BINDING PROTEIN9(ASCAB9) photosynthetic structural gene from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. We have compared rates of regulatory and structural gene evolution in the Hawaiian species to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in theASAP3/TM6andASAP1regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. An increase in nonsynonymous relative to synonymous nucleotide substitution rate is also evident in theASCAB9structural gene in the Hawaiian species, but not to the extent displayed in the regulatory loci. The significantly accelerated rates of regulatory gene evolution in the Hawaiian species may reflect the influence of allopolyploidy or of selection and adaptive divergence. The analyses suggest that accelerated rates of regulatory gene evolution may accompany rapid morphological diversification in adaptive radiations.}, number={18}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Barrier, M and Robichaux, RH and Purugganan, MD}, year={2001}, month={Aug}, pages={10208–10213} } @article{remington_ungerer_purugganan_2001, title={Map-based cloning of quantitative trait loci: progress and prospects}, volume={78}, number={3}, journal={Genetical Research}, author={Remington, D. L. and Ungerer, M. C. and Purugganan, M. D.}, year={2001}, pages={213–218} } @article{barrier_friar_robichaux_purugganan_2000, title={Interspecific evolution in plant microsatellite structure}, volume={241}, ISSN={["0378-1119"]}, DOI={10.1016/S0378-1119(99)00463-1}, abstractNote={Several intragenically linked microsatellites have been identified in the floral regulatory genes A. sandwicense APETALA1 (ASAP1) and A. sandwicense APETALA3/TM6 (ASAP3/TM6) in 17 species of the Hawaiian and North American Madiinae (Asteraceae). Thirty-nine microsatellite loci were observed in the introns of these two genes, suggesting that they are hotspots for microsatellite formation. The sequences of four of these microsatellites were mapped onto the phylogenies of these floral regulatory genes, and the structural evolution of these repeat loci was traced. Both nucleotide substitutions and insertion/deletion mutations may be responsible for the formation of perfect microsatellites from imperfect repeat regions (and vice versa).}, number={1}, journal={GENE}, author={Barrier, M and Friar, E and Robichaux, R and Purugganan, M}, year={2000}, month={Jan}, pages={101–105} } @misc{lawton-rauh_alvarez-buylla_purugganan_2000, title={Molecular evolution of flower development}, volume={15}, ISSN={["0169-5347"]}, DOI={10.1016/S0169-5347(99)01816-9}, abstractNote={Flowers, as reproductive structures of the most successful group of land plants, have been a central focus of study for both evolutionists and ecologists. Recent advances in unravelling the genetics of flower development have provided insight into the evolution of floral structures among angiosperms. The study of the evolution of genes that control floral morphogenesis permits us to draw inferences on the diversification of developmental systems, the origin of floral organs and the selective forces that drive evolutionary change among these plant reproductive structures.}, number={4}, journal={TRENDS IN ECOLOGY & EVOLUTION}, author={Lawton-Rauh, AL and Alvarez-Buylla, ER and Purugganan, MD}, year={2000}, month={Apr}, pages={144–149} } @article{juenger_purugganan_mackay_2000, title={Quantitative trait loci for floral morphology in Arabidopsis thaliana}, volume={156}, number={3}, journal={Genetics}, author={Juenger, T. and Purugganan, M. and MacKay, T. F. C.}, year={2000}, month={Nov}, pages={1379–1392} } @misc{purugganan_2000, title={The molecular population genetics of regulatory genes}, volume={9}, ISSN={["1365-294X"]}, DOI={10.1046/j.1365-294x.2000.01016.x}, abstractNote={Abstract}, number={10}, journal={MOLECULAR ECOLOGY}, author={Purugganan, MD}, year={2000}, month={Oct}, pages={1451–1461} } @article{purugganan_boyles_suddith_2000, title={Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea}, volume={155}, number={2}, journal={Genetics}, author={Purugganan, M. D. and Boyles, A. L. and Suddith, J. I.}, year={2000}, pages={855–862} } @article{lowman_purugganan_1999, title={Duplication of the Brassica oleracea APETALA1 floral homeotic gene and the evolution of domesticated cauliflower}, volume={90}, number={5}, journal={Journal of Heredity}, author={Lowman, A. C. and Purugganan, M. D.}, year={1999}, pages={514–520} } @article{barrier_baldwin_robichaux_purugganan_1999, title={Interspecific hybrid ancestry of a plant adaptive radiation: Allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications}, volume={16}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a026200}, abstractNote={The polyploid Hawaiian silversword alliance (Asteraceae), a spectacular example of adaptive radiation in plants, was shown previously to have descended from North American tarweeds of the Madia/Raillardiopsis group, a primarily diploid assemblage. The origin of the polyploid condition in the silversword alliance was not resolved in earlier biosystematic, cytogenetic, and molecular studies, apart from the determination that polyploidy in modern species of Madia/Raillardiopsis arose independent of that of the Hawaiian group. We determined that two floral homeotic genes, ASAP3/TM6 and ASAP1, are found in duplicate copies within members of the Hawaiian silversword alliance and appear to have arisen as a result of interspecific hybridization between two North American tarweed species. Our molecular phylogenetic analyses of the ASAP3/TM6 loci suggest that the interspecific hybridization event in the ancestry of the Hawaiian silversword alliance involved members of lineages that include Raillardiopsis muirii (and perhaps Madia nutans) and Raillardiopsis scabrida. The ASAP1 analysis also indicates that the two species of Raillardiopsis are among the closest North American relatives of the Hawaiian silversword alliance. Previous biosystematic evidence demonstrates the potential for allopolyploid formation between members of the two North American tarweed lineages; a vigorous hybrid between R. muirii and R. scabrida has been produced that formed viable, mostly tetraporate (diploid) pollen, in keeping with observed meiotic failure. Various genetic consequences of allopolyploidy may help to explain the phenomenal evolutionary diversification of the silversword alliance.}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Barrier, M and Baldwin, BG and Robichaux, RH and Purugganan, MD}, year={1999}, month={Aug}, pages={1105–1113} } @article{purugganan_suddith_1999, title={Molecular population genetics of floral homeotic loci: departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana}, volume={151}, number={2}, journal={Genetics}, author={Purugganan, M. D. and Suddith, J. I.}, year={1999}, pages={839–848} } @article{lawton-rauh_buckler_purugganan_1999, title={Patterns of molecular evolution among paralogous floral homeotic genes}, volume={16}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a026193}, abstractNote={The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congeneric species Arabidopsis lyrata. Analysis of these loci between these two Arabidopsis species, as well as three other more distantly related taxa, reveal contrasting dynamics of molecular evolution between these paralogous floral regulatory genes. Among the four loci, the CAL locus evolves at a significantly faster rate, which may be associated with the evolution of genetic redundancy between CAL and AP1. Moreover, there are significant differences in the distribution of replacement and synonymous substitutions between the functional gene domains of different floral homeotic loci. These results indicate that divergence in developmental function among paralogous members of regulatory gene families is accompanied by changes in rate and pattern of sequence evolution among loci.}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Lawton-Rauh, AL and Buckler, ES, IV and Purugganan, MD}, year={1999}, month={Aug}, pages={1037–1045} } @article{purugganan_suddith_1998, title={Molecular population genetics of the Arabidopsis CAULIFLOWER regulatory gene: Nonneutral evolution and naturally occurring variation in floral homeotic function}, volume={95}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.95.14.8130}, abstractNote={ The evolution of interspecies differences in morphology requires sufficient within-species variation in developmental regulatory systems on which evolutionary forces can act. Molecular analyses of naturally occurring alleles of the Arabidopsis thaliana CAULIFLOWER locus reveal considerable intraspecific diversity at this floral homeotic gene, and the McDonald–Kreitman test suggests that this gene is evolving in a nonneutral fashion, with an excess of intraspecific replacement polymorphisms. The naturally occurring molecular variation within this floral regulatory gene is associated with functionally different alleles, which can be distinguished phenotypically by their differential ability to direct floral meristem development. }, number={14}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Purugganan, MD and Suddith, JI}, year={1998}, month={Jul}, pages={8130–8134} } @misc{purugganan_1998, title={The molecular evolution of development}, volume={20}, ISSN={["0265-9247"]}, DOI={10.1002/(SICI)1521-1878(199809)20:9<700::AID-BIES3>3.0.CO;2-K}, abstractNote={Morphological differences between species, from simple single‐character differences to large‐scale variation in body plans, can be traced to changes in the timing and location of developmental events. This has led to a growing interest in understanding the genetic basis behind the evolution of developmental systems. Molecular evolutionary genetics provides one of several approaches to dissecting the evolution of developmental systems, by allowing us to reconstruct the history of developmental genetic pathways, infer the origin and diversification of developmental gene functions, and assess the relative contributions of various evolutionary forces in shaping regulatory gene evolution. BioEssays 20:700–711, 1998. © 1998 John Wiley & Sons, Inc.}, number={9}, journal={BIOESSAYS}, author={Purugganan, MD}, year={1998}, month={Sep}, pages={700–711} } @article{purugganan_1997, title={The MADS-box floral homeotic gene lineages predate the origin of seed plants: Phylogenetic and molecular clock estimates}, volume={45}, ISSN={["1432-1432"]}, DOI={10.1007/PL00006244}, abstractNote={Flower development in angiosperms is controlled in part by floral homeotic genes, many of which are members of the plant MADS-box regulatory gene family. The evolutionary history of these developmental genes was reconstructed using 74 loci from 15 dicot, three monocot, and one conifer species. Molecular clock estimates suggest that the different floral homeotic gene lineages began to diverge from one another about 450-500 mya, around the time of the origin of land plants themselves.}, number={4}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Purugganan, MD}, year={1997}, month={Oct}, pages={392–396} } @article{swaffield_purugganan_1997, title={The evolution of the conserved ATPase domain (CAD): Reconstructing the history of an ancient protein module}, volume={45}, ISSN={["0022-2844"]}, DOI={10.1007/PL00006259}, abstractNote={The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases, while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory, NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change that characterize the AAA proteins.}, number={5}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Swaffield, JC and Purugganan, MD}, year={1997}, month={Nov}, pages={549–563} }