@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 The pathways responsible for flowering time in Arabidopsis thaliana comprise one of the best characterized genetic networks in plants. We harness this extensive molecular genetic knowledge to identify potential flowering time quantitative trait genes (QTGs) through candidate gene association mapping using 51 flowering time loci. We genotyped common single nucleotide polymorphisms (SNPs) at these genes in 275 A. thaliana accessions that were also phenotyped for flowering time and rosette leaf number in long and short days. Using structured association techniques, we find that haplotype-tagging SNPs in 27 flowering time genes show significant associations in various trait/environment combinations. After correction for multiple testing, between 2 and 10 genes remain significantly associated with flowering time, with CO arguably possessing the most promising associations. We also genotyped a subset of these flowering time gene SNPs in an independent recombinant inbred line population derived from the intercrossing of 19 accessions. Approximately one-third of significant polymorphisms that were associated with flowering time in the accessions and genotyped in the outbred population were replicated in both mapping populations, including SNPs at the CO, FLC, VIN3, PHYD, and GA1 loci, and coding region deletions at the FRI gene. We conservatively estimate that ∼4–14% of known flowering time genes may harbor common alleles that contribute to natural variation in this life history trait.}, 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={Molecular population genetic analysis of three chromosomal regions in Arabidopsis thaliana suggested that balancing selection might operate to maintain variation at three novel candidate adaptive trait genes, including SOLUBLE STARCH SYNTHASE I (SSI), PLASTID TRANSCRIPTIONALLY ACTIVE 7(PTAC7), and BELL-LIKE HOMEODOMAIN 10 (BLH10). If balanced polymorphisms are indeed maintained at these loci, then we would expect to observe functional variation underlying the previously detected signatures of selection. We observe multiple replacement polymorphisms within and in the 32 amino acids just upstream of the protein–protein interacting BELL domain at the BLH10 locus. While no clear protein sequence differences are found between allele types in SSI and PTAC7, these two genes show evidence for allele-specific variation in expression levels. Geographical patterns of allelic differentiation seem consistent with population stratification in this species and a significant longitudinal cline was observed at all three candidate loci. These data support a hypothesis of balancing selection at all three candidate loci and provide a basis for more detailed functional work by identifying possible functional differences that might be selectively maintained.}, 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={The evolution from outcrossing based on self-incompatibility (SI) to a selfing system is one of the most prevalent transitions in flowering plants. It has been suggested that the loss of SI in Arabidopsis thaliana is associated with pseudogene formation at the SCR male component of the S locus. Recent work, however, suggests that alternative alleles with large deletions at the S locus are also present and may be responsible for the evolution of self-compatibility in this species. We demonstrate that most of these deletion alleles are evolutionarily derived from an S haplotype (haplogroups A) that already possessed the SCR pseudogene. This haplotype and its deletion variants are nearly fixed in Europe. Together with previous transgenic data, these results suggest that the pseudogenization of ΨSCR1 gene changed the SI phenotype in the majority of A. thaliana accessions, and was a critical step in the evolution of selfing in this species. Two other haplogroups (B and C) were also identified, the former of which contains a novel and possibly functional SCR allele. In contrast to haplogroups A, these two haplogroups are found primarily in Africa and Asia. These results suggest that self-compatibility, which appears to be fixed in this species, arose multiple times with different genetic bases, and indicates that a species-specific trait is associated with parallel evolution at the molecular level.}, 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 Major differences exist between plants and animals both in the extent of microRNA (miRNA)-based gene regulation and the sequence complementarity requirements for miRNA-messenger RNA pairing. Whether these differences affect how these sites evolve at the molecular level is unknown. To determine the extent of sequence variation at miRNAs and their targets in a plant species, we resequenced 16 miRNA families (66 miRNAs in total) and all 52 of the characterized binding sites for these miRNAs in the plant model Arabidopsis (Arabidopsis thaliana), accounting for around 50% of the known miRNAs and binding sites in this species. As has been shown previously in humans, we find that both miRNAs and their target binding sites have very low nucleotide variation and divergence compared to their flanking sequences in Arabidopsis, indicating strong purifying selection on these sites in this species. Sequence data flanking the mature miRNAs, however, exhibit normal levels of polymorphism for the accessions in this study and, in some cases, nonneutral evolution or subtle effects on predicted pre-miRNA secondary structure, suggesting that there is raw material for the differential function of miRNA alleles. Overall, our results show that despite differences in the architecture of miRNA-based regulation, miRNAs and their targets are similarly constrained in both plants and animals.}, 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={The impact of gene flow and population size fluctuations in shaping genetic variation during adaptive radiation, at both the genome-wide and gene-specific levels, is very poorly understood. To examine how historical population size and gene flow patterns within and between loci have influenced lineage divergence in the Hawaiian silversword alliance, we have investigated the nucleotide sequence diversity and divergence patterns of four floral regulatory genes (ASAP1-A, ASAP1-B, ASAP3-A, ASAP3-B) and a structural gene (ASCAB9). Levels and patterns of molecular divergence across these five nuclear loci were estimated between two recently derived species (Dubautia ciliolata and Dubautia arborea) which are presumed to be sibling species. This multilocus analysis of genetic variation, haplotype divergence and historical demography indicates that population expansion and differential gene flow occurred subsequent to the divergence of these two lineages. Moreover, contrasting patterns of allele- sharing for regulatory loci vs. a structural locus between these two sibling species indicate alternative histories of genetic variation and partitioning among loci where alleles of the floral regulatory loci are shared primarily from D. arborea to D. ciliolata and alleles of the structural locus are shared in both directions. Taken together, these results suggest that adaptively radiating species can exhibit contrasting allele migration rates among loci such that allele movement at specific loci may supersede genetic divergence caused by drift and that lineage divergence during adaptive radiation can be associated with population expansion.}, 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}, 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 Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (∼150 kb) and indica (∼75 kb). LD extends over a shorter distance in O. rufipogon (≪40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.}, 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 Association mapping focused on 36 genes involved in branch development was used to identify candidate genes for variation in shoot branching in Arabidopsis thaliana. The associations between four branching traits and moderate-frequency haplogroups at the studied genes were tested in a panel of 96 accessions from a restricted geographic range in Central Europe. Using a mixed-model association-mapping method, we identified three loci—MORE AXILLARY GROWTH 2 (MAX2), MORE AXILLARY GROWTH 3 (MAX3), and SUPERSHOOT 1 (SPS1)—that were significantly associated with branching variation. On the basis of a more extensive examination of the MAX2 and MAX3 genomic regions, we find that linkage disequilibrium in these regions decays within ∼10 kb and trait associations localize to the candidate genes in these regions. When the significant associations are compared to relevant quantitative trait loci (QTL) from previous Ler × Col and Cvi × Ler recombinant inbred line (RIL) mapping studies, no additive QTL overlapping these candidate genes are observed, although epistatic QTL for branching, including one that spans the SPS1, are found. These results suggest that epistasis is prevalent in determining branching variation in A. thaliana and may need to be considered in linkage disequilibrium mapping studies of genetically diverse accessions.}, 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={We investigated the distributions of genetic and phenotypic variation for two Yellowstone National Park populations of the heterocyst-forming cyanobacterium Mastigocladus (Fischerella) laminosus that exhibit dramatic phenotypic differences as a result of environmental differences in nitrogen availability. One population develops heterocysts and fixes nitrogen in situ in response to a deficiency of combined nitrogen in its environment, whereas the other population does neither due to the availability of a preferred nitrogen source. Slowly evolving molecular markers, including the 16S rRNA gene and the downstream internal transcribed spacer, are identical among all laboratory isolates from both populations but belie considerable genetic and phenotypic diversity. The total nucleotide diversity at six nitrogen metabolism loci was roughly three times greater than that observed for the human global population. The two populations are genetically differentiated, although variation in performance on different nitrogen sources among genotypes could not be explained by local adaptation to available nitrogen in the respective environments. Population genetic models suggest that local adaptation is mutation limited but also that the populations are expected to continue to diverge due to low migratory gene flow.}, 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 Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.}, 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={High-diversity genes represent an important class of loci in organismal genomes. Since elevated levels of nucleotide variation are a key component of the molecular signature for balancing selection or local adaptation, high-diversity genes may represent loci whose alleles are selectively maintained as balanced polymorphisms. Comparison of 4300 random shotgun sequence fragments of the Arabidopsis thaliana Ler ecotype genome with the whole genomic sequence of the Col-0 ecotype identified 60 genes with putatively high levels of intraspecific variability. Eleven of these genes were sequenced in multiple A. thaliana accessions, 3 of which were found to display elevated levels of nucleotide polymorphism. These genes encode the myb-like transcription factor MYB103, a putative soluble starch synthase I, and a homeodomain-leucine zipper transcription factor. Analysis of these genes and 4-7 flanking genes in 14-20 A. thaliana ecotypes revealed that two of these loci show other characteristics of balanced polymorphisms, including broad peaks of nucleotide diversity spanning multiple linked genes and an excess of intermediate-frequency polymorphisms. Scanning genomes for high-diversity genomic regions may be useful in approaches to adaptive trait locus mapping for uncovering candidate balanced polymorphisms.}, 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={RNA viruses are characterized by high genetic variability resulting in rapid adaptation to new or resistant hosts. Research for plant RNA virus genetic structure and its variability has been relatively scarce compared to abundant research done for human and animal RNA viruses. Here, we utilized a molecular population genetic framework to characterize the evolution of a highly pathogenic plant RNA virus [Tomato spotted wilt virus (TSWV), Tospovirus, Bunyaviridae]. Data from genes encoding five viral proteins were used for phylogenetic analysis, and for estimation of population parameters, subpopulation differentiation, recombination, divergence between Tospovirus species, and selective constraints on the TSWV genome. Our analysis has defined the geographical structure of TSWV, attributed possibly to founder effects. Also, we identify positive selection favouring divergence between Tospovirus species. At the species level, purifying selection has acted to preserve protein function, although certain amino acids appear to be under positive selection. This analysis provides demonstration of population structuring and species-wide population expansions in a multisegmented plant RNA virus, using sequence-based molecular population genetic analyses. It also identifies specific amino acid sites subject to selection within Bunyaviridae and estimates the level of genetic heterogeneity of a highly pathogenic plant RNA virus. The study of the variability of TSWV populations lays the foundation in the development of strategies for the control of other viral diseases in floral crops.}, 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 The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an ∼65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.}, 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={There is growing interest in the evolutionary dynamics of molecular genetic pathways and networks, and the extent to which the molecular evolution of a gene depends on its position within a pathway or network, as well as over-all network topology. Investigations on the relationships between network organization, topological architecture and evolutionary dynamics provide intriguing hints as to how networks evolve. Recent studies also suggest that genetic pathway and network structures may influence the action of evolutionary forces, and may play a role in maintaining phenotypic robustness in organisms.}, 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={Molecular EcologyVolume 12, Issue 5 p. 1109-1112 Merging Ecology, Molecular Evolution, and Functional Genetics Michael Purugganan, Michael Purugganan Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695–7614, USASearch for more papers by this authorGreg Gibson, Corresponding Author Greg Gibson Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695–7614, USAG. Gibson. Fax: (919) 515-3355; E-mail: ggibson@unity.ncsu.eduSearch for more papers by this author Michael Purugganan, Michael Purugganan Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695–7614, USASearch for more papers by this authorGreg Gibson, Corresponding Author Greg Gibson Department of Genetics, North Carolina State University, Gardner Hall, Raleigh, NC 27695–7614, USAG. Gibson. Fax: (919) 515-3355; E-mail: ggibson@unity.ncsu.eduSearch for more papers by this author First published: 14 April 2003 https://doi.org/10.1046/j.1365-294X.2003.01851.xCitations: 48Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume12, Issue5May 2003Pages 1109-1112 RelatedInformation}, 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={Genome-wide duplication (polyploidization) is prevalent in a large number of eukaryotic organisms and is particularly widespread in flowering plants. Polyploid species appear to vary from their diploid progenitors in a variety of ecologically important traits, suggesting that genome duplications provide a mechanism for ecological diversification. Studies of nucleotide variation at duplicate genes that arise via polyploidization allow us to infer the evolutionary forces that act on these polyploid loci. In an effort to examine the evolutionary dynamics of homoeologous loci, molecular population genetic analyses were undertaken for duplicate regulatory genes in the allopolyploid Hawaiian silversword alliance, a premier example of adaptive radiation. The levels and patterns of nucleotide variation for the floral homeotic genes ASAPETALA1 (ASAP1) and ASAPETALA3/TM6 (ASAP3/TM6) were studied in two species representing different lineages within the Hawaiian silversword alliance: Argyroxiphium sandwicense ssp. macrocephalum and Dubautia ciliolata ssp. glutinosa. Homoeologueous copies of ASAP1 and ASAP3/TM6 show differing levels and patterns of nucleotide polymorphism. Duplicate ASAP1 copies have similar levels of nucleotide diversity and haplotype structure in both species; by contrast, duplicate ASAP3/TM6 genes display different levels and patterns of variation in D. ciliolata ssp. glutinosa. Additionally, D. ciliolata ssp. glutinosa appears to be segregating for a moderate frequency null allele in one ASAP3/TM6 homoeologue. These results suggest that differing evolutionary forces can affect duplicate loci arising from allopolyploidization.}, 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}, 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 the Arabidopsis APETALA3 (ASAP3/TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL 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 the ASAP3/TM6 and ASAP1 regulatory 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 the ASCAB9 structural 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={Regulatory loci, which may encode both trans acting proteins as well as cis acting promoter regions, are crucial components of an organism's genetic architecture. Although evolution of these regulatory loci is believed to underlie the evolution of numerous adaptive traits, there is little information on natural variation of these genes. Recent molecular population genetic studies, however, have provided insights into the extent of natural variation at regulatory genes, the evolutionary forces that shape them and the phenotypic effects of molecular regulatory variants. These recent analyses suggest that it may be possible to study the molecular evolutionary ecology of regulatory diversification by examining both the extent and patterning of regulatory gene diversity, the phenotypic effects of molecular variation at these loci and their ecological consequences.}, 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.}, 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}, 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}, number={5}, journal={JOURNAL OF MOLECULAR EVOLUTION}, author={Swaffield, JC and Purugganan, MD}, year={1997}, month={Nov}, pages={549–563} }