Research Topics
Genomes and GenesSpecies | Douglas E SoltisSummaryAffiliation: University of Florida Country: USA Publications
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Publications
A genome triplication associated with early diversification of the core eudicotsYuannian Jiao
Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
Genome Biol 13:R3. 2012..Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear...
Origin and early evolution of angiospermsDouglas E Soltis
Department of Botany, University of Florida, Gainesville, FL 32611, USA
Ann N Y Acad Sci 1133:3-25. 2008..Variation in spatial expression of floral regulators may control major differences in floral morphology between basal angiosperms and eudicot models...
The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expressionDouglas E Soltis
Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
Trends Plant Sci 12:358-67. 2007..g. Amborella) result from a gradient in the level of expression of floral organ identity genes across the developing floral meristem...- The ABC model and its applicability to basal angiospermsDouglas E Soltis
Department of Botany, University of Florida, Gainesville, FL 32611, USA
Ann Bot 100:155-63. 2007..We offer 'fading borders' as a testable hypothesis for the basal-most angiosperms and, by inference, perhaps some of the earliest (now extinct) angiosperms... - Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogeneticsDouglas E Soltis
Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
Trends Plant Sci 9:477-83. 2004..We provide a conspicuous example that includes Amborella, the putative sister of all other extant angiosperms, highlighting the limits of phylogenetics when whole genomes are used but taxon sampling is poor... - Comparative phylogeography of unglaciated eastern North AmericaDouglas E Soltis
Department of Botany, University of Florida, Gainesville, FL 32611, USA
Mol Ecol 15:4261-93. 2006..Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers... - On the origins of species: does evolution repeat itself in polyploid populations of independent origin?D E Soltis
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Cold Spring Harb Symp Quant Biol 74:215-23. 2009..This methodology is particularly promising for groups such as Tragopogon for which limited genetic and genomic resources are available... - The role of phylogenetics in comparative geneticsDouglas E Soltis
Department of Botany and the Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
Plant Physiol 132:1790-800. 2003 - Floral gene resources from basal angiosperms for comparative genomics researchVictor A Albert
Natural History Museum, University of Oslo, NO 0318 Oslo, Norway
BMC Plant Biol 5:5. 2005.... - An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markersCharlotte Lindqvist
Natural History Museum, University of Oslo, PO Box 1172 Blindern, 0318 Oslo, Norway
BMC Plant Biol 6:16. 2006..We constructed an EST library from developing fleshy nutlets of Stenogyne rugosa principally to identify genetic markers for the Hawaiian endemic mints... - On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae)Jennifer A Tate
Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
BMC Plant Biol 9:80. 2009..dubius and T. pratensis less than 80 years ago... - Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploidsHana Malinska
Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi Laboratory of Molecular Epigenetics, Kralovopolska 135, CZ 61265 Brno, Czech Republic
BMC Evol Biol 10:291. 2010..We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids... - Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiospermsJ Gordon Burleigh
National Evolutionary Synthesis Center NESCent, Durham, NC 27705, USA
BMC Evol Biol 9:61. 2009..We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al... - Phylogeny and domain evolution in the APETALA2-like gene familySangtae Kim
Department of Botany, University of Florida, Gainesville, USA
Mol Biol Evol 23:107-20. 2006..Our expression studies show that the euAP2 homologue from Amborella trichopoda, the putative sister to all other angiosperms, is expressed in all floral organs as well as leaves... - The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm historyLaura M Zahn
Department of Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, 16802, USA
Genetics 169:2209-23. 2005..Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower... - Phylogeographical structure and temporal complexity in American sweetgum (Liquidambar styraciflua; Altingiaceae)Ashley B Morris
Department of Biology, University of South Alabama, Mobile, AL 36688, USA
Mol Ecol 17:3889-900. 2008..These patterns reflect a dynamic biogeographical history for eastern North American trees, and emphasize the importance of the inclusion of a temporal component in any phylogeographical study... - Persea americana (avocado): bringing ancient flowers to fruit in the genomics eraAndré S Chanderbali
Department of Botany, University of Florida, Gainesville, FL, USA
Bioessays 30:386-96. 2008.... - Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)Jin Koh
Department of Biology, University of Florida, Gainesville, Florida 32611, USA
BMC Genomics 11:97. 2010..dubius and T. porrifolius... - Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirusRichard J A Buggs
Department of Biology, University of Florida, Gainesville, FL 32611, USA
New Phytol 186:175-83. 2010..Our study shows that tissue-specific silencing, and even apparent subfunctionalization, can arise rapidly in the early generations of natural allopolyploidy... - Comparison of next generation sequencing technologies for transcriptome characterizationP Kerr Wall
Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
BMC Genomics 10:347. 2009..19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis... - Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flowerAndré S Chanderbali
Department of Biology and Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Proc Natl Acad Sci U S A 107:22570-5. 2010..However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants... - Widespread genome duplications throughout the history of flowering plantsLiying Cui
Department of Biology, The Pennsylvania State University, University Park 16802, USA
Genome Res 16:738-49. 2006..We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella... - Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plantRichard J A Buggs
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Curr Biol 21:551-6. 2011..Our results suggest that regulation of gene expression is relaxed in a concerted manner upon hybridization, and new patterns of partitioned expression subsequently emerge over the generations following allopolyploidization... - Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent originRichard J A Buggs
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Curr Biol 22:248-52. 2012..The high frequency of single-allele losses detected and low frequency of changes fixed within populations provide evidence for ongoing evolution... - The Amborella genome: an evolutionary reference for plant biologyDouglas E Soltis
Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
Genome Biol 9:402. 2008..The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics... - Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae)André S Chanderbali
Department of Biology and Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Proc Natl Acad Sci U S A 106:8929-34. 2009.... - The age of the angiosperms: a molecular timescale without a clockCharles D Bell
Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, Florida 32611, USA
Evolution 59:1245-58. 2005.... - Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulatorsSangtae Kim
Department of Botany, University of Florida, Gainesville, FL 32611, USA
Plant J 43:724-44. 2005.... - Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plantsMi Jeong Yoo
Department of Botany, University of Florida, Gainesville, FL 32611, USA
BMC Plant Biol 6:3. 2006..Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences... - Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploidJennifer A Tate
Department of Botany, University of Florida, Gainesville, Florida 32611, USA
Genetics 173:1599-611. 2006..Synthetic F(1) hybrids between putative diploid progenitors are additive of their parental genomes, suggesting that polyploidization rather than hybridization induces genomic changes in Tragopogon... - Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotypingRichard J A Buggs
Department of Biology, University of Florida, Gainesville, 32611, USA
Mol Ecol 19:132-46. 2010..These methods could be applied to any organism, allowing efficient and cost-effective generation of genetic markers... - Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae)Mi Jeong Yoo
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Plant J 64:687-98. 2010..Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology... - Phylogenetic relationships among early-diverging eudicots based on four genes: were the eudicots ancestrally woody?Sangtae Kim
Department of Botany, University of Florida, Gainesville, FL 32611, USA
Mol Phylogenet Evol 31:16-30. 2004..Furthermore, Ranunculales may not be ancestrally herbaceous, as long maintained. The woody habit appears to have been ancestral for several major clades of eudicots, including Caryophyllales, and asterids... - Missing links: the genetic architecture of flowers [correction of flower] and floral diversificationDouglas E Soltis
Dept Botany and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
Trends Plant Sci 7:22-31; dicussion 31-4. 2002.... - Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parentsJin Koh
Department of Biology, University of Florida, Gainesville, FL 32611, USA
New Phytol 196:292-305. 2012..mirus was not associated with hybridization itself, but occurred subsequent to both hybridization and polyploidization. This study has shown the utility of proteomics in the analysis of the evolutionary consequences of polyploidy... - Towards a comprehensive integration of morphological and genetic studies of floral developmentMatyas Buzgo
Department of Botany and the Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 8526, USA
Trends Plant Sci 9:164-73. 2004..Taxa occupying key phylogenetic positions offer great potential for generating hypotheses about the regulation of floral development... - Dynamics of polyploid formation in Tragopogon (Asteraceae): recurrent formation, gene flow, and population structureV Vaughan Symonds
Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
Evolution 64:1984-2003. 2010..Our data also indicate a lack of gene flow among polyploid plants of independent origin, even when they co-occur, suggesting potential reproductive barriers among separate lineages in both polyploid species... - Phylogeny of Opuntia s.s. (Cactaceae): clade delineation, geographic origins, and reticulate evolutionLucas C Majure
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Am J Bot 99:847-64. 2012..Evolutionary relationships in these stem succulents have been insufficiently studied; thus, delimitation of Opuntia s.s. and major subclades, as well as the biogeographic history of this enigmatic group, remain unresolved... - Angiosperm phylogeny: 17 genes, 640 taxaDouglas E Soltis
Department of Biology, University of Florida, Gainesville, Florida 32611 8525, USA edu
Am J Bot 98:704-30. 2011..In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses... - Using plastid genome-scale data to resolve enigmatic relationships among basal angiospermsMichael J Moore
Department of Botany and Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
Proc Natl Acad Sci U S A 104:19363-8. 2007..The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 +/- 4.8 and 140.3 +/- 4.8 Mya... - Polyploidy and angiosperm diversificationDouglas E Soltis
Department of Botany, University of Florida, Gainesville, Florida 32611 USA
Am J Bot 96:336-48. 2009.... - Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)Michael Chester
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Proc Natl Acad Sci U S A 109:1176-81. 2012..A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression... - Rapid and accurate pyrosequencing of angiosperm plastid genomesMichael J Moore
Department of Botany, University of Florida, Gainesville, FL 32611, USA
BMC Plant Biol 6:17. 2006.... - Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data setsPaul S Manos
Department of Biology, Duke University, Durham, NC 27708 0338, USA
Syst Biol 56:412-30. 2007..Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages... - Recent long-distance dispersal overshadows ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales)Joshua W Clayton
Department of Botany, University of Florida, Gainesville, FL 32611 7800, USA
Syst Biol 58:395-410. 2009..Notable dispersals are inferred to have occurred across the Atlantic Ocean in both directions, as well as between Africa and Asia, and around the Indian Ocean basin and Pacific islands... - Floral variation and floral genetics in basal angiospermsPamela S Soltis
Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
Am J Bot 96:110-28. 2009..We conclude with a set of evo-devo case studies in which floral genetics have been linked to variation in floral morphology... - Microsatellite marker development for the federally listed Prunus geniculata (Rosaceae)Charlotte C Germain-Aubrey
Department of Biology, University of Florida, Gainesville, Florida 32611, USA
Am J Bot 98:e58-60. 2011..To investigate levels and geographic partitioning of genetic variation in this species, we developed microsatellite markers for P. geniculata and its sister species, P. maritima... - Microsatellite marker development for Galax urceolata (Diapensiaceae)Stein V Servick
Department of Biology, University of Florida, Gainesville, Florida 32611, USA
Am J Bot 98:e48-50. 2011..Microsatellite markers were developed for Galax urceolata to investigate genetic diversity, population structure, and polyploid origins (auto- vs. allopolyploid), and to estimate the minimum number of independent cytotype origins... - Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)Jim Leebens-Mack
Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
OMICS 10:231-7. 2006..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors... - 'Living stones' reveal alternative petal identity programs within the core eudicotsSamuel F Brockington
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Plant J 69:193-203. 2012.... - The role of hybridization in plant speciationPamela S Soltis
The Genetics Institute, Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
Annu Rev Plant Biol 60:561-88. 2009..The time is therefore right for a review of the role of hybridization in plant speciation... - Does hybridization between divergent progenitors drive whole-genome duplication?Richard J A Buggs
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Mol Ecol 18:3334-9. 2009..The data simply demonstrate that hybridization between divergent parents has a higher probability of successfully producing a species if followed by polyploidization... - An assessment of karyotype restructuring in the neoallotetraploid Tragopogon miscellus (Asteraceae)Michael Chester
Department of Biology, University of Florida, Gainesville, FL 32611, USA
Chromosome Res 21:75-85. 2013..We consider these findings in relation to the gene loss reported previously for T. miscellus... - Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approachDouglas E Soltis
Department of Biology, University of Florida, Gainesville, Florida 32611 USA
Am J Bot 100:916-29. 2013..Our results indicate that in some cases the evolution of angiosperms might be conditioned by constraints that have been so far overlooked... - Complex pigment evolution in the CaryophyllalesSamuel F Brockington
Department of Biology, University of Florida, Gainesville, FL 32611, USA
New Phytol 190:854-64. 2011..Given these insights from molecular phylogenetics and comparative genetics, we discuss outstanding questions and define key goals for future research... - Genetic variability of an unusual apomictic triploid cactus--Haageocereus tenuis Ritter--from the Coast of Central PeruMónica Arakaki
Department of Biology, University of Florida, Gainesville, FL 32611, USA
J Hered 104:127-33. 2013..Other prostrate species of Haageocereus are suspected to be occasional apomicts. This phenomenon has significant implications for the evolutionary biology and ecology of Haageocereus and other clonal Cactaceae... - Relationships within Cornales and circumscription of Cornaceae-matK and rbcL sequence data and effects of outgroups and long branchesJenny Qiu Yun Xiang
Department of Botany, North Carolina State University, Raleigh, NC 27695 7612, USA
Mol Phylogenet Evol 24:35-57. 2002.... - Molecular phylogeny, biogeography, and systematics of Dicerandra (Lamiaceae), a genus endemic to the southeastern United StatesLuiz O Oliveira
Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
Am J Bot 94:1017-27. 2007..A revised subgeneric classification is presented to reflect the annual and perennial clades... - Characterization of polymorphic microsatellite loci in Haageocereus (Trichocereeae, Cactaceae)Mónica Arakaki
Department of Biology, University of Florida, Gainesville, Florida 32611 USA
Am J Bot 97:e17-9. 2010..Conclusions: These markers will facilitate analysis of genetic diversity, hybridization, and population differentiation throughout Haageocereus and Espostoa...