Comparison of next generation sequencing technologies for transcriptome characterization (2009)
Wall, P Kerr, Leebens-Mack, Jim, Chanderbali, André S, Barakat, Abdelali, Wolcott, Erik, Liang, Haiying, ...
Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared...
Tate, Jennifer A, Joshi, Prashant, Soltis, Kerry A, Soltis, Pamela S, Soltis, Douglas E
Abstract Background Polyploidy (whole-genome duplication) is an important speciation mechanism, particularly in plants. Gene loss, silencing, and the formation of novel gene complexes are some of the...
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms (2009)
Burleigh, J Gordon, Hilu, Khidir W, Soltis, Douglas E
Abstract Background Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing...
Clayton, Joshua W., Soltis, Pamela S., Soltis, Douglas E.
Detailed biogeographic studies of pantropical clades are still relatively few, and those conducted to date typically use parsimony or event-based methods to reconstruct ancestral areas. In this...
Rodrigo Vergara, Marc C. Minno, Maria Minno, Douglas E. Soltis, Pamela S. Soltis
Imperata cylindrica (cogongrass) is an invasive weed long established in the southeastern US, and considerable effort is devoted to its control. Two native species, I. brevifolia (California...
Does Phylogenetic Distance Between Parental Genomes Govern the Success of Polyploids (2008)
Pamela S. Soltis, Evgeny V. Mavrodiev, V. Vaughan Symonds, Douglas E. Soltis
It has long been suggested that phylogenetic divergence between parental species determines the likelihood of their producing a successful polyploid, with closely related parents less likely to form...
The Amborellagenome: an evolutionary reference for plant biology (2008)
Soltis, Douglas E, Albert, Victor A, Leebens-Mack, Jim, Palmer, Jeffrey D, Wing, Rod A, DePamphilis, Claude W, ...
Abstract The nuclear genome sequence of Amborella trichopoda , the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
Douglas E. Soltis, Evgeny V. Mavrodiev, Jeff J. Doyle, Jason Rauscher, Pamela S. Soltis
The impact of unknowingly including a hybrid or an allopolyploid in which rDNA homogenization (via gene loss, concerted evolution, or some other mechanism) has not occurred to completion in a...
Resolving an Ancient, Rapid Radiation in Saxifragales (2008)
Jian, Shuguang, Soltis, Pamela S., Gitzendanner, Matthew A., Moore, Michael J., Li, Ruiqi, Hendry, Tory A., ...
Despite the prior use of ∼ 9000 bp, deep-level relationships within the angiosperm clade, Saxifragales remain enigmatic, due to an ancient, rapid radiation (89.5 to 110 Ma based on the fossil...
The ABC Model and its Applicability to Basal Angiosperms (2007)
Soltis, Douglas E., Chanderbali, André S., Kim, Sangtae, Buzgo, Matyas, Soltis, Pamela S.
Background Although the flower is the central feature of the angiosperms, little is known of its origin and subsequent diversification. The ABC model has long been the unifying paradigm for floral...
Manos, Paul S., Soltis, Pamela S., Soltis, Douglas E., Manchester, Steven R., Oh, Sang-Hun, Bell, Charles D., ...
It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character...
Rapid and accurate pyrosequencing of angiosperm plastid genomes (2006)
Moore, Michael J, Dhingra, Amit, Soltis, Pamela S, Shaw, Regina, Farmerie, William G, Folta, Kevin M, ...
Abstract Background Plastid genome sequence information is vital to several disciplines in plant biology, including phylogenetics and molecular biology. The past five years have witnessed a dramatic...
Lindqvist, Charlotte, Scheen, Anne-Cathrine, Yoo, Mi-Jeong, Grey, Paris, Oppenheimer, David G, Leebens-Mack, James H, ...
Abstract Background The endemic Hawaiian mints represent a major island radiation that likely originated from hybridization between two North American polyploid lineages. In contrast with the...
Leebens-Mack, Jim, Vision, Todd, Brenner, Eric, Bowers, John E., Cannon, Steven, Clement, Mark J., ...
In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal...
Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinasegenes in plants (2006)
Yoo, Mi-Jeong, Albert, Victor A, Soltis, Pamela S, Soltis, Douglas E
Abstract Background The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In...
3/SHAGGY-like kinase genes in plants (2006)
Mi-jeong Yoo, Victor A Albert, Pamela S Soltis, Douglas E Soltis, Douglas E Soltis
Phylogenetic diversification of glycogen synthase kinase
Widespread genome duplications throughout the history of flowering plants (2006)
Cui, Liying, Wall, P. Kerr, Leebens-Mack, James H., Lindsay, Bruce G., Soltis, Douglas E., Doyle, Jeff J., ...
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth–death model to identify evidence for genome duplication in...
Widespread genome duplications throughout the history of flowering plants (2006)
Cui, Liying, Wall, P. Kerr, Leebens-Mack, James H., Lindsay, Bruce G., Soltis, Douglas E., Doyle, Jeff J., ...
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth–death model to identify evidence for genome duplication in...
Phylogeny and Domain Evolution in the APETALA2-like Gene Family (2006)
Kim, Sangtae, Soltis, Pamela S., Wall, Kerr, Soltis, Douglas E.
The combined processes of gene duplication, nucleotide substitution, domain duplication, and intron/exon shuffling can generate a complex set of related genes that may differ substantially in their...
Divergence Times and Historical Biogeography of Nymphaeales (2005)
Mi-Jeong Yoo, Charles D. Bell, Pamela S. Soltis, Douglas E. Soltis
THE AGE OF THE ANGIOSPERMS: A MOLECULAR TIMESCALE WITHOUT A CLOCK (2005)
Charles D. Bell, Douglas E. Soltis, Pamela S. Soltis
The age of the angiosperms has long been of interest to botanists and evolutionary biologists. Many early efforts to date the age of the angiosperms and evolutionary divergences within the angiosperm...
Floral gene resources from basal angiosperms for comparative genomics research (2005)
Albert, Victor A, Soltis, Douglas E, Carlson, John E, Farmerie, William G, Wall, P Kerr, Ilut, Daniel C, ...
Abstract Background The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and...
Phylogeny and Domain Evolution in the APETALA2-Like Gene Family (2005)
Kim, Sangtae, Soltis, Pamela S., Wall, Kerr, Soltis, Douglas E.
The combined processes of gene duplication, nucleotide substitution, domain duplication, and intron/exon shuffling can generate a complex set of related genes that may differ substantially in their...
Phylogeny and Domain Evolution in the APETALA2-Like Gene Family (2005)
Kim, Sangtae, Soltis, Pamela S., Wall, Kerr, Soltis, Douglas E.
The combined processes of gene duplication, nucleotide substitution, domain duplication, and intron/exon shuffling can generate a complex set of related genes that may differ substantially in their...
Geraldine A. Allen, Douglas E. Soltis, Pamela S. Soltis
We investigated phylogenetic relationships within Erythronium using DNA sequences from the chloroplast gene matK and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. Erythronium,...
Applying the Bootstrap in Phylogeny Reconstruction (2003)
Soltis, Pamela S., Soltis, Douglas E.
With the increasing emphasis in biology on reconstruction of phylogenetic trees, questions have arisen as to how confident one should be in a given phylogenetic tree and how support for phylogenetic...
Mark E. Mort, Douglas E. Soltis, Pamela S. Soltis, Javier Francisco-Ortega, Arnoldo Santos-Guerra
The Macaronesian clade of Crassulaceae comprises four genera (Aichryson, Aeonium, Greenovia, and Monanthes) that are largely endemic to Macaronesia, a region encompassing the Azores, Madeira, and the...
Savolainen, Vincent, Chase, Mark W., Salamin, Nicolas, Soltis, Douglas E., Soltis, Pamela S., López, Andrés J., ...
Patterns of Embryological and Biochemical Evolution in the Asterids (2001)
Dirk C. Albach, Pamela S. Soltis, Douglas E. Soltis
The Monopetalae or Sympetalae have been resurrected recently as the Asteridae s.l., a large clade that includes almost all sympetalous angiosperms. Phylogenetic analyses of a large, combined data set...
Phylogeny of Saxifragales (Angiosperms, Eudicots): Analysis of a Rapid, Ancient Radiation (2001)
Fishbein, Mark, Hibsch-Jetter, Carola, Soltis, Douglas E., Hufford, Larry
Rapid, ancient radiations pose one of the most difficult challenges for phylogenetic estimation. We used DNA sequence data of 9,006 aligned base pairs from five genes (chloroplast atpB, matK, rbcL,...
Comparison of Three Methods for Estimating Internal Support on Phylogenetic Trees (2000)
Mort, Mark E., Soltis, Pamela S., Soltis, Douglas E., Mabry, Michelle L.
Savolainen, Vincent, Chase, Mark W., Hoot, Sara B., Morton, Cynthia M., Soltis, Douglas E., Bayer, Clemens, ...
Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528–580) and (2) the 18S...
Soltis, Douglas E., Soltis, Pamela S., Mort, Mark E., Chase, Mark W., Savolainen, Vincent, Hoot, Sara B., ...
To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and...
A biosystematic study of Sullivantia and related studies in the saxifragaceae / (1980)
Thesis (Ph. D.)--Indiana University, 1980.
Thesis (Ph. D.)--Indiana University, 1980.
A biosystematic study of Sullivantia and related studies in the Saxifragaceae / (1980)
Photocopy. Ann Arbor, Mich. : University Microfilms International, 1982. 22 cm.
The role of genetic and genomic attributes in the success of polyploids
Soltis, Pamela S., Soltis, Douglas E.
In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to polyploidy, one on occurrence and nature and one on distribution...
Soltis, Pamela S., Soltis, Douglas E., Savolainen, Vincent, Crane, Peter R., Barraclough, Timothy G.
Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are...
The root of the angiosperms revisited
Zanis, Michael J., Soltis, Douglas E., Soltis, Pamela S., Mathews, Sarah, Donoghue, Michael J.
Most recent phylogenetic analyses of basal angiosperms have converged on the placement of Amborella as sister to all other extant angiosperms. However, certain recent studies suggest that Amborella...
Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid
Haufler, Christopher H., Soltis, Douglas E.
Homosporous ferns have usually been considered highly polyploid because they have high chromosome numbers (average n = 57.05). In angiosperms, species with chromosome numbers higher than n = 14...
Darwin's abominable mystery: Insights from a supertree of the angiosperms
Davies, T. Jonathan, Barraclough, Timothy G., Chase, Mark W., Soltis, Pamela S., Soltis, Douglas E., Savolainen, Vincent
Angiosperms are among the major terrestrial radiations of life and a model group for studying patterns and processes of diversification. As a tool for future comparative studies, we compiled a...
Floral gene resources from basal angiosperms for comparative genomics research
Albert, Victor A, Soltis, Douglas E, Carlson, John E, Farmerie, William G, Wall, P Kerr, Ilut, Daniel C, ...
Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants
Yoo, Mi-Jeong, Albert, Victor A, Soltis, Pamela S, Soltis, Douglas E
Zahn, Laura M., Kong, Hongzhi, Leebens-Mack, James H., Kim, Sangtae, Soltis, Pamela S., Landherr, Lena L., ...
Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the “floral state” by contributing to floral organ and meristem identity. SEP genes have not been detected in...
Lindqvist, Charlotte, Scheen, Anne-Cathrine, Yoo, Mi-Jeong, Grey, Paris, Oppenheimer, David G, Leebens-Mack, James H, ...
Rapid and accurate pyrosequencing of angiosperm plastid genomes
Moore, Michael J, Dhingra, Amit, Soltis, Pamela S, Shaw, Regina, Farmerie, William G, Folta, Kevin M, ...
Tate, Jennifer A., Ni, Zhongfu, Scheen, Anne-Cathrine, Koh, Jin, Gilbert, Candace A., Lefkowitz, David, ...
On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations...
Widespread genome duplications throughout the history of flowering plants
Cui, Liying, Wall, P. Kerr, Leebens-Mack, James H., Lindsay, Bruce G., Soltis, Douglas E., Doyle, Jeff J., ...
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth–death model to identify evidence for genome duplication in...
The role of genetic and genomic attributes in the success of polyploids
Soltis, Pamela S., Soltis, Douglas E.
In 1950, G. Ledyard Stebbins devoted two chapters of his book Variation and Evolution in Plants (Columbia Univ. Press, New York) to polyploidy, one on occurrence and nature and one on distribution...
Soltis, Pamela S., Soltis, Douglas E., Savolainen, Vincent, Crane, Peter R., Barraclough, Timothy G.
Many efforts to date evolutionary divergences by using a molecular clock have yielded age estimates that are grossly inconsistent with the paleontological evidence. Such discrepancies often are...
The root of the angiosperms revisited
Zanis, Michael J., Soltis, Douglas E., Soltis, Pamela S., Mathews, Sarah, Donoghue, Michael J.
Most recent phylogenetic analyses of basal angiosperms have converged on the placement of Amborella as sister to all other extant angiosperms. However, certain recent studies suggest that Amborella...
Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid
Haufler, Christopher H., Soltis, Douglas E.
Homosporous ferns have usually been considered highly polyploid because they have high chromosome numbers (average n = 57.05). In angiosperms, species with chromosome numbers higher than n = 14...
Darwin's abominable mystery: Insights from a supertree of the angiosperms
Davies, T. Jonathan, Barraclough, Timothy G., Chase, Mark W., Soltis, Pamela S., Soltis, Douglas E., Savolainen, Vincent
Angiosperms are among the major terrestrial radiations of life and a model group for studying patterns and processes of diversification. As a tool for future comparative studies, we compiled a...
Floral gene resources from basal angiosperms for comparative genomics research
Albert, Victor A, Soltis, Douglas E, Carlson, John E, Farmerie, William G, Wall, P Kerr, Ilut, Daniel C, ...
Zahn, Laura M., Kong, Hongzhi, Leebens-Mack, James H., Kim, Sangtae, Soltis, Pamela S., Landherr, Lena L., ...
Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the “floral state” by contributing to floral organ and meristem identity. SEP genes have not been detected in...
Widespread genome duplications throughout the history of flowering plants
Cui, Liying, Wall, P. Kerr, Leebens-Mack, James H., Lindsay, Bruce G., Soltis, Douglas E., Doyle, Jeff J., ...
Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth–death model to identify evidence for genome duplication in...
Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants
Yoo, Mi-Jeong, Albert, Victor A, Soltis, Pamela S, Soltis, Douglas E
Tate, Jennifer A., Ni, Zhongfu, Scheen, Anne-Cathrine, Koh, Jin, Gilbert, Candace A., Lefkowitz, David, ...
On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations...
Lindqvist, Charlotte, Scheen, Anne-Cathrine, Yoo, Mi-Jeong, Grey, Paris, Oppenheimer, David G, Leebens-Mack, James H, ...
Rapid and accurate pyrosequencing of angiosperm plastid genomes
Moore, Michael J, Dhingra, Amit, Soltis, Pamela S, Shaw, Regina, Farmerie, William G, Folta, Kevin M, ...
Matyášek, Roman, Tate, Jennifer A., Lim, Yoong K., Šrubařová, Hana, Koh, Jin, Leitch, Andrew R., ...
We analyzed nuclear ribosomal DNA (rDNA) transcription and chromatin condensation in individuals from several populations of Tragopogon mirus and T. miscellus, allotetraploids that have formed...
The Amborella genome: an evolutionary reference for plant biology
Soltis, Douglas E, Albert, Victor A, Leebens-Mack, Jim, Palmer, Jeffrey D, Wing, Rod A, DePamphilis, Claude W, ...
The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
Moore, Michael J., Bell, Charles D., Soltis, Pamela S., Soltis, Douglas E.
Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the...
Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
Lim, K. Yoong, Soltis, Douglas E., Soltis, Pamela S., Tate, Jennifer, Matyasek, Roman, Srubarova, Hana, ...
Rosid radiation and the rapid rise of angiosperm-dominated forests
Wang, Hengchang, Moore, Michael J., Soltis, Pamela S., Bell, Charles D., Brockington, Samuel F., Alexandre, Roolse, ...
The rosid clade (70,000 species) contains more than one-fourth of all angiosperm species and includes most lineages of extant temperate and tropical forest trees. Despite progress in elucidating...
Chanderbali, André S., Albert, Victor A., Leebens-Mack, Jim, Altman, Naomi S., Soltis, Douglas E., Soltis, Pamela S.
The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ...