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Douglas E. Soltis

Bio: Douglas E. Soltis is an academic researcher from Florida Museum of Natural History. The author has contributed to research in topics: Phylogenetic tree & Phylogenetics. The author has an hindex of 127, co-authored 612 publications receiving 67161 citations. Previous affiliations of Douglas E. Soltis include University of Kansas & University of Wisconsin-Madison.


Papers
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Journal ArticleDOI
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.

7,299 citations

Journal ArticleDOI
05 May 2011-Nature
TL;DR: Comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages are used to elucidate two groups of ancient gene duplications, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms.
Abstract: Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages to elucidate two groups of ancient gene duplications-one in the common ancestor of extant seed plants and the other in the common ancestor of extant angiosperms. Gene duplication events were intensely concentrated around 319 and 192 million years ago, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms, respectively. Significantly, these ancestral WGDs resulted in the diversification of regulatory genes important to seed and flower development, suggesting that they were involved in major innovations that ultimately contributed to the rise and eventual dominance of seed plants and angiosperms.

1,763 citations

Journal ArticleDOI
TL;DR: An attempt to improve methods of analysis of fern enzymes in starch gel electrophoresis by experimenting with modifications of the method of sample preparation outlined by Soltis et al. (1980), and determining gel and electrode buffers that provide clear starch gel enzyme banding for 22 enzyme systems in ferns.
Abstract: The homosporous pteridophytes have been largely uninvestigated by electrophoresis, despite the fact that they offer many exciting research possibilities (Soltis et al., 1980). The paucity of electrophoretic studies of ferns and fern allies may be due in large part to the high concentrations of condensed tannins that many species contain (Cooper-Driver, 1976 and pers. comm.). These compounds render enzymes inactive by binding with them following cellular disruption, thereby frustrating researchers who have attempted electrophoretic analysis utilizing standard methods of sample preparation. The method of sample preparation developed by Kelley and Adams (1977a, b) in their analysis of enzyme variation in Juniperus was an important procedural breakthrough in overcoming the difficulties that result from the liberation of large amounts of phenolic compounds during tissue preparation. Recently, a simplified version of that method was applied by Soltis et al. (1980) to fern leaf tissue, facilitating rapid preparation of active enzyme samples and thereby making electrophoretic analyses of large numbers of individuals more feasible. In an attempt to improve methods of analysis of fern enzymes in starch gel electrophoresis, we have experimented with modifications of the method of sample preparation outlined by Soltis et al. (1980). We also have examined several different methods of sample preparation such as those of Gottlieb (1981a), Mitton et al. (1979), and Werth et al. (1982), and have evaluated the relative merits of each with fern tissue. Finally, during the course of our electrophoretic investigations of ferns we found that standard gel and electrode buffers and staining schedules, such as those of Brewer (1970) and Shaw and Prasad (1970), often provided unsatisfactory results when applied to ferns. We have determined gel and electrode buffers, as well as staining schedules, that provide clear starch gel enzyme banding for 22 enzyme systems in ferns. Requests for advice resulting from the recent surge of interest in fern enzyme electrophoresis have prompted us to compile our procedural data so that other researchers can take advantage of our experimentation. We hope that these data will stimulate more extensive electrophoretic investigation of pteridophytes and other electrophoretically difficult taxa. Gottlieb (1981b) recently reviewed aspects of enzyme electrophoresis primarily in gymnosperms and angiosperms. His discussion is equally relevant to understanding the potential applications and limitations of electrophoretic evidence in pteridophytes. Since homosporous pteridophytes have high chromosome numbers, it is tempting to invoke polyploidy in interpreting their enzyme band patterns. It is well

1,432 citations

Journal ArticleDOI
TL;DR: A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA, rbcL, and atpB representing a total of 4733 bp is presented, resulting in the most highly resolved and strongly supported topology yet obtained for angiosPerms.

1,288 citations

Journal ArticleDOI
06 Feb 2014-Nature
TL;DR: It is shown that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing.
Abstract: Early flowering plants are thought to have been woody species restricted to warm habitats 1–3 . This lineage has since radiated into almost every climate, with manifold growth forms 4 . As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species’ traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully move di nto freezingprone environments by either possessing transport networks of small

1,221 citations


Cited by
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Journal ArticleDOI
TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

14,171 citations

Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

Journal ArticleDOI
TL;DR: ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Abstract: Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.

7,425 citations

Journal ArticleDOI
TL;DR: A revised and updated classification for the families of the flowering plants is provided in this paper, which includes Austrobaileyales, Canellales, Gunnerales, Crossosomatales and Celastrales.

7,299 citations