Publications (7)24.27 Total impact
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Article: A functional phylogenomic view of the seed plants.
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ABSTRACT: A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.PLoS Genetics 12/2011; 7(12):e1002411. · 8.69 Impact Factor -
Article: Growth and Care Instructions of a New Model Species—the Lycophyte Selaginella apoda
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ABSTRACT: Selaginella apoda has many advantages as a model species, including a short life cycle. In order to work effectively with a lycophyte model species, it is important to be able to grow the gametophytes and sporophytes quickly. In the case of S. apoda, the gametophytes grow quickly and have high fertilization success in warm nutrient enriched water. Sporophytes at the three root stage can be easily transplanted to soil. They grow well in moist containers at a wide range of temperatures. Treatment with 0.15% Previcur®N prevents most fungal contaminations.American Fern Journal 12/2010; · 0.41 Impact Factor -
Article: The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.
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ABSTRACT: Genome level analyses have enhanced our view of phylogenetics in many areas of the tree of life. With the production of whole genome DNA sequences of hundreds of organisms and large-scale EST databases a large number of candidate genes for inclusion into phylogenetic analysis have become available. In this work, we exploit the burgeoning genomic data being generated for plant genomes to address one of the more important plant phylogenetic questions concerning the hierarchical relationships of the several major seed plant lineages (angiosperms, Cycadales, Gingkoales, Gnetales, and Coniferales), which continues to be a work in progress, despite numerous studies using single, few or several genes and morphology datasets. Although most recent studies support the notion that gymnosperms and angiosperms are monophyletic and sister groups, they differ on the topological arrangements within each major group. We exploited the EST database to construct a supermatrix of DNA sequences (over 1,200 concatenated orthologous gene partitions for 17 taxa) to examine non-flowering seed plant relationships. This analysis employed programs that offer rapid and robust orthology determination of novel, short sequences from plant ESTs based on reference seed plant genomes. Our phylogenetic analysis retrieved an unbiased (with respect to gene choice), well-resolved and highly supported phylogenetic hypothesis that was robust to various outgroup combinations. We evaluated character support and the relative contribution of numerous variables (e.g. gene number, missing data, partitioning schemes, taxon sampling and outgroup choice) on tree topology, stability and support metrics. Our results indicate that while missing characters and order of addition of genes to an analysis do not influence branch support, inadequate taxon sampling and limited choice of outgroup(s) can lead to spurious inference of phylogeny when dealing with phylogenomic scale data sets. As expected, support and resolution increases significantly as more informative characters are added, until reaching a threshold, beyond which support metrics stabilize, and the effect of adding conflicting characters is minimized.PLoS ONE 02/2009; 4(6):e5764. · 4.09 Impact Factor -
Article: Nuclear genome size in Selaginella.
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ABSTRACT: Estimates of nuclear genome size for 9 Selaginella species were obtained using flow cytometry, and measurements for 7 of these species are reported for the first time. Estimates range from 0.086 to 0.112 pg per holoploid genome (84-110 Mb). The data presented here agree with the previously published flow cytometric results for S. moellendorffii. Within the 9 species sampled here, chromosome number varies from 2n = 16 to 2n = 27. Nuclear genome size appears to be strongly correlated with chromosome number (Spearman's rank correlation; p = 0.00003725). Cultivated S. moellendorffii lacks sexual reproduction--manifest by the production of abortive megasporangia. Flow cytometric data generated from a herbarium specimen of a fertile wild-collected S. moellendorffii are virtually indistinguishable from the data generated from fresh material (0.088 vs. 0.089 pg/1C). Therefore, the limited fertility observed in cultivated plants is probably not the result of abnormal chromosome number (e.g., induced by interspecific hybridization).Genome 05/2007; 50(4):351-6. · 1.65 Impact Factor -
Article: DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.
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ABSTRACT: Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.PLoS ONE 02/2007; 2(11):e1154. · 4.09 Impact Factor -
Article: Cataphylls of the Middle Triassic cycad Antarcticycas schopfii and new insights into cycad evolution.
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ABSTRACT: Cataphylls associated with the Middle Triassic stem genus Antarcticycas are described, and their impact on understanding cycad evolution is discussed. The cataphylls of Antarcticycas are triangular in outline and flattened adaxially with lateral flanges. The outer surfaces are covered with a ramentum of filamentous hairs, the epidermis is a single cell layer thick, and the ground tissue is parenchymatous with mucilage canals and sclereids. Vascular bundles form a distinct inverted omega-shaped pattern characteristic of the Cycadales observed in petioles of extant species. The structures in Antarcticycas are interpreted as cataphylls based on overall morphology, presence of straight vascular strands in the cortex of the associated stem, and lack of fascicular cambia in the vascular bundles. Because much of the overall diversity of Cycadales is represented by fossils, integrating fossil taxa into explicit phylogenetic hypotheses is important for understanding cycad evolution. Therefore, character and minimum age mapping were performed on a phylogeny of extant and fossil taxa including Antarcticycas. The results suggest that major extant lineages of Cycadales had diverged by the Permian to Triassic and that certain synapomorphies for Cycadales had evolved by the Permian. Evidence of insect feeding on Antarcticycas suggests that associations between cycads and insects are ancient.American Journal of Botany 05/2006; 93(5):724-38. · 2.66 Impact Factor -
Article: Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes.
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ABSTRACT: A phylogenetic analysis of the Poales was conducted to assess relationships among Poaceae and allied families. The analysis included 40 taxa, representing all families of the Poales as circumscribed by the Angiosperm Phylogeny Group (APG), plus five of the six unplaced Commelinid families in the APG system. The data matrix included 98 informative characters representing variation in morphology and chloroplast genome structure (including three inversions in the chloroplast genome), and 563 informative characters derived from rbcL and atpA nucleotide sequences. Ecdeiocolea has the 6-kilobase (kb) chloroplast genome inversion previously reported in Joinvillea and Poaceae, and like Joinvillea it lacks the trnT inversion that occurs in grasses. Analysis of the morphological data places Poaceae in an unresolved relationship relative to several other taxa, including Joinvillea and Ecdeiocolea, while analysis of the molecular and combined data resolves Ecdeiocolea as sister of Poaceae, with Joinvillea the sister of this group. Although the 6-kb and trnT inversions are non-homoplasious in the phylogenies obtained in this study, the 28-kb inversion is optimized as having originated twice (once in Restionaceae and another time in the most recent common ancestor of Ecdeiocolea, Joinvillea, and the grasses); an alternative interpretation is that it arose once and was later lost in Anarthria. Ecdeiocolea shares with Poaceae the presence of operculate, annulate pollen that lacks scrobiculi, and a dry, indehiscent fruit.American Journal of Botany 01/2003; 90(1):93-106. · 2.66 Impact Factor
Top co-authors
Top Journals
- American Journal of Botany (2)
- PLoS ONE (2)
- American Fern Journal (1)
- Genome (1)
- PLoS Genetics (1)
Institutions
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2007
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New York Botanical Garden
New York City, NY, USA
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2006
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University of Kansas
- Department of Ecology and Evolutionary Biology
Lawrence, KS, USA
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2003
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American Museum of Natural History
New York City, NY, USA
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