Edward E. Schilling

Bio: Edward E. Schilling is an academic researcher from University of Tennessee. The author has contributed to research in topics: Viguiera & Genus. The author has an hindex of 27, co-authored 97 publications receiving 6040 citations. Previous affiliations of Edward E. Schilling include Michigan State University & University of Tübingen.

Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III

Abstract: Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL((UAG)), trnQ((UUG))-5'rps16, 3'trnV((UAC))-ndhC, ndhF-rpl32, psbD-trnT((GGU)), psbJ-petA, 3'rps16-5'trnK((UUU)), atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

Abstract: Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

Chemometrics, mathematics and statistics in chemistry

Abstract: Experimental Designs: Fractionals.- Multivariate Data Analysis in Chemistry.- Statistics Aand Chemistry, and the Linear Calibration Problem.- Chemometrics and Analytical Chemistry.- Multivariate Calibration.- Autocorrelation and Time Series Analysis.- Sampling.- Automatic Control of Chemical Processes.- Data Analysis in Chromatography.- Experimental Design: Response Surfaces.- Linear Models And Matrix Least Squares In Clinical Chemistry.- Data Analysis in Food Chemistry.- Multidimensional Data Representation in Medicinal Chemistry.- Analysis of Variance and Linear Models.- Cluster Analysis.- Operational Research.- Variation In Space: An Introduction to Regionalized Variables.- Three-Dimensional Graphics for Scientific Data Display and Analysis.- Teaching Chemometrics.

Everywhere but Antarctica: using a supertree to understand the diversity and distribution of the Compositae.

Abstract: s. Albuquerque, New Mexico, August 12-16, 2001. Botanical Society of America. Pp. 132. Panero, J.L., Baldwin, B.G., Schilling, E.E. & Clevinger, J.A. 2001c. Molecular phylogenetic studies of members of tribes Helenieae, Heliantheae, and Eupatorieae (Asteraceae). 3. General systematics and proposed taxonomic changes in current classification. In: Botany 2001 Abstracts. Albuquerque, New Mexico, August 12-16, 2001.s. Albuquerque, New Mexico, August 12-16, 2001. Botanical Society of America. Pp. 132. Panero, J. & Funk, V.A. 2002. Toward a phylogenetic subfamilial classification for the Compositae (Asteraceae). Proc. Biol. Soc. Wash. 115: 909-922. Pelser, P.B., Gravendeel, B. & Meijden, R. 2002. Tackling speciose genera: species composition and phylogenetic position of Senecio sect. Jacobaea (Asteraceae) based on plastid and nrDNA sequences. Amer. J. Bot. 89: 929939. Raven, P.H. & Axelrod, D.I. 1974. Angiosperm biogeography and past continental movements. Ann. Missouri Bot. Gard. 61: 539-673. Robinson, H. 1983. A generic review of the tribe Liabeae (Asteraceae). Smithsonian Contr. Bot. 54: 1-69. Robinson, H. 1999. Generic and subtribal classification of American Vernonieae. Smithsonian Contr. Bot. 89: 1-116. Rzedowski, J. 1972. Contribuciones a la fitogeografia floristica e historica de Mexico. III Algunas tendencias en la distribucion geografica y ecologica de las Compositae mexicanas. Ciencia (Mexico) 27: 123-132. Schmidt, G.J. & Schilling, E.E. 2000. Phylogeny and biogeography of Eupatorium (Asteraceae: Eupatorieae) based on nuclear ITS sequence data. Amer. J. Bot. 87: 716726. Scotese, C.R. 2002. PALEOMAP website. (http://www.scotese.com) Skavarla, J. 1977. Pollen Morphology. In: Heywood, V.H., Harborne, J.B. & Turner, B.L. (eds.), The Biology and Chemistry of the Compositae. Vol. 1. Academic Press, Lon-

Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III

Abstract: Although the chloroplast genome contains many noncoding regions, relatively few have been exploited for interspecific phylogenetic and intraspecific phylogeographic studies. In our recent evaluation of the phylogenetic utility of 21 noncoding chloroplast regions, we found the most widely used noncoding regions are among the least variable, but the more variable regions have rarely been employed. That study led us to conclude that there may be unexplored regions of the chloroplast genome that have even higher relative levels of variability. To explore the potential variability of previously unexplored regions, we compared three pairs of single-copy chloroplast genome sequences in three disparate angiosperm lineages: Atropa vs. Nicotiana (asterids); Lotus vs. Medicago (rosids); and Saccharum vs. Oryza (monocots). These three separate sequence alignments highlighted 13 mutational hotspots that may be more variable than the best regions of our former study. These 13 regions were then selected for a more detailed analysis. Here we show that nine of these newly explored regions (rpl32-trnL((UAG)), trnQ((UUG))-5'rps16, 3'trnV((UAC))-ndhC, ndhF-rpl32, psbD-trnT((GGU)), psbJ-petA, 3'rps16-5'trnK((UUU)), atpI-atpH, and petL-psbE) offer levels of variation better than the best regions identified in our earlier study and are therefore likely to be the best choices for molecular studies at low taxonomic levels.

Use of DNA barcodes to identify flowering plants

Abstract: Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

Genome evolution in polyploids

Abstract: Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.