The North American Astereae clade (Asteraceae: Astereae) represents an ecologically important lineage whose species frequently comprise early to mid-successional ecosystems primarily throughout the United States. In the eastern U.S., most species are perennial suffrutescent herbs whereas many in the western U.S. are shrubs or subshrubs, particularly in the Solidagininae s.l. The delimitation of this subtribe, however, has remained unclear as molecular phylogenetics have not resolved whether the Solidagininae s.s. and another clade, the Gutierrezia lineage, collectively form the Solidagininae s.l. To evaluate the relationships among and within these lineages, high-throughput sequencing was employed across the North American Astereae. Highthroughput sequencing was also used to clarify relationships of one taxonomically contentious genus within the Gutierrezia lineage, Euthamia. Additional Euthamia specimens were amplified via polymerase chain reactions for sequencing two loci to increase phylogenetic sampling within the genus. Subsequent species delimitations based on molecular phylogenetics and morphological evaluations from literature were used to model species distributions through ecological niche modeling. Niche comparisons via the R package ‘Humboldt’ further assessed whether the most closely related species differed considerably in their environmental niche occupation. These collectively outlined the distributions of all nine Euthamia species and indicated that hypothetical sister taxa have diverged environmentally for both allopatric and sympatric species.

Eukaryotic microalgae from the Red Sea were isolated, characterized and identified with the purpose of building a culture collection that will serve future research activities in the area of industrial microbiology. Seven sampling locations were surveyed using an in-house designed isolation protocol. Microalgae enrichment was carried out in vitro using the streak plate method and fluorescence activated cell sorting approaches. Colonial and cellular microscopy, growth media preference assays, as well as temperature, pH and salinity tolerance tests were carried out to describe the isolates. DNA extraction, PCR amplification, template sequencing and in silico analyses were carried out to identify the isolates and arrange them in a proper phylogenetic description. In total, 129 isolates were obtained. From these, only 39 were selected for characterization given their increased ability of accumulating large amounts of biomass in solid and liquid media in relatively short periods of time. All of these have a green color, are unicellular, non-motile, photosynthetic organisms and have a cell size ranging from 5 to 8 µm. More than half of them showed growth preference in Walne media, followed by F/2, MN and BG-11 SW. Maximum temperature tolerance of all organisms was around 38 ºC, while optimum growth was observed close to 25 ºC. pH preference was diverse and three groups were identified: acidic (6), intermediate (8 - 9) and alkaline (> 10) growing isolates. Salinity tests showed an overall growth preference at 25 PSU, approximately 10 units lower than that found at the sampling stations. Most isolates showed diminished growth at high salinity and high pH, except for OS3S1b which grew well in both cases, and could be an interesting strain to study further. Twenty four isolates were related to Ulvophyceae sp. MBIC10591 by BLAST approaches with a maximum identity of 96 - 97%. A maximum likelihood phylogenetic tree was created for these isolates, relative to the BLAST hits and to some model eukaryotic microalgae for positioning reference. It was shown that the 24 OS isolates are related to each other with a confidence value of 84%. Differential responses of all high biomass producing isolates towards abiotic stresses might suggest that each represents a distinct, novel, unclassified marine organism.

Canary grasses (Phalaris, Poaceae) include 21 species widely distributed throughout temperate and subtropical regions of the world with centers of diversity in the Mediterranean Basin and western North America. The genus contains annual/perennial, endemic/cosmopolitan, wild, and invasive species with basic numbers of x=6 (diploid) and x=7 (diploid/tetraploid/hexaploid). The latter display vastly greater speciation and geographic distribution. These attributes make Phalaris an ideal platform to study species diversification, dispersal, historic hybridization, polyploidy events, and chromosome evolution in the grasses. This body of research presents the first molecular phylogenetic and phylogeographic reconstruction of the genus based on the nuclear ITS and plastid trnT-F DNA regions allowing species relationships and the importance of polyploidy in speciation to be assessed. Divergence dates for the genus were determined using Bayesian methods (BEAST, version 1.6.2) and historic patterns of dispersal were analyzed with RASP (version 2.1b). Self-incompatibility and the feasibility of hybridization between major groups within the genus were studied with a series of greenhouse experiments. Acetocarmine and fluorescent staining techniques were used to study the morphology of the chromosomes in a phylogenetic context and the nuclear DNA content (C values) was quantified using flow cytometry. Four major clades were revealed in the genus with cytological and geographic affinities leading to the establishment of two subgenera and four sections in the first comprehensive infrageneric treatment of Phalaris. Divergence dating revealed a Miocene emergence (20.6-8.4 MYA) for the genus which is concurrent with studies of other genera in the Aveneae tribe. The hypothesis stating that Phalaris originated in the Mediterranean Basin and dispersed to the New World via a western route leading to a secondary center of diversification in western North America was supported by phylogeographic and cytological analyses. An empirical study comparing the weight, length, and width of the florets by morphological type and cytotype revealed significant differences that support a dispersal advantage among the New World and Arundinacea species. The x=6 species displayed greater intraspecific C value variation, higher DNA content per haploid chromosome set, and a distinct karyotype compared with the x=7 species indicating a complex history of chromosome evolution. / Ph. D.

No description available.

No description available.

No description available.

Dating of sequence divergence from different species, genes, and strains is now commonplace in biological studies aimed at deciphering micro- and macro-evolutionary temporal patterns. With sequencing becoming increasingly cheaper, molecular datasets are expanding quickly in size. This expansion has necessitated the development of innovative and efficient methods to make the inference of large timetrees feasible from genome-scale datasets that routinely contain hundreds of species. In my dissertation research, I have focused on developing such methods that improved the accuracy, precision, and speed of calculations needed for divergence time inference. I have also conducted large-scale data analyses to reveal fundamental patterns of molecular evolution. The following five related projects were pursued in this dissertation. (1) Development of a machine learning method (CorrTest) for detecting the best-fit model for describing the variation of molecular evolution rates among branches and lineages for large phylogenies. Computer simulations show that the machine learning method outperforms the currently available state-of-the-art methods and is computationally efficient. (2) Development of an analytical method and a new approach to utilize probability densities as calibrations to calculate confidence intervals reliably for RelTime, a non-Bayesian method. Empirical analysis shows that RelTime produces confidence intervals that are comparable to those generated by Bayesian methods, and simulation analysis shows that RelTime confidence intervals often contain the actual values. (3) Application of CorrTest on empirical datasets reveals the extensive autocorrelation in molecular rate in nucleotide and amino acid sequence evolution in diverse taxonomic groups, suggesting that rate autocorrelation is a common phenomenon throughout the tree of life. (4) Investigation of the impact of substitution model complexity on the accuracy and precision of divergence time estimation. Analyses of large-scale empirical data show that the selection of substitution model only has a limited impact on time estimation, as the extremely simple models yield divergence time estimates and credibility intervals remarkably similar to those obtained from very complex models. (5) Inventory of non-Bayesian methods for dating species divergences, including their statistical bases, their performance of estimating divergence times, and the software packages in which they are implemented. A guide has provided for the use of non-Bayesian dating methods to produce reliable divergence times. / Biology

<p> Three pieces of work are contained in this thesis. OGRe is a relational database that stores mitochondrial genomes of animals. The database has been operational for approximately five years and the number of genomes in the database has expanded to over 1000 in this period. However, sometimes, new genomes can not be added to the database because of small errors in the source ffies. Several improvements to the update method and the organizational structure of OGRe have been done, which are presented in the first part of this thesis. </p> <p> The second part of this thesis is a study on codon usage in mitochondrial genomes of mammals and fish. Codon usage bias can be caused by mutation and translational selection. In this study, we use some statistical tests and likelihood-based tests to determine which factors are most important in causing codon bias in mitochondrial genomes of mammals and fish. It is found that codon usage patterns seem to be determined principally by complex context-dependent mutational effects. </p> <p> The third part of this thesis is a phylogenetic study of 159 avian species obtained using mitochondrial rRNA sequences that were provided by Dr. van Tuinen. In this study, two methods are used: one considers sites of sequences as independently evolving; the other includes the secondary structure of rRNAs. Unfortunately, the amount of information in the rRNA sequences seems to be insufficient to determine the whole phylogeny of birds. However, our results make it clear that several traditionally defined orders are polyphyletic and therefore need to be redefined. </p> / Thesis / Master of Science (MSc)

Astilbe (Saxifragaceae) is a genus of herbaceous perennials widely cultivated for their ornamental value. The genus is considered taxonomically complex because of its geographic distribution, variation within species, and the lack of adequate morphological characters to delineate taxa. To date, an inclusive investigation of the genus has not been conducted. This study was undertaken to (a) develop a well-resolved phylogeny of the genus Astilbe using an expanded morphological data set and sequences from the plastid gene matK, (b) use single nucleotide polymorphisms to determine the lineages of cultivated varieties, and (c) successfully culture Astilbe in vitro and evaluate potential somaclonal variation of resulting Astilbe microshoots. Phylogenetic trees generated from a morphological character matrix of 28 character states divided Astilbe into three distinct clades. Relationships were well resolved among the taxa, though only a few branches had greater than 50% bootstrap support. There is evidence from the phylogeny that some described species may actually represent variation within populations of species. From our analysis I propose an Astilbe genus with 13 to 15 species and offer a key for distinguishing species and varieties. There was little matK sequence variation among taxa of Astilbe. Phylogeny of Astilbe generated from the maximum parsimony and maximum likelihood analysis of matK sequences resulted in a polytomy of seven Astilbe species, with relationships within the genus poorly resolved. A second phylogeny of 21 taxa of Astilbe was more informative, aligning cultivated varieties near species from which they were derived. The matK sequence variation for Astilbe taxa was aligned to reveal DNA polymorphisms. Closely related taxa retained polymorphisms at the same sites within the gene sequence. These polymorphic sites could potentially be utilized to confirm the lineage of popular cultivated Astilbe varieties. Propagation of Astilbe seedlings in tissue culture gave rise to various numbers of microshoots from each of 15 seedlings. Multivariate and cluster analysis of morphological characters from 138 plants derived from 15 seedlings revealed potential somaclonal variants. These variants were characterized by one or more of the following traits: dwarf habit, dark green leaves (high chlorophyll content), increased flowering, or larger plant size. Somaclonal variants with desirable phenotypes may be valuable for cultivar development. / Ph. D.

<p dir="ltr">Spread primarily through sex, members of the microfungal class Laboulbeniomycetes are parasitic on arthropods, where they form tiny, three-dimensional thalli on the host exoskeleton. While the study of Laboulbeniomycetes has had a renaissance in the age of molecular methods, so too has the Red Queen Hypothesis, a coevolutionary theory aimed at characterizing how biotic interactions shape the evolutionary trajectory of “players” over time. While the central dogma of “laboulbeniology” is that labouls do not cause a fitness disadvantage to the host in the wild, here we report the first genome annotation data of a Laboulbeniomycete genome, indicating the possibility of past antagonistic relationships with host species. Some of the genes predicted are homologous with that of highly pathogenic entomopathogenic species, such as those within <i>Cordyceps</i>. To understand why these seemingly benign parasites possess genes associated with pathogenicity, we reviewed recent advances in molecular methods for detecting Red Queen associations, and propose a new model we call “Sleeping Red Queens”. Using Laboulbeniomycete evolutionary history, we predict that antagonists who have adapted to each other over time to a benign state can “re-awaken” or transition to a more antagonistic mode due to environmental changes. The “Sleeping Red Queen” model of Laboulbeniomycetes is supported by research on laboul ecology under artificial conditions. The purpose of this work is to review the history of Laboulbeniomycetes, examine recent advances in molecular methods through the Red Queen lens, report on our new molecular data, and discuss how our new findings can be used to apply Red Queen theory to Laboulbeniomycetes, while also hypothesizing what these future analyses could reveal. With promising advances in next-generation sequencing, we believe our Sleeping Red Queen model will be advantageous for interpretation of future genomic and bioinformatic data of Laboulbeniomycetes.</p>