<p>The <italic>Polypodium vulgare<italic> complex (Polypodiaceae) comprises a well-studied group of fern taxa whose members are cryptically differentiated morphologically and have generated a confusing and highly reticulate species cluster. Once considered a single species spanning much of northern Eurasia and North America, <italic>P. vulgare<italic> has been segregated into approximately 17 diploid and polyploid taxa as a result of cytotaxonomic work, hybridization experiments, and isozyme studies conducted during the 20th century. Despite considerable effort, however, the evolutionary relationships among the diploid members of the <italic>P. vulgare<italic> complex remain poorly resolved, and several taxa, particularly allopolyploids and their diploid progenitors, remain challenging to delineate morphologically due to a dearth of stable diagnostic characters. Furthermore, compared to many well-studied angiosperm reticulate complexes, relatively little is known about the number of independently-derived lineages, distribution, and evolutionary significance of the allopolyploid species that have formed recurrently. This dissertation is an attempt to advance systematic knowledge of the <italic>Polypodium vulgare<italic> complex and establish it as a "model" system for investigating the evolutionary consequences of allopolyploidy in ferns. </p><p>Chapter I presents a diploids-only phylogeny of the <italic>P. vulgare<italic> complex and related species to test previous hypotheses concerning relationships within <italic>Polypodium<italic> sensu stricto. Analyses of sequence data from four plastid loci (<italic>atpA<italic>, <italic>rbcL<italic>, <italic>matK<italic>, and <italic>trnG-trnR<italic>) recovered a monophyletic <italic>P. vulgare<italic> complex comprising four well-supported clades. The <italic>P. vulgare<italic> complex is resolved as sister to the Neotropical <italic>P. plesiosorum<italic> group and these, in turn, are sister to the Asian endemic <italic>Pleurosoriopsis makinoi<italic>. Divergence time analyses incorporating previously derived age constraints and fossil data provide support for an early Miocene origin for the <italic>P. vulgare<italic> complex and a late Miocene-Pliocene origin for the four major diploid lineages of the complex, with the majority of extant diploid species diversifying from the late Miocene through the Pleistocene. Finally, node age estimates are used to reassess previous hypotheses, and to propose new hypotheses, about the historical events that shaped the diversity and current geographic distribution of the diploid species of the <italic>P. vulgare<italic> complex. </p><p>Chapter II addresses reported discrepancies regarding the occurrence of <italic>Polypodium calirhiza<italic> in Mexico. The original paper describing this taxon cited collections from Mexico, but the species was omitted from the recent <italic>Pteridophytes of Mexico<italic>. Originally treated as a tetraploid cytotype of <italic>P. californicum<italic>, <italic>P. calirhiza<italic> now is hypothesized to have arisen through hybridization between <italic>P. glycyrrhiza<italic> and <italic>P. californicum<italic>. The allotetraploid can be difficult to distinguish from either of its putative parents, but especially so from <italic>P. californicum<italic>. These analyses show that a combination of spore length and abaxial rachis scale morphology consistently distinguishes <italic>P. calirhiza<italic> from <italic>P. californicum<italic> and confirm that both species occur in Mexico. Although occasionally found growing together in the United States, the two species are strongly allopatric in Mexico, where <italic>P. californicum<italic> is restricted to coastal regions of the Baja California peninsula and neighboring Pacific islands and <italic>P. calirhiza<italic> grows at high elevations in central and southern Mexico. The occurrence of <italic>P. calirhiza<italic> in Oaxaca, Mexico, marks the southernmost extent of the P. vulgare complex in the Western Hemisphere.</p><p>Chapter III examines a case of reciprocal allopolyploid origins in the fern <italic>Polypodium hesperium<italic> and presents it as a natural model system for investigating the evolutionary potential of duplicated genomes. In allopolyploids, reciprocal crosses between the same progenitor species can yield lineages with different uniparentally inherited plastid genomes. While likely common, there are few well-documented examples of such reciprocal origins. Using a combination of uniparentally inherited plastid and biparentally inherited nuclear sequence data, we investigated the distributions and relative ages of reciprocally formed lineages in <italic>Polypodium hesperium<italic>, an allotetraploid fern that is broadly distributed in western North America. The reciprocally-derived plastid haplotypes of <italic>Polypodium hesperium<italic> are allopatric, with populations north and south of 42&#730; N latitude having different plastid genomes. Biogeographic information and previously estimated ages for the diversification of its diploid progenitors, lends support for middle to late Pleistocene origins of <italic>P. hesperium<italic>. Several features of <italic>Polypodium hesperium<italic> make it a particularly promising system for investigating the evolutionary consequences of allopolyploidy. These include reciprocally derived lineages with disjunct geographic distributions, recent time of origin, and extant diploid progenitor lineages. </p><p>This dissertation concludes by demonstrating the utility of the allotetraploid <italic>Polypodium hesperium<italic> for understanding how ferns utilize the genetic diversity imparted by allopolyploidy and recurrent origins. Chapter IV details the use of high-throughput sequencing technologies to generate a reference transcriptome for <italic>Polypodium<italic>, a genus without preexisting genomic resources, and compare patterns of total and homoeolog-specific gene expression in leaf tissue of reciprocally formed lineages of <italic>P. hesperium<italic>. Genome-wide expression patterns of total gene expression and homoeolog expression ratios are strikingly similar between the lineages--total gene expression levels mirror those of the diploid progenitor P. amorphum and homoeologs derived from <italic>P. amorphum<italic> are preferentially expressed. The unprecedented levels of unbalanced expression level dominance and unbalanced homoeolog expression bias found in <italic>P. hesperium<italic> supports the hypothesis that these phenomena are pervasive consequences of allopolyploidy in plants.</p> / Dissertation

abstract: Natural history is, and was, dependent upon the collection of specimens. In the nineteenth century, American naturalists and institutions of natural history cultivated and maintained extensive collection networks comprised of numerous collectors that provided objects of natural history for study. Effective networks were collaborative in nature, with naturalists such as Spencer Baird of the Smithsonian trading their time and expertise for specimens. The incorporation of Darwinian and Neo-Lamarckian evolutionary theory into natural history in the middle of the century led to dramatic changes in the relationship between naturalists and collectors, as naturalists sought to reconcile their observations within the new evolutionary context. This dissertation uses the careers of collectors Robert Kennicott, Frank Stephens, Edward W. Nelson, E.A. Goldman, and Edmund Heller as case studies in order to evaluate how the changes in the theoretical framework of late nineteenth century natural history led to advances in field practice by assessing how naturalists trained their collectors to meet new demands within the field. Research focused on the correspondence between naturalists and collectors, along with the field notes and applicable publications by collectors. I argue that the changes in natural history necessitated naturalists training their collectors in the basics of biogeography - the study of geographic distribution of organisms, and systematics - the study of the diversity of life - leading to a collaborative relationship in which collectors played an active role in the formation of new biological knowledge. The project concludes that the changes in natural history with regard to theory and practice gradually necessitated a more professional cadre of collectors. Collectors became active agents in the formation of biological knowledge, and instrumental in the formation of a truly systematic natural history. As a result, collectors became de facto field naturalists, the forerunners of the field biologists that dominated the practice of natural history in the early and middle twentieth century. / Dissertation/Thesis / Ph.D. History 2011

abstract: The power of science lies in its ability to infer and predict the existence of objects from which no direct information can be obtained experimentally or observationally. A well known example is to ascertain the existence of black holes of various masses in different parts of the universe from indirect evidence, such as X-ray emissions. In the field of complex networks, the problem of detecting hidden nodes can be stated, as follows. Consider a network whose topology is completely unknown but whose nodes consist of two types: one accessible and another inaccessible from the outside world. The accessible nodes can be observed or monitored, and it is assumed that time series are available from each node in this group. The inaccessible nodes are shielded from the outside and they are essentially ``hidden.'' The question is, based solely on the available time series from the accessible nodes, can the existence and locations of the hidden nodes be inferred? A completely data-driven, compressive-sensing based method is developed to address this issue by utilizing complex weighted networks of nonlinear oscillators, evolutionary game and geospatial networks. Both microbes and multicellular organisms actively regulate their cell fate determination to cope with changing environments or to ensure proper development. Here, the synthetic biology approaches are used to engineer bistable gene networks to demonstrate that stochastic and permanent cell fate determination can be achieved through initializing gene regulatory networks (GRNs) at the boundary between dynamic attractors. This is experimentally realized by linking a synthetic GRN to a natural output of galactose metabolism regulation in yeast. Combining mathematical modeling and flow cytometry, the engineered systems are shown to be bistable and that inherent gene expression stochasticity does not induce spontaneous state transitioning at steady state. By interfacing rationally designed synthetic GRNs with background gene regulation mechanisms, this work investigates intricate properties of networks that illuminate possible regulatory mechanisms for cell differentiation and development that can be initiated from points of instability. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2015

<p> "Bantu" is a term used to describe lineages of people in around 600 different ethnic groups on the African continent ranging from modern-day Cameroon to South Africa. The migration of the Bantu people, which occurred around 3,000 years ago, was influential in spreading culture, language, and genetic traits and helped to shape human diversity on the continent. Research in the 1970s was completed to geographically divide the Bantu languages into 16 zones now known as "Guthrie zones" (Guthrie, 1971). </p><p> Researchers have postulated the migratory pattern of the Bantu people by examining cultural information, linguistic traits, or small genetic datasets. These studies offer differing results due to variations in the data type used. Here, an assessment of the Bantu migration is made using a large dataset of combined cultural data and genetic (Y-chromosomal and mitochondrial) data. </p><p> One working hypothesis is that the Bantu expansion can be characterized by a primary split in lineages, which occurred early on and prior to the population spreading south through what is now called the Congolese forest (i.e. "early split"). A competing hypothesis is that the split occurred south of the forest (i.e. "late split"). </p><p> Using the comprehensive dataset, a phylogenetic tree was developed on which to reconstruct the relationships of the Bantu lineages. With an understanding of these lineages in hand, the changes between Guthrie zones were traced geospatially. </p><p> Evidence supporting the "early split" hypothesis was found, however, evidence for several complex and convoluted paths across the continent were also shown. These findings were then analyzed using dimensionality reduction and machine learning techniques to further understand the confidence of the model.</p><p>

abstract: Weevils are one of the most diverse groups of animals with thousands of species suspected to remain undiscovered. The Conoderinae Schoenherr, 1833 are no exception, being especially diverse and unknown in the Neotropics where they are recognizable for their unique behaviors and color patterns among weevils. Despite these peculiarities, the group has received little attention from researchers in the past century, with almost nothing known about their evolution. This dissertation presents a series of three studies that begin to elucidate the evolutionary history of these bizarre and fascinating weevils, commencing with an overview of their biology and classificatory history (Chapter 1). Chapter 2 presents the first formal cladistic analysis on the group to redefine the New World tribes Lechriopini Lacordaire, 1865 and Zygopini, Lacordaire, 1865. An analysis of 75 taxa (65 ingroup) with 75 morphological characters yielded six equally parsimonious trees and synapomorphies that are used to reconstitute the tribes, resulting in the transfer of sixteen genera from the Zygopini to the Lechriopini and four generic transfers out of the Lechriopini to elsewhere in the Conoderinae. Chapter 3 constitutes a taxonomic revision of the genus Trichodocerus Chevrolat, 1879, the sole genus in the tribe Trichodocerini Champion, 1906, which has had an uncertain phylogenetic placement in the Curculionidae but has most recently been treated in the Conoderinae. In addition to redescriptions of the three previously described species placed in the genus, twenty-four species are newly described and an identification key is provided for all recognized species groups and species. Chapter 4 quantitatively tests the similarity in color pattern among species hypothesized to belong to several different mimicry complexes. The patterns of 160 species of conoderine weevils were evaluated for 15 categorical and continuous characters. Non-metric multidimensional scaling (NMDS) is used to visualize similarity by the proximity of individual species and clusters of species assigned to a mimicry complex in ordination space with clusters being statistically tested using permutational multivariate analysis of variance (PERMANOVA). / Dissertation/Thesis / Doctoral Dissertation Evolutionary Biology 2019

Despite the association of the human gut microbiome and various diseases, a systematic definition of what constitutes a healthy human gut microbiome has not been established. This is crucial for microbiome research as it provides a basis for evaluating whether a given microbiome sample may deviate from the homeostasis state and is thus prone to the development of chronic diseases. This work aims to propose one such definition by using species/strain-resolved Genome-scale (GEM) models of metabolism. More specifically, we have constructed sample-specific GEMs from 30 healthy subjects using the taxonomic profiling of fecal metagenomic samples. We then computationally simulated these GEMs under a relevant diet (a supplemented typical Western diet) to determine which microbes in each sample contribute to the production of 17 key metabolites curated from literature and reported to be produced and secreted by the gut microbiota of healthy subjects. Beyond this pilot study, we plan to expand our analyses by creating samples-specific GEMs for a large-scale database of all publicly available metagenomic data from healthy subjects (~2,500 samples so far). We will additionally identify a core set of microbial species/strains that are necessary to perform all essential functions of a healthy microbiome. Taken together, this project offers a new paradigm to establish a healthy baseline microbiome definition by identifying generalized and personalized microbial blueprints that could serve as viable markers of health.

<p>The identification and quantification of protein-protein interactions in large scale is critical to understanding biological processes at a systems level. Current approaches for the analysis of protein -protein interactions are generally not quantitative and largely limited to certain types of interactions such as binary and strong binding interactions. They also have high false-positive and false-negative rates. Described here is the development of and application of mass spectrometry-based proteomics metehods to detect and quantify the strength of protein-protein and protein-ligand interactions in the context of their interaction networks. Characterization of protein-protein and protein-ligand interactions can directly benefit diseased state analyses and drug discovery efforts. </p><p>The methodologies and protocols developed and applied in this work are all related to the Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX) and Stability of Protein from Rates of Oxidation (SPROX) techniques, which have been previously established for the thermodynamic analysis of protein folding reactions and protein-ligand binding interactions. The work in this thesis is comprised of four parts. Part I involves the development of a Histidine Slow H/D exchange protocol to facility SURPEX-like measurements on the proteomic scale. The Histidine Slow H/D exchange protocol is developed in the context of selected model protein systems and used to investigate the thermodynamic properties of proteins in a yeast cell lysate. </p><p>In Part II an isobaric mass tagging strategy is used in combination with SPROX (i.e., a so-called iTRAQ-SPROX protocol) is used to characterize the altered protein interactions networks associated with lung cancer. This work involved differential thermodynamic analyses on the proteins in two different cell lines, including ADLC-5M2 and ADLC-5M2-C2. </p><p>Parts III and IV of this thesis describe the development and application of a SPROX protocol for proteome-wide thermodynamic analyses that involves the use of Stable Isotope Labeling by Amino acid in cell Culture (SILAC) quantitation. A solution-based SILAC-SPROX protocol is described in Part III and a SILAC-SPROX protocol involving the use of cyanogen bromide and a gel-based fractionation step is described in Part IV. The SILAC-SPROX-Cyanogen bromide (SILAC-SPROX-CnBr) protocol is demonstrated to significantly improve the peptide and protein coverage in proteome-wide SPROX experiments. Both the SILAC-SPROX and SILAC-SPROX-CnBr porotocols were used to characterize the ATP binding properties of yeast proteins. Ultimately, the two protocols enabled 526 yeast proteins to be assayed for binding to AMP-PNP, an ATP mimic. A total of 140 proteins, including 37 known ATP-binding proteins, were found to have ATP binding interactions.</p> / Dissertation

Doctor of Philosophy / Department of Biology / Ruth Welti / The molecular mechanisms by which plants respond to environmental stresses to sustain growth and yield have great importance to agriculture. Lipid metabolites are a major element of plant stress responses. The model plant Arabidopsis thaliana is well-suited to study stress-driven compositional dynamics, metabolism, and functions of lipid metabolites. When Arabidopsis plants were subjected to wounding, infection by Pseudomonas syringae pv tomato DC3000 expressing AvrRpt2 (PstAvr), infection by Pseudomonas syringae pv. maculicola (Psm), and low temperature, and 86 oxidized and acylated lipids were analyzed using mass spectrometry, different sets of lipids were found to change in level in response to the various stresses. Analysis of plant species (wheat versus Arabidopsis), ecotypes (Arabidopsis Columbia 0 versus Arabidopsis C24), and stresses (wounding, bacterial infection, and freezing) showed that acylated monogalactosyldiacylglycerol was a major and diverse lipid class that differed in acyl composition among plant species when plants were subjected to different stresses. Mass spectrometry analysis provided evidence that oxophytodienoic acid, an oxidized fatty acid, is significantly more concentrated on the galactosyl ring of monogalactosyldiacylglycerol than on the glycerol backbone. A mass spectrometry method, measuring 272 lipid analytes with high precision in a relatively short time, was developed. Application of the method to plants subjected to wounding and freezing stress in large-scale experiments showed the method produces data suitable for lipid co-occurrence analysis, which identifies groups of lipid analytes produced by identical or inter-twined enzymatic pathways. The mass spectrometry method and lipid co-occurrence analysis were utilized to study the nature of lipid modifications and the roles of lipoxygenases and patatin-like acyl hydrolases in Arabidopsis during cold acclimation, freezing, and thawing.

Evolutionary relationships between a group of organisms are commonly summarized in a phylogenetic (or evolutionary) tree. The goal of phylogenetic inference is to infer the best tree structure that represents the relationships between a group of organisms, given a set of observations (e.g. molecular sequences). However, popular heuristics for inferring phylogenies output tens to hundreds of thousands of equally weighted candidate trees. Biologists summarize these trees into a single structure called the consensus tree. The central assumption is that the information discarded has less value than the information retained. But, what if this assumption is not true? In this dissertation, we demonstrate the value of retaining and studying tree collections. We also conduct an extensive literature search that highlights the rapid growth of trees produced by phylogenetic analysis. Thus, high performance algorithms are needed to accommodate this increasing production of data. We created several efficient algorithms that allow biologists to easily compare, store and share tree collections over tens to hundreds of thousands of phylogenetic trees. Universal hashing is central to all these approaches, allowing us to quickly identify the shared evolutionary relationships contained in tree collections. Our algorithms MrsRF and Phlash are the fastest in the field for comparing large collections of trees. Our algorithm TreeZip is the most efficient way to store large tree collections. Lastly, we developed Noria, a novel version control system that allows biologists to seamlessly manage and share their phylogenetic analyses. Our work has far-reaching implications for both the biological and computer science communities. We tested our algorithms on four large biological datasets, each consisting of 20; 000 to 150; 000 trees over 150 to 525 taxa. Our experimental results on these datasets indicate the long-term applicability of our algorithms to modern phylogenetic analysis, and underscore their ability to help scientists easily exchange and analyze their large tree collections. In addition to contributing to the reproducibility of phylogenetic analysis, our work enables the creation of test beds for improving phylogenetic heuristics and applications. Lastly, our data structures and algorithms can be applied to managing other tree-like data (e.g. XML).

Biologists use ontologies as a method to organize and publish their acquired knowledge. Computer scientists have shown the value of ontologies as a means for knowledge discovery. This dissertation makes a number of contributions to enable systematic biologists to better leverage their ontologies in their research. Systematic biology, or phylogenetics, is the study of evolution. “Assembling a Tree of Life” (AToL) is an NSF grand challenge to describe all life on Earth and estimate its evolutionary history. AToL projects commonly include a study a taxon (organism) to create an ontology to capture its anatomy. Such anatomy ontologies are manually curated based on the data from morphology-based phylogenetic studies. Annotated digital imagery, morphological characters and phylogenetic (evolutionary) trees are the key components of morphological studies. Given the scale of AToL, building an anatomy ontology for each taxon manually is infeasible. The primary contribution of this dissertation is automatic inference and concomitant formalization required to compute anatomy ontologies. New anatomy ontologies are formed by applying transformations on an existing anatomy ontology for a model organism. The conditions for the transformations are derived from observational data recorded as morphological characters. We automatically created the Cypriniformes Gill and Hyoid Arches Ontology using the morphological character data provided by the Cypriniformes Tree of Life (CTOL) project. The method is based on representing all components of a phylogenetic study as an ontology using a domain meta-model. For this purpose we developed Morphster, a domain-specific knowledge acquisition tool for biologists. Digital images often serve as proxies for natural specimens and are the basis of many observations. A key problem for Morphster is the treatment of images in conjunction with ontologies. We contributed a formal system for integrating images with ontologies where images either capture observations of nature or scientific hypotheses. Our framework for image-ontology integration provides opportunities for building workflows that allow biologists to synthesize and align ontologies. Biologists building ontologies often had to choose between two ontology systems: Open Biomedical Ontologies (OBO) or the Semantic Web. It was critical to bridge the gap between the two systems to leverage biological ontologies for inference. We created a methodology and a lossless round-trip mapping for OBO ontologies to the Semantic Web. Using the Semantic Web as a guide to organize OBO, we developed a mapping system which is now a community standard. / text