Dissertations / Theses on the topic 'Biology|Systematic biology'

The brachyuran superfamily Palicoidea Števčić, 2005, commonly referred to as stilt-crabs, currently includes the families Crossotonotidae Moosa and Seréne, 1981 and Palicidae Bouvier, 1898, consisting of two and nine genera, respectively. Both genus and species level relationships remain largely enigmatic and are based primarily upon highly variable morphological characters. Molecular phylogenetic analyses, based on COI and 16S mitochondrial gene sequences, are used to clarify relationships among primarily western Atlantic species and to independently validate diagnostic morphological characters. The resultant molecular phylogenetic tree resolves three major clades: one grouping Palicus affinis, Palicus alternatus, and Palicus bahamensis; a second grouping Palicus faxoni and Palicus obesus; and the third grouping Crossotonotus sp., Pseudopalicus sp., Palicus cristatipes, and Palicus sica. Putative specimens of P. floridanus were positioned as sister species to other groups. Molecular phylogenetic evidence infers intrageneric evolutionary history of Palicus Philippi, 1838, concordant with relationships suggested by gonopod morphology of congeners. Gonopod morphology was found to be highly conserved within species, moderately conserved among species sharing a common clade, and divergent among species in different well-separated clades. Conversely, many morphological characters that have historically been applied to describe and identify palicids were found to be highly variable within species, inconsistently variable among species, and in some cases relatively conserved across divergent clades. On the basis of present molecular phylogenetic analyses, separation of the families Crossotonotidae and Palicidae may be supported only if further revisions to membership of the family Palicidae were to be undertaken. These revisions are deferred pending more robust genetic analyses.

Modern biological research is currently canalized into two main modes of research: detailed, mechanistic descriptions, or big data collection and statistical descriptions. The former has the advantage of being conceptually tractable and fitting into an existing scientific paradigm. However, these detailed descriptions can suffer from an inability to be understood in the larger context of biological phenomena. On the other hand, the big data approaches, while closer to being able to capture the full depth of biological complexity, are limited in their ability to impart conceptual understanding to researchers. We put forward examples of an intermediate approach. The goal of this approach is to develop models which can be understood as abstractions of biological phenomena, while simultaneously being conducive to modeling and computational approaches. Firstly, we attempt to examine the phenomenon of modularity. Modularity is an ubiquitous phenomenon in biological systems, but its etiology is poorly understood. It has been previously shown that organisms that evolved in environments with lower levels of stability tend to display more modular organization of their gene regulatory networks, although theoretical predictions have failed to account for this. We put forward a neutral evolutionary model, where we posit the process of genome expansion through gene duplications acts as a driver for the evolution of modularity. This process occurs through the duplication of regulatory elements alongside the duplication of a gene, causing sub-networks to be generated which are more tightly coupled internally than externally, which gives rise to a modular architecture. Finally, we also generate an experimental system by which we can verify our model of the evolution of modularity. Using a long term experimental evolution setup, we evolve E. coli under fluctuating temperature environments for 600 generations in order to test if there is a measurable increase in the modularity of the gene regulatory networks of the organisms. This data will also be used in the future to test other hypotheses related to evolution under fluctuating environments. The second such model is a computational model of the properties of bacterial growth as a function of temperature. We describe a model composed of a chain of enzyme like actions, where the output of each enzyme in the chain becomes the substrate of the following enzyme. Using well known temperature dependence curves for enzyme activity and no further assumptions, we are then able to replicate the salient properties of bacterial growth curves at varying temperatures, including lag time, carrying capacity, and growth rate. Lastly, we extend these models to attempt to describe the ability of cancer cells to alter their phenotypes in ways that would be impossible for normal cells. We term this model the phenotypically pliant cells model and show that it can encapsulate important aspects of cancer cell behavior.

The genus Ophiocordyceps contains the most diverse assemblage of fungi attacking ants worldwide and are remarkably well adapted to the specific ecologies of their hosts. Desmidiospora myrmecophila is closely related to ant-pathogenic species within Ophiocordyceps, possibly specific to queens, but the sheer infrequency of encounters and previously unsuccessful attempts to culture this fungus has precluded any meaningful assessment until now. A new record of Desmidiospora myrmecophila from Louisiana was found infecting a foundress Camponotus pennsylvanicus queen, the same host species favored by the more common and ubiquitous ant-pathogenic Ophiocordyceps unilateralis found in the same geographic locality. To evaluate a long-held assumption that these fungi represent synanamorphs of a single species, we sampled our Desmidiospora specimen along with the local O. unilateralis population for molecular comparison. We are able to present for the first time the in vitro characteristics and morphology of Desmidiospora myrmecophila as well as a phylogenetic context for this fungus based on combined molecular analysis of representative members of the Ophiocordycipitaceae. Our results place the Desmidiospora myrmecophila lineage within the genus Ophiocordyceps but with a basal affiliation to the ant-pathogen clade. These results further implicate Desmidiospora myrmecophila as an important and quintessential example of cryptic diversity among an already taxonomically diverse and ecologically important group of fungi.

Viral infection and the subsequent immune responses such as the expression of interferon beta (ifnb1) show extreme levels of cell to cell variability. A fraction of cells get infected and a fraction of infected cells induce an ifnb1 response. These responding cells then signal to coordinate appropriate immune responses required to clear infection. The mechanism of propagation of this response at the single cell level is critical to generate an appropriate defense against the virus, yet is incompletely understood.

Interesting work on cell to cell variability has been done using transfected ifnb1 reporter constructs. However, this approach has several limitations. The reporter systems introduce multiple copies of the reporter construct in each cell, which does not reflect the conditions in the intact cells where only two of the interferon promoter and gene are present. This alters the ifnb1 enhanceosome stoichiometry from the one present in a normal physiological environment, and potentially distorts the patterns of single cell responses observed. In addition, reporter constructs integrate the response that occur over many hours, which makes it difficult to measure the expression dynamics that occur early after exposure to infection. Such measurements in the intact cells would be helpful for understanding the mechanisms underlying the propagation of this immune response.

In order to obtain sensitive and accurate measurements of changes in gene expression in infected single cells, we used single-cell single-molecule mRNA imaging to directly and simultaneously count the transcripts of ifnb1 and that of a virus (Newcastle disease virus) gene Hemagglutinin-neuraminidase hn . This experimental approach enabled us to measure the single-cell responses from the very early stages of infection, in primary immune cells. Simultaneous measurement of ifnb1 and the viral gene hn high lighted the variation in responses across cells, the temporal evolution of the expression of the two genes and their single cell correlation following infection.

We find that the single cell ifnb1 response to virus infection shows a temporally dispersed (asynchronous) pattern. A small fraction of infected cells respond very early and more ifnb1 expressing cells are recruited at later time after infection. In contrast, the single ifnb1 response to the toll like receptor stimulant LPS, follows a highly synchronous pattern, where in a large number of cells showed an ifnb1 response around the same time after treatment. These results suggest that the temporal evolution of single cell ifnb1 responses was likely dependent on the type of the inducing stimuli. Furthermore we observed that extracellular signaling plays an important role in introducing cell-to-cell variability in ifnb1gene induction in response to virus infection. Inhibition of extracellular signaling converted the response to virus infection into an early synchronous LPS-like response. Thus extracellular signaling shapes the temporally dispersed pattern of single cell ifnb1 response to viral infection.

The pattern of ifnb1 responses to virus infection involves an increase in the amplitude of the response per cell as well as an increase in the number of responding cells over time of infection. These properties may enable cells to fine tune the ifnb1 responses gradually. This strategy of mounting an antiviral cytokine response may be useful in calibrating the immune response such that an appropriate antiviral response is generated and cellular toxicity resulting from excessive cytokine expression is usually avoided.

The integration of advances in computing technology with major innovations in sequence data collection and phylogenetic inference has revolutionized evolutionary biology in the 21^st century. In particular, the continual development of both theory and software that allow for more flexibility in utilizing molecular clock methods has radically transformed our understanding of the mode and tempo of diversification across the Tree of Life. Over the course of five chapters, this dissertation explores methodological challenges to phylogenetic inference with the aim of better understanding the evolutionary history of the Holocentridae (squirrelfishes and soldierfishes).

Chapter 1 begins by focusing on the problem of accommodating clade specific rate heterogeneity in molecular clock analyses. While various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, recently developed "uncorrelated relaxed clock" and "random local clock" models are predicted to perform better in the presence of lineage specific rate heterogeneity as these models relax assumptions of inheritance of nucleotide substitution rates between descendant lineages. Using simulations and two cetacean (whale and dolphin) datasets as a case study, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated; and provide suggestions for diagnosing extreme clade specific rate heterogeneity.

Homoplasy is another important, yet often overlooked, source of error in phylogenetic studies. Chapters 2 and 3 utilize phylogenetic informative approaches to screen nucleotide sequence data for homoplasious site patterns. Using phylogenetic informativeness profiles, chapter 2 reconciles two competing hypotheses of ray-finned fish divergence times by highlighting that mitogenomic based Jurassic and Triassic divergence time estimates for most major lineages of spiny-rayed (acanthomorph) fishes were an artifact of tree extension. Evolutionary relationships of early diverging acanthomorph fishes are also contentious, with molecular data supporting either holocentrids or a clade comprised of holocentrids and primarily deep-sea fishes as the sister lineage to the species-rich percomorpha. Chapter 3 reveals this conflict to also be largely driven by homoplasy and reconciles results based on previously published data with a 132 gene next-generation sequence dataset to identify the sister lineage of percomorph and the phylogenetic placement of holocentrid fishes.

Chapter 4 continues to explore holocentrid evolutionary relationships. Using a multi-locus dataset that includes all but one holocentrid genus, this chapter provides the first molecular phylogeny of the group. The systematics of holocentrid fishes has unstable for over 100 years. We demonstrate several of the key synapomorphies for holocentrid genera are in fact homoplasious. Likewise, several genera of holocentrine (squirrelfish) are rendered consistently paraphyletic by a series of maximum-likelihood and Bayesian analyses and we propose taxonomic revisions to reflect shared ancestry.

Chapter 5 further investigates the temporal history of holocentrid evolution. Contemporary holocentrid species richness is concentrated in the Indo-Australian Archipelago (IAA), yet these fishes also represent some of the most numerous fossil taxa in deposits of the Eocene West Tethyan biodiversity hotspot. Using likelihood-based methods integrated with a molecular timetree that incorporates fossils as tip taxa, we reconstruct the history of range evolution for these fishes. Following the collapse of the West Tethys, holocentrids exhibit a signature of increased range fragmentation, becoming isolated between the Atlantic and Indo-Pacific Ocean basins. However, rather than originating within the emerging IAA hotspot, the IAA appears to have acted as a reservoir for holocentrid diversity that originated in adjacent regions over deep evolutionary timescales. By integrating extinct lineages, these results provide a necessary historic perspective on the formation and maintenance of global marine biodiversity.

The Lesser Sunda Archipelago, also known as Nusa Tenggara, lies in the southeastern portion of Indonesia and extends between Bali in the west, and New Guinea in the east. While the Lesser Sundas themselves are oceanic islands that have never been land bridged to a continent the islands on either side do. Bali and the other Greater Sunda Islands of Java, Sumatra, and Borneo become periodically land bridged with Asia during glacial maxima forming the Sunda Shelf. New Guinea and Aru become periodically land bridged to Australia during glacial maxima and form the Sahul Shelf. Given their current orientation, the Lesser Sundas may act as ‘stepping stones’ for animals and plants dispersing between the Sunda and Sahul Shelves and may act as a two-way filter for organisms dispersing between two of the world’s great biogeographical realms. Alfred Russel Wallace’s discovery of a pattern of clinal mixture of species from different biogeographical realms was a key insight leading to his identification of the Wallace Line and to his creation of the field of biogeography. Even though the Lesser Sundas played a critical role in the development of the field, this region has received little subsequent attention from historical biogeographers and our current understanding of Lesser Sunda biogeography has only modestly improved relative to what was known at the time of Wallace. The reptiles and amphibians of the Lesser Sundas represent a particularly interesting group of vertebrates from a biogeographical standpoint because they appear to show distributional patterns that are most consistent with a stepping-stone model of island colonization caused by the two-way filter zone. In Chapter 1, I review the geological and biogeographical literature for the Lesser Sundas and use these sources to formulate hypotheses concerning the colonization of the archipelago by rafting terrestrial vertebrates. In Chapters 2 through 4, I investigate the possibility that flying lizards, forest skinks, and fanged frogs have colonized the archipelago in a stepping-stone manner using a phylogenomic approach (using sequence data from mtDNA and hundreds of nuclear loci) whereby the relationships among island-specific lineages can be used to infer the sequence of island colonization. Flying lizards of the genus Draco form a monophyletic group that colonized the western Inner Arc islands of Lombok or Sumbawa from the Sunda Shelf around 10 million years ago when Lombok and Sumbawa first became land-positive. Draco continued expanding eastward through the Inner Arc until they reached Lembata, while a series of dispersal events from Flores south to Sumba, east to Timor, north to Wetar, west to Alor, and finally west to Pantar (the island immediately west of Lembata). The islands of Sumbawa and Flores contain multiple non-sister lineages that are parapatrically distributed and are exchanging migrants within an island. Forest Skinks of the genus Sphenomorphus show relatively little morphological divergence across their range yet exhibit large levels of genetic divergence. The oldest lineages of Sphenomorphus within the Lesser Sundas occur on the islands of Lombok and Flores and they expanded eastward through the Inner Arc until they reached Pantar. But rather than reaching Alor from neighboring Pantar, Sphenomorphus dispersed from Flores south to Sumba, then east to Timor, Alor, and Wetar. There are multiple non-sister lineages of Sphenomorphus on Lombok, Flores, and Sumba, and estimates of migration between lineages within each island suggest that these lineages are not interbreeding. Fanged frogs of the genus Limnonectes have colonized the Inner Arc of the Lesser Sundas from the Sunda Shelf. It is possible that Limnonectes kadarsani and L. dammermani diverged in situ on Lombok after which L. kadarsani dispersed east all the way to Lembata. But rather although a tree topology consistent with a stepping-stone pattern of island colonization is suggested by the mtDNA data, the phylogenomic results suggest a leap-frog pattern where Lembata is derived from West Flores, and these two lineages are closer related to Sumbawa than they are to Eastern Flores. The parapatrically distributed lineages on Flores are experiencing asymmetrical gene flow with successful migrants moving from west to east. In summary, the oldest islands of the western Inner Arc tend to harbor the most divergent lineages for all three focal taxa, a pattern expected from lineages originating from the Sunda Shelf. In Draco and Sphenomorphus, the islands of the eastern Inner Banda Arc are colonized by way of the ‘Sumba Route’ where they disperse into the Outer Banda Arc island of Sumba and then move east to Timor, and finally north into the eastern Inner Arc. All three focal taxa show multiple non-sister lineages on some of the larger islands, suggesting either that multiple colonization events of a single island occurred, or possibly that formerly separated paleo-islands have since merged allowing for secondary contact of lineages that diverged in allopatry. These studies have shown that the biogeography of reptiles and amphibians within the Lesser Sundas is extremely complex. By examining biogeographical patterns across many co-distributed taxa these studies have the potential to provide insights into the geological history of the archipelago. From an evolutionary perspective, these studies highlight the presence of multiple independently evolving lineages within a currently described species occurring on the same island, which suggests that species diversity within reptiles and amphibians of the Lesser Sundas is underestimated.

Cystic fibrosis (CF) is the most common lethal autosomal recessive genetic disorder that affects the Caucasian population. CF is caused by mutations in the CF transmembrane conductance regulator (CFTR), and is characterized by a viscous airway surface liquid (ASL) that impairs mucociliary function and facilitates bacterial infection. The molecular mechanisms by which these symptoms result from CFTR malfunction are unclear. We hypothesized that expression and secretion of innate immune proteins is altered in CF ASL.

We sought to use cell culture models in which the only source of secreted proteins was differentiated airway epithelium. Since CFTR localizes to the apical surface of airway submucosal glands (SMG) and ciliated epithelium, cell culture models that recapitulate two parts of respiratory tract epithelium were studied: 1) SMG acini and 2) mucociliary epithelium.

We developed a three-dimensional system wherein CF (ΔF508/ΔF508) and non-CF human bronchial epithelial (HBE) cells differentiated on Matrigel into polarized glandular acini with mature lumens by two weeks with no significant variability in size. Bronchial acini expressed and secreted SMG proteins, MUC5B and lysozyme, at day 22, and exhibited vectorial secretions that were collected along with acinar cell lysates. Proteome profiling demonstrated unique protein signatures for each cellular space. However, abundant contaminating proteins from Matrigel and growth media were identified. Therefore, the ALI cell culture model of airway epithelium was chosen for quantitative proteomic comparison of CF and non-CF HBE apical secretions because the protein-rich media does not contact the apical surface.

CF and non-CF HBE cells were labeled by stable isotope labeling with amino acids in cell culture and differentiated at ALI. LC-MS/MS and bioinformatic analysis identified seventy-one proteins with altered levels in CF secretions (+/−1.5 fold-change; p-value<0.05). Validation with antibody based biochemical assays demonstrated increased levels of MUC5AC, MUC5B, fibronectin and MMP9, and increased proteolysis/activation of complement C3, in CF secretions. Overall, the function of altered proteins in the CF secretome is indicative of an airway epithelium in a state of repair and altered immunity in the absence of infection, suggesting the downstream consequences of mutated CFTR in CF airways set the stage for chronic inflammation and infection.

Bamboo corals are a family (Isididae Lamouroux, 1812) of cnidarian anthozoans in the subclass Octocorallia. They are distinct and easily recognizable because of their unique articulating skeleton, which alternates internodes of calcium carbonate with proteinaceous sclerite (microscopic skeletal elements)-free nodes, and which is currently the primary synapomorphy for the family. Isididae is further divided into four subfamilies (Circinisidinae, Isidinae, Keratoisidinae, Mopseinae) based on several characters, including sclerite shape, size, and placement, and skeleton morphology. The deep-sea bamboo corals are classified in the most morphologically diverse subfamily, Keratoisidinae Gray, 1970. Currently, there are eight genera within the subfamily, and they are primarily distinguished based on branching pattern. Members of the subfamily are found worldwide and at depths greater than 200 m. I use genetic data to evaluate the monophyly of the Isididae, the relationships of the subfamilies to each other and other octocorals, and the monophyly of the genera within the Keratoisidinae. One genus, Acanella, is a genetically monophyletic group with a distinct polyp morphology with needle-like sclerites running obliquely up the polyp body. Additionally, I propose an evaluation of the taxonomic ranks of the bamboo corals at the family, subfamily, genus, and species levels based on morphological characters, mitochondrial genome arrangement, and mtMutS haplotypes. Re-description and classification is needed at every taxonomic level to fully describe and capture the morphological and genetic diversity observed.

Taxonomic checklists are a fundamental and widely-used product of taxonomy, providing a list of recognized taxa within a taxonomic group in a particular geographical area. Series of taxonomic checklists provide snapshots of recognized taxa over a period of time. Identifying and classifying the changes between these checklists can provide information on rates of name, synonym and circumscription change and can improve aggregation of datasets reconciled to different checklists.

To demonstrate this, I used a series of North American bird checklists to test hypotheses about drivers of splitting rates in North America birds. In particular, I asked if splitting was predominantly undoing previous lumping that happened during the heyday of the modern synthesis. I found that bird species have been split at an accelerating rate since the 1980s. While this was partially the result of previously lumped species being resplit, most splits were unrelated to previous lumps and thus represent new discoveries rather than simply the undoing of previous circumscription changes. I also used a series of North American freshwater algal checklists to measure stability over fifteen years, and found that 26% of species names were not shared or synonymized over this period. Rates of synonymization, lumping or splitting of species remained flat, a marked difference from North American birds. Species that were split or lumped (7% of species considered) had significantly higher abundance than other species in the USGS NAWQA dataset, a biodiversity database that uses these checklists as an index. They were associated with 19% of associated observations, showing that a small number of recircumscribed species could significantly affect interpretation of biodiversity data.

To facilitate this research, I developed a software tool that could identify and annotate taxonomic changes among a series of checklists, and could use this information to aggregate biodiversity data, which will hopefully facilitate similar research in the future. My dissertation demonstrates the value of taxonomic checklists series to answer specific questions about the drivers of taxonomic change ranging from philosophical and technical changes to characteristics of species themselves such as their abundance.

This study investigates the eIF4E family members in Dinoflagellates. Dinoflagellates are eukaryotic algae with large genomes and a minimal role for transcriptional regulation. All mRNA in dinoflagellates is trans -spliced with a 22-nucleotide 5'-spliced-leader sequence bearing a multi-methylated cap. Like other eukaryotes, dinoflagellates encode multiple eIF4E family members that are anticipated to fulfill a range of functions. Three distinct and novel clades of eIF4E have been recognized in dinoflagellates that are separate from the three metazoan classes of eIF4E. The dinoflagellate Amphidinium carterae encodes eight eIF4E family members while Karlodinium veneficum encodes fifteen eIF4E family members. I assayed six of these family members from A. carterae for expression levels, m⁷GTP binding, yeast knockout complementation and affinity for three mRNA cap analogs using surface plasmon resonance (SPR). Transcripts of each are expressed through a diel cycle, but only eIF4E-1 family members and eIF4E-2a are expressed at the level of protein. Recombinant eIF4E-1 family members and eIF4E-3a, but not eIF4E-2a, are able to bind to m ⁷GTP-agarose beads. Of the clade 1 eIF4Es, only eIF4E-1a and -1d1 complement a S. cerevisiae strain conditionally deficient in functional eIF4E, consistent with their function as translation initiation factors. However, only eIF4E-1a can be recovered from A. carterae extracts by m⁷GTP affinity binding. Using SPR analysis, the affinity of A. carterae eIF4E-1a for m⁷GTP is lower than that of murine eIF4E-1A. By the same analysis, A. carterae eIF4E-1a has a higher affinity for m⁷GpppG than m⁷GTP. In addition, K. veneficum eIF4E-1a1 displays many of the same characteristics as A. carterae eIF4E-1a. Four eIF4E-1 and one eIF4E-2 family members from K. veneficum were characterized for m⁷GTP binding capacity, only the eIF4E-1 family members can be pulled down with m⁷GTP. Three eIF4E family members were tested for their ability to interact with a putative eIF4E-interacting protein, although none interacted. Overall, the eIF4E-1a sub-clade emerges with characteristics consistent with the role of a prototypical translation initiation factor. These initial analyses will allow for a better understanding of specific translational control of gene expression through mRNA recruitment in the unique dinoflagellate lineage.

Plumage color evolution in birds has been the focus of theoretical and empirical research on sexual selection since Darwin. Many of the yellow, orange, and red hues seen in bird plumage are the result of carotenoid pigmentation. While a great number of recent studies have examined the functions of carotenoid-based plumage coloration in a single species, few have examined the evolutionary history of this trait in a comparative phylogenetic context. Using the New World blackbirds as a model clade, I focus on two questions that a comparative phylogenetic approach can uniquely address. First, what is the history of evolutionary change in carotenoid color that led to the colors seen in extant blackbird taxa? Second, by what proximate mechanisms have carotenoid pigments evolved? In Chapter 1, I present an ancestral state reconstruction of carotenoid-based plumage coloration across the Icterid phylogeny, based on reflectance measurements of museum skins. My results show robust evidence that red coloration was gained repeatedly from a yellow common ancestor. In Chapter 2, I used pigment biochemistry of meadowlark (Sturnella) and Cacique (Cacicus) feathers to test whether independent gains of red coloration are the result of parallel or convergent metabolic mechanisms. Meadowlarks have evolved red coloration using a different set of carotenoids than caciques, but the caciques have evolved the same set of carotenoids twice. This suggests that red coloration evolved by convergent evolution among different blackbird clades, but evolved by parallel evolution within the caciques. Lastly, in Chapter 3 I examine the relationship between color and carotenoid pigmentation in orioles, a blackbird clade in which orange has been gained at least twice independently from a yellow common ancestor. I found red-producing keto-carotenoids only in orange species and never in yellow species. This result is a striking contrast to our expectation for a continuous gradient of a carotenoid pigment concentration. These results suggest that repeated gains of C4-oxygenation ability best explain evolutionary changes in orange coloration in orioles. To summarize, I showed using phylogenetic comparative methods that blackbirds have repeatedly evolved towards redder carotenoid coloration. Using HPLC biochemistry, I showed that each of these gains of orange and red coloration is likely the result of a gain of C4-oxygenation ability. The prevalence of gains of orange and red coloration suggests that there may be a directional bias towards evolving longer-wavelength carotenoid plumage. The research presented in these chapters provides the phylogenetic framework necessary for future studies to examine the functional causes underlying the repeated evolution of carotenoid-based coloration.

In the first chapter, we revise the taxonomy of a lineage of plant bugs (Hemiptera: Miridae) that has radiated in the islands of French Polynesia. Six species of endemic Pseudoloxops plant bugs were previously known from two islands in French Polynesia, indicating a small radiation. We collected ecological, morphological, molecular, and geographical data for hundreds of fresh and historical Pseudoloxops specimens, expanding the genus' range to nine islands in two archipelagoes (the Austral and Society Islands). We combined all of the above data sources in an iterative integrative taxonomy framework to test the six existing species hypotheses and to search for new diversity.

In the second chapter, we explore the relative importance of ecology and geographic isolation in this lineage to provide a first approximation of whether the radiation was adaptive or non-adaptive. We collected Pseudoloxops from a wide range of plants, with 27 species in 25 different plant families and 13 orders. We then inferred a combined Bayesian molecular phylogeny from three genes, including 25 of the 26 known Pseudoloxops species, to examine the roles of plant affiliation and geography (island distribution) in speciation. We reconstructed the ancestral states using parsimony for these two characters, and found 12 speciation events that were well-supported in the phylogeny. Both plant-switching and island-hopping were correlated with speciation. For the 7 speciation events for which we could unequivocally determine plant affiliation before and after speciation, 4 were associated with a plant shift. For the 8 speciation events where island distribution could be reconstructed, two involved shifts to a new island. There were 5 cases for which we could determine both character states before and after speciation. In three of them, speciation occurred within the same locality with a switch in plant taxonomic order, suggesting that the lineage has great dietary versatility. However, much more research into feeding needs to be conducted, as anecdotal evidence from Pseudoloxops outside of French Polynesia suggests they may be facultative predators. In the other two speciation events, there was neither a geographic shift nor a change in plant affiliation, suggesting some other mechanism for speciation. Based on our results, both plant-switching and geography have played a role in the diversification of this radiation.

In the third chapter, we address the larger societal impact of taxonomic and biodiversity research by examining the effect of a natural history-driven curriculum on elementary schoolchildren's scientific knowledge. While studies have demonstrated the potential for natural history education to improve children's attitudes towards and knowledge of science and nature, few studies have been done in areas where indigenous culture heavily influences children's worldview. The lead author taught a nine-month natural history/biodiversity class focused on insects and plants to fifth-graders at the Pao Pao elementary school on the French Polynesian island of Moorea and tested their scientific knowledge before and after receiving the program. We compared their results to a control that did not receive the program, and while both cohorts improved, the experimental group's improvement was significantly greater (mean of 82.2% vs. 30.5%). We performed a delayed post-test evaluation three years after the conclusion of the program with a subset of the experimental cohort to test their retention and interest in science. Finally, the qualitative coding of the experimental group's test and survey responses revealed both the influence of indigenous culture on their scientific understanding and the appeal of taxonomy and field trips to children. When prompted for an example of a native plant, 24% of the experimental group named a plant introduced by the Polynesians, suggesting the misconception that plants with a prevalent role in indigenous culture have always been there. In the follow-up survey, 36.7% mentioned the field trips among their memories of the course, and 20% gave full scientific names for species they recalled from the class. The latter contrasts with the commonly held belief that taxonomy is too arcane to connect with the general public. (Abstract shortened by UMI.)

Stochastic models of biochemical interactions elucidate essential properties of the network which are not accessible to deterministic modeling. In this thesis it is described how a network motif, the proportional-reversibility interaction with active intermediate states, gives rise to the ability for the variance of biochemical signals to be controlled without changing the mean, a property designated as mean-independent noise control (MINC). This noise control is demonstrated to be essential for macro-scale biological processes via spatial models of the zebrafish hindbrain boundary sharpening. Additionally, the ability to deduce noise origin from the aggregate noise properties is shown.

However, these large-scale stochastic models of developmental processes required significant advances in the methodology and tooling for solving stochastic differential equations. Two improvements to stochastic integration methods, an efficient method for time stepping adaptivity on high order stochastic Runge-Kutta methods termed Rejection Sampling with Memory (RSwM) and optimal-stability stochastic Runge-Kutta methods, are combined to give over 1000 times speedups on biological models over previously used methodologies. In addition, a new software for solving differential equations in the Julia programming language is detailed. Its unique features for handling complex biological models, along with its high performance (routinely benchmarking as faster than classic C++ and Fortran integrators of similar implementations) and new methods, give rise to an accessible tool for simulation of large-scale stochastic biological models.

Several new discoveries in Euphorbia L. subg. Chamaesyce Raf. sect. Anisophyllum Roeper for the Trans-Pecos region of Texas are documented. These include E. ophthalmica Pers., a species new to the Trans-Pecos from Marfa, Presidio County; E. abramsiana L.C. Wheeler new to Texas from Brewster and Presidio Counties; E. vermiculata Raf., new to Texas from Alpine, Brewster County; E. cryptorubra N.C. Taylor & M. Terry, a newly described species from southern Hudspeth County and northern Chihuahua, Mexico; notes on E. golondrina L.C. Wheeler including two potential novelties; and notes on E. fendleri Torr. & A. Gray, a problematic species complex. The sections concerning E. abramsiana and E. cryptorubra have been published Taylor and Terry (2016) in Phytoneuron and the Journal of the Botanical Institute of Texas respectively. Within E. golondrina and E. fendleri, there is much room for study, and directions for future investigations are indicated. Provided at the end is a key to all species now known for the Trans-Pecos region of Texas.

SEM observations have revealed unknown and previously undetected stages of the bloom-forming dinoflagellate Prorocentrum growing inside calcium carbonate-encrusted perithallial cells of the rhodolith-forming Lithothamnion sp. (Hapalidiaceae, Hapalidiales, Rhodophyta) in the NW Gulf of Mexico. Roundish structures inside the coralline cells were clustered together, surrounded by a thin membrane. Organized blebs, projections of the cytoplasm into the plasma membrane, as well as a suite of varying extracellular ornamentation patterns, were observed. Openings on the surface of some of the structures looked like characteristic thecal pores found in thecal plates of some dinoflagellates. DNA was extracted from inside the rhodolith and sequenced using dinoflagellate-specific cob1-primers. When blasting the resulting DNA sequences, it proved to be an exact match for Prorocentrum lima. Cells were isolated from inside the rhodoliths and cultured, revealing the presence of another set of endolithic life stages identified as Haptophyta (Prymnesiophyta), confirmed by single cell 18S rDNA sequencing. This research illustrates and illuminates newly found benthic life history stages of two ecologically important taxa of primary producers that also cause harmful algal blooms, such as the formation of red tides, fish kills, or shellfish poisoning events in the Gulf of Mexico.

Electrophysiological behaviors in cardiomyocytes, such as the action potential and calcium transient, are emergent properties arising from the interaction of an ensemble of ion channels, transporters, and pumps. In this Thesis, I integrate mathematical modeling with experiments to gain new insight into cardiac electrophysiology. Cardiomyocyte models are probed using population-based parameter sensitivity analysis to comprehensively generate quantitative predictions of how key behaviors are determined by the levels of ion channels, transporters, and pumps. Experimental tests ground these predictions in reality and provide opportunities for model improvement when predictions differ from experiments. In Chapter 2, this approach was applied to the determinants of calcium transient amplitude in rat cardiomyocytes. Experiments validated the unexpectedly large predicted effect of the transient outward potassium current on calcium transient amplitude in epicardial cardiomyocytes, but others demonstrated that the sarco/endoplasmic reticulum calcium ATPase had a much larger impact than predicted. Further exploration revealed that model calcium fluxes were inaccurately balanced, which we corrected to yield an improved model accurately reflecting our experiments and previous reports. In Chapter 3, the determinants of action potential duration in guinea pig cardiomyocytes predicted by parameter sensitivity analysis were tested using dynamic clamp, which found generally larger experimental effect sizes than predicted. We adjusted the model using a genetic algorithm to match our results, which led us to show that the overly stable model action potential resulted from higher levels of the slow delayed rectifier current than in our experiments. Subsequent analysis revealed how this current more effectively stabilizes the action potential than a related current, the rapid delayed rectifier. Finally, in Chapter 4 I take a global approach to model analysis, exploring competing models of the rabbit cardiomyocyte by comparing patterns of variability and correlations between behaviors across a population of models with randomly varied parameters. This found key experimentally testable differences between the models, representing a novel potential method for assessing how well these mathematical models represent the electrophysiological system of these cells. Overall, this work adds to our understanding of cardiac electrophysiology and represents a potential new paradigm for combining modeling and experiments to understand complex behaviors.

The BRCA1 and BRCA2 (BRCA) genes are two tumor suppressors that when mutated, predispose patients to breast and ovarian cancer. The BRCA genes encode proteins that mediate the repair of DNA double strand breaks. Functional loss of the BRCA genes is detrimental to the integrity of the genome because without access to functional BRCA protein, inefficient and error-prone repair pathways are used instead. These pathways, such as Non-homologous end joining, do not accurately repair the DNA, which can introduce mutations and genomic rearrangements. Ultimately the genome is not repaired faithfully and the predisposition to cancer greatly increases. In addition to their contribution to DNA repair, the BRCA genes have been shown to have transcriptional activity, and this functional role can also be a driving factor behind the tumor suppressor activity.

Robustness is the ability of a complex system to sustain viability despite perturbations to it. In the context of a complex disease such as cancer, robustness gives cancers the ability to sustain uncontrollable growth and invasiveness despite treatments such as chemotherapy that attempt to eliminate the tumor. A complex system is robust however can be fragile to perturbations that the system not optimized against. In cancers, these fragilities have the potential to be cancer specific targets that can eradicate the disease specifically.

Patients with mutations in BRCA tend to have breast and ovarian cancers that are difficult to treat; chemotherapy is the only option and no targeted therapies are available. Targeting the synthetic lethal interaction (SLI), a mechanism of robustness, between BRCA and PARP1 genes was clinically effective in treating BRCA-mutated breast and ovarian cancers. This suggests that understanding robustness in cancers can reveal potential cancer specific therapies.

In this thesis, a computational approach was developed to identify candidate mechanisms of robustness in BRCA-mutated breast and ovarian cancers using the publicly accessible patient gene expression and mutation data from the Cancer Genome Atlas (TCGA). Results showed that in ovarian cancer patients with a BRCA2 mutation, the expression of genes that function in the DNA damage response were kept at stable expression state compared to those patients without a mutation. The stable expression of genes in the DNA damage response may highlight a SLI gene network that is precisely controlled. This result is significant as disrupting this precision can potentially lead to cancer specific death. In breast cancers, genes that were differentially expressed in patients with BRCA mutations were identified. A Bayesian network was performed to infer candidate interactions between BRCA1 and BRCA2 and the differentially expressed FLT3, HOXA11, HPGD, MLF1, NGFR, PLAT, and ZBTB16 genes. These genes function in processes important to cancer progression such as apoptosis and cell migration. The connection between these genes with BRCA may highlight how the BRCA genes influence cancer progression.

Taken together, the findings of this thesis enhance our understanding of the BRCA genes and their role in DNA damage response and transcriptional regulation in human breast and ovarian cancers. These results have been attained from systems-level models to identify candidate mechanisms underlying robustness of cancers. The work presented predicts interesting candidate genes that may have potential as drug targets or biomarkers in BRCA-mutated breast and ovarian cancers.

Cancer is a leading cause of morbidity and mortality, and one in three individuals in the U.S. will be diagnosed with cancer in their lifetime. At the molecular level, cancer is driven by the activity of oncogenes and the loss of activity of tumor suppressors. The availability of genomic data from large sets of tumor tissue have facilitated the identification of subgroups of patients whose tumors share molecular patterns of expression. These molecular signatures, in turn, can help identify clinically-useful patient subgroups and inform potential therapeutic strategies against cancer.

In chapter 1, I review the current theories behind carcinogenesis, the molecular factors that regulate gene expression, and statistical methods for analyzing genomic data. In chapter 2, I describe an approach, termed oncomix, developed to identify oncogene candidates from expression data obtained from tumor and adjacent normal tissue. I apply oncomix to breast cancer expression data and identify an oncogene candidate, CBX2, whose expression is gained in a subset of breast tumors. CBX2 is expressed at low levels in most normal adult tissue, and the CBX2 protein contains a drug-targetable chromodomain, both of which are desirable properties in a potential therapeutic target. We then provide the first experimental evidence that CBX2 regulates the growth of breast cancer cells. In chapter 3, I develop a method for identifying nuclear hormone receptors whose expression is lost in endometrial cancers relative to normal tissue. I report, for the first time, that the loss of expression of Thyroid Hormone Receptor Beta (THRB) is associated with better 5-year survival in endometrial cancer. The loss of THRB expression is independent of the loss of estrogen and progesterone receptor expression, two genes whose loss of expression is known to be associated with poor survival. THRB expression could be considered as a biomarker to risk-stratify endometrial cancer patients. In Chapter 4, I develop a user-friendly application for visualizing chromosomal copy number state obtained from three types of copy number input in single cells – fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and whole genome sequencing (WGS). This web application, termed aneuvis, automatically creates novel visualizations and summary statistics from a set of user-uploaded files that contain chromosomal copy number information.

In this thesis, I develop new computational approaches for identifying candidate molecular regulators of cancer. I also develop a new user-friendly tool to enable biological researchers to identify aneuploidy and chromosomal instability within populations of single cells. Applying these tools to breast and endometrial cancer genomic datasets has highlighted novel aspects of breast and endometrial cancer biology and may inform novel therapeutic strategies based on molecular patterns of genomic heterogeneity. The freely available software developed as part of these projects has the potential to enable other researchers to advance our understanding of cancer genomics and to inform novel therapeutic strategies against cancer.

The lack of vaccines for emerging and re-emerging diseases highlights technical gaps and indicates a need for innovative approaches to produce new vaccines. Vaccines may be improved by knowledge of host responses to vaccination, disease pathogenesis, and the effect of age and genetics on vaccine outcome. This study?s purpose was to quantitatively assess the molecular epidemiology of Francisella tularensis (Ft) and Venezuelan Equine Encephalitis Virus (VEEV). Study results support the Epidemiology Nexus model which holds that association of changes in gene expression to vaccination facilitate understanding the mechanisms of immune development and link public health and disease epidemiology. My research questions assessed the relationship between gene expression following vaccination, the relationship between age and vaccine response, and the association between Human Leukocyte Antigen (HLA) allele and vaccine response. The study was a novel secondary analysis of human data subjected to ANOVA to measure association between treatment and outcome, correlation to measure association of age with vaccine outcome, and Mann-Whitney U tests to measure association of HLA allele with vaccine outcome. Both Ft and VEEV vaccination elicited significant changes in gene expression. A highly positive relationship between age and vaccine outcome was shown for VEEV. The results may affect positive social change by contributing to a growing compendium of evidence of vaccine efficacy mechanisms that may function to assure the public of vaccine safety, combat vaccine hesitancy, and promote vaccine acceptance, as well as contribute mechanistic knowledge to reduce developmental costs of novel vaccines.

There continues to be a lack of agreement concerning the precise phylogenetic placement of Proconsul despite the wealth of fossil material and the extensiveness of its study. The difficulty in resolving the phylogenetic status of this important and well represented Miocene catarrhine is a consequence of its apparent basal position relative to crown catarrhines. This position complicates the inference of character polarities. This dissertation tests three previously proposed hypotheses concerning the phylogenetic position of Proconsul: (1) Proconsul is a stem catarrhine; (2) Proconsul is a stem hominoid; and (3) Proconsul is a basal hominid, most closely related to extant great apes and humans. A phylogenetic analysis based on 719 characters drawn from the skull, forelimb, pelvis and foot, and sampling a diversity of extant anthropoid taxa, offers no compelling support for a hominoid clade that includes Proconsul. The radiation of crown catarrhines involved rapid evolutionary changes from the ancestral catarrhine morphotype, resulting in stem catarrhines appearing much more similar to each other, even where there are key synapomorphies linking them with crown clades. As a result, systematic analyses alone are insufficient to confidently support a single optimal phylogenetic hypothesis. Further exploration of the data, by combining inferred ancestral morphotypes with phenetic visualizations of character evolution, demonstrated that inclusion of Proconsul among Hominoidea or Hominidae pushed the ancestral catarrhine morphotype closer to these clades, respectively. Given a more comprehensive analysis of character evolution under each hypothesis, this dissertation supports the hypothesis that Proconsul is a stem catarrhine. In addition to helping clarify the long-running debate about the phylogenetic status of Proconsul, the results offer fresh insights into the early stages of hominoid evolution and demonstrate the importance of comprehensive phylogenetic analyses in helping to resolve the relationships of problematic stem taxa.

"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).

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.

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").

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.

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.