abstract: Teaching evolution has been shown to be a challenge for faculty, in both K-12 and postsecondary education. Many of these challenges stem from perceived conflicts not only between religion and evolution, but also faculty beliefs about religion, it's compatibility with evolutionary theory, and it's proper role in classroom curriculum. Studies suggest that if educators engage with students' religious beliefs and identity, this may help students have positive attitudes towards evolution. The aim of this study was to reveal attitudes and beliefs professors have about addressing religion and providing religious scientist role models to students when teaching evolution. 15 semi-structured interviews of tenured biology professors were conducted at a large Midwestern universiy regarding their beliefs, experiences, and strategies teaching evolution and particularly, their willingness to address religion in a class section on evolution. Following a qualitative analysis of transcripts, professors did not agree on whether or not it is their job to help students accept evolution (although the majority said it is not), nor did they agree on a definition of "acceptance of evolution". Professors are willing to engage in students' religious beliefs, if this would help their students accept evolution. Finally, professors perceived many challenges to engaging students' religious beliefs in a science classroom such as the appropriateness of the material for a science class, large class sizes, and time constraints. Given the results of this study, the author concludes that instructors must come to a consensus about their goals as biology educators as well as what "acceptance of evolution" means, before they can realistically apply the engagement of student's religious beliefs and identity as an educational strategy. / Dissertation/Thesis / Masters Thesis Biology 2014

<p>Our only example of life is that of Earth- which is a single lineage. We know very little about what life would look like if we found evidence of a second origin. Yet there are some universal features of geometry, mechanics, and chemistry that have predictable biological consequences. The surface-to-volume ratio property of geometry, for example, places a maximum limit on the size of unassisted cells in a given environment. This effect is universal, interesting, not vague, and not arbitrary. Furthermore, there are some problems in the universe that life must invariably solve if it is to persist, such as resistance to radiation, faithful inheritance, and resistance to environmental pressures. At least with respect to these universal problems, some solutions must consistently emerge.</p><p> In this dissertation, I develop and defend my own account of universal biology, the study of non-vague, non-arbitrary, non-accidental, universal generalizations in biology. In my account, a candidate biological generalization is assessed in terms of the assumptions it makes. A successful claim is accepted only if its justification necessarily makes reference to principles of evolution and makes no reference to contingent facts of life on Earth. In this way, we can assess the robustness with which generalizations can be expected to hold. I contend that using a stringent-enough causal analysis, we are able to gather insight into the nature of life everywhere. Life on Earth may be our single example of life, but this is merely a reason to be cautious in our approach to life in the universe, not a reason to give up altogether.</p> / Dissertation

abstract: The present study tested the hypothesis that women dress modestly to signal to other women that they pose no mate poaching threat and are sexually restricted, and that this is especially true for religious women. Participants were 392 Muslim women living in the United States. They read two passages describing fictional situations in which they met with a potential female friend and then indicated what kind of outfit they would wear in both situations. In one situation, the participant obtained a reputation for promiscuity; in the other situation, reputation was not mentioned. I predicted that participants would choose more modest outfits for the promiscuous reputation passage, because if women dress modestly to signal sexual restrictedness, then they should dress more modestly around women with whom they have a reputation for promiscuity—to counteract such a reputation, women may wish to send a strong signal that they are not promiscuous. The hypothesis was partially supported: Less religious women chose more modest outfits for the promiscuous reputation situation than they did for the no reputation situation. This suggests that some women dress modestly to signal sexual restrictedness to other women, but that this is especially true for women who are less religious, not more. More religious women dress more modestly than less religious women, but they may not dress modestly to signal sexual restrictedness. Two important goals for this area of research are to determine the proximate reasons that more religious women dress modestly and to investigate modest dress among non-Muslim religious women. / Dissertation/Thesis / Doctoral Dissertation Psychology 2020

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

abstract: Cancer is a disease which can affect all animals across the tree of life. Certain species have undergone natural selection to reduce or prevent cancer. Mechanisms to block cancer may include, among others, a species possessing additional paralogues of tumor suppressor genes, or decreasing the number of oncogenes within their genome. To understand cancer prevention patterns across species, I developed a bioinformatic pipeline to identify copies of 545 known tumor suppressor genes and oncogenes across 63 species of mammals. I used phylogenetic regressions to test for associations between cancer gene copy numbers and a species’ life history. I found a significant association between cancer gene copies and species’ longevity quotient. Additional paralogues of tumor suppressor genes and oncogenes is not solely dependent on body size, but rather the balance between body size and longevity. Additionally, there is a significance association between life history traits and genes that are both germline and somatic tumor suppressor genes. The bioinformatic pipeline identified large tumor suppressor gene and oncogene copy numbers in the naked mole rat (Heterocephalus glaber), armadillo (Dasypus novemcinctus), and the two-fingered sloth (Choloepus hoffmanni). These results suggest that increased paralogues of tumor suppressor genes and oncogenes are these species’ modes of cancer resistance. / Dissertation/Thesis / Pipeline results for cancer genes / Phylogenetic regressions with correction tests / Pipeline results for housekeeping genes / Masters Thesis Biology 2019

abstract: Regulation of transcription initiation is a critical factor in the emergence of diverse biological phenotypes, including the development of multiple cell types from a single genotype, the ability of organisms to respond to environmental cues, and the rise of heritable diseases. Transcription initiation is regulated in large part by promoter regions of DNA. The identification and characterization of cis-regulatory regions, and understanding how these sequences differ across species, is a question of interest in evolution. To address this topic, I used the model organism Daphnia pulex, a well-characterized microcrustacean with an annotated genome sequence and selected a distribution of well-defined populations geographically located throughout the Midwestern US, Oregon, and Canada. Using isolated total RNA from adult, female Daphnia originating from the selected populations as well as a related taxon, Daphnia pulicaria (200,000 years diverged from D. pulex), I identified an average of over 14,000 (n=14,471) promoter regions using a novel transcription start site (TSS) profiling method, STRIPE-seq. Through the identification of sequence architecture, promoter class, conservation, and transcription start region (TSR) width, of cis-regulatory regions across the aforementioned Daphnia populations, I constructed a system for the study of promoter evolution, enabling a robust interpretation of promoter evolution in the context of the population-genetic environment. The methodology presented, coupled with the generated dataset, provides a foundation for the study of the evolution of promoters across both species and populations. / Dissertation/Thesis / Masters Thesis Molecular and Cellular Biology 2020

What selective forces and molecular mechanisms govern the integration of worker body size and morphology, brain architecture, and behavior in insect societies? Workers of the remarkably polyphenic and socially complex fungus-growing leafcutter ant Atta cephalotes exhibit a striking agricultural division of labor. The number of morphologically distinct and behaviorally differentiated worker groups, adaptive mosaic neural phenotypes, and brain transcriptomes have not been examined and the influences of socioecological challenges on behavioral performance, cognition, and brain evolution are unclear. We quantified worker morphological and behavioral variation to assess the number of worker size classes and characterized their social roles. We discriminated multiple worker size groups using a Gaussian mixture model: mid-sized workers (“medias”) had the most diverse task repertories and serve dominant roles in leaf harvesting, whereas workers of other size classes performed fewer, more specialized behaviors. We used variation among tasks in sensorimotor functions and task performance frequencies to create an estimate of sensory integration and processing demands across worker size groups. This metric predicted that medias require the greatest neural investment due to the high diversity of sensory inputs and motor functions associated with their task set. We quantified the volumes of key neuropils in brains of workers of different sizes and determined their allometries, finding that our estimate corresponded to proportional investment in the mushroom bodies, a brain compartment responsible for learning, memory, and sensory integration, and identifying allometric scaling patterns in other brain centers. Additionally, we measured whole-brain gene expression and identified significant differences in expression levels for numerous genes likely to underpin behavior. Differences were most pronounced between the smallest (fungal gardener “minims”) and largest (defensive “majors”), although not all expression differences were driven by worker size. Overrepresented gene functional categories included those related to sensory processing (enriched in genes upregulated in medias and minims) and metabolism (enriched in genes upregulated in majors). These results identify the nature of selective forces favoring differentiation along morphological, neuroanatomical, behavioral, and molecular axes among A. cephalotes workers and the impact of advanced division of labor on brain evolution. / 2023-03-01T00:00:00Z

Regulation of smooth muscle contraction depends on the phosphorylated state of myosin light chain (MLC). Although there are many kinases responsible for phosphorylating MLC, the myosin phosphatase complex is solely accountable for its dephosphorylation. Myosin phosphatase, in turn, is tightly regulated by many proteins. One of them being the CPI-17 gene family, which inhibits myosin phosphatase. This family of proteins is composed of CPI-17 itself, PHI-1, KEPI, and GBPI. Zebrafish have two genes each of CPI-17 and PHI-1, which are expressed during early embryonic development. This study sets out to investigate whether the two isoforms of CPI-17 and PHI-1 have diverged in function or expression using zebrafish as a model organism. Through a series of biochemical tests and assays, we have determined that the two isoforms have diverged in their expression pattern from each other, however they have similar function.

Spiders are one of the most diverse clades of multicellular life on earth, and their success has been attributed to several key genomic features, such as weaving silk, deploying various forms of venom, and being able to metabolize many types of prey. We have created a database of whole genome information from ten spider species from across major branches of the spider tree of life to help contextualize the genomic events occurring along the evolutionary history of the spider clade. Genes from these ten spiders were clustered into gene families which were used to detect duplications, losses, and evidence of selection (dN/dS) along the branches of these spiders' phylogeny. These results also allow us to weigh in on a contentious taxonomic placement for one of these spiders, the Uloborus diversus, which we found to be paraphyletic with other orb-web weaving spiders. One future applications of this database will involve phenotype reconstruction, with the goal of forging a genotype to phenotype map. / Biology

Sexual dimorphism, i.e., differences in morphology, physiology, and behavior between conspecific males and females, is ubiquitous, extensive, and often species-specific, indicative of its rapidly evolving nature. Ever since Darwin first described a general theory of sexual selection to explain the extraordinary differences between males and females of the same species, biologists have proposed a variety of mechanisms ranging from runaway selection to good genes to sexual conflict. While a popular approach is studying the effects of sexual selection on different components of fitness, the results of these studies are generally difficult to interpret and are typically not generalizable across populations, let alone taxa. Recent advances in the “omics” field are transforming the way that we study patterns and processes involved in sexual selection. At the molecular level, sexual dimorphism is present in gene expression differences between the sexes, providing a powerful framework to study sexual selection. By studying genes that are sex-biased in expression, we will better understand the underlying genetic basis of traits that are sexually dimorphic. Alreadly, studies of sex-biased genes in model organisms, particularly Drosophila, have revealed that male-biased genes are among the most rapidly evolving functional classes of genes. However, while a number of intrinsic factors appear to correlate with evolutionary rate (e.g., gene expression level, codon bias), it is unclear whether any of these factors drive the rapid divergence of male-biased genes. Another important discovery is the prevalence of sex-biased gene expression. However, even with widespread sexual dimorphism at the phenotypic level, it remains unknown the extent to which sex-biased gene expression exists in humans and their primate relatives. In fact, studies of sexual dimorphism on a molecular level in primates have been very few, even though understanding this phenomenon in humans could further our knowledge of the nature of sex-biased phenotypes and diseases. In this thesis, I advance our knowledge of the genetic bases and mechanisms that shape sexual dimorphism. First, I review a classic framework that biologists have traditionally applied to define and partition fitness measures between males and females in the model system, Drosophila. Second, I apply a molecular framework to compare the relative roles of intrinsic factors on the evolutionary rate of rapidly evolving male-biased genes in Drosophila. Third, I review the current state of our knowledge of sexual dimorphism and sex-biased gene expression in humans. Fourth, I present a bioinformatics framework to identify the extent of sex-biased expression in primate tissue and to examine the selective forces involved in their evolution. Overall, I demonstrate the effectiveness of using a functional comparative genomics approach in studying the nature of sexual dimorphism at the molecular level across multiple taxa. / Biology