Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

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  • Population genomic inference of ecology, conservation, evolution, and demographic history of Atlantic seahorses and pipefishes (Syngnathidae)

    Author:
    Joel Boehm
    Year of Dissertation:
    2015
    Program:
    Biology
    Advisor:
    Michael Hickerson
    Abstract:

    In the Atlantic Ocean powerful directional ocean currents can play a significant role in the formation and persistence of marine species. Syngnathidae fishes have a sparse fossil record, high morphological plasticity, and many of these species are difficult to observe in the wild, therefore they frequently lack life history information and the status of regional lineages and species designations are often obscure. In this dissertation I explore the ecology, evolution, and conservation of primarily Atlantic seahorses (Hippocampus) and pipefish (Syngnathus) in four core chapters, using differing genetic datasets ranging from mitochondrial DNA to genome-wide RAD sequences. Most Synganthids have the potential to disperse passively by rafting on floating vegetation, and are direct developers, which is thought to limit their active mobility, yet many species have widespread distributions. The majority of genetic research on Syngnathids fishes has focused on Indo-Pacific species, however the Atlantic Ocean is home to dozens of species of pipefishes from nine genera and roughly 1/5th of the world's seahorses species. In Chapter 1, I use six loci to infer the species tree for all Atlantic seahorses and infer the demographic history and evolution of the "Hippocampus erectus complex." The results of this study support the establishment of an ancestral population of the H. erectus complex in the Americas, followed by the Amazon River outflow splitting it into Caribbean/North American H. erectus and South American H. patagonicus at a time of increased sedimentation and outflow. Following this split, colonization occurred across the Atlantic via the Gulf Stream currents with subsequent trans-Atlantic isolation. Based on the results of Chapter 1, the species H. erectus exhibited a panmictic genetic structure from Latin America to temperate New York waters. However, inhabitants of the temperate region are considered by some ecologists to be tropical vagrants that only arrive during warm seasons from the southern provinces and perish as temperatures decline. Contrary to the findings of Chapter 1, in Chapter 2, I use thousands of RADseq loci and show strong support that temperate inhabitants are genetically diverged from southern populations and are composed of an isolated and persistent ancestral gene pool. The aim of Chapter 3 is to investigate how major current forces as well as climatic and geographic processes have shaped the evolutionary and demographic history of western Atlantic seahorses (Hippocampus) and pipefishes (Syngnathus). This Chapter takes a comparative approach across five codistributed species (two seahorses and three pipefishes). Genomic patterns of subpopulation divergence and post-divergence gene flow may be shared amongst fish species with similar life history traits, however ecological differences (i.e., macroclimatic tolerance and rafting propensity) may impact the rates of gene exchange and/or isolation times between subpopulations. The result of this study show how directional ocean currents and the life history trait of rafting propensity impacts population divergence and connectivity, and predicts gene flow directionality and magnitude in four out of five of the focal taxa. Lastly in Chapter 4, I use a molecular forensics approach to track the U.S. dried seahorse trade. Due to global exploitation, the genus Hippocampus are the only fish to have all species listed under the Convention of International trade of endangered species (CITES). Millions of individuals are traded each year for the use in traditional Chinese medicine as well as for souvenirs and crafts. Using "DNA barcoding," while mentoring high school and undergraduate students, we identified and compared specimens collected from two primary U.S. dried seahorse end-markets: 1) traditional Chinese medicine and, 2) Internet and coastal souvenir retailers. The results of this study found a significant contrast in both the species composition and size of individuals being sold between each market.

  • Straight Record and The Paper Trail: From Depression Reporters to Foreign Correspondents

    Author:
    Magdalena Bogacka-Rode
    Year of Dissertation:
    2014
    Program:
    English
    Advisor:
    Jane Marcus
    Abstract:

    Straight Record and the Paper Trail: From Depression Reporters to Foreign Correspondents engages with Martha Gellhorn's The Face of War (1959), Virginia Cowles' Looking for Trouble (1941) and Josephine Herbst's The Starched Blue Sky of Spain and Other Memoirs (1991) as documentaries of struggle. Documentary as a mode of writing and image making reveals dissonance, contradictions and varied perspectives which undermine the official historical record. The three writers, I argue, by republishing their Spanish Civil War (SCW) journalism in book form intended to set their record straight. This was motivated by their commitment to the 1930s struggle and the need to recover much that had been relegated to the margins as human interest stories (HIS), or woman's angle. This patronizing and denigrating label which was applied to their SCW articles dismissed the documentary value of, what I call, their human experience record (HER), as an affectation of uninformed and class biased women writers. Their documentary texts, much like those of Nancy Cunard, Muriel Rukeyser, Gerda Taro, Gamel Woolsey and Virginia Woolf, were not composed under auspices of dominant party lines as they eschewed formal membership in political as well as international organizations. In these, they recognized the very same patriarchal constraints and limitations which they sought to expose using the `masters' tools' they acquired by belonging, or at least being able to pass for "daughters of educated men" yet remained fully aware that being citizens with passports they were in position to help, but by no means to become the face of the cause(Woolf). The main criticism of The Face of War, Looking for Trouble and The Starched Blue Sky of Spain and Other Memoirs has been that Gellhorn, Cowles and Herbst did not tell the whole truth, that dates and names of key players are missing, and that they had no definite answers about the politics and propaganda in Spain. But these were not the objectives these women set for themselves when they went to Spain and later when they decided to republish their SCW journalism. What Gellhorn, Cowles and Herbst omitted from journalism and their subsequent accounts in book form -- moments of doubt, consternation, idleness -- remains in their archival repositories, the recovery project of which this dissertation aims to initiate.

  • Parental Investment and Song Learning in Zebra Finches (Taeniopygia guttata)

    Author:
    Diane Bogdan
    Year of Dissertation:
    2009
    Program:
    Psychology
    Advisor:
    Cheryl Harding
    Abstract:

    Abstract PARENTAL INVESTMENT AND SONG LEARNING IN ZEBRA FINCHES (TAENIOPYGIA GUTTATA) By DIANE M BOGDAN Adviser: Professor Cheryl F. Harding In order to understand the effects of parental investment on learning, we conducted a series of experiments using zebra finches. The aspects of parental investment studied included deposition of maternally-derived hormones (MDH) into eggs, feeding and attention to chicks. Learning was assessed by song copying (mean accuracy, sequential matching and percent similarity to the father's song). We compared digit ratios, a marker for the amount of MDH chicks experienced in eggs, and song copying ability. Our data suggests that maternally-derived testosterone negatively affected the ability to sequentially match notes. To determine if parents were preferentially feeding chicks by hatch order, we weighed chicks at key developmental points prior to fledging. We found that chicks that hatched early were heavier than those who hatched late. Additionally, weight at day 10 was positively correlated with song learning. Acoustic cues are one obvious way that parents might differentiate chicks by hatch order. Therefore, we assessed the begging calls of 10 day old chicks. We found that early-hatched chicks begged at lower amplitudes than late-hatched chicks. We then conducted a playback experiment in which begging calls of 10 day old early- and late-hatched chicks were presented to breeding adults. Adults were more attentive during the early-hatched chicks' playbacks. To determine if attention, in the form of clumping or perching closely together, affected song learning, we observed family groups when chicks were beginning song acquisition (day 25). We found that while clumped with their mates, mothers clumped with first-hatched more than second- or third- hatched chicks. Moreover, clumping behavior was positively correlated with the percent similarity of song copying. Clumping with first-hatched sons may be a way for mothers to give additional access to the father and thereby enhance son's song learning. Finally, we used a multiple linear regression, combining all three forms of parental investment to determine which were more important in song learning. We found that digit ratio 2:3 was positively correlated with sequential matching, nestling weight positively correlated with mean accuracy and clumping with the mother positively correlated with the percent similarity score.

  • PREDICTING INTRODUCTIONS AND RANGE EXPANSIONS OF THE MONK PARAKEET WITH ECOLOGICAL NICHE MODELING AND LANDSCAPE GENETICS

    Author:
    Corentin Bohl
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Jason Munshi-South
    Abstract:

    The ability to predict species future geographic distributions is an important challenge in biogeography and conservation biology, with critical implications for pressing environmental issues, including the potential spread of invasive species. This research examines a two-step framework to build accurate predictions of the invasive potential of the monk parakeet (Myiopsitta monachus). This species, native to temperate South-America, has established several stable populations worldwide, and shares many of the typical traits of high-risk invaders. The proposed framework aims to 1) identify areas where the species is likely to thrive, and 2) determine which of these suitable areas the species can likely disperse to. Objective 1 requires identifying the environmental conditions suitable to the species, for which I used ecological niche modeling (Chapter 1 & 2). Objective 2 addresses the ability of the species to conquer new adjacent favorable areas via dispersal, a problem that can be addressed with landscape genetics (Chapter 3). In Chapter 1, I developed a null model approach to evaluate the performance and significance of ecological niche models. The results highlight the importance of accounting for both discrimination and overfitting and correctly estimating significance. In Chapter 2, I tested the effect of different model calibration strategies on transferability (the ability to predict independent data in different geographic regions). I used this information to make predictions about the global invasive potential of the monk parakeet. The best prediction was obtained with native calibration records and complex model settings. This prediction indicates several areas with conditions suitable for monk parakeets, including areas adjacent to existing introduced populations. In Chapter 3, I integrated ecological niche modeling and landscape genetics to make predictions about the landscape features that affect monk parakeet dispersal. I tested these predictions with genetic data from an introduced population in Florida, and assessed their significance with null models. Estimating resistance to dispersal with ecological niche modeling produced results equivalent to evaluating a range of alternative hypotheses with a stepwise regression model. The results indicate that monk parakeet may not be limited by distance and most landscape features and are likely to expand to adjacent suitable areas.

  • The Characterization of Black Inkjet Computer Printer Inks using Pyrolysis Gas Chromatography-Mass Spectrometry (Py-GC-MS), High Performance Liquid Chromatography (HPLC), Thin Layer Chromatography (TLC) and Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR FT-IR)

    Author:
    Michelle Boileau
    Year of Dissertation:
    2012
    Program:
    Criminal Justice
    Advisor:
    Thomas Kubic
    Abstract:

    Documents are prevalent in every aspect of daily life and hardly a day passes without using some sort of document. Problems arise, however, when the authenticity of these documents is raised. Forensic science has long been involved in the investigation and examination of suspect documents. One of the steps in the examination of questioned documents is for the examiner to analyze the type of material used to create the document. This could involve the analysis of the paper substrate and/or the medium used to create the written word, namely pen ink, typewriter ink or toner in photocopied documents. This is the age of the computer, and as a result new challenges are facing the questioned document examiner. With more and more individuals using computers to produce their documents, and with the advancement of more sophisticated computer and printer systems, it has become harder for the analyst to distinguish and possibly individualize a suspected document based on physical appearance alone. Once again, the forensic scientist must focus on the material used to produce the document, namely the computer printer ink. An examination of these ink samples may allow for the differentiation between the many manufacturers, as well as within the products of a specific manufacturer. In time, it may also be possible to date a computer printer generated document based on the drying and decomposition rates of the different computer printer ink components. Currently, this is unfortunately still just a theory. There have been few studies on the different types of computer printer inks and how, or if, they differ from each other. The identification of the various black inkjet computer printer ink manufacturers, and the creation of a classification procedure, is the first step in the analysis of a questioned inkjet produced document. The goal of this study was to produce a detailed document on the forensic identification of black inkjet computer printer inks, and this research succeeded in its goal. The analysis of the black inkjet computer printer ink samples by Thin Layer Chromatography (TLC), High Performance Liquid Chromatography (HPLC), Pyrolysis Gas Chromatography-Mass Spectrometry (Py-GC-MS) and Attenuated Total Reflection Fourier Transform Infrared Spectroscopy (ATR FT-IR) analytical methods resulted in the production of data that led to the establishment of a classification procedure that could assist the forensic scientist in the examination, identification and discrimination of the different inkjet computer generated documents they receive.

  • CANDIDA ALBICANS ALS5P AMYLOID IN HOST-MICROBE INTERACTIONS: A CEANORHABDITIS ELEGANS STUDY

    Author:
    MICHAEL BOIS
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    PETER LIPKE
    Abstract:

    Candida albicans, a dimorphic fungus and an opportunistic pathogen, possesses a myriad of adherence factors including members of the agglutinin-like sequence (Als) family of mannoproteins. The adhesin Als5p mediates adhesion to many substrates, and is upregulated during commensal interactions, but is downregulated during active C. albicans infections[1]. An amyloid forming core sequence at residues 325-331 has been shown to be important for Als5p function, because a single amino acid substitution at position 326 (V326N) greatly reduces Als5p-mediated adherence[2]. We evaluated the role of Als5p in host-microbe interactions, using Caenorhabditis elegans as a host model and feeding them Saccharomyces cerevisiae expressing Als5p on the surface. Als5p-expressing yeast had increased intestinal accumulation rates when compared to non-expressing S. cerevisiae or yeast expressing the amyloid deficient Als5pV326N, respectively. Surprisingly, this accumulation delayed S. cerevisiae-induced killing of C. elegans. Treatment with the amyloid-inhibiting dye Congo red or repression of Als5p expression abrogated the protective effect of Als5p. Being that reproductive fitness is the most important measure of a pathogen's impact on the host, we looked at oocyte quantity and quality[3]. Als5p had no effect on oocyte quantity or quality. In order to understand why nematodes exposed to Asl5p were able to harbor the cells expressing functional amyloid, we looked into the innate immune system of the nematode. Toll- Like receptors (TLRs) are important mediators of innate immune responses to Candida albicans, and several classes of scavenger receptors have been implicated in recognizing and reacting to a variety of ligands in humans[4]. The C. elegans genome encodes for a single TLR, TOL-1, and scavenger receptor CED-1[4,5]. CED-1 is the orthologue to mammalian scavenger receptor SCARF1 and is required for defense against Cryptococcus neoformans[4,6]. Our studies showed that CED-1 was necessary for prolonged survival in the presence of Als5p, and TOL-1 was required for death in C. elegans fed S. cerevisiae. We have further demonstrated the necessity of CED-1 and TIR-1 in phosphorylation of ERK-2/MPK-2. The SAM and TIR domains of TIR-1 were shown to be necessary in discriminating the presence of functional amyloid, and thus elicit specificity in downstream signaling. Remarkably, the presence of the HEAT/Armadillo domain, alone, was sufficient to increase levels of phosphorylated ERK-2/MPK-2 in nematodes fed any yeast strain in this study. This study is the first to show that expression of amyloid-forming Als5p in S. cerevisiae can: a) attenuate S. cerevisiae pathogenicity in C. elegans; b) move the yeast-host interaction towards hallmarks of commensalism; c) be discriminated against by host pathogen recognition receptors (PRRs) leading to a slower decline in viability; and d) can lead to distinct downstream MAPK responses.

  • The Interchange of Plain Velar and Aspirate in Kronos/Chronos: A Case for Etymological Equivalence

    Author:
    Roberto Bongiovanni
    Year of Dissertation:
    2014
    Program:
    Classics
    Advisor:
    Tamara Green
    Abstract:

    Despite the current state of uncertainty regarding the etymology of Kronos, the equivalence long familiar to the ancients between Kronos and Chronos is still a moot point. Arguments denying their etymological equivalence can no longer firmly rely on linguistic arguments. It is therefore necessary to examine the validity of the time-honored interpretation of Kronos as the personification of Time. The solution to this problem is of considerable importance to Classical studies, since it will not so much as contribute to a better understanding of the myth of Kronos, as the interpretation of Kronos as Time is already familiar from ancient sources, but it will demand a rereading of Hesiod's Theogony to account for the possible relation of its myth and symbols to comparable myths and symbols of the transitioning ages of the world and consequent calendrical corrections.

  • Manuel de la Cruz González: Transnationalism and the Development of Modern Art in Costa Rica

    Author:
    Lauran Bonilla-Merchav
    Year of Dissertation:
    2014
    Program:
    Art History
    Advisor:
    Anna Indych-López
    Abstract:

    While scholars are increasingly scrutinizing twentieth-century Latin American art and inserting it into the canon of modern art history, studies of the region usually leap from Mexico to South America, skipping Guatemala, El Salvador, Honduras, Belize, Nicaragua, Costa Rica, and Panama. This is not due to a lack of dedicated artistic effort in the isthmus, but rather to poor cultural infrastructure, which made being a modern artist in the region particularly challenging, and the underdeveloped state of local art histories, which have yet to traverse national borders. This oversight of Central American art makes it difficult to grasp the full scope of Latin America's adaptation of, and contribution to, international modernism. My dissertation counteracts the privileging of art from North and South America and introduces Costa Rican art history to an international audience by examining the art and life of Manuel de la Cruz González Luján (1909-1986), one of Costa Rica's most influential modern artists. It emphasizes the importance of the transnational cultural currents that influenced González and his colleagues, and systematically discusses two fundamental phases of artistic growth in the country, the 1930s and the 1960s. By placing González's artistic production within the socio-historic, cultural, and aesthetic contexts of Costa Rica, this dissertation is a groundbreaking case study of the development of modern art in this Central American nation. González prodded the boundaries of the provincial Costa Rican art world and moved beyond local frameworks to take part actively in the spread of modernist trends. He embraced regionalism, modernismo, and Latin American impressionism while in Costa Rica, and surrealism and geometric abstraction during the ten years he spent abroad in Cuba (1948-1950) and Venezuela (1950-1957). Upon his return, he shared his knowledge and experience of international modernism, but was faced with an unprepared and unpropitious artistic setting that neither accepted nor encouraged his geometric abstract art. What his story shows is that in order for a transnational style or idea to take hold in a country such as Costa Rica, which could be any "ex-centric" location, it is necessary to have a receptive context. This analysis of González's career thus highlights the tension of being a provincial artist, attuned to transnational cultural flows, yet challenged by the limitations of his environment.

  • Systematic Asymmetries in Perception and Production of L2 Inflections in Mandarin L2 Learners of English: The Effects of Phonotactics, Salience, and Processing Pressure on Inflectional Variability

    Author:
    Timothy Bonner
    Year of Dissertation:
    2013
    Program:
    Linguistics
    Advisor:
    Gita Martohardjono
    Abstract:

    The study of language production by adults who are learning a second language (L2) has received a good deal of attention especially when it comes to omission of inflectional morphemes within L2 utterances. Several explanations have been proposed for these inflectional errors. One explanation is that the L2 learner simply does not have the L2 syntactic or prosodic representation in his grammar leading to omission of surface inflections (Hawkins & Liszka, 2003; Goad, White, & Steele, 2003, respectively). Others attribute L2 errors to mapping problems between the lexicon and syntax (Prévost & White, 2000; Lardiere, 1998, 2003). Another potential explanation for the variable production of inflectional endings is that it may be due to performance factors as in Hopp (2009) and Martohardjono, Valian, and Klein (2012) or to "Extra-syntactic" factors as proposed in Klein (2004) or to syllable repairs due to L1 phonotactic interference as proposed in Davidson (2005, 2006a, 2006b). This dissertation claims that when L2 morphosyntactic representations are shown to be available in the L2 learner's grammar, L2 inflectional variability can be attributed to L1 phonotactic interference, salience of the L2 inflection, and performance factors leading to systematic, but asymmetrical patterns of perception and production of the allomorphs that represent the surface L2 inflections. The results revealed that the target inflections were not omitted across the board as would be expected under deficit accounts. On the contrary, repairs of the final target coda clusters (i.e., schwa epenthesis before and after the final inflectional consonant and devoicing of the word-final consonants) revealed patterns that are consistent with the degree of syllabicity (e.g., [Vd] vs. [t] and [d]) and sonority (e.g., [s] vs. [t]) of the allomorph or coda and are not indicative of morphosyntactic deficits. Importantly, schwa epenthesis was applied asymmetrically (i.e., particularly to stops [t] and [d]) in clusters that contained target codas and inflectional allomorphs in real, nonce, and monomorphemic items, and thus, this repair pattern is contra the Prosodic Transfer Hypothesis of Goad et al. (2003). Overall, this dissertation presents an alternative explanation for L2 inflectional errors outside of the morphosyntactic and prosodic deficit arguments.

  • THE VARIABLE GRAMMAR OF THE SPANISH SUBJUNCTIVE IN SECOND-GENERATION BILINGUALS IN NEW YORK CITY

    Author:
    Kevin Bookhamer
    Year of Dissertation:
    2013
    Program:
    Hispanic & Luso Brazilian Literatures & Languages
    Advisor:
    Ricardo Otheguy
    Abstract:

    This morphosyntactic dissertation study compares the use of MOOD (indicative & subjunctive) in first- and second-generation Spanish speakers in New York City. The data for this study are from a transcription of naturalistic Spanish conversations with New Yorkers of different generations, representing the six primary Spanish-speaking groups in NYC: Puerto Rican, Dominican, Mexican, Ecuadorian, Colombian and Cuban. We analyze data from 26 born in Latin America and 26 born or raised in NYC, totaling 52 transcriptions. The reference model is the mood usage of first-generation newcomers, not a standard Spanish normative framework. The objective was to examine the use of mood by way of descriptive and inferential analytical methods in order to determine whether or not the second-generation bilinguals' mood grammar has changed, and if so, to establish exactly where and how it differs from the first-generation. The research questions were: 1) Does the subjunctive use of second-generation NYC bilinguals differ from that of their first-generation NYC counterparts? 2) What are the syntactic and communicative contexts in which the subjunctive is used in the first and second generations? 3) What internal and external independent variables condition mood choice in both immigrant generational groups? 4) Is the second generation's use of mood such that grammatical command of mood appears developed and systematic? Or is there evidence of an incomplete or unsystematic mood grammar? Our findings corroborate the results from other studies centered on generational U.S. subjunctive use: the second generation generates fewer subjunctives and more indicatives than the first-generation, a finding supported by statistical significance. The two generations also differ significantly concerning the internal contexts where mood manifests, but command of mood does appear intact among the majority of the second generation, thus problematizing common notions such as attrition, incomplete acquisition, and to a degree, simplification. Furthermore, analyses concerning several external variables show that the first generation appears essentially homogenous with respect to their use of mood, whereas the second-generation displays far more variability. Finally, this dissertation contributes to the variationist-sociolinguistic knowledge of Spanish grammar in bilingual settings.