Alumni Dissertations

 

Alumni Dissertations

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  • IMPACTS OF HABITAT DEGRADATION ON FUNDULUS HETEROCLITUS (LINNAEUS) IN URBAN TIDAL SALT MARSHES IN NEW YORK

    Author:
    Daisuke Goto
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    William Wallace
    Abstract:

    Despite considerable improvements in water quality over the last few decades, the ecological integrity of benthic habitats in the Arthur Kill (AK), New York, USA, largely remains altered. This dissertation explores how altered ecological status of benthic habitats directly and indirectly (via food webs) affected a resident forage fish, mummichogs (Fundulus heteroclitus), in highly urbanized tidal salt marshes in AK. A substantial portion of total abundance and biomass of benthic macroinvertebrates (a primary prey resource for mummichogs) in AK were comprised of only a few opportunistic oligochaete and polychaete species. And these alterations in benthic macroinfaunal communities in AK were strongly associated with the sediment-associated mercury level. Alterations in the AK benthic macroinfaunal assemblages were generally reflected in diet habits and strategies of mummichogs; a generalized feeding strategy with a broad diet niche breadth of mummichogs shifted to more specialized strategies for many of the AK populations. Although decapods (especially Palaemonetes spp.) were the predominant prey for all populations of mummichogs, the length-specific maximum sizes of Palaemonetes spp. ingested by some of the AK populations of mummichogs were about 2-fold smaller than those ingested by the reference population. These shifts in feeding habits were compensated for with an increased consumption of polychaetes by most of the AK populations and polychaetes contributed up to more than 40% of their gut contents. Partial trophic decoupling between mummichogs and dominant benthic macroinvertebrates had further implications for biogeochemical cycling of trace metals and energy transfer in AK. Alterations in benthic macroinfaunal prey communities reduced trophic transfer efficiency (i.e., exposure levels) of metals to mummichogs. Furthermore, despite their compensatory food consumption, most of the AK populations of mummichogs had considerably elevated total metabolism, resulting in substantially reduced growth conversion efficiency. This reduction in energy conversion efficiency at the individual level can cascade through trophic chains, potentially leading to energetic bottlenecks at the community level. Altered salt marsh trophic structures in AK and their resultant impacts on mummichog (a crucial trophic link in urban estuaries) bioenergetics may thus disrupt energy translocation in this severely degraded coastal ecosystem.

  • IMPACTS OF HABITAT DEGRADATION ON FUNDULUS HETEROCLITUS (LINNAEUS) IN URBAN TIDAL SALT MARSHES IN NEW YORK

    Author:
    Daisuke Goto
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    William Wallace
    Abstract:

    Despite considerable improvements in water quality over the last few decades, the ecological integrity of benthic habitats in the Arthur Kill (AK), New York, USA, largely remains altered. This dissertation explores how altered ecological status of benthic habitats directly and indirectly (via food webs) affected a resident forage fish, mummichogs (Fundulus heteroclitus), in highly urbanized tidal salt marshes in AK. A substantial portion of total abundance and biomass of benthic macroinvertebrates (a primary prey resource for mummichogs) in AK were comprised of only a few opportunistic oligochaete and polychaete species. And these alterations in benthic macroinfaunal communities in AK were strongly associated with the sediment-associated mercury level. Alterations in the AK benthic macroinfaunal assemblages were generally reflected in diet habits and strategies of mummichogs; a generalized feeding strategy with a broad diet niche breadth of mummichogs shifted to more specialized strategies for many of the AK populations. Although decapods (especially Palaemonetes spp.) were the predominant prey for all populations of mummichogs, the length-specific maximum sizes of Palaemonetes spp. ingested by some of the AK populations of mummichogs were about 2-fold smaller than those ingested by the reference population. These shifts in feeding habits were compensated for with an increased consumption of polychaetes by most of the AK populations and polychaetes contributed up to more than 40% of their gut contents. Partial trophic decoupling between mummichogs and dominant benthic macroinvertebrates had further implications for biogeochemical cycling of trace metals and energy transfer in AK. Alterations in benthic macroinfaunal prey communities reduced trophic transfer efficiency (i.e., exposure levels) of metals to mummichogs. Furthermore, despite their compensatory food consumption, most of the AK populations of mummichogs had considerably elevated total metabolism, resulting in substantially reduced growth conversion efficiency. This reduction in energy conversion efficiency at the individual level can cascade through trophic chains, potentially leading to energetic bottlenecks at the community level. Altered salt marsh trophic structures in AK and their resultant impacts on mummichog (a crucial trophic link in urban estuaries) bioenergetics may thus disrupt energy translocation in this severely degraded coastal ecosystem.

  • Migration Plasticity as an Adaptation to Climate Change: The Spatial Distribution and Abundance of a Subset of Neotropical Migrant Landbirds Wintering in the Northeastern United States

    Author:
    Juliette Goulet
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Shaibal Mitra
    Abstract:

    There is a need for accurate predictions of the effects of climate change on wildlife populations. Bioclimatic relationships however are potentially complicated by various environmental factors operating at multiple spatial and temporal scales. Therefore, in order to test the hypothesis that climate constraints of winter bird distributions are modified by species-specific responses to weather and climate, I relied on Christmas Bird Count data (CBC). With nearly 100 years of data, the CBC is a valuable source of information on historic and recent changes in the status and distribution of birds during the early winter period in the United States and Canada. The first chapter is a regional study that asked whether seasonal weather fluctuations and/or a warming climate indicative of the supposed increase in December presence of seven neotropical migrant landbirds near the northern edge of their winter ranges. CBC data and historical weather data from the U.S. Historical Climatology Network (USHCN) were analyzed to confirm the northward shift in average abundance over time among species near the northern limits of their winter ranges. I determined whether there was a strong temporal autocorrelation and/or linear relationship of December bird abundance consistent across species near the northern limits of their ranges and found strong evidence in support of the hypothesis that the migratory behavior of many bird populations has recently changed in response to climate warming. In addition, the effects of localized, short-term weather variations due to climate change proved to be just as, if not more important as the long-term global warming trend on the distribution of these wintering bird populations. In the second chapter, Christmas Bird Count-style counts conducted in November, December and February on Block Island, Rhode Island across eighteen winters (1995 - 2013) were used to describe long-term trends in the species abundance and diversity of 103 species of landbirds on Block Island, as well as subsets of species defined by migratory status and expected geographic distribution. The objectives were to determine what the eighteen-year trends in composition and occurrence of landbirds on Block Island across the winter season were; establish whether there was any evidence of changes in phenology and migration strategy in the migratory species as witnessed by increasing numbers in abundance and diversity in November and December; ascertain if the data supported evidence of multiple species shifting their non-breeding ranges to higher latitudes; and figure out what the long-term trends in the actual landbird winter populations on Block Island can tell us about fluctuations in local weather patterns leading to range shifts and demographic changes in a number of migratory species. The third chapter, focused on the observed range shifts and demographic changes in a subset of migratory landbirds referred to as Half-Hardies. This group of species increased on Block Island between November and December, although southern New England is at, or near, the northern limit of their normal winter distributions and stereotyped southbound migration is typically expected to have been completed well before mid-November. In addition, the body measurements of, and hydrogen isotope concentrations of the feathers of two half-hardy species wintering within Sandy Hook National Park in New Jersey, provided evidence of facultative, post-migratory movements among this subset of landbird species. I confidently concluded that many of the Half-Hardies present in the Northeast during the winter months are not "passive victims", i.e. simply injured, diseased, or otherwise unfit individuals but are in fact adaptively exploiting a new resource and are benefitting by avoiding the cost of long distance migration while gaining an advantage by remaining closer to the breeding grounds. In addition, my results support the distinction between late migrants and half-hardy wintering species in northeastern North America while disproving the notion that the early-winter timing of CBCs exposes them to the presence of lingering southbound migrants. The fourth and last chapter took a look at some of the other criticisms of the Christmas Bird Count data. I described the correlations and linear relationships between warmer temperatures and lighter winds with the number of observers and foot miles covered; and the total number of landbirds observed. Although there was a strong correlation between wind speed on count day and the number of birds observed on that count, the loss of detections, i.e. the inability to detect birds at longer distances as the wind increases, was not significantly relevant, and the difference in the variations tended to even out. My results support that statistical analyses of CBC data are a powerful tool for the study of birds on a local level, and concludes that the CBC is a valuable source of information on historic and recent changes in the status and distribution of birds during the early winter period in the United States and Canada.

  • Foraging strategies and facilitative interactions among common (Sterna hirundo) and roseate terns (S. dougallii) in the Northwest Atlantic Ocean

    Author:
    Holly Goyert
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    Richard Veit
    Abstract:

    Marine resources are characteristically patchy and concealed beneath the surface of a "featureless" ocean, which makes facilitative species interactions especially advantageous to seabirds. My research addresses how behavioral mechanisms accommodate prey availability, or more specifically, how common (Sterna hirundo) and roseate terns (S. dougallii) locate and access food when it is not easily detectable. I study their foraging behavior and ecology from pre- to post-breeding, offshore in the pelagic realm (chapter 1), around the colony (chapter 2), and in nearshore waters (chapter 3). My first chapter tests the hypothesis that, as broadly-ranging seabirds, common and roseate terns forage over habitat where marine mammals and predatory fish help to find and access prey. I quantify the spatial association among foraging terns, tunas, dolphins, and their habitat, using Bayesian hierarchical models, and tests of behavioral community interactions. Facilitation explains how terns benefit from subsurface predators through local enhancement and commensal relationships: foraging tunas improve the detection and availability of prey by signaling their presence, and driving them to the surface. Chapter 2 evaluates the link between resource utilization and foraging strategy, measured by nest provisioning and patterns among foraging routes or feeding flocks. I propose that the opportunistic generalists, common terns, depend more on social cues than the specialists, roseate terns, which rely more heavily on spatial memory to find predictable prey. The results support this and suggest that increased breeding and foraging success in roseate terns relates to higher quality and abundance in their preferred prey, sandlance (Ammodytes spp.); in contrast, common terns seem to endure prey limitation through their use of local enhancement. In my third chapter, I hypothesize that habitat variability and prey availability predict interspecific differences in tern foraging. Behavioral tests and density-surface models, with distance sampling, show that foraging common and roseate terns respond positively to the distribution and abundance of each other and their preferred prey. Clearly, common and roseate terns use conspecifics, heterospecifics and subsurface predators to encounter prey via facilitation: such interactions create dynamic hotspots that need to be considered in an ecosystem approach to marine spatial planning.

  • Gender specific changes in key regulators of neurodevelopment and autistic behavioral pathology in mice exposed to water chlorination byproducts

    Author:
    Sara Rose Guariglia
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Guang Wen
    Abstract:

    Autism is a heterogeneous group of disorders with no definitive etiology. Out of concern for higher than expected prevalence, the Agency for Toxic Substances and Disease Registry (ATSDR) investigated the municipal water supply in Brick Township, New Jersey. The ATSDR found that two trihalomethanes (THMs), specifically chloroform and bromoform, as well as tetrachloroethylene (perchlorethylene; PCE), were present in concentrations that exceeded allowable maximum contaminant (MCL) values. In a related study, it was found that THMs and PCE act synergistically to increase the level of catalytic Protein Kinase A (PKA) in neurons of clam embryos. PKA is a key regulator of neurodevelopment, and it is hypothesized that abnormalities in PKA activity could induce both histopathological and biochemical manifestations that are found in autism. Based upon these findings, we hypothesized that THM/PCE exposure induces changes in key regulators of neurodevelopment and behavioral pathology similar to that which is found in autism. In our experiments we found that exposure to THM/PCE induces an increase in the level of catalytically active PKA in zebrafish neurons and increases PKA activity in microglia cell culture. In a mouse model, we found that exposure to THM/PCE via drinking water induces an increase in the activity of PKA in the cerebral cortex of male animals at postnatal day 4 (P4) and postnatal day 10 (P10). Females cortical PKA activity was unaffected by THM/PCE exposure. By P15, male cortical PKA activity is no longer affected by THM/PCE exposure and female cortical PKA activity remains unaffected. Behaviorally, we found that the THM/PCE exposed males develop autistic like behavioral pathology as they evidence deficits in communication and social behavior and demonstrate both perseverance behavior and anxiety. Again, this finding is gender specific, as female behavior is unaffected by THM/PCE exposure. These findings suggest that these chemicals may be involved in the etiology of autism and that males are more susceptible to this set of insults.

  • Gender specific changes in key regulators of neurodevelopment and autistic behavioral pathology in mice exposed to water chlorination byproducts

    Author:
    Sara Rose Guariglia
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Guang Wen
    Abstract:

    Autism is a heterogeneous group of disorders with no definitive etiology. Out of concern for higher than expected prevalence, the Agency for Toxic Substances and Disease Registry (ATSDR) investigated the municipal water supply in Brick Township, New Jersey. The ATSDR found that two trihalomethanes (THMs), specifically chloroform and bromoform, as well as tetrachloroethylene (perchlorethylene; PCE), were present in concentrations that exceeded allowable maximum contaminant (MCL) values. In a related study, it was found that THMs and PCE act synergistically to increase the level of catalytic Protein Kinase A (PKA) in neurons of clam embryos. PKA is a key regulator of neurodevelopment, and it is hypothesized that abnormalities in PKA activity could induce both histopathological and biochemical manifestations that are found in autism. Based upon these findings, we hypothesized that THM/PCE exposure induces changes in key regulators of neurodevelopment and behavioral pathology similar to that which is found in autism. In our experiments we found that exposure to THM/PCE induces an increase in the level of catalytically active PKA in zebrafish neurons and increases PKA activity in microglia cell culture. In a mouse model, we found that exposure to THM/PCE via drinking water induces an increase in the activity of PKA in the cerebral cortex of male animals at postnatal day 4 (P4) and postnatal day 10 (P10). Females cortical PKA activity was unaffected by THM/PCE exposure. By P15, male cortical PKA activity is no longer affected by THM/PCE exposure and female cortical PKA activity remains unaffected. Behaviorally, we found that the THM/PCE exposed males develop autistic like behavioral pathology as they evidence deficits in communication and social behavior and demonstrate both perseverance behavior and anxiety. Again, this finding is gender specific, as female behavior is unaffected by THM/PCE exposure. These findings suggest that these chemicals may be involved in the etiology of autism and that males are more susceptible to this set of insults.

  • SYSTEMATICS AND HISTORICAL BIOGEOGRAPHY OF AGKISTRODON CONTORTRIX AND AGKISTRODON PISCIVORUS

    Author:
    Timothy Guiher
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Frank Burbrink
    Abstract:

    Many studies have revealed that lineages currently inhabiting formerly glaciated areas were pushed into southern glacial refugia and have expanded into their modern range since the last glacial maximum. There have been few studies that compare the effects of glacial cycles on lineage diversification, historical demography and migration rates in closely related species with overlapping ranges. In this study I compare phylogeographic structure, historical demography, approximate lineage age, potential distributions, and migration rates in two closely related and broadly co-occurring venomous snakes in eastern North America, the cottonmouth (Agkistrodon piscivorus) and copperhead (A. contortrix) using multilocus coalescent approaches. It has recently been discovered that gene flow between closely related species with adjacent distributions may be common (Nosil 2008). However, the absence of gene flow is a primary assumption of many phylogeographic methods including species tree inference and Bayesian species delimitation. I provide a framework for examining species delimitation when gene flow between species is present and provide a taxonomic revision of A. contortrix and A. piscivorus. In addition, I explore whether hybrids between adjacent species inhabit unique environmental conditions not suitable to one or both species. Finally, I reveal that species diversification was likely a direct result of Pleistocene glacial cycles and that species with the closest proximity to formerly glaciated areas experienced population expansion following the retreat of the Laurentide Ice Sheet. A combination of population expansion out of refugia and niche expansion has resulted in hybridization between adjacent species where species distributions come into contact. It is not clear whether gene flow has persisted during speciation and subsequent interglacial periods or if it has only recently occurred following the last glacial maximum.

  • SYSTEMATICS AND HISTORICAL BIOGEOGRAPHY OF AGKISTRODON CONTORTRIX AND AGKISTRODON PISCIVORUS

    Author:
    Timothy Guiher
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Frank Burbrink
    Abstract:

    Many studies have revealed that lineages currently inhabiting formerly glaciated areas were pushed into southern glacial refugia and have expanded into their modern range since the last glacial maximum. There have been few studies that compare the effects of glacial cycles on lineage diversification, historical demography and migration rates in closely related species with overlapping ranges. In this study I compare phylogeographic structure, historical demography, approximate lineage age, potential distributions, and migration rates in two closely related and broadly co-occurring venomous snakes in eastern North America, the cottonmouth (Agkistrodon piscivorus) and copperhead (A. contortrix) using multilocus coalescent approaches. It has recently been discovered that gene flow between closely related species with adjacent distributions may be common (Nosil 2008). However, the absence of gene flow is a primary assumption of many phylogeographic methods including species tree inference and Bayesian species delimitation. I provide a framework for examining species delimitation when gene flow between species is present and provide a taxonomic revision of A. contortrix and A. piscivorus. In addition, I explore whether hybrids between adjacent species inhabit unique environmental conditions not suitable to one or both species. Finally, I reveal that species diversification was likely a direct result of Pleistocene glacial cycles and that species with the closest proximity to formerly glaciated areas experienced population expansion following the retreat of the Laurentide Ice Sheet. A combination of population expansion out of refugia and niche expansion has resulted in hybridization between adjacent species where species distributions come into contact. It is not clear whether gene flow has persisted during speciation and subsequent interglacial periods or if it has only recently occurred following the last glacial maximum.

  • PHYLOGENETICS AND BIOGEOGRAPHY OF MOUSE OPOSSUMS (DIDELPHIDAE: MARMOSA)

    Author:
    ELIECER GUTIERREZ
    Year of Dissertation:
    2012
    Program:
    Biology
    Advisor:
    Robert Anderson
    Abstract:

    This research focused on the systematics and biogeography of mouse opossums of the genus Marmosa (Mammalia: Didelphimorphia: Didelphidae), with special emphasis on species found in the complicated geography of north-central South America. Via the four chapters of this dissertation, I presented information obtained through fieldwork, examination of museum specimens, DNA sequencing, phylogenetic analyses, georeferencing (including consultation of field notes and collectors), and ecological niche modeling. In Chapter 1, I conducted phylogenetic analyses of species of Marmosa based on sequence data of the mitochondrial cytochrome-b gene (CYTB), in part to test the monophyly of species previously recognized based on morphological criteria. This study revealed the existence of unrecognized species and identified novel interspecific relationships. All trans-Andean species of the subgenus Marmosa were recovered as a clade, suggesting that the uplift of the Andes might have played an important role in the diversification of the genus. In Chapter 2, I documented the presence of M. waterhousei in the Venezuelan Andes. This finding implied that the species might have crossed the dry Depresión del Táchira during a glacial period. In Chapter 3, I investigated the phylogeography of M. robinsoni, a species predominately distributed across the dry forests of northern South America. I conducted phylogenetic analyses based on sequence data of one mitochondrial and one nuclear gene. The results confirmed the monophyly of a dry-forest clade formed by M. robinsoni and M. xerophila and showed the existence of two major clades within M. robinsoni that corresponded roughly to an east/west division. Results of ancestral area reconstructions identified multiple dispersal events out of the greater Maracaibo basin. Lastly, in Chapter 4 I used ecological niche modeling to test the geographic predictions of competition between a sister species pair, M. robinsoni and M. xerophila. The results strongly suggest that M. xerophila may isolate populations of M. robinsoni in the Península de Paraguaná of northern Venezuela--representing a novel example of geographic isolation caused by competition. Together, these studies contributed to a better understanding of the taxonomy, phylogenetics, and biogeography of the genus Marmosa; provide novel information relevant to the biogeography of dry-forest species in northwestern South America; and propose a refinement of the concept of ecological vicariance to incorporate the possibility that biotic interactions could lead to geographic isolation.

  • Evolutionary Analyses on the Core Genome of Borrelia burgdorferi: Elucidating the Genomics of Virulence

    Author:
    James Haven
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Weigang Qiu
    Abstract:

    ABSTRACT: Adaptive Evolution in Borrelia burgdorferi by: James Haven Advisor: Dr. Weigang Qiu The availability of multiple genomes of closely related pathogen strains makes it possible to identify genome-wide variations associated with strain-specific phenotypes such as pathogenicity and virulence. One main challenge of gene-trait associative mapping in bacterial species is finding a way to minimize the effect of linkage among loci due to pervasive clonal population structures. A second concern is to distinguish selective sequence variations from random, selectively neutral differences among strains. Here we identified adaptive, strain-specific nucleotide polymorphisms (SSNPs) on the core genome of Borrelia burgdorferi, the Lyme disease pathogen. We minimized the linkage effect by comparing the genomes of seven isolates representing four genospecies (B. burgdorferi sensu stricto, B. bissettii, B. afzelii, and B. garinii) and four clonal groups of a single species (A, C, E, and K clones of B. burgdorferi sensu stricto). Identification of selective nucleotide polymorphisms was achieved by applying codon-based, tests of positive selection based on rates of synonymous (KS) and nonsynonymous (KA) substitutions. We then tested for the presence of positive selection at 824 gene loci on the main chromosome, 68 loci on the linear plasmid lp54, and 26 loci on the circular plasmid cp26. Consequently, we identified 28 genes under positive selection without regard for lineage, 12 genes associated with genospecies divergence, and 7 genes associated with the adaptive divergence of B31, a highly invasive strain. We checked results by excluding loci with high alignment uncertainties, mapping positively selected sites on protein structure models, and evaluating the possibility of false positives. Cell envelope genes are significantly over-represented among the positively selected genes. Additional categories of interest are DNA metabolism, transcription, cell division, and regulation. Focused analyses on copy number variation of established immune elicitors and a survey of intraspecific recombination support a prominent role for adaptive evolution in the maintenance of the B. burgdorferi pathogen cycle. These findings highlight immune escape as a driver of positive natural selection via surface protein variation and possibly pathogen replication dynamics.