Alumni Dissertations

 

Alumni Dissertations

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  • Evolution of Song Culture in the Zebra Finch

    Author:
    Olga Feher
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Ofer Tchernichovski
    Abstract:

    Cumulative cultural evolution is when behavior in subsequent generations of learners builds on the accumulated information of previous generations to such an extent that no individual learner can produce the behavior on its own. Many examples exist in humans, but in nonhuman animals there are only a handful of suspected cases. Here, we provide the first demonstration of cumulative cultural evolution in the laboratory in nonhuman animals. We raised zebra finches in complete acoustic and social isolation to create "uncultured" animals. Isolate zebra finches sing unstructured songs that are different from wild-type songs in many aspects such as spectral details of syllables and syntactic organization. We developed an automated procedure to quantify the differences between isolate and wild-type song at different timescales of song structure: spectral features, duration of sounds, and song rhythm. We then used the isolate birds to teach their songs to juveniles who became the tutors for the next generations of learners and so on recursively. We followed the evolution of isolate song over multiple generations. We found that isolate song was gradually transforming into wild-type song over 3-4 learning generations. In addition to this experiment where we trained young birds in individual tutor-pupil pairs, we established a semi-natural colony with an isolate founder and tracked song changes over multiple generations of learners. In the colony, the song also progressed towards wild-type song in a few generations, but some of the details of the changes differed between the two conditions. The rapid evolution indicates that wild-type song culture is encoded in every bird, but it takes multiple generations to surface. The young birds used imitation biases to change isolate song features into wild-type features.

  • Evolution of Song Culture in the Zebra Finch

    Author:
    Olga Feher
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Ofer Tchernichovski
    Abstract:

    Cumulative cultural evolution is when behavior in subsequent generations of learners builds on the accumulated information of previous generations to such an extent that no individual learner can produce the behavior on its own. Many examples exist in humans, but in nonhuman animals there are only a handful of suspected cases. Here, we provide the first demonstration of cumulative cultural evolution in the laboratory in nonhuman animals. We raised zebra finches in complete acoustic and social isolation to create "uncultured" animals. Isolate zebra finches sing unstructured songs that are different from wild-type songs in many aspects such as spectral details of syllables and syntactic organization. We developed an automated procedure to quantify the differences between isolate and wild-type song at different timescales of song structure: spectral features, duration of sounds, and song rhythm. We then used the isolate birds to teach their songs to juveniles who became the tutors for the next generations of learners and so on recursively. We followed the evolution of isolate song over multiple generations. We found that isolate song was gradually transforming into wild-type song over 3-4 learning generations. In addition to this experiment where we trained young birds in individual tutor-pupil pairs, we established a semi-natural colony with an isolate founder and tracked song changes over multiple generations of learners. In the colony, the song also progressed towards wild-type song in a few generations, but some of the details of the changes differed between the two conditions. The rapid evolution indicates that wild-type song culture is encoded in every bird, but it takes multiple generations to surface. The young birds used imitation biases to change isolate song features into wild-type features.

  • C. elegans ADAMTS ADT-2 regulates body size and cuticle collagen organization

    Author:
    Thilini Fernando
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Cathy Savage-Dunn
    Abstract:

    The regulation of body size is a fundamental feature of animals critical to their survival and fitness, yet its underlying mechanisms remain poorly understood. In C. elegans, the DBL-1 signaling pathway plays a major role in growth control. The mechanisms by which other pathways regulate body size function, however, are less well understood. To identify additional genes involved in body size regulation, a genetic screen for small mutants was previously performed. One of the genes identified in that screen was sma 21. I now demonstrate that sma 21 encodes ADT-2, a member of the ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) family of secreted metalloproteases. ADAMTS proteins are believed to remodel the extracellular matrix (ECM) and may modulate the activity of extracellular signals. Genetic interactions suggest that ADT-2 acts in parallel with known size regulatory pathways. I further demonstrate that ADT-2 activity is required for normal cuticle collagen fibril organization and adt-2 regulatory sequences drive expression in glial-like cells. ADT-2::GFP fusion protein is localized in the alae and the annuli of the cuticle. We therefore show that ADT-2 is secreted into the cuticle where it may act to proteolytically process secreted collagen or other ECM molecules required for normal cuticle structure and body size.

  • C. elegans ADAMTS ADT-2 regulates body size and cuticle collagen organization

    Author:
    Thilini Fernando
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Cathy Savage-Dunn
    Abstract:

    The regulation of body size is a fundamental feature of animals critical to their survival and fitness, yet its underlying mechanisms remain poorly understood. In C. elegans, the DBL-1 signaling pathway plays a major role in growth control. The mechanisms by which other pathways regulate body size function, however, are less well understood. To identify additional genes involved in body size regulation, a genetic screen for small mutants was previously performed. One of the genes identified in that screen was sma 21. I now demonstrate that sma 21 encodes ADT-2, a member of the ADAMTS (a disintegrin and metalloprotease with thrombospondin motifs) family of secreted metalloproteases. ADAMTS proteins are believed to remodel the extracellular matrix (ECM) and may modulate the activity of extracellular signals. Genetic interactions suggest that ADT-2 acts in parallel with known size regulatory pathways. I further demonstrate that ADT-2 activity is required for normal cuticle collagen fibril organization and adt-2 regulatory sequences drive expression in glial-like cells. ADT-2::GFP fusion protein is localized in the alae and the annuli of the cuticle. We therefore show that ADT-2 is secreted into the cuticle where it may act to proteolytically process secreted collagen or other ECM molecules required for normal cuticle structure and body size.

  • The effects of chronic habitat degradation on the physiology and metal accumulation of eastern oysters (Crassostrea virginica) in the Hudson Raritan Estuary

    Author:
    Allison Fitzgerald
    Year of Dissertation:
    2013
    Program:
    Biology
    Advisor:
    William Wallace
    Abstract:

    The Hudson Raritan Estuary (HRE) was once home an abundant population of the eastern oyster, Crassostrea virginica. Years of habitat degradation, via removal of habitat and shell substrate, overfishing of the population, and inputs of organic and inorganic contaminants, all led to the decline of this previous keystone species. The HRE today is a highly eutrophic environment, with increased sediment inputs, periods of low dissolved oxygen, algal blooms, and hotspots of contaminants throughout. The current study was designed to understand how a chronically degraded habitat, as is present in the HRE now, affects both juvenile and adult oyster physiology. There are three parts to this study: in the first, a large scale field transplant study was deployed to determine how juvenile oyster health and subcellular physiology are altered over a continuum of sites across the HRE, and if subcellular metal accumulation related to alterations in physiology. Using eight sites across the HRE, it was apparent that there are many site-specific factors that affect oyster physiology, and the synergistic effects of these abiotic and biotic factors together influence oyster physiology the most. There was no one factor that could be isolated as a key parameter to determine future oyster restoration. The second part used a field transplant study to examine the role of a degraded habitat on adult oysters and reproduction. Using Vitellogenin protein and energy expenditures to estimate oyster reproduction, it was seen that adult oysters respond much slower than juveniles and no differences were seen between highly degraded habitats and less degraded habitats. Thirdly, both juveniles and adults were observed to accumulate non-essential metals (Cd and Hg) in the field. In order to determine if metal accumulation is the sole cause of physiological alterations, a laboratory exposure was designed to determine if changes in subcellular physiology could be correlated specifically to subcellular accumulation of Cd or Hg, when no other abiotic factors are able to influence oyster health. It was observed that Cd accumulation lead to physiological changes, but Hg accumulation did not. Using this information about the site-specific nature of oyster physiology and how metal accumulation can alter physiology will allow researchers to choose future restoration sites and set up projects that will allow for maximum growth and survival.

  • EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS

    Author:
    Frank Fontanella
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Mark Siddall
    Abstract:

    EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS ADVISER: Dr. Mark E. Siddall The monotypic snake genus Diadophis Baird and Girard, 1853 is one of the most widely distributed and morphologically variable snakes throughout North America. This snake (Diadophis punctatus) exploits a variety of habitats and ecological niches ranging from the mixed hardwood forests of southern Canada to the desert of the Southwestern US and Central Mexico (excluding the northern Great Plains states. Ringneck snakes have traditionally been divided into 13 subspecies based on a combination of morphology and geography. This study has provided the first range-wide molecular study and provides a framework for the origin, evolution and biodiversity in the genus Diadophis. Analysis of mtDNA sequence data inferred 16 mtDNA lineages that replace each other geographically across the United States and into central Mexico. In contrast to previous hypothesis, ancestral area reconstructions inferred an origin for D. punctatus in the southeastern United States during the Miocene, followed by a southeast to northeast then westward directionality of historical migration. Demographic analyses indicate that independent lineages currently occupying previously glaciated or unsuitable areas in eastern, central and western U.S. underwent post-glacial population expansion likely from southern refugia during the late Pleistocene/early Holocene. Conversely, southern lineages display patterns consistent with long-term population stability. For the purposes of species delineation, ecological niche modeling does not show isolation due to unsuitable habitat. Ten novel microsatellite loci developed for this study suggest that most species boundaries are maintained through a balance of selection and dispersal in hybrid zones. Based on the geographic distribution of the mtDNA lineages and the microsatellite frequency data, we hypothesize that there are eight species within the genus Diadophis throughout the Eastern United States. This body of work provides a rich framework for further study including, examining species boundaries in the western lineages, determining population structure within species, and detailed examination of hybrid zones.

  • EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS

    Author:
    Frank Fontanella
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Mark Siddall
    Abstract:

    EVOLUTION, PHYLOGEOGRAPHY AND SPECIES BOUNDARIES OF THE RINGNECK SNAKE GENUS DIADOPHIS ADVISER: Dr. Mark E. Siddall The monotypic snake genus Diadophis Baird and Girard, 1853 is one of the most widely distributed and morphologically variable snakes throughout North America. This snake (Diadophis punctatus) exploits a variety of habitats and ecological niches ranging from the mixed hardwood forests of southern Canada to the desert of the Southwestern US and Central Mexico (excluding the northern Great Plains states. Ringneck snakes have traditionally been divided into 13 subspecies based on a combination of morphology and geography. This study has provided the first range-wide molecular study and provides a framework for the origin, evolution and biodiversity in the genus Diadophis. Analysis of mtDNA sequence data inferred 16 mtDNA lineages that replace each other geographically across the United States and into central Mexico. In contrast to previous hypothesis, ancestral area reconstructions inferred an origin for D. punctatus in the southeastern United States during the Miocene, followed by a southeast to northeast then westward directionality of historical migration. Demographic analyses indicate that independent lineages currently occupying previously glaciated or unsuitable areas in eastern, central and western U.S. underwent post-glacial population expansion likely from southern refugia during the late Pleistocene/early Holocene. Conversely, southern lineages display patterns consistent with long-term population stability. For the purposes of species delineation, ecological niche modeling does not show isolation due to unsuitable habitat. Ten novel microsatellite loci developed for this study suggest that most species boundaries are maintained through a balance of selection and dispersal in hybrid zones. Based on the geographic distribution of the mtDNA lineages and the microsatellite frequency data, we hypothesize that there are eight species within the genus Diadophis throughout the Eastern United States. This body of work provides a rich framework for further study including, examining species boundaries in the western lineages, determining population structure within species, and detailed examination of hybrid zones.

  • Phylogenetics, biogeography and co-adaptation between a Batesian model (Micrurus fulvius) and mimic (Lampropeltis triangulum)

    Author:
    Michael Friedman
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Rob DeSalle
    Abstract:

    The coral snake, Micrurus fulvius (Elapidae), and the scarlet king snake, Lampropeltis triangulum (Colubridae), members of a Batesian mimicry complex in the southeastern and southern United States were subjects of a study of model-mimic co-evolution. Inferring co-evolution required discovery of distinct terminals within each group, for posterior phylogenetic inference and analysis of co-variation of color patterns among sympatric populations of each species. In addition, haplotype and population differentiation were assessed. Also, hypotheses regarding selection on color patterns were tested. The latter included model-mimic tracking, environmental effects and frequency dependence of mimetic color pattern variation. Population Aggregation Analysis failed to diagnose terminals for either group. Haplotype and population genetic analyses showed both groups to be largely panmictic, with some north/south differentiation. Morphometric analyses of means and variations in proportions of color pattern components failed to reveal geographic tracking by mimics of models, but manifested possible independent geographic or environmental effects on each of the species. Frequency-dependent selection was falsified for color pattern variation in mimics.

  • Phylogenetics, biogeography and co-adaptation between a Batesian model (Micrurus fulvius) and mimic (Lampropeltis triangulum)

    Author:
    Michael Friedman
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Rob DeSalle
    Abstract:

    The coral snake, Micrurus fulvius (Elapidae), and the scarlet king snake, Lampropeltis triangulum (Colubridae), members of a Batesian mimicry complex in the southeastern and southern United States were subjects of a study of model-mimic co-evolution. Inferring co-evolution required discovery of distinct terminals within each group, for posterior phylogenetic inference and analysis of co-variation of color patterns among sympatric populations of each species. In addition, haplotype and population differentiation were assessed. Also, hypotheses regarding selection on color patterns were tested. The latter included model-mimic tracking, environmental effects and frequency dependence of mimetic color pattern variation. Population Aggregation Analysis failed to diagnose terminals for either group. Haplotype and population genetic analyses showed both groups to be largely panmictic, with some north/south differentiation. Morphometric analyses of means and variations in proportions of color pattern components failed to reveal geographic tracking by mimics of models, but manifested possible independent geographic or environmental effects on each of the species. Frequency-dependent selection was falsified for color pattern variation in mimics.

  • Islet-brain-2: a novel postsynaptic density protein linked to an autism spectrum disorder

    Author:
    Joanna Giza
    Year of Dissertation:
    2010
    Program:
    Biology
    Advisor:
    Mitchell Goldfarb
    Abstract:

    Islet-brain-2 (IB2) is a neuronal protein, whose functions are not well understood. Based upon its sequence homology to JNK-interacting protein 1 (JIP1) and biochemical studies, IB2 has been described as a putative scaffold for mitogen activated protein kinase (MAPK) signaling. IB2 has been documented to interact with a wide array of functionally unrelated proteins, which has complicated efforts to confirm its biochemical role in vivo. In order to investigate the IB2 function in the nervous system, we have generated Ib2 null mice. The mutants are viable and their expression of genes neighboring Ib2 is unaffected. Ib2 knockout mice display developmental delay in grip strength until 5 weeks (P35) of age. Their behavioral analysis following disappearance of this defect shows significant deficits in their motor learning abilities. In addition, mutant mice exhibit marked reduction in social interactions, delayed fear induced learning and unresponsiveness to the environment in various behavioral tasks. These complex atypical behaviors are reminiscent of autism spectrum disorders (ASDs). Interestingly, the human Ib2 gene resides within the deleted chr22qter region in Phelan-McDermid syndrome and patients with this disorder manifest similar deficits as observed in our Ib2 null mice, suggesting that Ib2 loss-of-function is a promising candidate model for this disorder. Recent developments in the ASDs field implicate as a major culprit defective synaptic function. Using brain fractionation and co-immunoprecipitation methods, we show that IB2 is an integral component of the postsynaptic density (PSD). Immunofluorescence shows IB2 concentrated within dendritic spine heads. Ib2 mutation did not alter expression levels of many other common PSD components such as PSD95 and AMPA-type and NMDA-type receptors subunits. Signaling analyses conducted in Ib2 null cultured cortical neurons failed to reveal deficits in NMDA-evoked signaling through known IB2-interacting partners TIAM1 and p38MAPK, suggesting that IB2 modulates synaptic and behavioral functions through as yet unknown molecular mechanisms.