Alumni Dissertations and Theses

 
 

Alumni Dissertations and Theses

Filter Dissertations and Theses By:

 
 
  • Functional Genomics of Cell Wall Biogenesis in Fungi

    Author:
    Edimarlyn Gonzalez
    Year of Dissertation:
    2009
    Program:
    Biology
    Advisor:
    Peter Lipke
    Abstract:

    In pathogenic fungi, glycosylphosphatidyl inositol cell wall proteins (GPI-CWPs) mediate adhesion of the fungus to a host during infection -a step that is necessary for the fungus to be able to initiate and establish infection. Genes involved in the biosynthetic pathway that incorporate GPI-CWPs to the wall thus represent excellent targets for antifungal drug design. A mechanistically-based genomic screen was developed and applied to search for genes involved in fungal cell wall biogenesis. Specifically, the screen identifies genes required for the cross-linking of glycoproteins (GPI-CWPs) to cell wall polysaccharides via GPI anchors. GPI-CWPs are the most abundant class of proteins at the wall and play both structural and biosynthetic functions. The rationale for the screening assay was that cells unable to properly cross-link GPI-CWPs to the wall would either retain a GPI-CWP reporter protein within the cell (hypo-excretors) or excrete the reporter protein into the growth medium (hyper-excretors), relative to wild type cells. This idea was validated in cell wall mutants known to hyper-excrete GPI-CWPs. To screen for the hypo- and hyper-excretion phenotypes, a GPI-CWP-marker protein was made by fusing the green fluorescent protein (GFP) to the carboxyl end of the GPI-CWP α-agglutinin. The marker protein was expressed in 178 gene deletants missing genes previously implicated in cell wall biogenesis and in corresponding wild type parental strains. Strains expressing the reporter protein were examined for deficiencies in anchoring the marker protein to the wall. The screen used conditions that facilitated sample processing at large-scale and enhanced marker protein yields while minimizing noise in marker protein expression. These conditions required expression of the reporter protein from the constitutive S. cerevisiae GPD1 promoter at lower temperature than the standard 30 0C in the presence of 1 M sorbitol, and growth of the cell cultures to similar cell concentrations in medium buffered to pH 6.5. Sample analysis at large scale was possible by growing the cells as 3 ml cultures in glass test tubes from which OD measurements were taken directly. Microliter volumes of cell-free supernatants were evaluated for GFP levels using a 96-well plate reader fluorimeter. Interesting mutants were subjected to secondary screens using anti-GFP antibodies and by collecting complete fluorescence spectra. The strains were also analyzed for cell surface fluorescence and levels of cytosolic and total protein in the culture medium. Deletions in MCD4, GPI13, TDH3 and GDA1 caused hyper-excretion of the reporter protein. MCD4 and GPI13 are essential genes that play a role in GPI-anchor biosynthesis, GDA1 is involved in GPI-CWP O-glycosylation and TDH3 is a glycolytic enzyme that resides at the cell wall and has been implicated in mediating adhesion of fungal cells to host surfaces. The genomic screen was performed without the use of pepstatin A, which was found to inhibit GFP degradation by extracellular protease activity and thus to enhance the sensitivity of the screening assay without affecting cell growth and viability. Identified mutants thus hyper-excrete large enough amounts of the GPI-CWP reporter protein to allow detection of the hyper-excretion phenotype even in the presence of GFP proteolysis. Deletion of the transglycosidases Dcwp1 and Dfg5p, suspected of playing a direct role in cross-linking GPI-CWPs to the cell wall, hyper-excreted the reporter protein when grown in the presence of pepstatin A. Gene deletants subjected to secondary screens exhibited 1.5-2.0 fold less fluorescence at the wall than wild type cells except for MCD4/mcd4 and GPI13/gpi13 cells which hyper-express the marker protein at the wall 2-4-fold relative to wild type cells. This increase may be in compensation for the high failure rate of adding the GPI-anchor to GPI-CWPs precursors. All strains examined showed less than wild type levels of the cytosolic marker, 3-phosphoglycerate kinase (PGK) and wild type levels of total protein in cell-free supernatants.

  • HOW IMPORTANT IS LAND-BASED FORAGING TO POLAR BEARS (URSUS MARITIMUS) DURING THE ICE-FREE SEASON IN WESTERN HUDSON BAY? AN EXAMINATION OF DIETARY SHIFTS, COMPOSITIONAL PATTERNS, BEHAVIORAL OBSERVATIONS AND ENERGETIC CONTRIBUTIONS.

    Author:
    Linda Gormezano
    Year of Dissertation:
    2014
    Program:
    Biology
    Advisor:
    Robert Rockwell
    Abstract:

    Trophic mismatches between predators and their prey are increasing as climate change causes decoupling of phenological relationships. Predators linked to the life histories of a particular prey will have a more difficult time persisting through environmental change unless they can alter their behavior to maintain the historical match or possess the ability to pursue alternate prey. Arctic predators typically possess flexible foraging strategies to survive in the labile environment, however, quantifying the limits of those strategies can be difficult when life history information is incomplete. In such cases, piecing together different aspects of a predator's foraging behavior, particularly when environmental effects are thought to induce the most nutritional stress, can serve as a basis to understand the species' resiliency in response to climate changes. Climate change is impacting the Hudson Bay region faster than any other portion of Arctic North America. As a consequence, polar bears (Ursus maritimus) in western Hudson Bay, near the southern extent of their range, are already experiencing a phenological mismatch with their primary prey, ringed seals (Phoca hispida). These polar bears have relied on the energy stores amassed from hunting seal pups in spring to sustain them through the ice-free season on land for 4 to 5 months. As climate change causes the ice in Hudson Bay to melt earlier in spring, polar bears are projected to have less time to hunt seal pups on the sea ice, leaving them with smaller energy reserves to sustain them for longer periods on land. As a result, body condition is expected to deteriorate, leading to eventual declines in reproduction and survival, unless alternative energy sources are utilized. Polar bears currently hunt and consume a variety of foods during the ice-free season. Few believe, however, that such foraging will compensate for projected energy deficits from lost seal hunting opportunities. This skepticism stems from the perceptions that polar bears are specially adapted to hunting seals on the ice, the behavior has always occurred, but only a few polar bears partake in it, breath-based carbon-isotope analyses suggest that energy expended on land is solely of marine (i.e., seal) origin, pursuing animals on land would be too energetically expensive for polar bears to experience any net gain and there is not enough energy in land-based food to compensate all polar bears in western Hudson Bay for the energy available from seals on the ice. Many of these arguments are premised on the idea that past (and even present) foraging behaviors are representative of how polar bears will respond to future climate-related changes. Alternatively, the past behaviors may have represented optimal foraging strategies when seals were relatively abundant and easy to catch. Rather than tie the polar bears' fate directly to deteriorating ice conditions and thus availability of a single prey, I consider a more mechanistic approach to evaluating polar bears' reaction to climate changes. In light of the shared genetic legacy with grizzly bears, I analyze different aspects of polar bears' current foraging behavior, as well as known physiological and energetic constraints, to consider an alternative future scenario by which polar bears might persist consuming land-based food during the ice-free season. I explore different aspects of land-based foraging and address aforementioned concerns regarding the potential value of terrestrial foods in a series of interrelated chapters. In the first chapter, I develop a comprehensive inventory of foods polar bears currently consume on land and compare them to those consumed approximately 40 years earlier, prior to the onset of climate changes, using morphological scat analysis. Changes in the polar bear diet between time periods are compared to changes in availability of specific prey items in the region (Chapter 1) as well as where and when they currently occur most abundantly in the landscape (Chapter 2). Based on compositional patterns, I explore the extent of diet mixing and its implications for weight gain (or rate of weight loss, Chapter 2). In addition to long-term changes in abundance that have made Lesser Snow Geese (Chen caerulescens caerulescens) more available since the 1960s, temporal shifts in their incubation period and earlier ice-breakup is creating a new trophic match between arriving polar bears and eggs. The potential energy available from this increasingly accessible resource and its implications for energy compensation are discussed in Chapter 3. In Chapter 4, I provide total energy values for populations of novel animal foods (snow geese, eggs, caribou (Rangifer tarandus) and vegetation (berries, Lyme grass seed heads (Leymus arenarius) that polar bears consume on land and determine what amounts of each, alone or in combination, would prevent adult males from starving to death as the ice-free season expands to a 180 days as predicted by Molnár et al. (2010). In Chapter 5, I reexamine available data on the energetic costs of locomotion at different speeds, develop a new predictive model and challenge past assertions by Lunn and Stirling (1985) that energetic inefficiencies would prevent a polar bear from profiting after a sustained chase. In Chapter 6, I present unpublished observations of polar bears foraging from land and in open water from the Hudson Bay Project archives and my personal observations. I describe different evolutionary pathways for the observed behavior in light of their recent divergence from grizzly bears and the implications of each for future polar bear persistence.

  • MyTH4 and FERM Have Overlapping and Distinct Roles in the Function of Myo1, a Class XIV Myosin in Tetrahymena thermophila

    Author:
    Michael Gotesman
    Year of Dissertation:
    2011
    Program:
    Biology
    Advisor:
    Ray Gavin
    Abstract:

    MyTH4 and FERM are conserved tail domains in myosin classes VII, X, XII, XIV, XV and in MyoG. Myo1, a class XIV myosin in Tetrahymena thermophila, contains MyTH4 and FERM. Previous studies have shown that Myo1 localizes to phagosomes, the cytoskeleton, and the macronucleus, and that phagosome trafficking and division of the macronucleus are affected in a MYO1 knockout. To investigate the roles for MyTH4 and FERM in the function of Myo1, GFP-tagged MyTH4, FERM, and truncated FERM were separately overexpressed in Tetrahymena. Actin antibody coprecipitated tubulin, GFP-MyTH4, and GFP-FERM. GFP-MyTH4 and GFP-FERM cosedimented with either exogenous microtubules or exogenous F-actin. GFP-MyTH4 localized to phagosomes and colocalized with antitubulin to intranuclear microtubules. Overexpression of GFP-MyTH4 inhibited the organization of the parallel array of intranuclear microtubules that form prior to division of the macronucleus. Cells that failed to form the parallel array of microtubules did not advance in nuclear division. Overexpression of GFP-MyTH4 did not affect phagosome recycling. Overexpressed GFP-FERM localized to phagosomes, cytoskeleton, and intranuclear puncta and did not affect division of the macronucleus. Overexpression of truncated GFP-FERM did not localize to the cytoskeleton or nucleus and led to the accumulation of phagosomes at the membrane recycling site in the posterior of the cell. It is unlikely that the overexpression phenotypes are nonspecific effects of GFP. Localization of GFP-fusions is consistent with the localization of full-length Myo1, and overexpression phenotypes mimic the knockout phenotype. Furthermore, GFP-MyTH4 from Myo9, another Tetrahymena myosin, did not localize in Tetrahymena thermophila. We conclude that MyTH4 and FERM have overlapping roles as indicated by the interaction with actin and tubulin. However, MyTH4 and FERM appear to have distinct roles in the function of Myo1. MyTH4 affects the organization of microtubules involved in macronuclear division, whereas FERM affects recycling of phagosomes and is required for localization to the cytoskeleton.

  • 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.

  • 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.