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- All Subjects: Genetics
- Genre: Academic theses
- Creators: Liu, Li
- Creators: Pratt, Stephen
- Member of: ASU Electronic Theses and Dissertations
- Resource Type: Text
Description
How a colony regulates the division of labor to forage for nutritional resources while accommodating for changes in colony demography is a fundamental question in the sociobiology of social insects. In honey bee, Apis mellifera, brood composition impacts the division of labor, but it is unknown if colonies adjust the allocation of foragers to carbohydrate and protein resources based on changes in the age demography of larvae and the pheromones they produce. Young and old larvae produce pheromones that differ in composition and volatility. In turn, nurses differentially provision larvae, feeding developing young worker larvae a surplus diet that is more queen-like in protein composition and food availability, while old larvae receive a diet that mimics the sugar composition of the queen larval diet but is restrictively fed instead of provided ad lib. This research investigated how larval age and the larval pheromone e-β ocimene (eβ) impact foraging activity and foraging load. Additional cage studies were conducted to determine if eβ interacts synergistically with queen mandibular pheromone (QMP) to suppress ovary activation and prime worker physiology for nursing behavior. Lastly, the priming effects of larval age and eβ on worker physiology and the transition from in-hive nursing tasks to outside foraging were examined. Results indicate that workers differentially respond to larvae of different ages, likely by detecting changes in the composition of the pheromones they emit. This resulted in adjustments to the foraging division of labor (pollen vs. nectar) to ensure that the nutritional needs of the colony's brood were met. For younger larvae and eβ, this resulted in a bias favoring pollen collection. The cage studies reveal that both eβ and QMP suppressed ovary activation, but the larval pheromone was more effective. Maturing in an environment of young or old larvae primed bees for nursing and impacted important endocrine titers involved in the transition to foraging, so bees maturing in the presence of larvae foraged earlier than control bees reared with no brood.
ContributorsTraynor, Kirsten S. (Author) / Page, Robert E. (Thesis advisor) / Hölldobler, Berthold (Committee member) / Pratt, Stephen (Committee member) / Liebig, Jürgen (Committee member) / Brent, Colin (Committee member) / Baluch, Page (Committee member) / Arizona State University (Publisher)
Created2014
Description
Gene-centric theories of evolution by natural selection have been popularized and remain generally accepted in both scientific and public paradigms. While gene-centrism is certainly parsimonious, its explanations fall short of describing two patterns of evolutionary and social phenomena: the evolution of sex and the evolution of social altruism. I review and analyze current theories on the evolution of sex. I then introduce the conflict presented to gene-centric evolution by social phenomena such as altruism and caste sterility in eusocial insects. I review gene-centric models of inclusive fitness and kin selection proposed by Hamilton and Maynard Smith. Based their assumptions, that relatedness should be equal between sterile workers and reproductives, I present several empirical examples that conflict with their models. Following that, I introduce a unique system of genetic caste determination (GCD) observed in hybrid populations of two sister-species of seed harvester ants, Pogonomyrmex rugosus and Pogonomyrmex barbatus. I review the evidence for GCD in those species, followed by a critique of the current gene-centric models used to explain it. In chapter two I present my own theoretical model that is both simple and extricable in nature to explain the origin, evolution, and maintenance of GCD in Pogonomyrmex. Furthermore, I use that model to fill in the gaps left behind by the contributing authors of the other GCD models. As both populations in my study system formed from inter-specific hybridization, I review modern discussions of heterosis (also called hybrid vigor) and use those to help explain the ecological competitiveness of GCD. I empirically address the inbreeding depression the lineages of GCD must overcome in order to remain ecologically stable, demonstrating that as a result of their unique system of caste determination, GCD lineages have elevated recombination frequencies. I summarize and conclude with an argument for why GCD evolved under selective mechanisms which cannot be considered gene-centric, providing evidence that natural selection can effectively operate on non-heritable genotypes appearing in groups and other social contexts.
ContributorsJacobson, Neal (Author) / Gadau, Juergen (Thesis advisor) / Laubichler, Manfred (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2012
Description
Childhood Apraxia of Speech (CAS) is a severe motor speech disorder that is difficult to diagnose as there is currently no gold-standard measurement to differentiate between CAS and other speech disorders. In the present study, we investigate underlying biomarkers associated with CAS in addition to enhanced phenotyping through behavioral testing. Cortical electrophysiological measures were utilized to investigate differences in neural activation in response to native and non-native vowel contrasts between children with CAS and typically developing peers. Genetic analysis included full exome sequencing of a child with CAS and his unaffected parents in order to uncover underlying genetic variation that may be causal to the child’s severely impaired speech and language. Enhanced phenotyping was completed through extensive behavioral testing, including speech, language, reading, spelling, phonological awareness, gross/fine motor, and oral and hand motor tasks. Results from cortical electrophysiological measures are consistent with previous evidence of a heightened neural response to non-native sounds in CAS, potentially indicating over specified phonological representations in this population. Results of exome sequencing suggest multiple genetic variations contributing to the severely affected phenotype in the child and provide further evidence of heterogeneous genomic pathways associated with CAS. Finally, results of behavioral testing demonstrate significant impairments evident across tasks in CAS, suggesting underlying sequential processing deficits in multiple domains. Overall, these results have the potential to delineate functional pathways from genetic variations to the brain to observable behavioral phenotypes and motivate the development of preventative and targeted treatment approaches.
ContributorsVose, Caitlin (Author) / Peter, Beate (Thesis advisor) / Liu, Li (Committee member) / Brewer, Gene (Committee member) / Arizona State University (Publisher)
Created2018
Description
Persistent cooperation between unrelated conspecifics rarely occurs in mature eusocial insect societies. In this dissertation, I present evidence of non-kin cooperation in the Nearctic honey ant Myrmecocystus mendax. Using microsatellite markers, I show that mature colonies in the Sierra Ancha Mountain of central Arizona contain multiple unrelated matrilines, an observation that is consistent with primary polygyny. In contrast, similar analyses suggest that colonies in the Chiricahua Mountains of southeastern Arizona are primarily monogynous. These interpretations are consistent with field and laboratory observations. Whereas cooperative colony founding was observed frequently among groups of Sierra Ancha foundresses, founding in the Chiricahua population was restricted to individual foundresses. Furthermore, Sierra Ancha foundresses successfully established incipient laboratory colonies without undergoing queen culling following emergence of the first workers. Multi-queen laboratory Sierra Ancha colonies also produced more workers and repletes than haplometrotic colonies, and when brood raiding was induced between colonies, queens of those with more workers had a higher survival probability.
Microsatellite analyses of additional locations within the M. mendax range suggest that polygyny is also present in some other populations, especially in central-northern Arizona, albeit at lower frequencies than that in the Sierra Anchas. In addition, analyses of multiple types of genetic data, including microsatellites, the mitochondrial barcoding region, and over 2000 nuclear ultra-conserved elements indicate that M. mendax populations within the southwestern U.S. and northwestern Mexico are geographically structured, with strong support for the existence of two or more divergent clades as well as isolation-by-distance within clades. This structure is further shown to correlate with variation in queen number and hair length, a diagnostic taxonomic feature used to distinguish honey ant species.
Together, these findings suggest that regional ecological pressures (e.g. colony density , climate) may have acted on colony founding and social strategy to select for increasing workforce size and, along with genetic drift, have driven geographically isolated M. mendax populations to differentiate genetically and morphologically. The presence of colony fusion in the laboratory and life history traits in honey ant that are influenced by colony size, including repletism, brood raiding, and tournament, support this evolutionary scenario.
Microsatellite analyses of additional locations within the M. mendax range suggest that polygyny is also present in some other populations, especially in central-northern Arizona, albeit at lower frequencies than that in the Sierra Anchas. In addition, analyses of multiple types of genetic data, including microsatellites, the mitochondrial barcoding region, and over 2000 nuclear ultra-conserved elements indicate that M. mendax populations within the southwestern U.S. and northwestern Mexico are geographically structured, with strong support for the existence of two or more divergent clades as well as isolation-by-distance within clades. This structure is further shown to correlate with variation in queen number and hair length, a diagnostic taxonomic feature used to distinguish honey ant species.
Together, these findings suggest that regional ecological pressures (e.g. colony density , climate) may have acted on colony founding and social strategy to select for increasing workforce size and, along with genetic drift, have driven geographically isolated M. mendax populations to differentiate genetically and morphologically. The presence of colony fusion in the laboratory and life history traits in honey ant that are influenced by colony size, including repletism, brood raiding, and tournament, support this evolutionary scenario.
ContributorsEriksson, Ti (Author) / Gadau, Jürgen (Thesis advisor) / Taylor, Jay (Thesis advisor) / Fewell, Jennifer (Committee member) / Hӧlldobler, Bert (Committee member) / Johnson, Robert (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2018
Description
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes can result in unequal gene expression between the sexes (e.g., between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression which prevents deleterious side effects from having too much or too little expression of genes on sex chromsomes. The green anole is part of a group of species that recently underwent an adaptive radiation. The green anole has XX/XY sex determination, but the content of the X chromosome and its evolution have not been described. Given its status as a model species, better understanding the green anole genome could reveal insights into other species. Genomic analyses are crucial for a comprehensive picture of sex chromosome differentiation and dosage compensation, in addition to understanding speciation.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
ContributorsRupp, Shawn Michael (Author) / Wilson Sayres, Melissa A (Thesis advisor) / Kusumi, Kenro (Committee member) / DeNardo, Dale (Committee member) / Arizona State University (Publisher)
Created2016
Description
Speech sound disorders (SSDs) are the most prevalent type of communication disorder in children. Clinically, speech-language pathologists (SLPs) rely on behavioral methods for assessing and treating SSDs. Though clients typically experience improved speech outcomes as a result of therapy, there is evidence that underlying deficits may persist even in individuals who have completed treatment for surface-level speech behaviors. Advances in the field of genetics have created the opportunity to investigate the contribution of genes to human communication. Due to the heterogeneity of many communication disorders, the manner in which specific genetic changes influence neural mechanisms, and thereby behavioral phenotypes, remains largely unknown. The purpose of this study was to identify genotype-phenotype associations, along with perceptual, and motor-related biomarkers within families displaying SSDs. Five parent-child trios participated in genetic testing, and five families participated in a combination of genetic and behavioral testing to help elucidate biomarkers related to SSDs. All of the affected individuals had a history of childhood apraxia of speech (CAS) except for one family that displayed a phonological disorder. Genetic investigation yielded several genes of interest relevant for an SSD phenotype: CNTNAP2, CYFIP1, GPR56, HERC1, KIAA0556, LAMA5, LAMB1, MDGA2, MECP2, NBEA, SHANK3, TENM3, and ZNF142. All of these genes showed at least some expression in the developing brain. Gene ontology analysis yielded terms supporting a genetic influence on central nervous system development. Behavioral testing revealed evidence of a sequential processing biomarker for all individuals with CAS, with many showing deficits in sequential motor skills in addition to speech deficits. In some families, participants also showed evidence of a co-occurring perceptual processing biomarker. The family displaying a phonological phenotype showed milder sequential processing deficits compared to CAS families. Overall, this study supports the presence of a sequential processing biomarker for CAS and shows that relevant genes of interest may be influencing a CAS phenotype via sequential processing. Knowledge of these biomarkers can help strengthen precision of clinical assessment and motivate development of novel interventions for individuals with SSDs.
ContributorsBruce, Laurel (Author) / Peter, Beate (Thesis advisor) / Daliri, Ayoub (Committee member) / Liu, Li (Committee member) / Scherer, Nancy (Committee member) / Weinhold, Juliet (Committee member) / Arizona State University (Publisher)
Created2020
Description
All biological processes like cell growth, cell differentiation, development, and aging requires a series of steps which are characterized by gene regulation. Studies have shown that gene regulation is the key to various traits and diseases. Various factors affect the gene regulation which includes genetic signals, epigenetic tracks, genetic variants, etc. Deciphering and cataloging these functional genetic elements in the non-coding regions of the genome is one of the biggest challenges in precision medicine and genetic research. This thesis presents two different approaches to identifying these elements: TreeMap and DeepCORE. The first approach involves identifying putative causal genetic variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. TreeMap performs an organized search for individual and multiple causal variants using a tree guided nested machine learning method. DeepCORE on the other hand explores novel deep learning techniques that models the relationship between genetic, epigenetic and transcriptional patterns across tissues and cell lines and identifies co-operative regulatory elements that affect gene regulation. These two methods are believed to be the link for genotype-phenotype association and a necessary step to explaining various complex diseases and missing heritability.
ContributorsChandrashekar, Pramod Bharadwaj (Author) / Liu, Li (Thesis advisor) / Runger, George C. (Committee member) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2020