Matching Items (4)
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- All Subjects: Mesoamerica
- All Subjects: Sex Chromosomes
- Genre: Academic theses
- Creators: Wilson, Melissa A
- Creators: Abbott, David
- Member of: Theses and Dissertations
Description
Unlike traditional frontier studies that treat the frontier as monolithic and focus on core-periphery interactions involving colonialism and acculturation, this dissertation seeks to characterize the internal social dynamics of frontier regions using the collective social identification framework. Concentrating on the intraregional and intrasite scales makes it possible to directly evaluate the bottom-up processes involved in the formation of collective social identities within frontier zones (i.e., sociopolitical development divorced from core-centric actions). Derived from social science research aimed at understanding the development of modern nation-states and social movements, the theoretical framework implemented in this research centers on the idea that sustained collective action depends on the degree to which groups of individuals share networks of social interaction (i.e., relational identification) and recognize membership in the same social categories (i.e. categorical identification). Applying this model to the site of La Quemada, Zacatecas, Mexico, provides a methodology for assessing the potential for collective action through time and across spatial scales based on the degree of categorical commonality or the strength of relational connections among the site’s inhabitants.
Dating to the Epiclassic period (600-900 CE), La Quemada was founded during the cultural florescence of the northern frontier of Mesoamerica, but the site was abandoned ca. 800-900 CE while other polities persisted. Therefore, it is hypothesized that a change in how the occupants of La Quemada identified with one another decreased the potential for collective action over time and contributed to site abandonment. Material proxies in the form of ceramic-style categories (i.e., shared styles expressing categorical affiliation) and fabric classes (i.e., shared pastes indicative of relational networks) are used to assess the temporal and spatial consistency of social identification at multiple socio-spatial scales within the site of La Quemada. The results of this research, however, find that despite fluctuations in the expression of categorical identification among La Quemada residents it was the strength of their relational ties that gave them the capacity to recover. Furthermore, the capacity for collective action was high preceding site abandonment, suggesting that a disruption in the social fabric of La Quemada did not contribute to its decline and abandonment.
Dating to the Epiclassic period (600-900 CE), La Quemada was founded during the cultural florescence of the northern frontier of Mesoamerica, but the site was abandoned ca. 800-900 CE while other polities persisted. Therefore, it is hypothesized that a change in how the occupants of La Quemada identified with one another decreased the potential for collective action over time and contributed to site abandonment. Material proxies in the form of ceramic-style categories (i.e., shared styles expressing categorical affiliation) and fabric classes (i.e., shared pastes indicative of relational networks) are used to assess the temporal and spatial consistency of social identification at multiple socio-spatial scales within the site of La Quemada. The results of this research, however, find that despite fluctuations in the expression of categorical identification among La Quemada residents it was the strength of their relational ties that gave them the capacity to recover. Furthermore, the capacity for collective action was high preceding site abandonment, suggesting that a disruption in the social fabric of La Quemada did not contribute to its decline and abandonment.
ContributorsTorvinen, Andrea (Author) / Nelson, Ben A. (Thesis advisor) / Abbott, David (Committee member) / Michelak, Konstantina-Eleni (Committee member) / Peeples, Matthew (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
The regulation of gene expression, timing, location, and amount of a given project, ultimately affects the cellular structure and function. More broadly, gene regulation is the basis for cellular differentiation and development. However, gene expression is not uniform among individuals and varies greatly between genetic males and females. Males are hemizygous for the X chromosome, whereas females have two X chromosome copies. Contributing to the sex differences in gene expression between males and females are the sex chromosomes, X and Y. Gene expression differences on the autosomes and the X chromosome between males (46, XY) and females (46, XX) may help inform on the mechanisms of sex differences in human health and disease. For example, XX females are more likely to suffer from autoimmune diseases, and genetic XY males are more likely to develop cancer. Characterizing sex-specific gene expression among human tissues will help inform the molecular mechanisms driving sex differences in human health and disease. This dissertation covers a range of critical aspects in gene expression. In chapter 1, I will introduce a method to align RNA-Seq reads to a sex chromosome complement informed reference genome that considers the X and Y chromosomes' shared evolutionary history. Using this approach, I show that more genes are called as sex differentially expressed in several human adult tissues compared to a default reference alignment. In chapter 2, I characterize gene expression in an early formed tissue, the human placenta. The placenta is the DNA of the developing fetus and is typically XY male or XX female. There are well-documented sex differences in pregnancy complications, yet, surprisingly, there is no observable sex difference in expression of innate immune genes, suggesting expression of these genes is conserved. In chapter 3, I investigate gene expression in breast cancer cell lines. Cancer arises in part due to the disruption of gene expression. Here I show 19 tumor suppressor genes become upregulated in response to a synthetic protein treatment. In chapter 4, I discuss gene and allele-specific expression in Nasonia jewel wasp. Chapter 4 is a replication and extension study and discusses the importance of reproducibility.
ContributorsOlney, Kimberly (Author) / Wilson, Melissa A (Thesis advisor) / Hinde, Katherine (Committee member) / Buetow, Kenneth (Committee member) / Banovich, Nicholas (Committee member) / Arizona State University (Publisher)
Created2021
Description
Tuberculosis (TB) is a deadly disease that infects millions of people annually. TB has a global distribution and remains a significant cause of mortality, despite decades of eradication campaigns and antibiotic development. TB is caused by genetically similar pathogens in the Mycobacterium tuberculosis complex (MTBC), and human infections are generally caused by human-associated strains, although humans can contract animal-associated strains. Skeletal evidence of TB on archaeological human skeletal remains and evolutionary dating of MTBC genomes reveal that TB has afflicted humans for approximately 6,000 years. Previous research has shown that MTBC pathogens were introduced into the Americas through a zoonotic transmission from seals and sea lions along the coasts of South America by at least 1000 CE. Characterizing the introduction and enigmatic intercontinental spread of a successful zoonotic transmission over hundreds of years provides valuable insight into the potential of zoonotic MTBC infections. Through the recovery and phylogenomic analysis of the first ancient MTBC genomes (n = 2) from pre-contact North America, I establish that there were multiple contemporaneous MTBC lineages circulating in human populations in the Americas. The high genomic diversity and deep divergence of strains from Mesoamerica suggest that TB was endemic in the region. To reveal the impact of TB within a Mesoamerican city, I examined human skeletons (n = 137) for evidence of disease from sacrificial and natural mortality burial contexts within Tlatelolco, a ceremonial precinct and interregional marketplace at the heart of the Aztec Empire (1300-1521 CE). I found that TB disproportionately affected sacrificial victims, who also exhibited evidence of food insecurity and resource inequality. These results mirror the socioeconomic patterns of TB distribution today. Further, I sampled broadly from sacrificial victims with skeletal evidence of TB not only for biomolecular confirmation of MTBC but also to uncover associations between skeletal TB manifestation and ability to recover ancient MTBC DNA. I identify 10 additional cases of MTBC at Tlatelolco and link ancient MTBC DNA recovery to TB skeletal lesion characteristics and age-at-death of the infected individual. Overall, this body of work combines paleogenomic and paleopathological data to highlight the impact of ancient TB zoonoses.
ContributorsBlevins, Kelly Elaine (Author) / Buikstra, Jane E (Thesis advisor) / Stone, Anne C (Thesis advisor) / Ávila-Arcos, María C (Committee member) / Smith, Michael E (Committee member) / Wilson, Melissa A (Committee member) / Arizona State University (Publisher)
Created2021