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- All Subjects: Genetics
- Creators: Buikstra, Jane E.
- Member of: ASU Electronic Theses and Dissertations
- Resource Type: Text
Description
Studies of ancient pathogens are moving beyond simple confirmatory analysis of diseased bone; bioarchaeologists and ancient geneticists are posing nuanced questions and utilizing novel methods capable of confronting the debates surrounding pathogen origins and evolution, and the relationships between humans and disease in the past. This dissertation examines two ancient human diseases through molecular and bioarchaeological lines of evidence, relying on techniques in paleogenetics and phylogenetics to detect, isolate, sequence and analyze ancient and modern pathogen DNA within an evolutionary framework. Specifically this research addresses outstanding issues regarding a) the evolution, origin and phylogenetic placement of the pathogen causing skeletal tuberculosis in New World prior to European contact, and b) the phylogeny and origins of the parasite causing the human leishmaniasis disease complex. An additional chapter presents a review of the major technological and theoretical advances in ancient pathogen genomics to frame the contributions of this work within a rapidly developing field. This overview emphasizes that understanding the evolution of human disease is critical to contextualizing relationships between humans and pathogens, and the epidemiological shifts observed both in the past and in the present era of (re)emerging infectious diseases. These questions continue to be at the forefront of not only pathogen research, but also
bioarchaeological and paleopathological scholarship.
bioarchaeological and paleopathological scholarship.
ContributorsHarkins, Kelly M (Author) / Buikstra, Jane E. (Thesis advisor) / Stone, Anne C (Thesis advisor) / Knudson, Kelly (Committee member) / Kumar, Sudhir (Committee member) / Krause, Johannes (Committee member) / Arizona State University (Publisher)
Created2014
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 transition from Late Antiquity to Early Medieval Europe (ca. AD 400-900) is often characterized as a period of ethnogenesis for a number of peoples, such as the Franks. Arising during protracted contact with the Roman Empire, the Franks would eventually form an enduring kingdom in Western Europe. However, there is little consensus about the processes by which they formed an ethnic group. This study takes a fresh look at the question of Frankish ethnogenesis by employing a number of theoretical and methodological subdisciplines, including population genetics and ethnogenetic theory. The goals of this work were 1) to validate the continued use of biological data in questions of historical and archaeological significance; and 2) to elucidate how Frankish population structure changed over time.
Toward this end, measurements from the human dentition and crania were subjected to rigorous analytical techniques and interpreted within a theoretical framework of ethnogenetic life cycles. Results validate existing interpretations of intra-regional biological continuity over time. However, they also reveal that 1) there are clear biological and geographical differences between communities, and 2) there are hints of diachronic shifts, whereby some communities became more similar to each other over time. These conclusions complement current ethnohistoric work arguing for the increasing struggle of the Frankish kingdom to unify itself when confronted by strong regionally-based politics.
Toward this end, measurements from the human dentition and crania were subjected to rigorous analytical techniques and interpreted within a theoretical framework of ethnogenetic life cycles. Results validate existing interpretations of intra-regional biological continuity over time. However, they also reveal that 1) there are clear biological and geographical differences between communities, and 2) there are hints of diachronic shifts, whereby some communities became more similar to each other over time. These conclusions complement current ethnohistoric work arguing for the increasing struggle of the Frankish kingdom to unify itself when confronted by strong regionally-based politics.
ContributorsCarver, Charisse (Author) / Stojanowski, Christopher M (Thesis advisor) / Scott, Rachel E. (Thesis advisor) / Buikstra, Jane E. (Committee member) / Arizona State University (Publisher)
Created2015