Matching Items (3)
Description
Although the Caribbean has been continuously inhabited for the last 7,000 years, European contact in the last 500 years dramatically reshaped the cultural and genetic makeup of island populations. Several recent studies have explored the genetic diversity of Caribbean Latinos and have characterized Native American variation present within their genomes. However, the difficulty of obtaining ancient DNA from pre-contact populations and the underrepresentation of non-Latino Caribbean islanders in current research have prevented a complete understanding of genetic variation over time and space in the Caribbean basin. This dissertation uses two approaches to characterize the role of migration and admixture in the demographic history of Caribbean islanders. First, autosomal variants were genotyped in a sample of 55 Afro-Caribbeans from five islands in the Lesser Antilles: Grenada, St. Kitts, St. Lucia, Trinidad, and St. Vincent. These data were used to characterize genetic structure, ancestry and signatures of selection in these populations. The results demonstrate a complex pattern of admixture since European contact, including a strong signature of sex-biased mating and inputs from at least five continental populations to the autosomal ancestry of Afro-Caribbean peoples. Second, ancient mitochondrial and nuclear DNA were obtained from 60 skeletal remains, dated between A.D. 500–1300, from three archaeological sites in Puerto Rico: Paso del Indio, Punta Candelero and Tibes. The ancient data were used to reassesses existing models for the peopling of Puerto Rico and the Caribbean and to examine the extent of genetic continuity between ancient and modern populations. Project findings support a largely South American origin for Ceramic Age Caribbean populations and identify some genetic continuity between pre and post contact islanders. The above study was aided by development and testing of extraction methods optimized for recovery of ancient DNA from tropical contexts. Overall, project findings characterize how ancient indigenous groups, European colonial regimes, the African Slave Trade and modern labor movements have shaped the genomic diversity of Caribbean islanders. In addition to its anthropological and historical importance, such knowledge is also essential for informing the identification of medically relevant genetic variation in these populations.
ContributorsNieves Colón, Maria (Author) / Stone, Anne C (Thesis advisor) / Pestle, William J. (Committee member) / Benn-Torres, Jada (Committee member) / Stojanowski, Christopher (Committee member) / Arizona State University (Publisher)
Created2017
Description
Mycobacterium leprae, the causative agent of Hansen’s disease (leprosy), has plagued humans and other animal species for millennia and remains of concern to public health throughout the world today. Recent research into the expanded use of medical tissues preserved as formalin-fixed, paraffin-embedded samples (FFPE), opened the door for the study of M. leprae DNA from preserved skin samples. However, problems persist with damage to the DNA including fragmentation and cross linkage. This study evaluated two methods commonly used for the recovery of host DNA from FFPE samples for their efficacy in extracting pathogen DNA (hot alkaline lysis protocol and QIAGEN QIAamp FFPE DNA kit). Twenty FFPE skin samples collected from 1995-2015 from human subjects in the Pacific Islands suffering from M. leprae infection, each exhibiting a range of bacillary loads, were analyzed to determine which extraction method was most successful in terms of ability to consistently yield reliable, robust traces of M. leprae infection. This study further examined these samples to understand the phylogeny of leprosy in the region, where gaps in the evolutionary history of M. leprae persist. DNA recovery from paired samples was similar using either method. However, by extending the incubation time of post-paraffin removal sample lysis, both protocols were more likely to yield positive traces of M. leprae, with this enhancement being especially evident in paucibacillary samples with low bacterial presence. The qPCR assay findings suggest that the hot alkaline procedure is most likely to yield positive identification of infection in these traditionally challenging samples.
ContributorsKing, Felicia Clarice (Author) / Stone, Anne (Thesis advisor) / Wilson, Melissa (Committee member) / Buetow, Ken (Committee member) / Arizona State University (Publisher)
Created2023
Description
Recovering high-quality DNA from thermally altered human remains poses a significant challenge for research and law enforcement agencies due to high levels of DNA degradation resulting from exposure to extremely high temperatures (e.g., fire). The current standard practice for the DNA identification of badly burned skeletal remains is to extract DNA from dense cortical bone collected from recovered skeletal elements. Some of the problems associated with this method are that it requires specialized equipment and training, is highly invasive (involving the physical destruction of sample material), time-consuming, and does not reliably guarantee the successful identification of the remains in question. At low-medium levels of thermal exposure, charred tissue is often adhered to these skeletal remains and typically discarded. In cases where burned/charred tissue is recoverable, it has the potential to be a more efficient alternative to the sampling of cortical bone. However, little has been done to test the viability of thermally altered soft tissue in terms of DNA identification to date. Burned/charred tissue was collected from skeletal samples provided by the University of Tennessee Forensic Anthropology Center, as a part of a controlled burn from donor individuals, for downstream laboratory processing and DNA analysis as part of the Stone Lab (Arizona State University, School of Human Evolution and Social Change). DNA from this charred tissue was extracted using the Qiagen DNeasy Blood and Tissue Kit, and resulting yields were quantified via fluorometry using the Qubit Fluorometer 2.0 and Agilent TapeStation 4200 High-Sensitivity D5000 assay. It was found that between the temperatures of ~200-300 ℃ (burn category 2) and ~300-350 ℃ (burn category 3), tissue was the most efficient extraction type, especially from tissue taken from the surface of the ilium and the rib. As for bone, both the Dabney and the Loreille protocol performed similarly, so choice in extraction type comes down to personal preference, type of equipment on hand, and training. Although, for samples with low input material, the Dabney protocol is optimal.
ContributorsCoffman, Amber (Author) / Stone, Anne C (Thesis advisor) / Parker, Cody (Committee member) / Kanthaswamy, Sreetharan (Committee member) / Arizona State University (Publisher)
Created2023