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Development and Evaluation of Genomic Tools and Technology for North American Bison Conservation
No full textNorth American bison fulfill many roles in society as livestock, wildlife, a spiritual symbol, and the US National Mammal, making its preservation vital to multiple groups. Over the last 25 years, genetic technologies have been instrumental for the development of successful, long-term management strategies for the species. This work advances bison research into the genomic era by creating innovative tools and technologies for conservation and production, including assembling a highly contiguous chromosome-level reference genome, developing a robust single nucleotide polymorphism (SNP) panel for population management, and assessing bison herds across North America to understand degree of hybridization, genetic diversity, health, and demographic history within this species. Comprehensive whole genome sequencing from bison representative of the major lineages revealed evidence for recent introgression in all samples, including those previously thought to be free from a history of hybridization. These finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last two centuries. The developed high-quality genome assembly, which exceeds previous assemblies, provides a platform to evaluate the conservation, ecological, evolutionary, and population genomics of this species. This genome's utility was demonstrated when the causative mutation for albinism was identified as a de novo nonsynonymous SNP contained in a compiled genomic variant database. Additionally, construction of a novel SNP-based platform facilitated the assessment of population genetic parameters, establishing baseline data for important populations to inform genetic diversity preservation strategies. This platform was employed to examine Yellowstone National Park bison dynamics, revealing multiple historical lineages but currently represent only a single interbreeding metapopulation. These findings have significant implications for future management and conservation of this historically important and iconic bison herd. The overarching aim of these studies is to develop novel genomic technologies and techniques for a deeper understanding of bison genomics, contributing to effective long-term conservation plans. Therefore, the culmination of these investigations provides highly robust and informative genomic resources for further studies on this North American species
Muon Event Display for the Forward Muon Region in the CMS Experiment at the HL-LHC
Get PDFThe Large Hadron Collider (LHC) is the world���s largest particle collider, located at CERN in Geneva, Switzerland. One of its main experiments is the Compact Muon Solenoid (CMS), a general-purpose detector used to make precision measurements of high energy particle collisions. These measurements are used to study the fundamental particles in nature, which leads to a deeper understanding of physical phenomena and may uncover some of the mysteries of the universe, such as the Higgs mechanism and matter-antimatter asymmetry. To improve the precision of these studies, the LHC will be upgraded in the upcoming High-Luminosity LHC (HL-LHC) project, which will increase the luminosity of the accelerator and therefore the probability of observing rare events that may reveal new physics. As part of the HL-LHC upgrade, the CMS experiment will install new detectors at its endcap section and improve the electronics of existing detectors, in order to maintain good detector efficiency in the higher rate environment. The CMS muon upgrade will include improvement of the current muon endcap trigger algorithm, responsible for construction of muon track segments through the detectors, as it is expected to see some inefficiencies occurring at higher luminosities. To aid with the development of improved reconstruction algorithms, event visualization tools are useful in identifying sources of inefficiencies in the algorithm. In this thesis project, improvements to existing detector visualization tools are developed, which are capable of detailed analysis of individual muon events and identification of these inefficiencies. These tools are tested with real and simulated data to ensure their capabilities of identifying known inefficiencies, and to verify these tools for further use in improvement of the CMS muon endcap trigger
