Population Genetic Structure of Ixodes pacificus Ticks and Detection of Their Pathogens In-Silico
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Authors
McVicar, Molly Elizabeth
Issue Date
2024
Type
Thesis
Language
en_US
Keywords
Ixodes , Ixodes pacificus , population genetics , tick-borne pathogens , ticks
Alternative Title
Abstract
Ticks are hematophagous ectoparasites responsible for the transmission of several serious illnesses in humans, domestic animals, livestock, and wildlife. As climate changes and ticks are introduced into new areas by their host, regions unfamiliar with tick-borne disease become vulnerable to potential public health crises. The movement and subsequent adaptation to the new environment by ticks can be modeled using genetic information and can be used to inform public health agencies of the risk of encountering ticks. Using Restriction-site DNA sequencing (RAD-seq) (Chapter 2), tick migration, phylogenetic relationships, population structure, clustering patterns, and isolation by distance can be analyzed and allow researchers to predict tick movement and risk for disease. Even further, performance of Genome Wide Association Studies (GWAS) will allow researchers to find genes with significant single-nucleotide polymorphisms (SNPs) and identify traits affected in different populations of ticks. Understanding how ticks are adapting to their environment, or their host associations can assist in developing new and effective tick control strategies. The research detailed in this thesis aims to understand 1) population structure of Ixodes pacificus in the western United States, and 2) a novel method of detecting tick-borne pathogens in-silico. In Chapter 2, we aimed to understand if I. pacificus, the western black-legged tick, has a population structure and if there is genetic differentiation between tick populations. Using Restriction site Associated DNA sequencing (RAD-seq), we identified three main populations of ticks and a pattern which suggests ticks are rapidly expanding into new areas in Oregon and Washington. Additionally, California populations appear to be more established, insinuating that ticks have been moving south to north. This information allows for us to track tick movement and assess tick encounter risk in new, high-risk areas. In Chapter 3, we attempted to utilize HISAT2, a sensitive and rapid genome aligner, to detect tick-borne pathogens computationally (in-silico). Pathogen genomes were aligned to RAD-seq reads to detect pathogen signatures in our samples. HISAT2 successfully detected two tick-borne pathogens, but depending on the species or type of pathogen it could either not distinguish between species or cannot detect their presence accurately. Utilizing a simple bioinformatic tool to test hundreds of samples at a time could speed up the time it takes to diagnosis and treat the pathogen, as well as decrease the need for specialized staff. More work is needed in the future to assess whether using bioinformatic tools to detect and diagnosis tick-borne pathogens and illnesses is a viable route to take in regards to tick-borne disease testing. The following studies are vital in understanding the basic biology, pathogen prevalence, and population dynamics of and in I. pacificus and have given us crucial insight into this tick.