Graduate Defense: Carlos Dave Dumaguit

Thesis Information

Title: Genomic Underpinning Of Drought-Associated Phenotypes In A Keystone Shrub Species Of Western North America

Program: Master of Science in Biology

Advisor: Dr. Sven Buerki, Biological Sciences

Committee Members: Dr. Stephen Novak, Biological Sciences; and Dr. Marcelo Serpe, Biological Sciences

Abstract

Anthropogenic climate warming and habitat loss threaten species and ecosystem sustainability. Given this, it is urgent to determine whether populations can adapt at a rate sufficient to combat climate change or if human intervention is needed to preserve ecosystem health. Assessing if populations could adapt includes inferring whether key phenotypic traits associated to abiotic tolerance are under genetic control and therefore heritable. This thesis focused on the imperiled western North American sagebrush steppe and its widespread eponymous keystone species Artemisia tridentata, commonly known as big sagebrush. To determine the adaptive capacity of any population, standing phenotypic variation across its climatic range must be known, allowing for predictions into performance under climate change conditions. For sagebrush populations, we investigated phenotypic trait variation by examining leaf stomata density and size to infer water use efficiency as well as xylem diameter to infer relative risk of embolism, then used comparative genomic analyses to test for signature of natural selection driven by climatic conditions. A common garden greenhouse experiment included 41 seedlings from four populations in Idaho, Nevada, and Utah, representing a potential evapotranspiration gradient. If distinct phenotypes were observed under optimum conditions, then this would provide evidence for genetic control of these traits. Light microscopy was applied on leaf epidermis and roots to record phenotypes and comparative statistical analysis was conducted to determine phenotypes at population level. This study showed that seedlings from Utah exhibited significantly more dense stomata, increasing transpiration water loss, but greater allocation of large diameter xylem, mitigating risk of embolism. In contrast, seedlings from Idaho and Nevada exhibited significantly less stomata density, decreasing transpiration water loss, and greater allocation of small diameter xylem mitigating embolism. The genetic underpinning of phenotypes was investigated by reconstructing 12 individual genomes from three significantly different stomata phenotypes by applying a reference-based approach using Illumina short reads. To test for signature of local adaptation, single nucleotide polymorphisms were called for a principal component analysis. The latter analysis returned the same climatic and phenotypic clustering as previously observed with Utah seedlings being separated from those from Idaho and Nevada. Combining phenotypic and genomic data support a hypothesis of genetically controlled phenotypic traits reflecting local adaptation. In all populations, individuals with less dense and smaller sized stomata increasing drought tolerance as well as smaller diameter xylem with greater tolerance to embolism exist. Future work should explore gene expression responsible for phenotypic trait development under controlled drought, with continued work informing practices to improve ecosystem recovery in the face of climate change.