Abstract
Advancements in DNA sequencing technologies have provided increased resolution and identification of genomic markers, which is particularly important for species of conservation concern. These technological advancements provide opportunities to identify previously understudied or elusive taxa, obtain more accurate estimates of neutral processes (e.g., gene flow, connectivity), and observe the effects of environmental change and biodiversity loss on species and ecosystems. With these improved insights, we can better inform our management strategies to conserve threatened species and systems.In my first chapter, we developed, optimized, and validated a Genotyping-by-thousands sequencing (GT-seq) panel for the federally threatened northern Idaho ground squirrel (Urocitellus brunneus) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016-2020 had 73% genotyping success, while samples collected from hair from 2002-2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and FST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative FIS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. We found our GT-seq panel is an effective and efficient genotyping tool and our results provide insights for applying GT-seq to minimally invasive DNA sampling techniques in other rare mammals.
In my second chapter, we applied the GT-seq panel developed in Chapter 1 to inform recovery action for the northern Idaho ground squirrel. We evaluated genetic diversity, structure, connectivity, and effective population size to address species recovery goals. We delineated conservation units: (1) three evolutionarily significant units that represent long-term population structure and variation, (2) nine management units that reflect current demographic connectivity and restrictions to gene flow, and (3) three adaptive units that capture adaptive differentiation across the species range. Effective populations sizes per management units were small overall, indicating recovery goals have not been reached. Our results support that connectivity within evolutionarily significant units should be maintained through the restoration of dispersal corridors. We recommend further sampling of subpopulations that harbor unique adaptive differentiation and subpopulations that are geographically isolated. We intend for future samples to be genotyped with the same GT-seq panel to detect dispersal, assess effective population size, monitor the effects of inbreeding, and evaluate adaptive differentiation to monitor the effects of management action and environmental change. Our findings highlight the value of using genomic data to evaluate recovery goals for threatened species.
In my third chapter, we explored how genetic variation in a foundation species can impact community structure through indirect interactions. Big sagebrush (Artemisia tridentata) is a prolific foundation species in western North America facing widespread anthropogenic threats. Big sagebrush’s complex genome, complicated hybridization events, and diverse associated organisms make it an ideal system to explore how intraspecific variation of a foundation species influences community dynamics. We characterized taxonomic composition of microbial and arthropod communities associated with big sagebrush individuals across elevational transects and a common garden. We hypothesized (1) microbial and arthropod richness would be lower at high elevations, (2) microbial and arthropod richness would be higher on big sagebrush individuals with higher ploidy, and (3) big sagebrush ancestral groups would support different microbial and arthropod richness. Microbial and arthropod community richness were more consistent than expected across big sagebrush genetic variables and environmental variables. However, we were limited by confounded variables and low sample sizes of hybrids in big sagebrush to make robust conclusions. Our work suggests there may not be a strong community genetics effect on the microbial and arthropod communities in this system. Nevertheless, this study serves as an exploration of the sagebrush steppe ecosystem through the lens of landscape community genomics.