Environmental Determinants of American Pika (\u3ci\u3eOchotona princeps\u3c/i\u3e) Distribution and Abundance Across the Northern Portion of the Greater Yellowstone Ecosystem

Over the next century, temperatures are expected to rise by 1-4 °C in the Greater Yellowstone Ecosystem of the American West, and by even larger amounts in montane habitats. This warming may cause species that live there to acclimate, adapt, move, or disappear. Understanding the degree to which species\u27 distributions are tied to temperature and other aspects of the environment is key to developing effective conservation plans. American pikas (Ochotona princeps) are small alpine lagomorphs restricted to cooler talus habitats. Pikas have exhibited varying responses across their range to the changing climate, suggesting that their distributions are not simply limited by climate. In this thesis, I explored how landscape, climate, vegetation, habitat connectivity and activity constraints are related to pika distribution and abundance in the northern range of the Greater Yellowstone Ecosystem including the Beartooth Plateau, Washburn Mountain, and Bunsen-Hoodoo area. To determine the environmental variables that best explain pika distribution and abundance, I compared statistical models with different sets of environmental variables and field measurements of occupancy and pika latrine densities, as a proxy for pika density. The strongest predictor of pika occupancy was the timing of peak vegetation cover (measured as the maximum Normalized Difference Vegetation Index), with higher occupancy at sites with later peaks in vegetation cover. Habitat connectivity, measured by the percentage of talus within 1 km of each site, was the second strongest predictor of occupancy, with occupancy increasing with the amount of nearby talus. Neither maximum summer temperatures nor the number of hours pikas could be active during the summer were strong predictors of occupancy. Overall, there was a higher probability of occupancy at sites with increased connectedness to surrounding talus, peak primary productivity later in the year, and large amounts of seasonal precipitation. The necessity of large seasonal precipitation may be detrimental for pika populations because, under future climate scenarios, this area is expected to become drier. The two strongest predictors of latrine density, and likely pika density, were the area of talus sites and the forage quality, as measured by the ratio of forbs to graminoids. Latrine density was greater in areas of higher amounts of forbs compared to graminoids, flatter slopes and smaller talus areas. As with site occupancy, summer temperatures and activity hours were not the strongest predictors of latrine density. Instead, winter temperatures and winter and summer precipitation were the strongest climate predictors of latrine density. In conclusion, forage quality and habitat connectivity appear to drive the distribution and abundance of pikas in the Greater Yellowstone Region. In particular, the Beartooth Plateau appears to provide a refugia for pikas under the present and potentially the future climate. Summer temperatures do not appear to limit pikas in this region; instead they are limited by winter climate. Ultimately, identifying areas of large connectivity, such as the Beartooth Plateau, and high forage quality, will be necessary for future protection of this species

Validation of Bacteroidales quantitative PCR assays targeting human and animal fecal contamination in the public and domestic domains in India.

We compared host-associated Bacteroidales qPCR assays developed in the continental United States and Europe for the purpose of measuring the effect of improved sanitation on human fecal exposure in rural Indian communities where both human and animal fecal loading are high. Ten candidate Bacteroidales qPCR assays were tested against fecal samples (human, sewage, cow, buffalo, goat, sheep, dog and chicken) from a test set of 30 individual human, 5 sewage, and 60 pooled animal samples collected in coastal Odisha, India. The two universal/general Bacteroidales assays tested (BacUni, GenBac3) performed equally well, achieving 100% sensitivity on the test set. Across the five human-associated assays tested (HF183 Taqman, BacHum, HumM2, BacH, HF183 SYBR), we found low sensitivity (17 to 49%) except for HF183 SYBR (89%), and moderate to high cross-reactivity with dog (20 to 80%) and chicken fecal samples (60 to 100%). BacHum had the highest accuracy (67%), amplified all sewage samples within the range of quantification (ROQ), and did not cross-react with any fecal samples from cows, the most populous livestock animal in India. Of the ruminant- and cattle-associated assays tested (BacCow, CowM2), BacCow was more sensitive in detecting the full range of common Indian livestock animal fecal sources, while CowM2 only detected cow sources with 50% sensitivity. Neither assay cross-reacted with human sources. BacCan, the dog-associated assay tested, showed no cross-reactivity with human sources, and high sensitivity (90%) for dog fecal samples. Overall, our results indicate BacUni, BacHum, HumM2, BacCan and BacCow would be the most suitable MST assays to distinguish and quantify relative amounts of human-associated and livestock/domestic animal-associated contributions to fecal contamination in Odisha, India

Recruiting Diverse Smokers: Enrollment Yields and Cost

To help tobacco control research better include vulnerable populations, we sought to identify effective ways to recruit diverse smokers. In 2014–2015, we recruited 2149 adult cigarette smokers in California and North Carolina, United States, to participate in a randomized trial of pictorial cigarette pack warnings. The most effective means of recruiting smokers were the classified advertising website Craigslist (28% of participants), word of mouth (23%), Facebook (16%), and flyers or postcards (14%). Low-income and African American smokers were more likely to respond to interpersonal contact (including staff in-person recruitment and word of mouth) than were high-income and non-African American smokers (all p < 0.05). Hispanic and gay, lesbian, and bisexual smokers were more likely to be recruited by Craigslist than non-Hispanic and straight smokers (both p < 0.05). Of the recruitment methods requiring cost, the cheapest was Craigslist ($3–7 per smoker). The most expensive methods were newspaper ads in California ($375 per smoker) and staff in-person recruiting in North Carolina ($180 per smoker). Successfully recruiting diverse smokers requires using multiple methods including interpersonal, online, and other media. Craigslist and word of mouth are especially useful and low-cost ways to recruit diverse smokers

Twenty year comparison of reproduction and habitat characteristics of Gopherus polyphemus between two sites of varying management

The effects of fire on Gopherus polyphemus populations in a sandhill habitat, specifically their reproductive success, has not been extensively studied in Georgia. Here we present data on a long term comparison of the reproduction and habitat use under different management: long term active fire management vs limited management approach. Reproductive output, population structure, and habitat quality were compared over a 20 year period (1994 to 2014). The project took place at two sites: Fort Stewart Army Reserve (FSAR) which is managed aggressively for tortoises and George L Smith State Park (GLS) which only recently received some management for its population. Female tortoises at FSAR are significantly larger than females at GLS (GLS: 29.08±0.327cm, n=69, FSAR: 30.49±0.107cm, n=301, p=.0002). When the data was pooled, there was a significant difference in clutch size (GLS: 4.83± 0.177 eggs, n=44, FSAR: 6.565± 0.113 eggs, n=194). The linear regression of clutch size and carapace length show weak positive correlations for GLS and FSAR (r²=0.0129, 0.1401 respectively). Analysis of Covariance showed significant heterogeneity of the slopes suggesting that the larger females at FSAR are producing larger clutch sizes which is not seen at GLS (p=0.0368). Habitat results were similar to the 1994-1996 study. There was a significant difference in canopy and ground cover between the burrows and random points at GLS but not at FSAR. Tortoises at both sites are selecting habitat with low canopy and available ground forage however tortoises at FSAR are able to find more favorable available habitat throughout their range

Effects of salinity and transparent exopolymer particles on formation of aquatic aggregates and their association with norovirus

Human noroviruses (NoVs) are responsible for 50% of food-related disease outbreaks and are notably associated with shellfish consumption. Despite the detrimental health impacts of human NoV-contaminated seafood to public health, there is a lack of knowledge on the physicochemical conditions that govern NoV transmission in aquatic ecosystems. In the present study, we investigated the propensity for NoVs to associate with aquatic aggregates, which have been shown to efficiently deliver nano-sized particles to shellfish. Specific physicochemical conditions characteristic of shellfish cultivation waters, specifically salinity and transparent exopolymer particles (TEP), were targeted in this study for investigating aggregate formation and NoV association dynamics. Murine norovirus (MNV) was used in aggregation experiments as a model surrogate for NoVs. Results demonstrate increased aggregate formation as a function of increasing salinity and TEP concentrations, as well as greater numbers of MNV genomes incorporated into aggregates under conditions that favor aggregation. As aggregate formation was enhanced in waters representing optimal conditions for shellfish production, specifically saline and high TEP waters, the implications to virus transport and shellfish food safety are profound: more aggregates implies increased scavenging of virus particles from surrounding waters and therefor greater risk for bivalve contamination with nano-sized pathogens. These novel data provide insight into where and when NoVs are most likely to be ingested by shellfish via contaminated aggregates, thereby informing best management and water quality monitoring practices aimed at providing safe seafood to consumers

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study