Publication List

Colusa grass, Neostapfia colusana, is a listed California endangered plant endemic to the vernal pools of California. Vernal pool habitat is highly degraded and threatened by further anthropological development, with only 10% of its historical range remaining. With only 42 confirmed extant populations, it is a major conservation concern to understand patterns of genomic diversity. Here we report the first complete genome assembly of Colusa grass. The assembly includes two haplotypes: haplotype one spans 2.13 Gb with contig N50 of 10.62 Mb, scaffold N50 of 112.31 Mb, and BUSCO completeness of 98.1%. Haplotype two spans 2.04 Gb with contig N50 of 10.05 Mb and scaffold N50 of 138.31 Mb, with a BUSCO completeness of 97.6%. This genome assembly will allow for in-depth analysis of genomic variation and gene flow in populations of this threatened grass and will be a major asset to studies supporting its conservation. This genome was assembled as part of the California Conservation Genomics Project, which contributes to a collection of resources and tools to support state-wide conservation efforts.

Plant species richness patterns across vernal pool complexes are regulated by dynamic hydrologic processes, yet these controls remain difficult to quantify across space in ways that inform monitoring and conservation. In this study, we test whether microtopographic features can serve as proxies for hydrologic processes that shape plant species richness patterns. We evaluate this hypothesis by modeling relationships between unmanned aerial vehicle light detection and ranging (UAV-LiDAR)-derived microtopographic features and vascular, forb, and graminoid plant species richness across a vernal pool complex in central California, USA. We obtained plant assemblage data from surveys of 224 vernal pools in 2018 and 2019 and collected UAV-LiDAR data over the study area in 2020. We derived 11 features from UAV-LiDAR data and applied a recursive feature elimination procedure to optimize richness estimates. Poisson generalized linear models and a bootstrap cross-validation approach were used to construct species richness models for each plant functional type. Microtopographic features related to hydrologic connectivity, soil moisture gradients, and hydroperiod described substantial variation in vascular plant species richness patterns (median training r2 = 0.35, median validation r2 = 0.28) and were accurate to within 2–3 species per pool, consistent with similar ecological remote sensing efforts in tall prairie, salt meadow, and other grassland ecosystems. Forb richness, which disproportionately contribute to vascular plant richness, was highest in low-lying, hydrologically connected, and topographically uniform areas characteristic of vernal pools. Conversely, graminoid richness was higher at elevated, low-slope positions, such as mound tops across the mound–swale topography of the study area. These contrasting responses support the hypothesis that microtopography shapes hydrological niches favoring water-tolerant forbs in frequently inundated areas and graminoids in comparatively drier areas. Importantly, quantifying the link between microtopography and plant richness responses provides an ecologically grounded basis for managers to guide vernal pool conservation and restoration using microtopographic datasets.

One of the key uncertainties in climate change models is how microbes will adapt to rising temperatures. Large-scale comparisons of bacterial thermal performances show a clear boundary between mesophiles and thermophiles. Here, we investigated whether phylogenetic constraints limit the adaptive potential of bacteria to warming soils. Focusing on copiotrophs within Gammaproteobacteria, we found that both thermal optima and upper thermal limits are constrained; variation in these traits decreases above 42°C across the phylogeny, with minimal influence of present-day bioclimatic variables. This, along with the reduced thermal safety margins found in fluctuating hot climates, suggests that many isolates may already be maladapted to local temperature variability. Our findings indicate that these constraints interact with the geometry of thermal performance curves, imposing a trade-off between high-temperature performance and the risk of substantial fitness losses above Topt. Overall, this work underscores potential limits to thermal adaptation and their implications for bacterial fitness.Competing Interest StatementThe authors have declared no competing interest.John Templeton Foundation, https://ror.org/035tnyy05, 63455U.S. National Science Foundation, https://ror.org/021nxhr62, 2316731

This paper proposes a digital twin (DT) framework for point source applications in environmental sensing (ES). The DT concept has become quite popular among process and manufacturing industries for improving performance and estimating remaining useful life (RUL). However, environmental behavior, such as in gas dispersion, is ever changing and hard to model in real-time. The DT framework is applied to the point source environmental monitoring problem, through the use of hybrid modeling and optimization techniques. A controlled release case study is overviewed to illustrate our proposed DT framework and several spatial interpolation techniques are explored for source estimation. Future research efforts and directions are discussed.

Nearly 90% of California’s vernal pool habitat has been destroyed by human activity in the past 100 years. The University of California, Merced manages one of the largest actively protected vernal pool habitats in the state, the UC Merced Vernal Pools and Grassland Reserve (MVPGR), aimed at conserving rare native species and landscapes through research, teaching, and outreach. Because the reserve was only recently established, little is known about the interannual patterns of vernal pool plants occupying the region. Consequently, the phenological and demographic responses of the native species inhabiting the MVPGR to reduced precipitation, biological invasions, and cattle grazing has not been quantified. The goal of this dissertation is to investigate the composition, flowering time, and invasion intensity of vernal pool plant communities across multiple climate years. Chapter 1 focuses on two wildflowers native to California, Limnanthes douglassi ssp. rosea (meadowfoam) and Trifolium variegatum (whitetip clover), and quantifies each species’ phenological response to variable precipitation and temperature across 7 years. Additionally, population size of both focal species in response to competition and eutrophication were assessed. I found that both meadowfoam and whitetip clover flower earlier in response to lower precipitation. Chapter 2 focuses on plant community responses to abiotic and biotic dynamics across zones within pools, which are established by soil texture and flooding gradients. Chapter 2 expands upon Chapter 1 by characterizing the community composition, invasion intensity, and interannual flowering trends of 42 plant species across three zones: pool bottom, edge and upland. I found a distinct plant community occupying each zone, and each zone responded uniquely to invasion and winter precipitation. The pool bottom plant community flowered earlier in response to lower winter precipitation, whereas native species in the upland plant community were negatively associated with non-native species richness. No correlations were found between precipitation and the floral phenology of upland species, and neither was there a correlation between non-native species richness and native biodiversity patterns in the pool bottom. The findings elucidate the sensitivities and ramifications of climate change, invasion, and eutrophication amongst ‘zones of vegetation’ on the UCMGVPR. Conserving the native species also requires community participation in the management and legislative process, and ideally the scientific process. Chapter 3 examines several recruitment and retention methods for a community science project involving UC Merced undergraduates and provides guidance on how to achieve a long lasting and high engagement project. I found that in-person presentations achieved a recruitment rate than email flyers. In addition, giving volunteers the freedom to decide the time and date they volunteer and providing periodic updates in the form of a newsletter can improve retention rate of volunteers at different stages.

Biogeographic patterns in microorganisms are poorly understood, despite the importance of microbial communities for a range of ecosystem processes. Our knowledge of microbial ecology and biogeography is particularly deficient in rare and threatened ecosystems. We tested for three ecological patterns in microbial diversity and community composition within ephemeral wetlands—vernal pools—located across Baja California (Mexico) and California (USA): 1) habitat filtering; 2) a latitudinal diversity gradient; and 3) distance-decay in community composition. Paired water and soil samples were collected along a latitudinal transect of vernal pools, and bacterial and archaeal communities were characterized using 16S rDNA sequencing. We identified two distinct microbial communities, with one community present in the soil matrix that included archaeal and bacterial soil taxa, and another community present in the overlying water that was dominated by common freshwater bacterial taxa. Aquatic microbial communities were more diverse in the north and displayed a significant but inverted latitudinal diversity pattern. Aquatic communities also exhibited a significant distance-decay pattern, with geographic proximity explaining 9%, and precipitation explaining 16% of community variation. Collectively these results indicate greater sensitivity to spatial and environmental variation in vernal pool aquatic microbial communities than in soil microbial communities. We conclude that vernal pool aquatic microbial communities can display distribution patterns similar to those exhibited by larger organisms, but differ in some key aspects, such as the latitudinal gradient in diversity.

The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.[Evolution; open science; phylogenetics; Python; taxonomy.

This study investigates the ability of machine learning models to retrieve the surface soil moisture of a grassland area from multispectral remote sensing carried out using an unoccupied aircraft system (UAS). In addition to multispectral images, we use terrain attributes derived from a digital elevation model and hydrological variables of precip- itation and potential evapotranspiration as covariates to pre- dict surface soil moisture. We tested four different machine learning algorithms and interrogated the models to rank the importance of different variables and to understand their rela- tionship with surface soil moisture. All the machine learning algorithms we tested were able to predict soil moisture with good accuracy. The boosted regression tree algorithm was marginally the best, with a mean absolute error of 3.8 % vol- umetric moisture content. Variable importance analysis re- vealed that the four most important variables were precip- itation, reflectance in the red wavelengths, potential evap- otranspiration, and topographic position indices (TPI). Our results demonstrate that the dynamics of soil water status across heterogeneous terrain may be adequately described and predicted by UAS remote sensing and machine learn- ing. Our modeling approach and the variable importance and relationships we have assessed in this study should be use- ful for management and environmental modeling tasks where spatially explicit soil moisture information is important.

California’s vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species- specific assays for four of California’s vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

The introduction of exotic species to new regions offers opportunities to test fundamental questions in ecology, such as the context-dependency of community structure and assembly. Annual grasslands provide a model system of a major unidirectional introduction of plant species from Europe to North America. We compared the community structure of grasslands in two Mediterranean regions by surveying plots in Spain and in California with similar environmental and management conditions. All species found in Spanish grasslands were native to Spain, and over half of them (74 of 139 species) are known to have colonized California. In contrast, in California, over half of the species (52 of 95 species) were exotic species, all of them native to Spain. Nineteen species were found in multiple plots in both regions (i.e., shared species). The abundance of shared species in California was either similar to (13 species) or greater than (6 species) in Spain. In California, plants considered pests were more likely than non-pest species to have higher abundance. Co-occurring shared species tended to maintain their relative abundance in native and introduced communities, which indicates that pools of exotic species might assemble similarly at home and away. These findings provide interesting insights into community assembly in novel ecosystems. They also highlight an example of startling global and local floristic homogenization.

The avifauna of the University of California’s Merced Vernal Pools and Grassland Reserve in eastern Merced County was observed and documented over a three-year period (2013-2015). Several additional surveys made in other years were also included in this analysis. Eighty-nine species were observed using Reserve habitats. Twelve species used the Reserve for nesting, 38 species were local breeders, and 39 species were considered non-breeding migrants. The largest species groups were waterbirds and grassland specialists. Vernal pools, cattle stock ponds, and an irrigation canal are important aquatic habitats for birds and their occurrence added significantly to the overall diversity. Abundance and habitat usage are discussed and compared with several other regional avifaunal assessments.

<h3>Abstract</h3> <p>Global change is leading to habitat shifts that threaten species persistence throughout California’s unique ecosystems. Baseline biodiversity data provide opportunities for ecosystems to be managed for community complexity and connectivity. In 2017, the University of California Conservation Genomics Consortium launched the California Environmental DNA (CALeDNA) program, a community science initiative monitoring California’s biodiversity through environmental DNA (eDNA)—DNA shed from organisms through fur, mucus, spores, pollen, etc. Community scientists collect soil and sediment samples, then researchers analyze the eDNA in the samples and share results with the public. The results are catalogues of thousands of organisms per sample, ranging from microbes to mammals. The CALeDNA website presents biodiversity inventories in a platform designed for the public and researchers alike, as well as user-friendly analysis tools and educational modules. Here, we present CALeDNA as a scalable community science framework that can harmonize with future biodiversity research and education initiatives.</p>

The Biota Project communicates science to populations historically ignored by the scientific community. The Biota Project is comprised of a team of young professionals from a myriad of backgrounds and locations with interests in promoting science accessibility and equity. We do this by highlighting research conducted by scientists from underrepresented groups in relatable yet underrated locations with the intention of increasing the participation of underrepresented populations in science. The Biota Project centers on the scientific definition of symbiosis as a tool for both educating and learning from its followers. We deliver stories on the environments of our own backyards by merging art and science and distributing these publicly available stories widely online through short films, media clips, drawings, paintings, blogs, and e-newsletters. This project demonstrates a fresh, transferable perspective on strengthening science communication in a way that conjoins scientific discovery with social justice through the promotion of critical thinking by its target audience. Likewise, contributors learn how to better support local communities with each new story and environment. The Biota Project thus sets a symbiotic tone for re-calibrating the balance between academics, researchers, and local communities. When science is made relevant through understanding, its quality and significance are enhanced, and public recognition of its value is increased.

We used data collected by automated recorders to generate baseline estimates of occupancy for >80 songbird species in the Great Valley. Site-level detection probabilities were high for the majority of songbirds, providing support for the effectiveness of automated recorders as a monitoring tool. Further, our research highlights potential starting points for reconciling the Great Valley when the goal is to increase the distribution and richness of songbirds. These include increasing natural and agricultural heterogeneity, and conserving remnant forests and natural vegetation throughout the region. We encourage CDFW to use our estimates as baselines, thus setting the stage for long-term monitoring of songbird communities in the region. A long-term monitoring program would provide the agency with the empirical data needed to evaluate the processes driving the songbird populations, such as trends in occupancy and drivers of local colonization and extinction probabilities.

Accurate and precise measurements of wind are important for understanding atmospheric transport, especially when trying to localize and quantify natural gas emissions from pipeline leaks. This work looks at the applicability of measuring wind speed and direction with mini ultrasonic anemometers on-board small unmanned aerial systems. The 'prop wash effect' from propeller air intake mixing of the wind is quantified through experiments for a multi-rotor platform in a low cost wind tunnel (LCWT). Trisonica and FT742SM sensors are compared through wind tunnel experiments for accuracy confirmation. The validation of measuring wind conditions on-board is compared with accepted estimation techniques for VTOL and fixed wing platforms.

Executive Summary 1. In response to the drought State of Emergency declared in 2014, California's Department of Fish and Wildlife (CDFW) prioritized monitoring of wildlife populations and their associations with drought stressors and habitat features. As part of this effort, CDFW initiated Terrestrial Species Stressor Monitoring (TSM) surveys in 2016 to collect baseline data on wildlife species in the Mojave Desert and Great Valley ecoregions. In this report, we present our analysis of camera trap data from the 2016-17 TSM surveys. For each ecoregion, our objectives were to estimate the occupancy and richness of terrestrial mammal species weighing >0.5kg and to evaluate community and species-specific responses to climate and habitat variables. 2. We deployed camera traps at 320 and 265 sites across the Mojave Desert and Great Valley ecoregions, respectively, in the springs of 2016 and 2017. We used this camera trap data, in combination with multi-species hierarchical occupancy models, to estimate and evaluate mammal distributions. 3. Sixteen and 22 species of terrestrial mammals (>0.5kg) were photographed in the Mojave Desert and Great Valley ecoregions, respectively, with camera-specific estimates of species richness ranging from 0-13. Black-tailed jackrabbits (ψ = 0.73) and kit foxes (ψ = 0.34) had the highest estimated occupancies in the Mojave, whereas coyotes (ψ = 0.49) and raccoons (ψ = 0.45) had the highest estimated occupancies in the Great Valley. The mammal community in the Mojave tended to be positively associated with elevation and negatively associated with mean temperature and distance to pinyon juniper forest. The mammal community in the Great Valley, alternatively, tended to be positively associated with crop diversity and negatively associated with natural vegetative cover. 4. Our results suggest projected increases in temperature will negatively influence the Mojave Desert's mammal community, and consequently, that the protection of climate refugia (e.g., high elevations, shaded areas, and permanent water sources) may be an increasingly important conservation strategy. This is particularly true for some species in the region, like deer, Audubon's cottontail, and bobcat, which appeared to be more vulnerable to projected climate changes than species like the kit fox. 5. In the Great Valley, our results suggest that the remnant mammal community is adept at accessing resources and surviving in this human-modified, agricultural landscape. Working with landowners to diversify agricultural practices and maintain habitat heterogeneity is important, however, as heterogeneity within and among croplands positively influences the mammal community. 6. Biodiversity loss, climate change, and anthropogenic pressures on ecosystems are accelerating. The infrastructure required to monitor changes in biodiversity and species' vulnerability to stressors, however, is often lacking. Our analysis demonstrates the utility of camera traps and multi-species occupancy models for monitoring terrestrial mammals, including elusive species. Expanding beyond our snapshot in time however, requires long-term data. With longer-term data (e.g., >5 years), we can develop an understanding of the processes occurring within these ecoregions including trends in species' occupancy and the influence of climate, environment, and humans on mammal communities. This information in turn, would allow managers to track, improve, and adapt management actions aimed at addressing the loss of wildlife populations. (PDF) Evaluating mammalian diversity in the Mojave Desert and Great Valley ecoregions of California using camera trap surveys. Available from: https://www.researchgate.net/publication/328252602_Evaluating_mammalian_diversity_in_the_Mojave_Desert_and_Great_Valley_ecoregions_of_California_using_camera_trap_surveys [accessed Dec 11 2018].

Vernal pool landscapes are rare and highly modified. The Merced Vernal Pools and Grassland Reserve consists of 6,500 protected acres, preserving sensitive vernal pool habitat and organisms. The Reserve contains a number of modified stock ponds that have caused extensive alteration of the historic landscape to capture and retain water for longer periods than the seasonal wetland complexes dispersed throughout the site. Using a combination of empirical data and 2D hydrodynamic modeling, our project seeks to better understand how water moves throughout the UC Merced Vernal Pools and Grassland Reserve in order to evaluate the feasibility of potential hydrological restoration activities and develop a better understanding of potential management strategies. This study aims to assess the feasibility of restoring or enhancing existing natural vernal pool complexes through increased inundation by reconnecting historical channels via small alterations in previously modified terrain.A 2D hydrodynamic model was developed using HEC-RAS rain-on-grid methodology to assess the restorative potential of a vernal pool complex at Avocet Pond in the Merced Vernal Pools and Grassland Reserve. In this currently modified system, levees disconnect natural channels and reroute overland flows into the stock pond which behaves as a reservoir, removing water from downstream landscape processes. Increased inundation to natural habitats benefits native vernal pool species whose life histories are integrally tied to finite and variable hydroperiods. Invasive plant and animal species may be reduced through the reduction of perennial stock pond hydroperiods and increased inundation and hydrologic connectivity of wetland features. Base case hydroecological conditions were established as the formative basis for evaluating the benefit of various restoration scenarios. Proposed restoration scenarios implemented simple terrain modifications such as small breaks in conveyance levees or notching stock pond berms. Model simulations suggest that historical flow paths can be reconnected through minimal terrain alteration resulting in increased inundation to wetlands and other downstream environments and reduction of overall stock pond inflows and hydroperiod. Results of this study will serve as a demonstration of landscape scale restoration of a vernal pool grassland habitat that has been altered through past land uses so that similar restoration assessment methodology can be implemented on other preserved lands in the state.

Vernal pools are shallow, seasonal wetlands, underlined by an impermeable or slowly permeating layer, that form in depression pools. Vernal pools in California have been decimated by land developments. This has caused increased habitat fragmentation for vernal pool species. A thorough understanding of the vernal pools hydrology is imperative to their continued survival, as they are important refugia for endangered, endemic vernal pool species. The purpose of my research is to study the hydrological connectivity of two three–vernal pool series. My results show that vernal pools are hydrologically connected to each other and to the landscape. There are several variables that determine its degree of hydrological connectivity– shallow subsurface confining layer, perched groundwater and surface water flow, inundation, and location. Understanding the hydrology of this unique environment is imperative to the success of vernal pools and its species, as they undergo habitat loss and stresses associated with climate change.

A miniature in-situ CH4concentration measurement instrument based upon tunable laser spectroscopy (TLS) was developed and applied in numerous field campaigns. The instrument, a 3.4 μm laser spectrometer developed at NASA Jet Propulsion Lab (JPL), is lightweight (250g), low power (<; 8 W), and high sensitivity (10 ppb s-1). The payload was further developed and integrated onto a small UAV at UC Merced, rendering an overall payload weight of 400 g and real-time data acquisition. The remarkable characteristics of the instrument and prior investigative work regarding sensor placement yielded excellent trial and field results, which are presented in this work.

Residual Dry Matter (RDM) was monitored in 2013, 2014, and 2015 on the Vernal Pools and Grassland Reserve (Reserve), University of California, Merced. RDM monitoring was conducted to assess cattle grazing on the 6,561 acre (2,656 hectares) Reserve; grazing is a requirement of the Reserve Management Plan, and state and federal wetland permits. A herd of about 1,600 dairy cattle grazes the Reserve for about six months each year. Triplicate RDM samples were collected at 55 sites in 2013, 67 sites in 2014, and 71 sites in 2015. Mean overall RDM was 760 lbs./acre (853 kg/ha) in 2013; 430 lbs./acre (482 kg/ha) in 2014; and 956 lbs./acre (1,072kg/ha) 2015. Lower RDM levels in 2013 and 2014 were attributed to low rainfall rather than to overutilization by cattle. High RDM levels in 2015, more than twice the levels of 2014, were attributed to lower grazing pressure. Mean grass height was about 2.7 in. (6.9 cm) over the three years. For comparative purposes, RDM and grass heights were monitored annually on ungrazed grasslandoutside the Reserve along La Paloma Road. RDM and grass heights were much higher at these ungrazed locations than in the Reserve. The primary environmental purpose for cattle grazing on the Reserve is to prevent pervasive, non-native, European grasses from growing into the thousands of rare and protected vernal pools found there. Without grazing, excessive grass growth can lead to thatch (phytomass) build up in pools; reduction of rare, endemic wetland plants via competition; reduced hydroperiod; and overall degradation of the aquatic environment. Low RDM levels and overutilization by grazing cattle, therefore, are more desirable from a vernal pool ecosystem perspective than are higher RDM levels and underutilization. RDM monitoring took place during an historic drought (2013-2015) in California in which annual precipitation in eastern Merced County was only 29% to 67% of the long term mean. Low rainfall leads to low RDM levels. RDM levels were 5% below the Management Plan target of 800 lbs./acre in 2013 and about 20% above this target in 2015. We conclude, based on our RDM monitoring, that grazing appears to comply with Management Plan guidelines, although grazing was uneven across the Reserve. Whether the current grazing operations actually result in desirable ecological conditions with in the vernal pools has not yet been determined.

Over the past decade, the rapid rise of Unmanned Aircraft Systems (UASs) has blossomed into a new component of the aviation industry. Though regulations within the United States lagged, the promise of the ability of Small Unmanned Aircraft Systems (SUASs), or those UAS that weigh less than 55 lbs, has driven significant advances in small scale aviation technology. The dream of a small, low-cost aerial platform that can fly anywhere and keep humans safely away from the `dull, dangerous and dirty' jobs, has encouraged many to examine the possibilities of utilizing SUASin new and transformative ways, especially as a new tool in remote sensing. However, as with any new tool, there remains significant challenges in realizing the full potential of SUAS-based remote sensing. Within this dissertation, two specific challenges are addressed: validating the use of SUAS as a remote sensing platform and improving the safety and management of SUAS. The use of SUAS in remote sensing is a relatively new challenge and while it has many similarities to other remote sensing platforms, the dynamic nature of its operation makes it unique. In this dissertation, a closer look at the methodology of using SUAS reveals that while many viewSUAS as an alternative to satellite imagery, this is an incomplete view and that the current common implementation introduces a new source of error that has significant implications on the reliability of the data collected. It can also be seen that a new approach to remote sensing with an \gls{SUAS} can be developed by addressing the spatial, spectral and temporal factors that can now be more finely adjusted with the use of SUAS. However, to take the full advantage of the potential of SUAS, they must uphold the promise of improved safety. This is not a trivial challenge, especially for the integration into the National Airspace System (NAS) and for the safety management and oversight of diverse UAS operations. In this dissertation, the challenge of integrating SUAS in the NAS is addressed by presenting an analysis of enabling flight operations at night, developing a swarm safety management system for improving SUAS robustness, investigating the use of new technology on SUAS to improve air safety, and developing a novel framework to better understand human-SUAS interaction. Addressing the other side of safety, this dissertation discusses the struggle of large diverse organizations to balance acceptance, safety and oversight for UAS operations and the development of a novel implementation of a UAS Safety Management System.

Researchers have described major declines in breeding populations of American Kestrels (Falco sparverius) since the 1960s in the western United States, including parts of California (Hamerstrom et al. 1973, Sauer et al. 1997, Pandolfino 2008, Farmer and Smith 2009, Smallwood et al. 2009). In California, habitat loss and lack of nesting sites are considered the most likely causes of declines (Smallwood et al. 2009). In response, many organizations are working to expand populations by placing nest boxes in suitable areas and monitoring them to determine nesting success (http://kestrel.peregrinefund.org/). We describe results from 2015 and 2016, the second and third year of a study on American Kestrel breeding productivity at the Merced Vernal Pools and Grassland Reserve near the University of California, Merced (UCM). In the first year, 2014, kestrels occupied six of ten available nest boxes and fledged 15 young (Swarth et al. 2014). In January 2015, we added 20 more nest boxes to the Reserve. Study goals were to assess the population’s response to the increase in boxes, measure nest box occupancy and breeding productivity, band nestlings and adults, assess recapture rates of previously banded birds, and provide a hands-on research experience for UCM students.

Abstract The use of unmanned aerial systems (UASs) for remote sensing applications has increased significantly over the last decade. As more and more applications are developed and documented, the need for a guide for the development of a UAS remote sensing methodology has become apparent. A well-developed methodology is critical for the success of the project as it defines with clarity the end goal, the implementation, and the data collection strategy and provides metrics for success and project completion. Failure to accurately develop a methodology can lead to significant development delays, spiraling costs, or complete project failure. In this chapter, a guide to developing UAS remote sensing methodology is presented, focusing specifically on common UAS applications and payload equipment.

In light of recent U.S. Federal Aviation Administration (FAA) notices, there is a surge in the research and development of the `micro' class sUAS for commercial purposes. Natural gas production and distribution companies in particular are making an effort to develop aerial leak detection methods with sUAS. These efforts require a comprehensive evaluation of sUAS capabilities and the environmental disturbances introduced by the sUAS in order to accurately utilize data collected via onboard in situ methane gas sensors. Though many commercially available sUAS are on the market, the shape and arrangement of any system has significant impact on the aircraft's ability to accurately sense gas leaks. This paper explores using a 3DRobotics Iris+ quadcopter for gas sensing, paying particular attention to propeller disturbances introduced by the sUAS. The paper defines certain operating conditions in which the influence of propellers can be ignored. These results can be used in gas leak applications by examining the overall airflow dynamics of a commercially available rotary sUAS.

American Kestrel populations have declined since the 1960s, and the cause has yet to be identified. To further comprehend the decline of the American Kestrel, my study examined kestrel breeding productivity including occupancy, hatching success, and fledging success in nest boxes in conjunction with the identification of dietary resources. In this thesis, I monitored and documented the breeding success of the American Kestrel from nest boxes on the UC Merced’s Vernal Pools and Grassland Reserve from 2014-2016. I also analyzed food resources of the population and of individuals to quantify intraspecific and temporal dietary variation. I employed a multi-faceted approach to fully examine diet composition, breadth, and variation within a population. I used pellet and prey remain analysis as well as stable isotope analysis of carbon, nitrogen, and hydrogen in feathers and prey items. Nest box occupancy increased over the three-year study period from 60% to 80%. In 2016, the hatching and fledging success decreased drastically from 68% to 44% and 100% to 69%, respectively. Predation and nest failures occurred more frequently in 2016 compared to 2015 and 2014. Based on examination of prey and pellet remains diet composition was similar in 2015 and 2016, kestrel’s consumed mostly spiders, orthopterans, and small birds. In 2016, late nesting kestrels (May and June) consumed a greater number of orthopterans compared to kestrels that nested earlier in the season who ate spiders. Stable isotope analyses revealed that adults may feed at a higher trophic level than nestlings. Stable isotope mixing models indicated that adult diets in 2015 and 2016 were composed principally of orthopterans (2015 = 25-59%, 2016 = 18-60%) and birds (2015 = 28-58%, 2016 = 15-60%). In 2015, nestling diets were similar to adult diet with slightly different proportions of orthopterans (18-72%) and birds (17-47%). In 2016 nestlings, diets were comprised of orthopterans (15-58%) and mammals (9-56%). Overall, American Kestrels colonized the nest boxes rapidly, however, reducing predation of eggs and nestlings by mitigating predator access to nest boxes is crucial to increasing hatching and fledging success on the Merced Vernal Pools and Grassland Reserve. In terms of dietary resources, invertebrates are the largest proportion of the kestrel diet. Vertebrate consumption could also be an important factor in kestrel diet due to the higher amount of biomass in vertebrate prey. Preservation of key prey items is crucial to the conservation of the American Kestrel population. Changes in dietary resource abundance could be a predominant factor influencing the decline of the species.

PREMISE OF THE STUDY: Project Baseline is a seed bank that offers an unprecedented opportunity to examine spatial and temporal dimensions of microevolution during an era of rapid environmental change. Over the upcoming 50 years, biologists will withdraw genetically representative samples of past populations from this time capsule of seeds and grow them contemporaneously with modern samples to detect any phenotypic and molecular evolution that has occurred during the intervening time. METHODS: We carefully developed this living genome bank using protocols to enhance its experimental value by collecting from multiple populations and species across a broad geographical range in sites that are likely to be preserved into the future. Seeds are accessioned with site and population data and are stored by maternal line under conditions that maximize seed longevity. This open-access resource will be available to researchers at regular intervals to evaluate contemporary evolution. KEY RESULTS: To date, the Project Baseline collection includes 100–200 maternal lines of each of 61 species collected from over 831 populations on sites that are likely to be preserved into the future across the United States (∼78,000 maternal lines). Our strategically designed collection circumvents some problems that can cloud the results of “resurrection” studies involving naturally preserved or existing seed collections that are available fortuitously. CONCLUSIONS: The resurrection approach can be coupled with long-established and newer techniques over the next five decades to elucidate genetic change and thereby vastly improve our understanding of temporal and spatial changes in phenotype and the evolutionary processes underlying it.

Unmanned Aerial Systems are currently in use for a wide variety of applications with digital cameras and thermal cameras, but recent advances in Short Wave Infrared (SWIR) imaging systems or imagers have led to their commercial availability. The SWIR spectrum is a reflected light region and similar to near-infrared (NIR) is invisible to human eyes. The unique properties of this spectrum such as penetration of haze and smoke and its high sensitivity to moisture make it a potentially significant addition to small UAS (sUAS) applications. The use of sUASs to provide higher temporal and spatial resolutions has the potential for new applications otherwise impossible. In this paper, a tutorial introduction to the SWIR spectrum and its enabled potential applications for small UASs is presented. Furthermore this paper outlines how sUAS remote sensing applications stand to benefit from the use of SWIR imaging systems, as the effectiveness of SWIR bands in satellite imagery for metrics related to water content have already been demonstrated. Results from real world sUAS flight missions are included.

This report summarizes a survey project that used remotely-placed, automatic wildlife cameras to detect the possible presence of the San Joaquin kit fox (Vulpes macrotis mutica) at athe Merced Vernal Pools and Grassland Reserve, Merced, California. This subspecies has experienced population declines for many decades. By the 1950s the principal factors leading to this decline were habitat loss, degradation, and fragmentation associated with agricultural, industrial, and urban development in the San Joaquin Valley. More than 95% of potential kit fox habitat in the San Joaquin Valley has been converted to irrigated agriculture or to urban and industrial uses. Shoooting, trapping, poisoning, electrocution, and road kills are additional human-induced mortality factors. Natural mortality factors include predation, starvation, flooding, disease, and drought. In 1967 the San Joaquin kit fox was listed as a federal endangered species and in 1971 the state of California listed it as threatened. The San Joaquin kit fox has been sighted in several areas in eastern Merced County, but there have been no recent confirmed sightings or direct evidence of their occurrence in the Reserve. From March 2014 t May 2015 we placed auatomatic Bushnell brand wildlife cameras at 24 locations for a total of 35 deployments. Cameras were operated in a the field for over 12,600 hours. For this effort, 418 photographs and 274 videos have been archived. We captured photographic images of 9 mammal species, 26 bird species, and a single amphibian. No kit foxes were detected.

Night time flights are a relatively untouched field of application for small unmanned aerial systems (sUASs) in part due to the risks associated. However, there are many opportunities for agricultural, environmental or surveillance applications when night flying missions can be valuable or necessary. Undoubtedly, there are many risks associated with flying a sUAS at night that must be thoroughly addressed to ensure the safety to the public and property. While the U.S. Federal Aviation Administration (FAA) currently has severe restrictions for night flying missions, it is necessary to investigate methods to enable them in a safe manner. This paper, for the first time, introduces the development of a lighting system for a sUAS operating within line of sight and the development of mission protocols to address the human factors. The paper is based on the developments in night flying airworthiness and efforts in obtaining an FAA COA for night flying operations.

A leakage wetland on the north eastern edge of Lake Yosemite, Merced County, California, between the extensive grasslands of the Cyril Smith Trust Lands and the Gallo Brothers Ranch and the deep waters of Lake Yosemite,appears to be an important habitat for water birds. This wetland is about 1 km north west of UC Merced’s Vernal Pools and Grassland Reserve. I surveyed the birds at this wetland to collect information on avian abundance and diversity. A portion of this wetland has been proposed by the US Fish and Wildlife Service and California Audubon for consideration as a nesting habitat restoration project for the threatened Tricolored Blackbird. In anticipation of this future action, we wanted to understand the current bird use of this wetland. I documented the birds and their activities on fifteen weekly surveys between November 2014 and April 2015. Fifty one species and 2,100 individuals were documented. The muddy shoreline attracted various species of Calidris sandpipers and other shorebirds. Green -winged Teal and Bufflehead sought the shallow waters for food and places to rest. Northern Harriers, White-tailed Kites and other raptors were seen searching for prey or perching on fence posts. A Peregrine was seen on one day. We found that this small wetland supported a rich diversity and sizeable numbers of birds. Shallow wetlands are not common in eastern Merced County, making this an important habitat for waterbirds.

In spring 2014, the Reserve initiated a conservation project to expand American Kestrel (Falco sparverius) nesting populations into the Merced Vernal Pools and Grassland Reserve and to monitor their breeding success. Kestrels are common nesting birds in eastern Merced County, but there was no evidence that they currently nested in the Reserve. Kestrels are often seen foraging in the Reserve; we have observed them on 45 of 105 bird surveys conducted between January 2013 and August 2014 (Swarth unpubl. data). The maximum observed on one day was 12 in July 2013. The 6,500 acres in the Reserve represent a vast area of suitable nesting habitat for this small falcon. In February and March 2014, a team of undergraduate students fabricated and erected ten handcrafted; wooden nest boxes in the Reserve. The boxes were strategically placed on existing fence posts and were monitored in May and June. The objectives of this study were: •to attract kestrels to new, man-made nest boxes in the Reserve •to measure nesting productivity in the boxes •to band the kestre l chicks •to band any adults that could be captured at the nest Kestrels nested in 6 of 10 nest boxes and they produced a total of 15 fledged young which we banded. We also captured seven adults (6 females and one male) and placed bands on four birds. Three of the adult females had been banded on the Flying M Ranch; two in 2012 and one in 2013. This report summarizes the results of our study, the first conservation project to take place in the new Merced Vernal Pools and Grassland Reserve.

Patterns of dispersal and gene-flow in freshwater invertebrates have often been difficult to interpret. Despite the assumed high potential for dispersal, populations of freshwater invertebrates display high genetic differentiation over small distances. There have been several explanations posed for this gene flow dispersal paradox, including strong priority effects or low realized dispersal. This study explores the spatial genetic structure of the freshwater invertebrate Branchinecta lynchi, a threatened vernal pool inhabitant, at two scales with a goal to determine the scale at which gene flow is important in shaping these patterns. Vernal pools were sampled at two different localities the San Luis National Wildlife Refuge Complex and a preserve adjacent to the University of California, Merced. Individuals were genotyped using both the mitochondrial cytochrome oxidase I subunit (COI) and nuclear amplified fragment length polymorphisms (AFLPs). Pairwise Fst values showed that genetic structure for this species was high, however, the only geographic pattern that emerged was isolation by distance at the local scale for the COI marker. Discrepancies between mitochondrial and AFLP markers may be explained several ways, including genotyping error, sex-biased dispersal and/or the longer time to equilibrium of the nuclear genome. These results suggest that gene flow is important at the local scale, at least for mitochondrial DNA, while historical colonization patterns are likely maintained at the regional scale by priority effects. I infer that maintaining connectivity among vernal pool complexes through local dispersal vectors should be a management priority.

The vernal pool fairy shrimp (Branchinecta lynchi) (Eng et al. in J Crustac Biol 10:247–277, 1990) is broadly distributed throughout California’s Central Valley with disjunct populations in southern California and southern Oregon. A survey of genetic variation at the mitochondrial cytochrome c oxidase subunit I (COI) gene was conducted from individuals collected throughout the range of the species. Phylogenetic analysis of unique haplotypes could not resolve any significant genetic partitions below the species level. A detailed analysis of samples from two pools indicates that sample sizes underestimate overall variation, but that the general phylogeographic pattern still holds. Evidence was found for a putative long-distance dispersal event between Central Valley sites and the Oregon site. These results indicate that geographically limiting stochastic colonization followed by local diversification may be important in governing current genetic structure for this species. Future and current conservation/restoration efforts should recognize the geographic limitations to population structure for this species and focus on local endemic genetic variation.

Vernal pools are seasonal wetlands that harbor rare and endemic plants and animals. In California, vernal pools are often associated with Mima mounds, roughly circular soil mounds, found in grassland landscapes. The processes that form and maintain the mound-pool complexes have not yet been conclusively identified, even though such information is necessary to understand the effects that land use and climate change may have on the resilience and longevity of these important landscapes. One hypothesis for the origin and persistence of Mima mound—vernal pool systems proposes that pocket gophers (Rodentia: Geomyidae) maintain and possibly create the mounds by preferentially translocating soils towards mound centers as an adaptive response to perched water tables. The topographic characteristics and above-ground gopher activity of one of the largest remaining Mima mound—vernal pool systems in California were studied in order to investigate the gopher hypothesis. A detailed topographic survey of a 3,507 m2 region was conducted near the city of Merced, CA. Downslope erosion rates off Mima mounds were estimated using a mass balance model that incorporates a diffusive sediment transport law. The median calculated net erosion rate was 15 cm of soil per 1,000 years, while the measured rate of above-ground gopher sediment movement was approximately 57 cm of soil per 1,000 years. Assuming that some portion of the gopher sediment movement is in an upslope direction, these results suggest that gopher soil transport may be large enough to compensate for erosion, and this activity may play a dominant role in maintaining Mima mound—vernal pool systems. The results of this study were used to guide the development of a quantitative model of gopherdriven sediment transport on Mima mound—vernal pool landscapes. This model will be used to infer the origin of the landscapes and the rates of processes critical to their continued functioning and will also help to determine, quantitatively, the role of burrowing animals as “keystone” species on these landscapes.