Doctor of Philosophy

dissertationContemporary climate change is occurring at an unprecedented rate and is already dramatically affecting biodiversity worldwide. However, despite many well-documented changes, relatively little is known about specific mechanisms by which climate affects species. Investigating survival and recruitment in sub-optimal habitat can be as illuminating as population declines or extinctions, in terms of identifying mechanisms by which climate impacts species distributions. This dissertation incorporates aspects of global change ecology, disturbance ecology, and animal behavior to understand mechanisms of survival and recruitment of a climate-sensitive small mammal, the American pika (Ochotona princeps), in atypical habitats. I first elucidate mechanisms underlying low-elevation pika survival in the Columbia River Gorge, Oregon. This region is characterized by a high degree of moss cover, which appears to promote pika survival in two ways. First, by consuming the moss, which is available year-round, pikas are released from constructing large food caches for winter, a hallmark of their behavior in typical habitats. Second, the moss mediates the microclimates relevant to the species, in some cases completely decoupling ambient temperatures from those measured in the pikas’ rocky habitat. Pikas in this habitat also exhibit a high degree of behavioral plasticity in foraging strategy and microhabitat selection. Finally, I had a unique opportunity to build upon these results by investigating how pikas recolonize habitat severely disturbed by wildfire. Pikas quickly recolonized seemingly barren habitat, but animal abundance did not increase until after a threshold in vegetation availability was reached. Defining these habitat thresholds will significantly advance our understanding of pikas’ resource requirements and their sensitivity to disturbance. These results will also inform practical conservation measures for this species and other small alpine animals

Squirreling from Afar: Adapting Squirrel-Net Modules for Remote Teaching and Learning

The shift from face-to-face instruction to remote teaching and learning has proven to be a challenging endeavor for many reasons, including lack of time, resources, and inspiration. Lab courses, the “hands-on” portion of many curricula, may be especially difficult to adapt to online learning given the common use of specialized equipment, materials, and techniques that require close supervision. Without the time and resources to creatively modify existing activities or create new ones, remote lab courses run the risk of becoming less effective, equitable, and/or engaging. Squirrel-Net has created four field-based activities for biology labs that are easy to implement, highly flexible for different course aims, and readily adaptable to a remote learning environment. In this essay, we briefly summarize the modules and propose several ways that each can be adjusted to accommodate online teaching and learning. By providing authentic learning opportunities through distance delivery we hope to promote widespread student engagement and creative solutions for instructors

How Many Squirrels Are in the Shrubs? A Lesson Plan for Comparing Methods for Population Estimation

Estimating the population sizes of animals is a key skill for any student interested in ecology, conservation, or management. However, counting animals in natural habitats is difficult, and the many techniques that exist each rely on assumptions that can bias results. Most wildlife courses teach one or two of these methods, but rarely are students given an opportunity to compare approaches and explore how underlying assumptions affect the accuracy of estimates. Here, we describe a hands-on activity in which students estimate the size of a single population of animals using multiple methods: strip censuses, scat counts, and camera traps. They then compare the estimates and evaluate how the assumptions of each model (e.g., random use of habitats and animal behavior) bias the results. Finally, students submit their data to a national database that aggregates observations across multiple institutions as part of Squirrel-Net (http://squirrel-net.org). They can then analyze the national dataset, permitting exploration of these questions across a broader variety of habitats and species than would be possible at any single institution. Extensions of this activity guide students to enumerate the advantages and disadvantages of each method in different contexts and to select the most appropriate method for a given scenario. This activity and the database focus on estimating population sizes of squirrels, which are diurnal, charismatic, easily identified, and present in a wide range of habitats (including many campuses), but the same methods could be broadly used for other terrestrial species, including birds, amphibians, reptiles, or invertebrates

Squirrels in Space: Using Radio Telemetry to Explore the Space Use and Movement of Sciurid Rodents

Biotelemetry is used by researchers to track the interactions of animals with each other and the environment. While advancing technology has led to the development of numerous biotelemetry tools, radio telemetry remains the most common method for tracking small animals. Moreover, telemetry tracking of animal movement is an important skill for entry-level positions in wildlife biology. Thus, hands-on experience using radio telemetry provides students with an advantage as they pursue careers in wildlife biology, as well as an opportunity to build science process skills. We present a lesson in which students use radio telemetry to track animals; collect, analyze and interpret spatial data; and consider its applications to local wildlife management and conservation. Students submit their data to a national database collecting observations from multiple institutions as part of Squirrel-Net (http://squirrel-net.org). The aggregated data allows students to generate and test hypotheses across a broader variety of species and habitats than would be possible at any single institution. The lesson is designed for adaptation to diverse educational contexts, from a single two-hour laboratory period (basic skills acquisition) to a semester-long student-driven research project (open inquiry Course-based Undergraduate Research Experience, or CURE). Although this activity and the national database focus on spatial data for squirrels, which are diurnal, charismatic, easily identified, and present on most college campuses, the same methods and materials can be modified for any animal capable of carrying a radio transmitter and being safely tracked by students

Sorry to Eat and Run: A Lesson Plan for Testing Trade-off in Squirrel Behavior Using Giving Up Densities (GUDs)

All animals need to find and compete for food, shelter, and mates in order to survive and reproduce. They also need to avoid being eaten by predators. Optimal foraging theory provides a framework to examine the trade-offs individuals make while foraging for food, taking into account an animal’s body condition, predation pressure, quality of food resources, and food patch availability in the habitat. Here we describe an activity that uses Giving Up Densities (GUDs), which could be used as part of a course-based undergraduate research experience (CURE) or as a stand-alone activity. GUDs provide an experimental approach to quantify the costs and benefits of foraging in a particular patch and is simple to measure in that it is literally the density of food remaining in a patch. However, its interpretation allows students to compare foraging decisions under different environmental conditions, between species, or with different food sources. This activity was designed to study the foraging behavior of squirrels, which are active during the day, forage on seeds, and are found on and around many college campuses, but it can be adapted to nocturnal animals, birds, or other vertebrates. This module is hands-on. Students weigh seeds, sift sand, walk out into the field with bags of sand and trays, and analyze data. The module can be designed at various levels of inquiry to suit the needs of a particular class. Further, students can work individually, in pairs, or in teams. Finally, students and instructors are encouraged to upload their data to a national dataset, which is available to instructors for use in the classroom to broaden the possible hypotheses and analyses students can explore

An Introduction to the Squirrel-Net Teaching Modules

Although course-based undergraduate research experiences (CUREs) are gaining popularity in biology, most are designed for benchwork-based laboratory courses while few focus on field-based skills. Many barriers to implementing field CUREs exist, including the difficulty in designing authentic research that can be accomplished in a limited lab timeframe, permitting and liability issues, and problems gathering sufficient data to meaningfully analyze. Squirrel-Net (http://squirrel-net.org) is a consortium of mammalogists from eight different institutions who have worked to overcome these limitations through four field-based CUREs focused on sciurid rodents (e.g., squirrels, chipmunks, marmots, prairie dogs). Each module is linked to a national dataset, allowing for broader and more complex hypotheses and analyses than would be possible from a single institution. Modules have been field tested at different institutions and are easily implemented and highly flexible for different courses, levels of inquiry, habitats, and focal species. Beyond the basic lesson plan, each module also provides suggestions for adaptation at different levels of inquiry and scaffolding across a course or an entire curriculum. Moreover, our website provides templates to help lower barriers to CURE implementation (e.g., selecting a field site and writing institutional animal care protocols). Here, we introduce Squirrel-Net and give an overview of the four CURE modules. Additionally, we demonstrate how the modules can be used singly or together to provide authentic research experiences to a diversity of undergraduates

Squirreling Around for Science: Observing Sciurid Rodents to Investigate Animal Behavior

Hands-on research experiences are important opportunities for students to learn about the nature of inquiry and gain confidence in solving problems. Here, we present an inquiry-based lesson plan that investigates the foraging behavior of sciurid rodents (squirrels) in local habitats. Squirrels are an ideal study system for student research projects because many species are diurnal, easy to watch, and inhabit a range of habitats including college campuses. In this activity, instructors identify appropriate field sites and focal species, while students generate questions and brainstorm predictions in small groups regarding factors that might influence behavioral trade-offs in sciurids. Students conduct observational surveys of local squirrels in pairs using a standardized protocol and upload their data to a national database as part of the multi-institutional Squirrel-Net (http://squirrel-net.org). Instructors access the nationwide dataset through the Squirrel-Net website and provide students with data for independent analysis. Students across the country observe and record a range of squirrel species, including behaviors and habitat characteristics. The national dataset can be used to answer student questions about why squirrels behave in the way they do and for students to learn about authentic analyses regarding behavior trade-offs. Additionally, the lesson is designed to be modified across a range of inquiry levels, from a single two-hour laboratory activity to a unit- or semester-long student-driven course-based research experience. Our activity highlights the value of using observational data to conduct research, makes use of the Squirrel-Net infrastructure for collaboration, and provides students equitable access to field-based projects with small mammals

Temporal vs. spatial variation in stress-associated metabolites within a population of climate-sensitive small mammals

Temporal variation in stress might signify changes in an animal&rsquo;s internal or external environment, while spatial variation instress might signify variation in the quality of the habitats that individual animals experience. Habitat-induced variationsin stress might be easiest to detect in highly territorial animals, and especially in species that do not take advantage ofcommon strategies for modulating habitat-induced stress, such as migration (escape in space) or hibernation (escape intime). Spatial and temporal variation in response to potential stressors has received little study in wild animals, especiallyat scales appropriate for relating stress to specific habitat characteristics. Here, we use the American pika (Ochotona princeps),a territorial small mammal, to investigate stress response within and among territories. For individually territorial animalssuch as pikas, differences in habitat quality should lead to differences in stress exhibited by territory owners. We indexedstress using stress-associated hormone metabolites in feces collected non-invasively from pika territories every 2 weeks fromJune to September 2018.We hypothesized that differences in territory qualitywould lead to spatial differences in mean stressand that seasonal variation in physiology or the physical environment would lead to synchronous variation across territoriesthrough time.We used linear mixed-effects models to explore spatiotemporal variation in stress using fixed effects of day-ofyearand broad habitat characteristics (elevation, aspect, site), aswell as local variation in habitat characteristics hypothesizedto affect territory quality for this saxicolous species (talus depth, clast size, available forage types). We found that temporalvariation within territories was greater than spatial variation among territories, suggesting that shared seasonal stressors aremore influential than differences in individual habitat quality. This approach could be used in other wildlife studies to refineour understanding of habitat quality and its effect on individual stress levels as a driver of population decline.</p

microfluidic platform for 3-D neuron culture

Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007.Includes bibliographical references (p. 51-53).Neurodegenerative diseases typically affect a limited number of specific neuronal subtypes, and the death of these neurons causes permanent loss of a specific motor function. Efforts to restore function would require regenerating the affected cells, but progress is limited by a narrow understanding of the mechanisms that underlie the generation of these neurons from their progenitor cells. In order to prevent neuronal degeneration and potentially repair or regenerate the damaged motor output circuitry, it will be necessary to understand the molecular and genetic factors that control, direct, and enhance differentiation, axonal projection and connectivity. While techniques are available to separate specific populations of neurons once they are fully-differentiated, current methods make it nearly impossible to monitor or control the development of a neural precursor in standard open culture. To carry out directed differentiation experiments effectively, it will be critical to control how signals are introduced to the cells. In this study, we present a microfluidic system to address the limitations of previous research.(cont.) The device is capable of generating a controlled gradient of chemoattractant or growth factor of interest and directing axonal growth through an extra-cellular matrix material. Once the cells have grown into the device, signals and gradients can be applied directly to either the cell bodies or the axons. This device will serve as a platform technology for future experimentation with biomaterial scaffolds for neural tissue engineering, drug design or testing, and eventually directed differentiation of neural precursor cells.by Johanna Varner.M.Eng

The importance of biologically relevant microclimates in species distribution models and habitat suitability assessments

Data SetPredicting habitat suitability under climate change is vital to conserving biodiversity. However, current species distribution models rely on coarse scale climate data, whereas fine scale microclimate data may be necessary to assess habitat suitability and generate predictive models. Here, we evaluate disparities between temperature data at the coarse scale from weather stations versus fine-scale data measured in microhabitats relevant to a climate-sensitive mammal, the American pika (Ochotona princeps). We collected temperature data in occupied habitats predicted to be suitable (high elevation) and unsuitable (low elevation) by the bioclimatic envelope approach. At low elevations, talus surface and interstitial microclimates drastically differed from nearby weather stations and ambient temperatures measured on-site. Interstitial talus temperatures were decoupled from high ambient temperatures, resulting in disparities up to 30°C between these two measurements. Microhabitat temperatures were also highly heterogeneous, such that temperature measurements within the same patch of talus were not more correlated than measurements at distant patches. Experimental manipulations revealed that vegetation cover can cool the talus surface by 10°C during the summer, which may contribute to this spatial heterogeneity. Finally, low elevation microclimates were milder and less variable than typical alpine habitat, suggesting that, counter to species distribution model predictions, these seemingly unsuitable habitats may actually be better refugia under climate change. These results highlight the importance of fine-scale microhabitat data in habitat assessments and underscore the notion that some critical refugia may be counterintuitive