<p>Western Pond Turtles, <i>Emys</i> (<i>Actinemys</i>) <i> marmorata</i>, were captured (n=173) in 2011 (wet year) and 2012&ndash;2013 (successively drier drought years) along upper Coyote Creek, an intermittent stream in central California. Males outnumbered females 2.8:1, juveniles less than 120 mm long made up 26% of captures, growth rates varied among individuals, and little growth occurred in turtles older than 10 years. I radio-tracked turtles from May 2011 through August 2013 to ascertain movements and seasonal habitat use. Males had much larger home ranges than females (means of 2281 m for males and 501 m for females in 2012), and males moved extensively in April and May, during the apparent breeding season. Turtles preferred deep and complex pools, complex runs, and backwaters. Turtles left the stream for upland habitats in late spring and summer as stream flow ceased and pool connectivity was broken. There was substantial variation in departure dates among individuals and between wetter and drier reaches. Mean departure date was 16 August in 2011, but decreased to 20 July in 2012 and 28 June in 2013, as the drought intensified. Upland sites were mostly within 100 m of the stream, beneath dried leaves and/or thatch, and on slopes varying from flat to over 40%. Turtles remained upland for almost seven months in 2011&ndash;2012, although there was much variation. Mean return to stream dates were 27 February (males) and 16 March (females). </p>

<p> As the southern sea otter (<i>Enhydra lutris nereis</i>) range expands into northern and southern California, it will encounter estuaries that have been historically occupied by sea otters. Understanding how otters use re-colonized estuarine environments will inform how estuaries might be managed to encourage future sea otter range expansion. This project addressed the question: how do southern sea otters use space in the unique estuarine habitats of Elkhorn Slough? I compared the locations and behaviors of 25 individual sea otters of different status (male, female, and female with pup) among eelgrass, saltmud, saltmarsh, tidal creek, and main channel habitats in Elkhorn Slough. From these data I created a synoptic model to predict space use for resident otters of Elkhorn Slough based on sex, behavior, home range, and habitat distribution. Ninety percent home ranges calculated from the model indicated that females used larger home ranges than males in the slough, but both sexes had smaller home range areas than otters using the rocky outer-coast habitats of the Monterey Peninsula. In Elkhorn Slough, important habitats associated with resting included tidal creeks (for females only) and eelgrass, whereas the main channel was important for foraging behaviors of both sexes. Although using land habitats, sea otters were most likely to be found within 50 m of water. Protection of similar resting and foraging habitats in prey-rich estuaries colonized in the future will promote southern sea otters recovery by allowing them to re-colonize historically important estuarine habitats. </p>

<p> Evolutionary biologists are supremely interested in the events that cause populations to diverge and speciate, and the mechanisms that maintain divergence over time. Here, I investigate the evolutionary history of a boreal bird species complex. Boreal bird species are co-distributed, diverged during the Pleistocene, and generally have patterns of genetic divergence that are consistent with a single &ldquo;boreal&rdquo; clade in northern and eastern North America. The Gray-cheeked Thrush species complex, however, shows a possible species break in eastern North America between the Bicknell&rsquo;s Thrush (<i> Catharus bicknelli</i>) and Gray-cheeked Thrush (<i>Catharus minimus </i>). Using population genetic and genomic analyses of the largest sampling to-date of either species, I find that the eastern break indeed coincides with a species-level divergence, although low levels of admixture in a few individuals and one probable hybrid hint at the possibility of occasional hybridization. Species distribution models (SDMs) of the Last Glacial Maximum revealed that divergence may have been maintained by residence in different late-Pleistocene refugia. However, because speciation occurred mid-Pleistocene, I examined the geographical context of divergence of the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush using multivariate analyses and ecological niche modeling techniques of local-scale habitat data and broad-scale climate and tree species distributions. Local-scale habitat analyses reveal that the thrushes breed at sites with unique tree species composition, physiognomy (forest structure), and ground cover characteristics; furthermore broad-scale analyses reveal that niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in their speciation. This dissertation supports the hypothesis that the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush are distinctive species that breed in divergent local- and broad-scale niches and emphasizes that this species-level divergence seems unique among boreal bird species.</p>

<p>The decline of the Oregon Spotted Frog (<i>Rana pretiosa</i>), a Pacific Northwest endemic now federally listed as threatened, has been attributed to several aspects of ecosystem alteration, primarily habitat degradation and loss. The introduced American Bullfrog (<i>Rana (Aquarana) catesbeiana </i>) has been widely implicated in those declines, but the basis of that contention has been difficult to characterize. The bullfrog occurring at every site of recent Oregon Spotted Frog extirpation has focused concern about its impact. </p><p> Here, I present a suite of interconnected studies that examine the behavioral ecology of both species to better understand the potential for bullfrog-mediated Oregon Spotted Frog extirpation. I quantified Oregon Spotted Frog anti-predator behavior from the only known population successfully co-occurring with bullfrogs (Conboy Lake) and a population devoid of bullfrog impact (Big Marsh), and compared these behaviors to the predatory traits of the bullfrog. The initial study revealed that captive-reared individuals from the Oregon Spotted Frog population that has successfully co-occurred with bullfrogs respond faster to a predatory stimulus (measured as latency to response) than Oregon Spotted Frogs from a population not to exposed to bullfrogs. Subsequent field investigations of the approach distance allowed by a predator stimulus before taking evasive action (termed the flight initiation distance: FID) conducted with the Oregon Spotted Frog population co-occurring with bullfrogs first demonstrated that FID of recently metamorphosed bullfrogs is consistently greater than that of recently metamorphosed Oregon Spotted Frogs. Further, examination of FID across all post-metamorphic age classes of Oregon Spotted Frogs revealed that older frogs do not allow as close approach as recently metamorphosed Oregon Spotted Frogs. This age class shift in FID did not occur in the Oregon Spotted Frog population not exposed to bullfrogs. In the latter population, FID did not differ among age classes. </p><p> Since the bullfrog might be driving this age-based change in anti-predator behavior, I explored the variation in strike distance of bullfrogs from the site of co-occurrence in both the field and laboratory to determine the extent of overlap with Oregon Spotted Frog FID. I found that the bullfrog strike distance significantly overlaps the FID of all ages of Oregon Spotted Frogs from the bullfrog-free site but only that of youngest (recently metamorphosed) frogs at the site of co-occurrence. Older Oregon Spotted Frogs from the site of co-occurrence generally escaped at distances greater than the strike distance of bullfrogs. </p><p> I also collected > 880 bullfrogs from the site of co-occurrence and analyzed the stomach contents to assess their dietary trends. I found that bullfrogs consume Oregon Spotted Frogs at the site, but do not eat the larger (older) frogs. Moreover, the body size ratio between Oregon Spotted Frogs as prey and bullfrogs as predators suggests that nearly all of the adult size distribution of bullfrogs at Conboy would be incapable of preying on adult Oregon Spotted Frogs. </p><p> Collectively, these studies strongly suggest that bullfrogs have altered the escape behavior of Oregon Spotted Frogs at Conboy Lake and that most adult Oregon Spotted Frogs at Conboy may have a size-based release from predation by bullfrogs. Implicit in this finding is that bullfrogs may pose a real threat via predation to other Oregon Spotted Frog populations with which they might come into contact where the distribution of bullfrog body sizes differ substantially from that at Conboy Lake. </p>

<p> Culverts are ubiquitous in urban and natural environments, installed to provide road access and erosion control, but often impact fish movements in freshwater habitats. Effects of culverts on marine and estuarine fish are not well-studied. This study aimed to understand the potential impacts of a culvert, which connects a large tidal bay and a coastal lagoon, on the movements of several species of fish. Habitat characteristics of both sites were analyzed to better understand these movements, including water parameters, sediment characteristics, and zooplankton, benthic macroinvertebrate, and small fish communities. The two habitats differed in terms of temperature, salinity, dissolved oxygen, zooplankton abundance, and community composition of zooplankton, benthic macroinvertebrates, and small fish. The culvert and associated grate limited large fish from moving between the two habitats likely due to body size and other morphological characteristics. Removing this barrier and replacing it with an open channel would increase connectivity between these two habitats which could improve trophic quality in the lagoon habitat and increase functionality overall.</p><p>

<p> Information about population dynamics, life history variation, and connectivity patterns of threatened cutthroat trout (<i>O. clarkii</i> spp.) is critical for effective management and restoration. The Lahontan cutthroat trout (<i>O. c. henshawi;</i> LCT) is classified as threatened under the Endangered Species Act due to widespread extirpations across its range, and is at increased risk due to drought, habitat fragmentation, and climate change. This study was conducted in the Summit Lake Basin, NV (USA), which has a population of LCT that resides in Summit Lake and its tributary stream network. The objectives of this research were to (1) examine the population dynamics of stream- and lake-dwelling LCT in the context of drought, (2) quantify the amount of stream-resident versus adfluvial life histories in an adfluvial spawning tributary, and (3) identify the level of population connectivity between stream-resident and adfluvial components of the population. Chapter 1 shows that stream-dwelling trout were more resilient to drought disturbance and that drought refugia in the stream contribute to their resilience. Chapter 2 provides evidence for stream-residency in addition to high population connectivity across the lake and stream environments that is likely to increase in high flow years. While LCT and other cutthroat species have innate characteristics that allow them to persist in dynamic and harsh environments, this research highlights the importance of drought refugia and landscape connectivity to the long-term persistence and viability of co-occurring adfluvial and stream-resident fish.</p><p>

<p> Infectious disease can play a vital role in species conservation, as some diseases can cause massive population die-offs. In North American tortoises, population declines have been attributed to an upper respiratory tract disease, but the importance of this disease within and among tortoise hosts is controversial. In this dissertation, I use samples from the upper respiratory tract of wild tortoises representing multiple species in the genus <i>Gopherus</i> to answer questions regarding pathogen prevalence and co-infection, pathogen genetic diversity, and the ecology of pathogens within the upper respiratory tracts of tortoises. Using genetic methods including polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and 454-pyrosequencing, the data presented herein supports hypotheses that pathogens in this disease system interact with each other and with other microbes in the respiratory tract differently in different tortoise host species. </p><p> In this system, both transmission and disease progression are found to be extremely slow in these long-lived hosts. Though pathogens were widespread among the sampled tortoises, few individuals were found with clinical signs of disease. Few individuals capable of transmitting disease (requiring nasal mucus and pathogen), along with few opportunities for pathogen transmission (requiring long periods of direct contact), indicate that it is unlikely for tortoises to fully clear themselves of these microbes without risk of the pathogen&rsquo;s extinction. If this is the case, then it is likely that more tortoises than we can detect have these microbes in their upper respiratory tracts. With this in mind, and considering the abundance of visibly healthy tortoises over ill tortoises, my collaborators and I suspect that pathogens in this system likely form commensal relationships with their hosts much of the time, until a stressor alters the system and leads to a parasitic interaction. </p><p> The results of this dissertation indicate that this disease is context dependent, depending on the host and likely other microbes in the community. Our understanding of the ecology of this disease system would greatly benefit from experimental inoculation and long-term resampling studies.</p><p>

<p>Within the San Francisco Bay Area, Western Snowy Plovers (<i>Alexandrinus nivosus nivosus</i>) nest and winter in former salt ponds. They face a number of threats including human-altered habitats and high levels of predation by mesopredators and raptors. The South Bay Salt Pond Restoration Project (the Project) is a large wetland restoration project that will change and potentially eliminate Snowy Plover habitat in the region. As the Project returns salt ponds to tidal wetland, there will be less of the dry, flat, and sparsely vegetated habitat that plovers need for breeding and wintering habitat. A greater understanding of the specific microhabitat requirements for high quality plover foraging sites is needed. In particular, it is important for managers to understand what constitutes high quality wintering habitat for Snowy Plover numbers. This study assessed the characteristics at sites where Snowy Plovers winter in former salt ponds, especially habitat traits related to promoting plover foraging. Analysis of plover foraging habitat showed that plovers were associated with increasing plant height, water cover, and distance from perches and levees. This information is designed to inform restoration and management decisions in efforts to meet Snowy Plover recovery goals in the South San Francisco Bay. </p>

<p> Several avian species exhibit reduced hatching success as a result of mercury contamination, but the mechanism by which this occurs is unknown. We examined egg turning rates and egg temperatures, two important determinants of egg hatchability, in relation to egg mercury contamination of Forster&rsquo;s terns (<i>Sterna forsteri</i>) in San Francisco Bay. Here, we used artificial eggs containing a data logger with a 3-D accelerometer, a magnetometer, and a temperature thermistor to monitor parental incubation behavior (sampled at 1 Hz) of 186 tern nests. Overall, adults turned their eggs an average of 3.8 &plusmn; 0.8 SD turns h^-1, which is nearly two times higher than that of other seabirds. Egg turning rates also increased with nest initiation date. Changes about the yaw axis (side-to-side egg movements) were the most prominent aspect of egg turning (224 &plusmn; 4.7 degrees h^-1), though roll and pitch (up-and-down movements) also showed substantial changes (149 &plusmn; 2.5 degrees h^-1 and 89 &plusmn; 1.1 degrees h^-1, respectively). Despite the high variability in egg turning rates among individuals (SD = 0.8 turns h^-1), the rate of turning was not correlated with mercury concentrations in surrogate eggs collected from the same nest. Our results indicate that egg turning rates in Forster&rsquo;s terns are high, but unrelated to mercury contamination.</p>

<p> The bog turtle (<i>Glyptemys muhlenbergii</i>) is listed as threatened under the U.S. Endangered Species Act primarily because of the loss and degradation of its specialized wetland habitat. Adequate nesting habitat may be a limiting factor for bog turtle recovery, and nesting habitat creation or expansion may be an effective conservation tool but only if managers understand nesting behaviors, habitat requirements, and threats to nest success. The objective of this study was to understand the nesting ecology of the bog turtle and to use this information to suggest improvements to bog turtle management. I used radio telemetry to locate nesting females. I then used nest location and maternal genetic microsatellite data to investigate nest-site fidelity and natal homing. I collected microhabitat data at each nest and random points in both spring and fall at three spatial scales to understand nest-site selection. I also studied nest success with and without predator excluder cages to determine if predator excluders reduced predation or altered nest conditions. I found evidence that females display nest-site fidelity to nest-site areas but no evidence for natal homing. Bog turtles nested in relatively small patches of habitat in close proximity to water or saturated soil with low densities of woody stems and low percent cover of woody vegetation, forbs, and ferns. Predator excluders reduced predation by &sim;40% while having no effect on nest temperatures, incubation periods, or underlying (disregarding predation) nest success. Given the results of this research, I conclude that the creation of new nesting areas could be a viable conservation tool, as females do not always return to the same nest-site area. Managers should create or maintain small patches of open-canopy habitat with reduced woody vegetation in areas that have consistent moisture from spring to fall. Increasing the availability of nesting areas may eventually lead to increases in recruitment, but if predation pressures are high, managers should also deploy predator excluders. This is the first study to examine the behavioral drivers of bog turtle nest-site selection and the efficacy of predator excluders on bog turtle nests.</p>