Habitat loss is one of the main threats to global biodiversity and ecosystem services. Human development, resource extraction, and climate change all contribute to the degradation or loss of ecosystems worldwide and in California. To counter these impacts, development may be regulated by following a general mitigation hierarchy where the priority is to first avoid injury to natural resources, then minimize remaining impacts, and finally, compensate for any unavoidable losses. This last step, known as compensatory mitigation, can offset environmental impacts through the restoration, enhancement, preservation, or creation (i.e., establishment) of habitat. My research focuses on three aspects of this process: the quantification of impacts to habitat, the cumulative effects of the permitted development, and strategies to improve outcomes of restoration projects. In Chapter 1, I review the cumulative impacts of development permitted by the California Coastal Commission between 2010 and 2018. Wetland habitat was the most frequently impacted, and mitigation usually took the form of restoration and was predominantly on-site and in-kind. I also provide recommendations for improving the compensatory mitigation process. In Chapter 2, I review metrics and tools that quantify impacts to seagrasses, kelps, and other macroalgae. I provide a list and chart to identify tools and applications best suited for ecological valuation and equivalency analysis for mitigation. In Chapter 3, I demonstrate restoration actions that can establish cover and survivorship of a dominant species at a restored tidal marsh in central California. Irrigation and larger plants provided the most cost-effective strategies in the short-term, when compensatory mitigation projects are likely to be held to performance standards. The topics of this thesis are varied but all relate back to the process of compensatory mitigation, the goal of which is to ensure the persistence of natural resources for present and future generations.

In the face of swift anthropogenic change, it is essential to examine the broad ecological context for species of concern using a variety of approaches in order to understand their interactions in a natural context. Host-pathogen relationships offer a close interaction to examine how each are acted upon by biotic and abiotic conditions. Batrachochytrium dendrobatidis, an emerging infectious disease of amphibians, has been implicated with wholesale loss and marked declines in amphibian species across the globe, thus understanding its dynamics across amphibian hosts and in complex, natural environments is a key area for conservation focus.

For this dissertation, I tested the importance of various biotic and abiotic factors in the relationship between B. dendrobatidis and three co-occurring amphibian hosts, as well as across metrics of host physiological health. In Chapter 1, I ranked environmental conditions that favor B. dendrobatidis success in two native and one introduced amphibian tadpole species. I found top models favoring B. dendrobatidis infection included: a) a positive relationship with amphibian community diversity, b) elevated B. dendrobatidis infection in co-occurring infected amphibian species, and c) a varying, but strong relationship with assorted vegetative cover types. In Chapter 2, I asked which factor, Bd infection, amphibian community diversity, and predator diversity, best explained tadpole physiological metrics including, body condition, total white blood cell count, and neutrophil to lymphocyte ratio, for three species of tadpole.

The most important factors predicting tadpole body condition varied markedly by species. Tadpole body condition was positively correlated with Bd infection and predator diversity for the introduced Lithobates catesbeiana, negatively correlated with amphibian community diversity for Rana draytonii, and positively correlated with predator diversity index for Pseudacris regilla.

While the only factor that impacted neutrophil to lymphocyte ratios was Bd infection in bullfrogs, with white blood cell counts, I again saw a difference in the way the different species responded to the various stressors in their environment. Bd infection was the top driver in elevating white blood cell counts in P. regilla, while only amphibian diversity had this effect for R. draytonii. Predator diversity had a negative effect on white blood cell counts in L. catesbeiana. This diversity of responses is useful from a management perspective, as it may allow conservation practitioners to shift habitat suitability to species of interest. Given the differences in how the amphibians respond, a handful of concrete management recommendations for native amphibians emerge:

1. Decrease Bd by decreasing co-occurring species; provide ponds specialized for species in a site, thus decreasing in-pond diversity, but maintaining amphibian diversity across the site

2. Increase sunning sites for R. draytonii and P. regilla and maintain habitat complexity

3. Create or maintain smaller, exposed, ephemeral ponds for P. regilla

4. Create or maintain larger, shallower, ephemeral ponds for R. draytonii

4. Improve water quality for R. draytonii

5. Decrease amphibian species diversity by controlling introduced species, particularly bullfrog tadpoles, adults, and introduced fish

My dissertation demonstrates the importance of taking a broad approach to examine ecological relationships by designing studies across various species, combining perspectives such as pathogen success and metrics of host physiological stress, and taking into account a suite of likely interacting biotic and abiotic factors. Broad studies such as this can help to avoid spurious conservation decisions given limited time and resources to protect rapidly declining species.

Disease outbreaks are becoming more frequent as anthropogenic changes to ecosystem function stress species and create conditions favorable for pathogen infection. Marine outbreaks that were once locally constrained are re-emerging as large-scale epidemics with heightened mortality, decimating populations across multiple ocean basins. Effective prediction of future disease impacts requires a better understanding of their causes and consequences. In this dissertation, I explore the connections between environmental conditions, recovery of decimated host populations, and multispecies interactions to examine how a marine epidemic affects marine communities. I focus on a recent Sea Star Wasting Syndrome outbreak in rocky intertidal habitats along the Pacific coast of North America, with emphasis in Central California. Sea stars are an iconic intertidal species to many coastal visitors. Their absence has generated heightened public awareness of current challenges to ocean health, providing many opportunities for engagement in the process and outcomes of ecological research.

In my first chapter, I use data from long-term ecological monitoring to assess the recovery of sea star populations and predation pressure in the years immediately following the outbreak. I show that while sea star numbers are rebounding, these populations are made of smaller individuals that do consume the same amount of food. In my second chapter, I explore potential conditions associated with outbreak timing using data from citizen scientists and researchers combined. I identified associations between Sea Star Wasting Syndrome appearance, low tide exposure duration, proximity to other infected sites, and chlorophyll a concentration, though the relative importance of these factors varied across geographic regions of the coast. In my third chapter, I take advantage of a natural experiment created by the loss of predatory sea stars to measure the consequences of the outbreak on the intertidal community. I found that while mussels, the sea stars’ primary prey, had increased their coverage, they had not displaced the species living below the mussel bed. At local field sites, mussel increases were positively correlated with mussel recruitment and not pre-outbreak sea star levels. However, a coast-wide scale, pre-outbreak sea star density was positively correlated with pre-outbreak sea star density. Finally, I conclude with key insights from this work. My dissertation provides evidence that sea star wasting does not have uniform causes or population-level and community-level consequences across coastal regions. I discuss the value of long-term ecological monitoring and citizen science as critical information sources in the process of evaluating disease impacts.

A central goal of ecology is to understand the causes of spatial and temporal variation in the composition and structure of ecological communities. One way a species distribution may vary within its range is through changes in its vertical distribution. Variation in vertical distributions can influence local species abundance, which in turn can determine species ranges and the structure of communities. For my dissertation research, I investigated latitudinal gradients of rocky intertidal community structure along 5500km of coastline in the northeast Pacific Ocean. The spatially explicit design of this study allows the explicit answering of many ecological questions at a fine resolution for a large suite of species across their geographic range. By mapping the x, y, and z coordinates of intertidal species at cm scale accuracy, I determined the distribution patterns for abundance, vertical extent, and upper vertical limit of species across their range. I find the abundant center distribution, ramped south distribution and non-directional distribution are the most common distribution patterns. The distribution patterns are consistent for the majority of species between abundance, vertical extent and upper vertical limit. Next, I test the explicit hypothesis that vertical distribution of species varied progressively with latitude using linear regressions, which examined the relationship between community similarity and the vertical distribution of species. For many of the abundant species of intertidal invertebrates and algae that constitute those communities, sites that have a similar vertical distribution of species also have a similar community structure. Finally, I focus on central California to determine how the vertical distribution of species is explained by environmental factors. Of the nine abiotic factors investigated, reef slope, rock color, solar incidence, rock hardness and reef length explained the variability of species' upper limit. These abiotic factors influence the temperature of the reef which relates to desiccation stress. Whereas the vertical extent of species is explained by aspects of the reef's geomorphology that influences the abundance and reach of mobile consumers such as reef slope and rugosity. Across 32̊ of latitude, species' vertical distribution change in relation to abiotic forces and underlie the community structure patterns within the rocky intertidal.

The giant kelp, Macrocystis pyrifera, exists as one species with distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is unclear. One ecomorph (“pyrifera”) has a conical, mound-shaped base while the other (“integrifolia”) has a flattened, elongated base that forms denser kelp beds. My research on the drivers of these distinct phenotypes can inform decisions about management and restoration of kelp populations, as well as selective breeding for certain traits in aquaculture. First, I assessed the patterns of giant kelp ecomorph spatial distribution and genetic differentiation across its Western Hemisphere range. I collected samples from 18 kelp populations in Chile and California and used whole-genome sequencing to evaluate the degree of genetic divergence among populations. My results demonstrate that “pyrifera” and “integrifolia” are genetically distinguishable, yet divergence patterns differ between Northern and Southern Hemispheres. Next, I empirically tested the effect of local environment on giant kelp morphology. I collected reproductive tissue from adult individuals of both ecomorphs naturally occurring at the same location, cultured the spores in the laboratory, and outplanted the resulting baby kelp to the seafloor in a common ocean environment. Weekly monitoring revealed distinguishing morphological features at multiple developmental stages, ultimately culminating in morphologically distinct adults which also differed in reproductive timing. By including a mixed treatment with equal numbers of spores from each ecomorph, I observed the morphologies that emerge in a competitive context. This study also revealed for the first time how the characteristic “integrifolia” morphology forms in nature. Finally, I investigated ecomorph variation in production of alginate, one of the most commercially important chemicals from kelp. I compared alginate yield and composition of “pyrifera” and “integrifolia” populations across varied environments using kelp samples from 15 populations (a subset of those used in the genetic differentiation study). Alginate yield and composition were significantly different between the two morphs and were also related to the depth at which the kelp grew. Collectively, this work reveals a genetic basis to giant kelp morphology as well as eco-physiological divergence between the two ecomorphs, giving reason to consider them as distinct species.

Solving the environmental problems created by the increasing impact of humans on our planet will require a collaborative effort between scientists, practitioners, and policymakers. In this dissertation, I provide an example of how ecologists can contribute to and benefit from environmental problem solving. I focus on rocky intertidal habitats along the coast of central California (USA), which have high levels of biological diversity and provide a rich environment for education, research, and recreation. These habitats are negatively affected by a number of anthropogenic activities and, as a result, there is a growing interest in restoration strategies, particularly for addressing the impacts of oil spills.

In the following chapters, I explore connections between ecological concepts, restoration science, and mitigation policy to guide management of rocky intertidal habitats. In my first data chapter, I experimentally test the success and benefits of using adult mussel transplants to restore mussel bed communities following disturbance events. Results show mussel transplants provide restoration benefits in areas where recovery is slow but that these benefits are limited by local mussel recruitment dynamics and likely many other environmental and biological characteristics. In my second data chapter, I examine the importance of positive species interactions (i.e. facilitation) during the mussel recruitment stage. These interactions have not been well-described and may provide important insights for mussel bed restoration. I use a combination of field surveys and experiments to evaluate how environmental stress, mussel ontogeny, and organismal movement interact to determine the importance of facilitation during mussel recruitment. I show these interactions shift from neutral to positive with increasing tidal elevation and that ontogenetic shifts in recruit survival and growth modify interactions with different facilitator species. This suggests mussels may move between multiple facilitators throughout the juvenile stage. In the third data chapter, I examine and challenge the mitigation policy and science guiding compensatory restoration of rocky intertidal habitats following oil spills. I do this by reviewing Natural Resource Damage Assessment (NRDA) cases for oil spills in California. I summarize NRDA documentation and show, while tools for injury assessment in rocky intertidal habitats have increased in recent decades, there remain few proposed restoration projects to compensate the public for these injuries. I suggest a more cooperative and flexible approach will be needed to advance compensatory restoration in marine habitats. Finally, I conclude by discussing the key insights from this work and future research directions for rocky intertidal restoration and management.

Estuaries are among the most productive ecosystems on the planet and provide many important functions to the benefit of humans. Estuaries, however, are also under multiple anthropogenic threats, such as habitat degradation, pollution, eutrophication, and trophic downgrading through overharvesting of marine predators. These threats to estuaries come with a heavy cost through the loss of key ecosystem functions and services. The purpose of my dissertation was to characterize how anthropogenic threats affect estuarine communities in Elkhorn Slough, an estuary that provides habitat to a great diversity of organisms but is under threat through extreme nutrient loading and habitat modification.

In my first chapter I investigated how bottom-up (nutrients) and top-down (predation) forcing interact to influence seagrass beds. Using the recovery of sea otters (Enhydra lutris) I demonstrated that top predators can mediate the harmful effects of nutrient loading and eutrophication to eelgrass (Zostera marina) beds through the removal of crabs, which frees mesograzers to perform an important function: removing shade-causing algal epiphytes from seagrass leaves. I followed up on these results for my second chapter to develop a mechanistic understanding of eelgrass resilience in face of macroalgal blooms (Ulva spp.) that coincide with peak eelgrass production. Using a series of field experiments I demonstrated that sea otters can promote both eelgrass and Ulva at a seagrass-macroalgal ecotone, a process that benefits eelgrass resilience by enhancing Ulva's mesograzer assemblage that lowers the epiphyte load on eelgrass.

For my third and final chapter I used a 40 year data set of fish, water quality, and climate indices to determine the long-term effects of hypoxia on two important ecosystem services: the provision of biodiversity and nursery function. My results demonstrated that anthropogenic nutrient loading and subsequent hypoxia negatively impacted fish diversity and the nursery function for English sole (Parophrys vetulus). Despite ever increasing nutrient inputs, hypoxia was highly variable in time and space, and was mediated by climate, specifically El Niño events that increase flushing through increased precipitation as well as suppressing upwelling that brings hypoxic water from the deep sea. The suppression of hypoxia through El Niño events was a consistent pattern across estuaries in the northeast Pacific, providing important insight as to how climate change will affect anthropogenic threats to ecosystem services provided by estuaries.

My dissertation unravels some of the mysteries underlying ecosystem resilience in face of anthropogenic threats. Systems like Elkhorn Slough are critical for informing research and management as to how ecosystems function under intense stress. The rarity of available long-term data, along with the recovery of a foundation species - Zostera marina - and a model top predator - Enhydra lutris - made it possible to tease apart processes and mechanisms driving resilience over meaningful time scales. Furthermore, my dissertation highlights the importance of studying systems where resilience and recovery are occurring, as they will provide insight to inform management and policy in a world of increasing anthropogenic threats and changing climate.