The built environment, especially roads, urban and suburban development, can reduce the ability for wildlife to move across landscapes. Maintaining landscape connectivity has become a central theme in ecology and conservation, as corridors of intact habitat help maintain ecosystem functionality and, in the face of climate change, may provide migration paths for species. However, the influence of the built environment on connectivity is rarely quantified using empirical data informed by species detection, movement, or genetic structure. Rather, structural connectivity, as opposed to functional connectivity, is estimated using land cover alone. Structural connectivity estimates offer a simple and potentially powerful approach with fewer data requirements for wildlife corridor planning; however, models of structural connectivity are rarely if ever evaluated with empirical species data, limiting our understanding of their reliability and utility. This dissertation fills this gap by investigating the influence of human land use and habitat fragmentation on landscape connectivity using a suite of quantitative modeling approaches and mammals as the focal species, including cross comparisons among these approaches. Specifically, three methods that vary in levels of biological information are used to evaluate how well structural connectivity models perform for individual species, as well as their relationship to functional connectivity.

To begin with, the utility of a structural connectivity model based on the distribution and intensity of land use is evaluated by comparing model predictions to observed land use by a generalist carnivore, the puma (Puma concolor). Findings from this study indicate that generic landscape permeability models can be used with confidence as a guide when prioritizing habitat corridors for biodiversity conservation across fragmented landscapes. Next, the utility of structural connectivity models is further evaluated by examining how the inclusion of specific human land use variables affects model accuracy in a species distribution model for gray fox (Urocyon cinereoargenteus). Findings from this study indicate that species distribution models generated in human-dominated landscapes have higher accuracy when informed by indices of land use. Finally, a combination of spatial and genetic methods is used to evaluate the influence of roads on the functional connectivity for a small mammal, California ground squirrels (Otospermophilus beecheyi). Findings from this study indicate that a combined spatial and genetic approach can be used to identify locations where roads act as barriers.

Given the importance of habitat fragmentation, there is a pressing need to rapidly develop and utilize connectivity assessment methods in conservation planning. Research findings presented here have already impacted mammal conservation planning and management in California in the following specific ways. The structural connectivity model was used to identify priority habitat linkages for inclusion in the Conservation Blueprint for Santa Cruz County, and the combined genetic and spatial approach was used by the Santa Clara County Open Space Authority, CA to identify corridors and restore connectivity in an area with an existing road network. Beyond these regional impacts, future conservation planning worldwide can benefit from using readily available data collected by citizen scientists as input in predictive mapping to increase the sample size and spatial coverage for species distribution modeling.

This dissertation addresses the role that dynamic flow characteristics play in shaping the potential for significant ecosystem benefits from floodplain restoration. Mediterranean-climate river systems present challenges for restoring healthy floodplains because of the inter and intra-annual variability in stream flow, which has been dramatically reduced in an effort to control flooding and to provide a more consistent year-round water supply for human use. Habitat restoration efforts require that this reduced stream flow be altered in order to recover more naturally dynamic flow patterns and reconnect floodplains. This thesis defines and takes advantage of an eco-hydrology modeling framework to reveal how the ecological returns of different hydrologic alterations or restoration scenarios--including changes to the physical landscape and flow dynamics--influence habitat connectivity for freshwater biota. A method for quantifying benefits of expanding floodplain connectivity can highlight actions that might simultaneously reduce flood risk and restore ecological functions, such as supporting fish habitat benefits, food web productivity, and riparian vegetation establishment.

Pending climate change increases the uncertainty of restoration treatment outcomes yet must be addressed as part of the restoration planning process. An ecologically-oriented assessment of the current and potential future stream flow characteristics of selected Central Valley rivers makes it clear that climate change will affect future floodplain habitat function. Findings show that the low emissions (warm-wet) climate change scenario allows for higher flows at longer durations compared to the historical post-dam record and the high emissions (hot-dry) scenario. In fact, the low-emissions scenario flows might be more similar to pre-dam flow regimes--peak magnitudes in particular--than to the current regulated flow regime. The high emissions scenario can serve as a measure for the lower bounds of functional floodplain area for ecological benefit. Planning for potential impacts of climate change on flow dynamics will be essential if restoration managers are to minimize negative consequences of climate change and maximize the potential benefits that it may offer for species recovery.

Efforts to plan and evaluate floodplain reconnection projects for ecological benefits have been hindered by a lack of metrics that allow for comparisons among alternative restoration sites with respect to the type and quality of dynamic habitat potential. This dissertation presents a framework for quantifying the benefits of floodplain restoration projects by coupling the spatial and temporal characteristics of floodplains to express the functional habitat they create. First, habitat was quantified using Area-Duration-Frequency (ADF) curves for several durations and across multiple frequencies of flood occurrence. From these data, a value was then generated for expected annual habitat (EAH). The method has advantages in framing the potential restored area in terms of probabilities based on dynamics of flow timing, durations, and frequencies. The EAH metric captures a comprehensive picture of the likelihood of flooded areas appearing in any given year. This method can be used to design projects to meet specific and measurable habitat objectives. These methods and new metrics provide a transparent and replicable means to examine the effects and relative importance of policy decisions and river restoration projects.

To illustrate this modeling method, statistical flow characteristics needed to support floodplain benefit for species were coupled with topographic alteration scenarios for increasing beneficial habitat along the Vernalis to Mossdale corridor on the San Joaquin River, California. Findings for a suite of species that span a range of necessary flow requirements exemplify a wide array of impacts associated with flow scenarios for the San Joaquin River system. Most importantly, the modeled results predict significant declines in the availability of required flow related habitat conditions for splittail spawning and rearing and Chinook salmon rearing in the future under two climate change scenarios. Physical habitat restoration must be paired with additional in-stream flows to meet frequency, duration, and seasonal requirements for these species. Thus, restoration treatment considerations for floodplain habitat should not only include physical alterations for additional channel floodplain connectivity, but also restore a more natural flow regime to increase habitat area and frequency of inundation.

Restoration planning often fails to follow strategies based on assessments of ecological benefit outcomes and cost effectiveness. A hydro-ecological approach was applied to multiple modeled floodplain restoration sites along California's Sacramento River and was integrated with socio-economic considerations into a prioritization scheme. The new EAH and ADF metrics were used to assess probabilities for ecological outcomes for increased salmon rearing habitat and combined with land value cost for parcels in the restoration areas. The model was used to assess individual and cumulative benefits of 26 floodplain rehabilitation options involving levee setbacks and examine the consequences of changing topography and climate for floodplain habitat along a large expanse of the Sacramento River. Cumulative effects of projects implemented concurrently showed only small changes in functional floodplain habitat creation. Climate change flow scenarios for this section of the Sacramento River indicate that the functional EAH habitat under a low emissions (warm-wet) regime overlaps with that created for restoration sites under the current flow regime. However, the high emissions (hot-dry) regime will create less functional habitat and serves as a good lower bound of expectations for any restoration plan. By adding to ecological outcome measures and integrating environmental benefits into a cost effectiveness ratio, some projects' priority rankings shift. Thus, cost effectiveness is relevant for informing decisions about restoration site priorities and could improve the way funds are allocated to restoration options. This study advances mitigation planning at a local and regional scale by providing tools for quantitative estimates of potential habitat that could be restored, for assessing projects individually and cumulatively, and for comparing and prioritizing sites using an analytical cost effectiveness approach.

In sum, this dissertation presents a modeling framework and new quantitative metrics that can be used to plan and evaluate floodplain restoration projects that address connectivity and dynamic flows, whether they are the result of climate change or prescribed reservoir release flows. Restoration options for multiple locations in California's Central Valley were investigated to demonstrate the utility of this approach. The method has advantages in estimating the potential restored area in terms of probabilities based on dynamics of flow timing, durations, and frequencies. Ultimately, using integrative hydro-ecological models offers support for decision makers considering where to rehabilitate floodplain processes upon which biological and social benefits depend.

Anthropogenic climate change poses an existential threat to biodiversity that is compounded by habitat conversion, disease, and other disturbances. Understanding the ecological needs of sensitive species and identifying priority habitat is vital for wildlife conservation. However, there is growing recognition that the traditional conservation emphasis on protected areas is not sufficient to sustain biodiversity. We also need to understand the habitat value of working lands and incorporate these areas in conservation planning. My dissertation explores these themes through the lens of bats in the California coast redwood ecosystem. Bats are extremely sensitive to climate and habitat disturbance, making them useful indicators of ecosystem health. Coast redwood forests may provide critical habitat for bats under climate change because coastal effects on temperature and fog patterns buffer the coast from the extreme temperatures and drought experienced inland. Although 13 species of bats are found in coast redwood forests, bats are an especially elusive taxon and much about their basic ecology remains unknown. In addition to climate change, hibernating bat populations in North America are threatened by an emerging disease called white-nose syndrome. The disease has newly spread to the west coast, heightening the urgency to understand the ecology of western bat populations.

I conducted research on the factors shaping habitat suitability for bats across the coast redwood ecosystem, the environmental drivers behind species activity, and how species activity patterns shift seasonally. In Chapter 1, a large landscape field study demonstrates that both working forests and protected areas provide valuable summer bat habitat, but species vary significantly in their sensitivity to microclimate and forest habitat conditions. In Chapter 2, I complement conventional, ground-level acoustic survey techniques with canopy-level monitoring. This comparison reveals that treetop deployment methods significantly increase the detection of tree-roosting and migratory species across all forest management types and all seasons, revealing new insights about niche partitioning and seasonal bat activity. In Chapter 3, the results of winter bat activity surveys were examined in relation to microclimate, and daytime maximum temperature was determined to be the variable that best explained variation in nightly probability of bat acoustic presence. The winter data also show that 11 bat species are detected in coast redwood forests during the winter, but species vary in their winter activity levels, which may have ramifications for population susceptibility to white-nose syndrome. In the final chapter, the implications for bat conservation of laws and policies regulating California timberland are discussed, and ways to improve protections are recommended based on scientific understanding of species ecology.

Taken together, the findings from this dissertation highlight the value of coastal forests as habitat for bat species threatened by climate change and emerging diseases. Species of special concern are present and active in coast redwood forests year-round. However, the presence of high-flying species was found to be systematically underestimated by ground-level survey methods, especially during the winter. Standard survey protocols may thus bias assessment of forest use and management impacts by primarily detecting species that make frequent use of understory habitat. The results of this research that includes year-round, canopy-level monitoring and advanced approaches to statistical analysis can be used to improve bat monitoring efforts and identify priority habitat to conserve bat species under global change.

In many parts of coastal California, agricultural water needs during the summer are met by tapping riparian and groundwater resources, which has led to documented decreases in stream flow during the dry season. This has consequences for salmon, including sudden drying of habitat, higher water temperatures and changes in the invertebrate prey base. We developed a new, spatially explicit analytical tool to quantify and map human and environmental needs, model daily stream-flow rates, and estimate regulatory flow requirements and cumulative impacts of reservoirs. This tool is part of a decision support system that can be integrated in a Geographic Information System (GIS) with other restoration considerations. This research provides a basis for placing additional reservoir storage where projects are not likely to affect adult salmon passage, while reducing water demand from surface and subsurface flows during spring and summer, ultimately improving both habitat for salmonids and water supply for growers.

The goal of conservation biology is to understand and prevent the loss of biological diversity. Modern conservation science relies heavily on four major quantitative methods: reserve site selection algorithms, species distribution models, population viability analyses, and species-area relationships. These methods, however, have several longstanding and unresolved shortcomings, including extensive data requirements, long computation times, and important simplifying assumptions, that limit their ability to inform conservation decisions in many real landscapes. This dissertation develops new approaches in quantitative ecology that address these shortcomings through the use of simulation modeling, probability theory, machine learning, modern statistics, and economic input-output analysis.

Chapter 2 examines the optimal design of reserve networks for preventing extinction of terrestrial mammal species, demonstrating that the match between a species' body size and the spatial scale of a landscape can be used to determine which species will benefit from a clustered reserve network design. Chapter 3 derives two new macroecological metrics, similar to the species-area relationship, that provide probabilistic estimates of single-species extinction risks and community-wide extinction rates in landscapes undergoing habitat loss. Chapter 4 uses data from acoustic surveys to examine the road ecology of California bats, finding that total bat activity, and the activity of four common species, is decreased in the vicinity of large highways. Chapter 5 presents a "wildlife footprint" analysis that combines global bird and mammal range maps, data on the human appropriation of net primary productivity, and economic input-output tables to link specific human consumption activities to decreases in wild bird and mammal populations.

Agriculture is a primary driver of global change and biodiversity loss. Several approaches have been proposed to enhance biodiversity conservation in agriculture in order to protect ecosystems while maintaining agricultural production, a critical strategy to stave off a sixth mass extinction.

Globally, I reviewed 205 studies to evaluate different conservation strategies within agroecosystems that may impact bird conservation. The results reveal that agroecological practices such as increasing structural heterogeneity in agricultural fields, eliminating reliance on agrochemical inputs, and providing supplementary habitat within farms can enhance bird wildlife within agroecosystems. Interestingly, there is a paucity of studies quantifying the influence of vineyards on bird communities in Mediterranean-climate ecosystems.

Human settlement preference for mediterranean type ecosystems globally has resulted in constant agricultural pressure on these areas. These ecosystems have high rates of endemic biota and include some of the 35 global conservation priority sites. This dissertation addresses the influence of the vineyards on wildlands and vice versa in two new world mediterranean-climate regions, Chile and California. I evaluated the impact of vineyards on bird communities using two natural experiments across gradients of increasing vineyard proportion in the landscape. The first study, conducted in oak woodland fragments surrounded by a vineyard matrix in California, revealed that a subset of birds were significantly associated with increasing vineyard proportion. These birds, designated as agricultural adapters, negatively interacted with the rest of the bird community, revealing a secondary mechanism of the influence of agricultural land use change, in addition to the well-characterized primary mechanism involving loss of habitat. Secondly, in Chile, I assessed the influence of surrounding native Matorral vegetation and habitat fragments within vineyards on birds. Findings showed that proportion of fragments within the vineyard and the proportion of native vegetation surrounding vineyards increase abundance of endemics, insectivores, granivores, and omnivores, indicating that the proportion of fragments can be managed to enhance conservation efforts within vineyard landscapes. Lastly, I compared the influence of vineyards on bird communities in Chile and California. Results from this comparative study reveal that vineyards significantly influence bird communities in both study regions, increasing the abundance of agriculturally adapted species. Co-occurrence analysis showed that these agricultural adapter species are often found together and, importantly, negatively interact with other species in surrounding natural areas.

These results provide new insight for conservation efforts in agroecosystems as well as information to guide conservation strategies in mediterranean-climate agroecosystems. Specifically, the results suggest that conservation efforts should emphasize the importance of large patches of native vegetation and maintaining fragments of native vegetation within vineyards. These results can help conservation practitioners and farmers promote biodiversity conservation in agricultural landscapes.

This dissertation addresses the complex relationships between human water demands and ecosystem water needs in the Mediterranean-climate region of northern California. Through a combination of long-term ecological data analysis, hydrologic modeling, and field studies of ecological-flow relationships, the research presented examines the challenges and opportunities for managing water to sustain freshwater ecosystems, with a particular emphasis on the environmental flow requirements of steelhead trout (Oncorhynchus mykiss). In coastal California watersheds, stream flows are increasingly impacted by small-scale withdrawals from agriculture and residential water users. While the effects of large dams have been extensively-studied, relatively little is known about the cumulative impacts of small-scale water-management practices on freshwater ecosystems. Analysis of a long-term record of fish count data revealed a strong positive relationship between stream flow and the over-summer survival of juvenile salmon and provided evidence that insufficient stream flows during the spring and summer rearing period has become an important limiting factor to threatened steelhead trout populations. These finding suggest that changes in water use practices that maintain dry season flows are critical for salmon population recovery.

A reduction in dry season water diversions could potentially be achieved by increasing local storage capacity in ponds, which could be filled during the wet season when there is greater water availability. However, increased water storage has the potential to impair winter flows, which are important for fish passage and spawning and the maintenance of habitat heterogeneity. To quantify the trade-offs between alternative water management strategies, an integrated management framework is introduced that simultaneously considers the temporal and spatial dynamics of flow regimes, and the water needs of both human and natural systems. The management framework relies on a watershed hydrologic routing model, which is useful for representing the temporal and spatial distribution of water availability and predicting the impacts of water diversions across the stream network. An examination of the potential impacts of water management practices in a Sonoma County, California watershed demonstrated that the location and size of water storage projects influences the magnitude and duration of stream flow impacts. The findings also illustrated trade-offs between environmental flow protections and the ability for water users to meet storage demands.

Managing stream flows for ecological benefits requires an understanding of flow-habitat relationships at scales relevant to individual organisms. To assess the flow needs of adult salmon for their upstream migration, a new approach was developed for mapping stream channel topography and modeling flows in relation to fish passage suitability. The approach relies on high-resolution measurements of stream channel topography derived from terrestrial LiDAR surveys. A two-dimensional hydraulic model was then used to simulate flows in several survey reaches and identify the minimum flow required to maintain a continuous migration path of suitable passage depths for adult salmon. The modeling approach is compared to a regional formula used by State of California resource agencies to estimate salmon passage flow needs. While the results were similar, improvements to State's regional formula could be made by explicitly incorporating a variable describing channel typology.

In sum, these studies quantify the response of a threatened salmon species to flow variation, illustrate the relationships between water management and ecologically-important flow dynamics, and establish a new approach for evaluating biological flow thresholds, all of which are critical for improving the management of freshwater ecosystems in Mediterranean-climate regions.

Ecosystem restoration is increasingly used as a tool to offset the contemporary loss of habitat or help address past ecosystem destruction. However, given the complex, interconnected nature of ecosystem processes, restoration outcomes are notoriously variable. In certain ecosystems, minimal intervention may be able to produce desired restoration outcomes, but in others even high levels of intervention may not achieve restoration goals. Significant uncertainties remain about restoration trajectories over time and space. In order to effectively deliver the benefits these projects purport to offer, a detailed scientific understanding of restoration trajectories is necessary to inform the practice of ecological restoration moving. To better understand the factors influencing restoration trajectories in California’s San Francisco Bay (SF Bay), I compare change in vegetation over time at an older restoration and reference site using field data, explore rates of change at a recently established wetland restoration site in the context of a historic drought using remote sensing of satellite imagery, and compare seed dispersal across three restoration and two reference sites. Addressing these questions will aid in the management of these projects and design of future project which will help improve conservation outcomes and address impacts associated with sea level rise and increased climate variability.

While ecosystem development can take decades if not centuries, most restoration projects are minimally monitored, and a five-year window for assessment is often the best-case funding scenario. This means that detailed temporal studies of restoration projects are rare, which is particularly problematic in variable areas where climate cycles proceed at decadal scales. To address this gap, I worked with a vegetation field data set collected most years between 1990 and 2005 at an established restoration site initiated in 1975 (Muzzi Marsh) and a historical reference wetland (China Camp) in Marin County, CA. To determine the factors influencing reference and restoration trajectories, I examined changes in plant community identity in relation to annual salinity levels in the SF Bay, annual rainfall, and tidal channel structure. Over the entire study period, both sites experienced significant directional change away from the 1990 community. Community change was accelerated following low salinity conditions that resulted from strong El Niño events in 1994–1995 and 1997–1998. Overall rates of change were greater at the restoration site and driven by a combination of dominant and sub-dominant species, while change at the reference site was driven by sub-dominant species. Sub-dominant species first appeared at the restoration site in 1996 and incrementally increased during each subsequent year, whereas sub-dominant species cover at the reference site peaked in 1999 and subsequently declined.

In addition to the later-stage restoration dynamics highlighted above, climate variability may also influence the early stages of restoration site development. At a developing restoration site in the SF Bay, I use object-based image analysis (OBIA) and change analysis of high-resolution IKONOS and WorldView-2 satellite imagery to explore whether mean annual rates of change from mudflat to vegetation are lower during drought years with higher salinity (2011-2015) compared to years with lower salinity (2009-2011). I found that vegetation increased at a mean rate of 1979 m2/year during California’s historic drought, 10.4 times slower than the rate of 20580 m2/year between 2009 and 2011 when the state was not in drought. Vegetation was significantly concentrated in areas in closer to channel edges, where salinity stress is ameliorated, and the magnitude of the channel effect increased in the 2015 image.

Seed dispersal is another critical but understudied mechanism driving restoration site development. Where and when seeds arrive at a restoration site can have major implications for how a restoration project proceeds. In my final chapter, I explore seed dispersal over a chronosequence of three restoration sites and two reference sites at Eden Landing Ecological Reserve (Hayward, CA), part of the South Bay Salt Pond Restoration Project. I find that seeds of wetland species in the restoration sites were significantly aggregated in areas with vegetation cover above 30%, and that many study plots were completely devoid of wetland seeds. Vegetation cover was significantly related to channel proximity and relative elevation at the sites. Reference sites contained significantly more seeds than restoration sites, but density was low overall at the reference sites. The oldest restoration site had statistically equivalent seed density compared to one of the reference sites. Across all sites, the pioneer dominant species Salicornia pacficia was the most common seed species, and sub-dominant species were only found in a single plot in the restoration sites and in overall low densities in the reference sites. These results highlight the fact that seeds or seedlings may need to be added to developing restoration sites, and that manipulating elevation and channel structure may be important for accelerating the rate of vegetation development.

ArticleOpen AccessPublished: 24 April 2020Topography and human pressure in mountain ranges alter expected species responses to climate changePaul R. Elsen, William B. Monahan & Adina M. Merenlender 

Nature Communications volume 11, Article number: 1974 (2020) Cite this article

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Abstract

Climate change is leading to widespread elevational shifts thought to increase species extinction risk in mountains. We integrate digital elevation models with a metric of human pressure to examine changes in the amount of intact land area available for species undergoing elevational range shifts in all major mountain ranges globally (n = 1010). Nearly 60% of mountainous area is under intense human pressure, predominantly at low elevations and mountain bases. Consequently, upslope range shifts generally resulted in modeled species at lower elevations expanding into areas of lower human pressure and, due to complex topography, encountering more intact land area relative to their starting position. Such gains were often attenuated at high elevations as land-use constraints diminished and topographic constraints increased. Integrating patterns of topography and human pressure is essential for accurate species vulnerability assessments under climate change, as priorities for protecting, connecting, and restoring mountain landscapes may otherwise be misguided.