Billions of birds fatally collide with human-made structures each year. These mortalities have impacts on species of conservation concern and potentially on avian populations as a whole. This source of human-wildlife conflict also places economic and operational constraints on various human industries. Furthermore, with continued increases in urbanization, the rate and extent of collisions continues to increase. Efforts to reduce collisions have largely centered on making structures more visible to birds but have been met with limited success. Currently, there is a call for solutions to be tailored to both the environmental context of hazardous structures and to the sensory ecology of at-risk birds. In Chapter 1, we review how and why sensory ecology will help reduce in-flight collision risk for birds. A growing understanding of the sensory systems of birds and of the interface between these systems and the environment will enable the design of appropriate warning and deterrent signals. In particular, we review avian auditory and visual sensory ecology to better understand the susceptibility of birds to collisions and to recommend effective signal design. We highlight the ubiquity and salience of multi-modal signals in avian ecology and evolution, particularly as warning signals, and propose the use of multi-modal signals in mitigating collisions. We encourage the use of animal behavior frameworks to assess collision risk and collision mitigation approaches. Behavioral analyses offer numerous advantages over traditional collision measures, such as mortality estimates. Behavioral data can be generated quickly, render large sample sizes, and allow more nuanced perspectives of the context-dependence of collisions. In Chapter 2, we investigate the use of acoustic signals to reduce avian collisions with structures in open airspace. Birds have largely evolved without tall human-made structures in their flight paths and, consequently, avian perception and behavior may not be suitably primed to detect these novel hazards. Our previous work in captive settings showed that acoustic signals aid in drawing the attention of flying birds to potential collision hazards, influencing flight behavior. The current work corroborates these findings in a field setting. We projected acoustic signals into open airspace surrounding communication towers and quantified movement patterns of birds, to indicate potential collision avoidance behavior. Our results show a ~15% reduction in overall bird activity surrounding towers during sound treatment conditions, compared with control trials. Furthermore, flight movement patterns during sound treatments were characterized by significantly greater distances from and greater displacement of travel direction relative to towers, compared with control trials. Flights during sound treatments also showed significantly slower velocities, compared with control trials. Lower frequency sound stimuli (4-6 kHz) produced larger effect sizes than higher frequency stimuli (6-8 kHz). Results also co-varied with tower location and data collection date, reinforcing an appreciation of the context-dependent nature of collision risk. Our findings will inform the field of avian sensory ecology and help to assess the use of acoustic signals in collision mitigation measures.

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To understand native species persistence in transformed landscapes we must evaluate how individual behaviors interact with landscape structure through ecological processes such as habitat selection. Rapid, widespread landscape transformation may lead to a mismatch between habitat preference and quality, a phenomenon known as ecological traps that can have negative outcomes for populations. I applied this framework to the study of birds inhabiting landscapes dominated by forest remnants and shade coffee plantations, a tropical agroforestry system that retains important portions of native biodiversity. I used two different approaches to answer the question: What is the role of habitat selection in the adaptation of native species to transformed landscapes? First, I present the results of a simulation model used to evaluate the effects of landscape structure on population dynamics of a hypothetical species under two mechanisms of habitat selection. Then I present the analyses of seven years of capture-mark-recapture and resight data collected to compare habitat preference and quality between shade coffee and forest for twelve resident bird species in the Sierra Nevada de Santa Marta (Colombia). I provide evidence for the importance of including the landscape context in the evaluation of ecological traps and for using long-term demographic data when evaluating the potential of novel ecosystems and intermediately-modified habitats for biodiversity conservation. Beyond suggestions to improve bird conservation in shade coffee, my findings contribute to theory about ecological traps and can be applied to understand population processes in a wide variety of heterogeneous landscapes.

As sea level rise (SLR) affects coastal wetlands, ecosystem responses can include vertical accretion, landward transgression, or submergence. Sea level rise-induced transitions can alter key biogeochemical transformations within wetland soils, impacting the ability of these systems to provide ecosystem services, specifically carbon (C) storage and water quality regulation. Through a series of complementary laboratory and field-based studies, biogeochemical responses to salinity, vegetation shifts, and submergence were investigated. Changes in nutrient dynamics associated with saltwater intrusion were evaluated by artificially adding saline water to different freshwater wetland soil types, indicating that potential exports of critical nutrients (forms of nitrogen, phosphorus, and C) out of freshwater wetland soils is mediated by soil type. A controlled laboratory experiment was conducted to determine the potential degradability of C stored within submerging coastal wetland soils under both aerobic and anaerobic conditions. Under aerobic conditions, 66% more carbon dioxide was produced than under anaerobic conditions and 4x greater carbon dioxide was produced at 90-100cm depths than at the surface. At the same site, the degradability of carbon stores was examined through organic matter fractionation, stable isotopic examination, and determining the abundance of key microbial genes. Both total soil C and stores of bioavailable nutrients increased with depth, while organic matter quality decreased. Finally, the biogeochemical impacts of two separate vegetation transitions occurring co-incidentally with sea level rise were investigated: mangrove encroachment into salt marsh, and more salt- and inundation-tolerant herbaceous encroachment into herbaceous marsh. Conclusions from these studies demonstrate that vegetation transitions alter both soil nutrient storage and fast-cycling nutrient pools, indicating that biogeochemical transitions occur in advance of changes in vegetative species dominance. Results from these chapters holistically address how biogeochemical functioning, specifically nutrient cycling, regulation of water quality, and C sequestration, within coastal wetlands responds to stressors associated with SLR.

Collisions with human-made structures are responsible for billions of bird deaths each year, resulting in ecological damage as well as regulatory and financial burdens to many industries. Acoustic warning signals can alert birds to obstacles in their flight paths in order to mitigate collisions, but these signals should be tailored to the sensory ecology of birds in flight. The effectiveness of various acoustic warning signals likely depends on the influence of background noise and the relative ability of various sound types to propagate within a landscape. I evaluated the ability of four sound signals to elicit collision-avoidant flight behaviors from birds released into a flight corridor containing a physical obstacle. I selected signals to test two frequency ranges (4-6 kHz or 6-8 kHz) and two temporal modulation patterns (broadband or frequency-modulated oscillating) to determine whether any particular combination of sound attributes elicited the strongest collision avoidance behaviors. I found that, relative to control flights, all sound treatments caused birds to maintain a greater distance from hazards and to adjust their flight trajectories before coming close to obstacles. There were no statistical differences among different sound treatments, but consistent trends within the data could suggest that the 4-6 kHz frequency-modulated oscillating signal elicited the strongest avoidance behaviors, followed by the 6-8 kHz broadband signal. I conclude that acoustic warning signals could be an effective avian collision deterrent in several contexts, and that the particular sound used in a warning signal may impact the detectability of the signal as well as the type of flight behaviors used to evade a collision. These findings can be used to design more effective warning signals and demonstrate the value of using behavioral data to assess collision risk.

With species increasingly becoming imperiled due to anthropogenic activities, conservation practitioners are tasked with determining conservation priorities in order to make the best use of limited resources. The United States’ Endangered Species Act (ESA) has two listing statuses into which imperiled species are placed to receive protections: Threatened or Endangered. In the first chapter, our objective was to identify differences between Threatened and Endangered species beyond what is outlined in their ESA definitions. To our knowledge, this is the first study to compare listing status for species protected by the ESA on the basis of types and number of threats they face. For six broad-scale threats (habitat modification, overutilization, pollution, species-species interactions, environmental stochasticity, and demographic stochasticity), we investigated whether there is a difference in the number and types of threats which impact Threatened and Endangered species at the time of their listing. We found that Threatened (X̄ = 2.9, SD = 1.4) and Endangered (X̄ = 3.0, SD = 1.1) species were faced by a similar number of threats at their time of their listing. The only broad-scale threat that disproportionately impacted Endangered species more than Threatened species was demographic stochasticity; Endangered species were 1.9 times (95% CI = 1.4 -2.7) more likely to have this threat than Threatened species. We found four finer-scale demographic stochasticity threats (few individuals in one population, few individuals in multiple populations, lack of reproduction, and genetic loss) to be strong predictors of Endangered status. The similarities in the number and types of broad-scale threats faced by Threatened and Endangered species suggest that changes recently made to the ESA may be detrimental to the recovery efforts of future Threatened species. In the second chapter, our objective was to identify temporal trends in threats facing the four major phyla protected by the United States Endangered Species Act: angiosperms, arthropods, mollusks, and vertebrates. For 24 threat types, we created models to determine whether there was a linear, quadratic, or pseudo-threshold association between year and the probability that a phylum was listed with a given threat. We were able to identify temporal trends for 79% of the 96 possible threat-phylum combinations. We found that angiosperms had the highest peak probability of being listed with the greatest number of threats (N = 10), followed by mollusks (N = 8) and more distantly by arthropods (N = 4) and vertebrates (N = 2). We found that vertebrates had the greatest number of threats (N = 16) for which the year with their greatest probability of their being listed with a threat was their most recent year of listing. The other three phyla were similar to each other for this metric, mollusks having 12 and angiosperms and arthropods each having 11 threats peak in their most recent year of listing. We only identified one threat/phylum combination for which the maximum probability of their being listed with a threat was in their first year of listing (i.e., the threat has been consistently decreasing): authorized take impacting angiosperms. Overall, we believe our findings can be used to assist conservation efforts by identifying which threats have been decreasing or stable over time and which have been increasing that are in need of more attention.

Apalachicola Bay, an estuary located in northwest Florida, is likely to experience an increase in climate change and human-induced stressors, such as sea level rise and changes in freshwater inflow, in the future. A coupled hydrodynamic and food web modeling approach was used to simulate future scenarios of low and high river flow and sea level rise in Apalachicola Bay from 2020 to 2049 and demonstrate the range of temporal and spatial changes in water temperature, salinity, fisheries species populations and the broader food web. Concurrent with model development, a survey of Apalachicola Bay stakeholders was conducted to assess stakeholder knowledge and concerns regarding species and environmental changes within the system. Model results indicated an increase in annual average biomass for white shrimp and blue crab under low river flow scenarios and decrease in Gulf flounder and red drum biomass. High river flow scenarios resulted in an increase in annual average biomass for blue crab and red drum and decrease for white shrimp and Gulf flounder. For all modeled simulations, the largest differences in future environmental variables and species biomasses were between scenarios of low and high river flow, rather than low and high sea level rise. Stakeholders anticipated a future reduction in river flow and increase in sea level rise as both having some negative impacts to the Franklin County economy and stakeholders' personal interaction with the Apalachicola Bay ecosystem. The use of the ensemble modeling approach combined with the stakeholder survey highlights the use of multiple knowledge types to better understand abiotic and biotic changes in the estuarine system. Results provide insight on the synergistic effects of climate change and human-induced stressors on both the estuarine food web and human community of Apalachicola Bay.

Climate change has caused gradual changes within marine environments within the last couple decades and is expected to continue to impact these ecosystems. Changes to these ecosystems are anticipated to emerge as adverse effects reach the lowest and highest levels within trophic food webs. For example, these environmental changes may change the abundance and distribution of species within their current geographic range. In extreme cases, climate change has already resulted in range shifts of terrestrial and marine species. A need for bioindicator species has emerged, so that they may be used to indicate when climate change may impact marine communities and whether these communities are at risk. Bioindicators are useful in that they can be early indicators for adverse effects and be used to indicate to decision-makers that intervention is needed before adverse effects can spread to the rest of a particular ecosystem. Bioindicators that are responsive to environmental changes are ideal for use. Mytilus edulis (blue mussels) and Donax variabilis (coquina clams) are two species that could potentially have use as bioindicators for climate change. However, it is not known how responsive the physiological condition of these species is to environmental changes. Our thesis objectives were to determine whether differences in the physiological condition and recruitment rate of blue mussels and coquina clams on the Eastern Shore are connected to seasonal water quality changes in the northern hemisphere Spring-Summer months and (2) to determine whether there have been long-term (9 years) changes in mussel and clam physiology and interpret these changes in the context of climate change. We found some evidence for a connection between blue mussel and coquina clam physiology and recruitment and seasonal changes in water quality on the Eastern Shore. We also found that blue mussel and coquina clam physiology did exhibit long-term spatiotemporal changes through time on Virginia’s Barrier Islands. Blue mussels showed an early indication of a possible range shift to come. On southern barrier islands, blue mussels either had lower physiological condition and recruit counts or had higher rates of decline in these metrics. Coquina clams on the other hand, only showed evidence of declines in their physiological condition at Hog Island. This could be an early sign of the sublethal impacts stemming from gradual environmental changes and may signal that blue mussels and coquina clams will continue to decline in quality and quantity in these areas of Virginia’s Eastern Shore. Declines in blue mussel quality and quantity could be worrisome as they not only provide several economic and ecological services that benefit humans, but also are an important food source for the migrating shorebird species that use Virginia Barrier Islands as a refueling station. While worrisome, this response in blue mussels does indicate that this species may be responsive to environmental changes. With additional targeted, experimental research, a framework could be established that uses blue mussel physiology to further indicate impacts of specific environmental conditions on Virginia’s Eastern Shore ecosystems.

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