Urbanization can affect species by introducing new selection pressures, such as noise pollution and different environmental transmission properties. These selection pressures can potentially trigger divergence between urban and non-urban populations of conspecifics. Songbirds in particular rely on their vocalizations to defend territories and attract mates. Urban songbirds have been shown in some species and some populations to increase the frequencies and reduce the length and trill rate of their songs. This study compares songs from four urban and three non-urban populations of dark-eyed juncos (Junco hyemalis) throughout Southern California. We examined song length, trill rate, minimum frequency, maximum frequency, and bandwidth frequency. All sites showed high variance in these traits. We also analyzed whether there were any differences between songs recorded from one urban junco population in San Diego nearly two decades ago and more recently collected data in 2018-2020. We found no significant differences across sites and between urban and non-urban populations in any of these song features; we also found no significant differences between San Diego junco songs from the 2006/2007 and the 2018-2020 field seasons. These findings partially support and partially are in contrast to previous urban junco song studies. To our knowledge, this is one of only a few studies that found no differences in any song traits examined from multiple urban populations and multiple non-urban populations of the same species.

Exposure to both antibiotics and changes in temperature can induce similar physiological responses in bacteria. Thus, changes in growth temperature could affect resistance to antibiotics. Previous studies have found that evolution under antibiotic stress causes shifts in optimal growth temperature of bacteria, but little is known if evolution under thermal stress affects antibiotic resistance. Examining 114 heat-adapted strains, we asked if evolution under thermal stress affects optimal growth temperature, if there are any correlations between heat adaptation and antibiotic resistance, and if antibiotic efficacy for these strains change depending on the local environment’s temperature. We found that: (1) most of the heat-adapted strains displayed a decrease in optimal growth temperature relative to the ancestor strain, (2) there were complex patterns of changes in antibiotic resistance when comparing the heat-adapted strains to the ancestor strain, and (3) there were no significant correlations between antibiotic resistance and changes in optimal growth temperature.

Urban areas often impose strong, novel selection pressures on wildlife. Phenotypic plasticity is an important mechanism helping enable organisms to colonize and establish populations in these novel environments. Phenotypic plasticity can be difficult to study in urban wildlife because many urban environmental variables are challenging to isolate and manipulate experimentally. The COVID-19 lockdowns created a natural experiment in which urban wildlife populations normally exposed to high levels of disturbance were released from stressors associated with humans. We took advantage of this to measure the territorial aggression responses of resident dark-eyed juncos (Junco hyemalis) on an urban college campus in in Los Angeles, USA. We assessed whether individual birds expressed aggression differently when relieved from frequent encounters with humans. We quantified their aggression using simulated territorial intrusions and compared measurements from the pre-pandemic year 2019 to those from the pandemic year 2021. We found that the population overall displayed significantly reduced aggression responses in 2021. Furthermore, individuals measured in both 2019 and 2021 showed significantly reduced aggression responses during 2021, demonstrating that individual birds maintain phenotypic plasticity in this trait. Our results show that human disturbance likely has a significant effect on the aggressive behavior of urban birds.

Widespread overuse and large-scale production of antibiotics create antibiotic pollution, disrupting environmental microbiota and creating a public health risk. Highly urbanized coastal environments can be under high impact from antibiotic pollution from many trails of polluted effluents and runoff. The city of Long Beach is one such coastal area under high impact, since it is highly urban, industrialized, and experiences frequent sewage spills. We collected water samples from the LA River in a transect running southwest into the San Pedro Channel in order to investigate (1) how does strength of antibiotic resistance change as distance from shore increases, and (2) does antibiotic resistance correlate with composition of the bacterial community. There was no consistent relationship between strength of antibiotic resistance and distance from shore. Instead, we found that bacteria from the Pacific Ocean showed higher antibiotic resistance than bacteria from the LA River in five out of eleven antibiotic treatments. We also found that the alpha diversity of bacterial communities was lower in the LA River samples compared, and alpha diversity positively correlated with strength of antibiotic resistance in four antibiotic treatments. Our findings highlight how prevalence of antibiotic pollution does not always follow a distance dilution, as well as the need for understanding the strength behind antibiotic resistance in marine bacteria.

Environmental stressors come in many different forms and affect every level of ecological organization. In a natural environment, organisms experience mixtures of stressors at various doses or strengths of exposure that could be constantly changing, both temporally and spatially. Complex environmental regimes and interactions among multiple stressors can have a profound effect on both the short-term fitness of organisms and their long-term evolutionary dynamics. This dissertation uses a bacterium-drug system to study drug-drug, drug-temperature, and gene-gene interactions. The first question we ask is how bacteria evolve to combat new stressors. Through an interaction network clustering approach followed by transcriptomic analysis, we show that Escherichia coli may have co-opted its cellular response to temperature stress for antibiotic stress because these stressors share similar physiological effects. We also found that antibiotic stress modifies the thermal response of E. coli by altering both its optimal growth temperature and temperature breadth. Next, we ask how we can identify and quantify dose-dependent drug interactions, including interactions among more than two components, i.e., higher-order interactions. To do this, we introduce a novel visual representation termed interaction landscape to directly map local dose-dependent interactions and the transitions between different interaction classes. Finally, we ask how gene-gene interactions change in fluctuating environments. We showed that changes in the type and magnitude of environmental fluctuations could affect fitness due to the differences in epistatic interactions of mutations. We quantify structural features of fitness landscapes by calculating the ruggedness across broad concentration gradients of various antibiotics. We show that fluctuating environments frequently lead to epistasis sign switches (from negative to positive or vice versa) on the pairwise level, as a potential mechanism to either promote specialization or maintain genetic variation. Overall, this dissertation combines experimental, mathematical, and computational biology to identify and understand the structures and patterns of interactions at different scales and their effects on the fitness and eco-evolutionary dynamics of bacterial populations.

Anthropogenic change alters environments and introduces novel stressors to multiple species and communities. Understanding how populations shift and cope in response to these stressors is essential to test evolution in real-time and predict our impacts on natural populations. In urban landscapes, populations that survive undergo rapid evolutionary and behavioral changes in response to strong selective pressures (Chapter 1). I am interested in how these populations respond to multiple stressors and in the patterns and processes underlying adaptive response to strong anthropogenic change. I led a reanalysis of population response data to multiple stressors across species and habitats from the last 25 years of studies by applying a new and generalizable framework—Rescaled Bliss Independence (RBI)—to evaluate stressor interactions (Chapter 2). We found that antagonism and additivity, rather than synergy, are the most frequent interaction types and that our novel method is likely to re-classify previously synergistic interactions as non-synergistic. I applied the RBI to three stressor combinations and found that antagonism was the dominant net interaction type, while synergy was the dominant emergent interaction type (Chapter 3). Next, I delved into one species to assess how populations respond to strong anthropogenic change in the wild. I tested four independent urban colonist populations of Dark-eyed Juncos (Junco hyemalis) to test if the birds have adapted morphological traits similarly in comparison to three non-urban populations or if similar environmental differences can result in different adaptations (Chapter 4). I found that there are complex patterns where some traits converge in some cities, while others are associated with urbanization generally. I quantified behavioral plasticity in response to the change in human activity due to COVID-19 restrictions (“the anthropause”) in one of the urban populations (Chapters 5 and 6). I found that fear response surprisingly decreased following campus re-opening, but didn’t change during the anthropause, posing new hypotheses to the development of a trait essential for urban living. I also found that novel urban nesting did not change during the anthropause, suggesting that novel nesting behavior is driven by landscape or urban predator effects, not human disturbance. This dissertation in sum investigates the patterns and processes underlying population response to novel stressors, with an emphasis on determining the predictability of how organisms respond to the growth of urbanization, a present threat to biodiversity.

Urbanization, characterized by the rapid growth of human development and resource consumption, not only replaces preexisting habitats but can also convert entire landscapes and their associated ecological services. As a result, these areas provide researchers with opportunities to study how wildlife species respond to novel habitat scenarios. In Chapter 1, we directly compared the House Sparrow’s (Passer domesticus) success among different habitat typologies in its native and non-native distributions. We related their numbers to environmental variables describing vegetation structure, urban infrastructure, and human activity. Our results are not only consistent with previous reports but also reveal some useful insights for the development of population management tools. In Chapter 2, we assessed the feasibility of using Google Street View as an ecological tool for gathering environmental data in different urban areas and typologies. Our results provide an optimistic look for GSV’s utilization as a powerful tool in the field of ecology.

The key to success in urban environments may be to be sufficiently plastic so as to tolerate direct disturbance by humans. By studying escape behavior we can ask how wildlife respond to threats such as humans, and by tracking individuals, we can study plasticity. We compared flight-initiation distance and distance fled from approaching humans across urban and non-urban populations of individually-marked dark-eyed juncos (Junco hyemalis) in southern California. We found that both populations primarily use information about proximity of an approaching threat to determine escape decisions. Attenuated flight initiation distance and distance fled indicates population-level habituation in urban juncos, yet urban juncos did not consistently habituate or sensitize when repeatedly tested. What explains this between-individual variability, whether there is an urban-rural gradient in within-population variation, and whether or not this individual variability has fitness consequences needs further study.

Urbanization is rapidly changing landscapes worldwide, driving phenotypic divergence in numerous urban wildlife populations. However, the strength and direction of this divergence may vary across and within cities. Here, we investigated the influence of fine-scale environmental variation on the morphological divergence of dark-eyed juncos (Junco hyemalis) across three Southern California cities. We explored how bill shape varies across three urban populations and one non-urban population, and we tested whether bill shape varies with fine-scale changes in resource availability across urban Los Angeles. Bill shape differed between urban and non-urban populations, but we did not observe expected patterns of bill shape divergence across cities. Bill shape variation also was not associated with fine-scale variation in resource availability within urban Los Angeles. Our findings suggest urban junco bill shape may be driven by non-adaptive processes, other environmental factors, or a more complex suite of urban selection pressures.

A central objective of ecology is to understand the factors, biotic and abiotic, that shape the survival and persistence of species. Developing such an understanding is particularly chal- lenging for organisms with complex life cycles, whose behavioral and physiological responses to the environment during one life stage can carry over to affect future life stages and scale up to affect population dynamics. Building on this understanding to then make predictions about how populations might respond to ongoing and future climate change is an additional defining challenge for contemporary ecological research.

The goal of my dissertation is to uncover behavioral and physiological mechanisms that shape survival, and evaluate the consequences of these processes for populations. Working across diverse taxa, I use statistical approaches to identify the behavioral mechanisms that affect survival and growth rate at the level of individuals, and develop a novel theoreti- cal framework of mathematical models that link behavior and physiology to demographic rates in order to quantify impacts at the population level. Chapter 1 introduces this novel theoretical framework, which incorporates temperature responses of the ectothermic (e.g. eggs, hatchlings) and endothermic (e.g. juveniles, adults) life stages that comprise the avian life cycle into a multi-season, stage-structured population model. I use this framework to compare the effects of different warming regimes, including deterministic increases to mean annual temperatures, seasonal differences in warming severity, and stochastic hot extremes. Using non-migratory arid-zone passerine birds as a case study, I find that stochastic hot extremes represent an immediate threat to population persistence and that realistic levels of warming over the next century may cause considerable – and in some cases, catastrophic – declines in abundance.

In Chapter 2, I expand this framework to account for the empirical observation that extreme temperatures can have persistent effects on a bird’s condition beyond the period of extreme temperature exposure. Focusing on temperature-induced condition changes for only the adult stage, I find that low levels of warming that are not enough to trigger acute increases in mortality rates can nevertheless cause adult condition to deteriorate and lead to declines in abundance. The severity of impacts from such condition changes on bird populations depends on two factors: first, on the negative consequences of being in poor condition for vital rates, and second, on how quickly adults in poor condition can recover to good condition under favorable environments. This work shows that failing to account for temperature-induced condition changes could lead to underestimation of warming costs to birds.

For Chapter 3, I turn my attention to the underlying factors that affect demographic rates. I focus on the juvenile stage of a territorial reef fish, which exhibits a trade-off between body size at the time of settlement on the reef and growth rate after settling, such that juvenile fish are more likely to survive if they are large at settlement but grow slowly. I assess possible behavioral mechanisms that give rise to this trade-off, and find that larger juveniles undertake foraging strategies that increase survival, but also experience higher costs from conspecific chasing, which reduce growth rate. Since water temperature during the larval (pre-settlement) period has been previously shown to determine size-at-settlement in this system, my work reveals how temperature effects during early life stages can impact survival and growth in a future life stage through condition and behavior.

Together, the chapters of my dissertation reveal an important role of temperature and be- havior interacting to affect vital rates that have downstream impacts on later life stages. My work underscores the value of integrating detailed empirical work on species with complex life histories with mechanistic models that scale individual-level mechanisms up to population dynamics.