Using multiple drugs in combination has been suggested as a possible solution to the antibiotic resistance problem. However, drug combinations introduce new factors to consider, including how the interactions among drugs influence the evolutionary process. Antibiotic combinations are considered additive if the combined effect is equivalent to the drugs acting independently, synergistic if more effective and antagonistic if less effective. This study examines the evolution of S. epidermidis in single drug, two-drug, and three-drug environments to determine how the interaction types may influence the rate of adaptation. The net interaction of a combination as well as the emergent interaction—the interaction that is uniquely due to all drugs being present in a combination that is not due to pairwise interactions, was examined. We find that in three-drug combinations, synergistic net interactions correlate with higher rates of adaptation, and the emergent interaction has no significant effect on the rates of adaptation.

Cultural values, such as machismo and marianismo, and its effects on women sexuality and reproduction have been well documented across studies. However, little is known about the effects of respecto and familismo on the age at first reproduction in Hispanic women. Additionally, the transition into new environments (i.e., migration into the United States) oftentimes place women in conflicting situations due to differences in their outside cultural environment versus their home environment which may likely result in cultural mismatches. The present study investigates the effects of cultural values and acculturation on the age at first reproduction in 114 Hispanic women in the U.S.. Including how the transition of Hispanic women into the U.S. may result in a cultural mismatch affecting their reproductive decisions and thus the rate of cooperative care they may later receive from the grandmother-to-be when conceiving and postpartum. Cultural values and acculturation did not significantly impact age at first reproduction in this cohort of women. While cooperative help from grandmothers-to-be appeared to be associated with younger age at first birth (>20), however, the model itself was not statistically significant.

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.