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An undisputable fact of the modern age is that human activities are now a major force shaping the biosphere. Some have called for a new geological epoch called the “Anthropocene” or the age of humans— the search is underway for a reliable and unambiguous mark in the geological record for the designation of this new epoch. As a biologist, however, I am reminded daily of the “marks” this age has left on the world around us. The American philosopher and ecologist Aldo Leopold perhaps said it best when he described an “ecological education” as “living alone in a world of wounds.” What follows in this dissertation is maybe best described as searching for wounds, for marks, in biological archives that allow us to better understand the ecosystems of the Anthropocene. My dissertation is focused primarily on studying the widespread crustacean zooplankter, Daphnia pulicaria. A common refrain in the following chapters will be to point out the function of this and related species in lake ecosystems and their value to the humans that enjoy and benefit from lakes. Daphnia in lakes are important for two reasons; first, they are keystone species of the pelagic food webs, connecting primary production from algae to higher trophic levels namely fish. Daphnia thus support the recreational and commercial fisheries of freshwater lakes. A knock-on benefit of Daphnia trophic position is they control the standing crop of algae in freshwater ecosystems and maintain water clarity, so lakes are not choked with noxious algal blooms. My dissertation is separated into three chapters. In the first chapter, I sequence, assemble, and annotate a genome for D. pulicaria using the latest long-read DNA sequencing technology. We use the genomic resources developed for this species to better understand its evolutionary history, especially its split from the closely related “sister” species D. pulex. This reference genome is important for enabling other work, a thread we pick up in the third and final chapter. In my second chapter, I chronicled the 175-years history of D. pulicaria and other Daphnia species in a small lake that will be the primary focus of the last two chapters. Tanners Lake is an ecosystem replete with wounds from the numerous human activities that dominate the landscape surrounding it. Due to their landscape position, lakes integrate vast amounts of information about their watersheds in their sediments. Tanners Lake records in its sediments the history of a landscape dominated by humans with the development of a major city surrounding it. Located just outside of Saint Paul, MN, Tanners Lake is impacted by two major human impacts inflicted on Northern Temperate Lakes. It is not only eutrophic, from the export of unprecedented amounts of nutrients but also it is severely salinized. Freshwater salinization is a consequence of the widespread use of de-icing salts on impervious surfaces such as roads and parking lots- a ubiquitous feature of human-dominated landscapes. I collected sediment cores from Tanners Lake to reconstruct the ecological dynamics of the Daphnia community across time in this lake by examining the abundance and diversity of resting eggs (encased in durable sclerotized structures called ephippia) across time in the core. I found that only modest changes in diversity and abundance occurred in the lake during salinization. This result suggests that Daphnia may be resilient to the threat of salinization- perhaps maintaining the ecosystems they support despite salinization. The results of my second chapter set up an important question to tackle in my third chapter. Since D. pulicaria remains in Tanners Lake despite salinization, is this population evolving higher tolerance to these conditions? We tackle this question using an approach that is somewhat unique to Daphnia, by hatching the eggs contained in the ephippia from across time. This method known as Resurrection Ecology, allows us to sample individuals from across time and study their phenotypes and genotypes. I hatched Daphnia from across approximately 25 years (~1994-2019) and resequenced their genomes. In addition, we also evaluated these D. pulicaria clones for their tolerance to salinity using phenotypic (i.e., survivorship) assays. I compiled this data set together to understand the evolution of this population through time. The genomic data supports the idea that salinity is a driving force for evolution in this population. In particular, genes related to osmoregulation and salinity tolerance are enriched within the statistical outliers. The phenotypic data supported this finding, as we observed that the salinity tolerance of modern Daphnia was higher than that of the ancestors hatched from the sediment. Interestingly, while I initially described this work as a search for ecological and or evolutionary wounds, I was surprised to find that while they exist in very real ways in the biological archives studied, they are not mortal. My research, taken together, suggests that Daphnia populations should have the potential to respond to human threats and evolve to maintain the ecosystems they support. However, this resiliency will be highly dependent on the speed and intensity of the threats that these systems will face, as well as the strength of the evolutionary forces (i.e., selection, drift, migration, mutation) that will shape the underlying genetic structure of these populations.

Freshwater salinization syndrome is a rising threat globally which results in increased ion concentrations in inland freshwaters. This syndrome threatens healthy aquatic ecosystems and can alter the perception of the potability of finished drinking water. The Occoquan Reservoir, located in Northern Virginia, is a freshwater system that is facing rising salinization. Stakeholders for the reservoir have been convened to address these rising salinization concerns. Among these stakeholders, there are a variety of viewpoints on the significance of the salinization, which is preventing a high level of convergence around this threat. To assist in contextualizing this system, empirical cumulative distribution functions were generated from data gathered from various governmental sources and compared the reservoir's watershed and finished drinking water ion concentrations. These analyses show that the watershed and finished drinking water have some of the highest concentrations of sodium and chloride statewide. Additional investigations determined the trend of sodium increases in finished drinking water since the 1980s. Monte Carlo simulations were ran to determined whether there would be risks to human from ingesting this water should this trend continued. Results from these analyses greatly varied due to the wide range in drinking water ingestion rates. The purpose of these analyses is to assist with stakeholder convergence around the level of threat salinization poses to the reservoir and to initiate discussions of what an acceptable threshold for management could be.

Human-induced environmental change creates novel stressors which populations have not experienced over the course of their evolutionary histories. These stressors are unique selective pressures which may alter species’ survival, growth, reproduction, or behaviors. Freshwater salinization is of growing interest in the scientific community because of the substantial increase in salinity concentrations from irrigation, mining runoff, groundwater pumping, and road salt use. Freshwater salinization is particularly harmful to zooplankton. Zooplankton are critically important to the health of freshwater ecosystems and maintaining ecosystem services such as fisheries, recreation, and clean drinking water. Recent research demonstrates that zooplankton may be capable of rapid adaptation to elevated salinity, which has implications for ecological stability. However, many questions remain regarding how changes in zooplankton tolerance to salinization alters survival, growth, reproduction, and behaviors. To address these important questions, I conduced two separate studies. My first chapter addresses how a multigenerational exposure to salt pollution alters the life history traits of zooplankton and if life history tradeoffs can promote ecological stability. I found that freshwater zooplankton are able to make life history tradeoffs to cope with low levels of salt stress. However, these tradeoffs only occurred in specific salt types and concentrations. Additionally, I found that prolonged, multigenerational exposure to salinity can lead to maladaptation where a long-term exposure history does not confer adaptation, but further reduces lifetime reproduction. My second chapter consists of two experiments to address how the non-consumptive effects of predation may interact with increased freshwater salinity, and a multigenerational exposure to salt pollution to affect 1) the population-level abundance of zooplankton, and 2) the anti-predatory escape behavior of zooplankton. I found in the abundance experiment that salinity and the non-consumptive effects of predation reduced zooplankton abundance 50%. Further, it appears that predation can likely mask the effect of salinity because the effects of salinity are sub-lethal relative to the lethality of predation. In the escape behavior experiment, I found that salinity decreased the vertical escape velocity of zooplankton following a physical disturbance reminiscent of a predation attempt. A prolonged multigenerational exposure to salinity further decreased the swimming velocities of zooplankton. However, when these treatments where combined with predator cues, I found that zooplankton swam at the same speed as control conditions lacking salinization or a predator cue. This finding suggests that predation is a driving force in the behavior of zooplankton and is able to mask the effect of salinity. Changes in zooplankton behavior due to human-induced stress and subsequent masking by natural stressors has implications for community interactions in human-dominated environments. My thesis demonstrates that dramatic effects on zooplankton biology and ecology can occur at environmentally relevant concentrations of salinity, and regulatory thresholds set by the United States Environmental Protection Agency are insufficient in protecting freshwater organisms from the adverse effects of freshwater salinization.

The accumulation of salts in plant rootzones, known as “salinization,” is often a gradual process that can degrade soil structure and cause permanent plant damage. Salinization caused by ever increasing water demands and an increasingly dry climate is becoming problematic for agriculture in semi-arid to arid regions, including California’s Central Valley, which produces about one-quarter of the United States' food supply and almost half of its nuts and fruits, including grapes, according to the USGS California website (https://ca.water.usgs.gov). While grapevines are considered moderately salt tolerant (Walker et al. 2002), the current rate of salinization in many of California's vineyards is contributing to reduced crop yields and lower fruit quality (Keller 2020). Once symptoms of salt toxicity appear on the leaves, vine growth and crop yield may already be in serious decline (Fort and Walker 2011). To prevent salt toxicity from occurring in grapevines, the Walker Lab at UC Davis is applying traditional plant breeding techniques to some of the native population of wild North American grapevine species to improve the salt tolerance of commercial rootstocks (Fort et al. 2013). In recent years, the Walker Lab discovered a wild grapevine species called Vitis acerifolia 9018, which has consistently proven to be more salt tolerant than the most salt tolerant commercial rootstocks (Chen 2021). These physiological traits could be bred into existing popular commercial rootstocks to improve their salt tolerance. The research for this thesis was performed to observe the stress response and compare the salt tolerance of the recently discovered salt tolerant wild rootstock V. acerifolia 9018, against commercial rootstocks widely planted in California and other salinization-affected places, including Ramsey, 1103 Paulson and 140 Ruggeri.

Salinization is a global threat to the ecological functioning and development of the coastal wetlands. Therefore, the study of salinity interaction between the wetland and the coastal estuary is crucial to determine the salinity distribution and its variation in the coastal wetlands. This study, preeminently, was conducted to investigate the distribution of salinity in the Mentor Marsh wetland using a hydrodynamic model. The marsh is a coastal estuary system located within the Ohio Lake Basin, which has been experiencing increased levels of salinity from the early 1960s, especially after the placement of salt mine tailings near the marsh. Consequently, increased salinity has been inducing drastic vegetative change throughout the Mentor Marsh and leading to the rapid development of Phragmites australis. When dry, Phragmites australis is very prone to catch fire.Ten monitoring stations were established within the Mentor Marsh to monitor the salinity and record the hourly salinity, water level, and stream temperature data. The graphical analysis of the observed salinity was performed at several locations within the western basin of Mentor Marsh. Furthermore, a three-dimensional hydrodynamic Environmental Fluid Dynamics Code Plus (EFDC+) model was developed for the western section of the Mentor Marsh utilizing the measured data from five monitoring stations of the western basin. Most of the meteorological data needed for this model were obtained from the National Oceanic and Atmospheric Administration (NOAA). While cloud cover and precipitation data were acquired from nearby airports, solar radiation data were obtained from the United States Department of Agriculture (USDA). Similarly, bathymetry data were prepared by integrating the shoreline GIS shapefile of the Lake Erie and Mentor Marsh with a detailed survey conducted in the marina and adjoining marsh in order to appropriately represent the bathymetry in the EFDC+ model. The water levels at Lake Erie and Mentor Marsh were recorded for the open boundary conditions, whereas the streamflow at Marsh Creek was simulated from the Soil Water Assessment Tools (SWAT) model for the upstream flow boundary conditions. The EFDC+ model was calibrated for water level, water temperature, and water salinity, and the performance of the model was assessed using the statistical parameters such as Coefficient of determination (R2), Nash-Sutcliffe efficiency (NSE), and root mean squared error (RMSE). The salinity distribution under different inflows conditions, and lake level rise scenario was simulated using the calibrated model. The analysis suggested that during high flow conditions of 21.48 m3/s, the advection of the low saline water from Marsh Creek was vigorous in comparison to the diffusion of salinity mixing by tidal influence resulting in the lower salinity distribution of below 0.375 ppt within the model domain. However, during the low flow conditions of 0.392 m3/s, diffusion of salinity mixing due to tidal influence was dominant. The average salinity distribution in the Mentor Marina and Mentor Marsh was 0.655 ppt. Similarly, during lake level rise scenario, the results indicated that the salinity was significantly decreased near Lake Erie relative to the Mentor Marsh and the junction of Mentor Marsh and Mentor Marina. The average decrease of salinity from the salinity during the base run was -45.8% near the Lake Erie, -29.7% at the junction of Mentor Marina and Mentor Marsh, -21.2% in the Mentor Marsh, and -4.4% in the Marsh Creek. Presumably, the analysis suggested that the road salt applications for the de-icing purpose were the prime reason for the salinity increase in the western basin. This study can be helpful to identify the interaction of salinity between Mentor Marsh, Marsh Creek, and Lake Erie, which will eventually assist the local stakeholders for their ongoing efforts of remediation of water quality within Mentor Marsh and avoid unwanted phragmites and fire in the future.

This study of the upper reaches of the Gila River basin in southwestern New Mexico reveals both spatial and seasonal patterns in physical and hydrochemical parameters. Monsoonal precipitation, temporal variability in water chemistry of streams in the upper Gila watershed is significantly impacted by surface runoff due to variability in landscape cover features, as well as surface area of the catchment. However, during base flow regimes spring inputs are the dominant drivers of solute concentrations and chemical variability. Geothermal sources play a major role in salinization of the southwestern stream systems. Prolonged water/rock interaction combined with high temperature, pressure result in chemical change which alters the composition of the surface runoff. This study investigates correlations of solute loading of the Gila River on temporal and spatial scales implementing geochemical, statistical and modeling analysis of the period of record. Significant spatial variability is evident by progressive downstream increases in solute concentrations. This report includes a 108 river mile reach of the upper Gila River. Regional climate change scenarios predict an increase occurrences of base flow regimes resulting in increased frequency of peak salinization. Implications of such scenarios could result in stress on a wide range of ecological communities and negative effects on water quality for downstream users. This study provides a crucial baseline information for determining system’s response to projected climate change, and data which allows to delineate natural salinization sources from anthropogenic impacts on water quality. .

The following research explores how abiotic and biotic processes interact to shape the distributions of the marsh-upland ecotone, a characteristic high marsh plant community in Pacific coast salt marshes that forms the transition zone between vegetated marsh plain and upland habitats. Understanding how abiotic and biotic ecological features interact to structure the marsh upland ecotone is necessary for predicting how the boundaries and distributions of this plant community will respond to disturbance, both human and natural, and for the design of effective strategies to restore and conserve degraded habitats. The abrupt boundaries, relatively simple community composition, and rapidly transitioning abiotic gradient of the marsh-upland ecotone make both observational and manipulative approaches feasible for addressing these research goals. Here both approaches are used to quantify the abiotic and biotic factors responsible for setting species distributions, to test how the relative influence of these factors changes across the underlying abiotic gradient resulting from variable tidal influence, and to design an effective restoration strategy for habitats degraded by disruption of the natural abiotic regime. These results challenge the applicability of a classic theoretical framework commonly applied to describe the structure of the marsh-upland ecotone, increase our understanding of the ecological processes, both biotic and abiotic, structuring the plant community of the marsh-upland ecotone, and optimize a time- and cost-effective restoration strategy to restore degraded ecotone habitats. This body of research significantly enhances our understanding of the complex abiotic and biotic processes structuring the marsh and also contributes to the understanding of how these processes structure species distributions in general.