Today, West Antarctica has been experiencing some of the most profound and rapid climate change on Earth, affecting biota from phytoplankton to seals. To better predict future changes in Antarctica with continued warming, a clear understanding of this region’s biogeochemistry and trophic dynamics is essential. Furthermore, studies of subfossils can reveal how species and their environment responded to past climate events, indicating how anthropogenic climate change might affect them.

The goals of this dissertation are threefold. First, bulk stable carbon and nitrogen isotope (δ13C and δ15N, respectively) analyses of zooplankton were performed to study spatial gradients in West Antarctica’s biogeochemistry. These analyses also established isotopic baselines for this area, critical for accurate assessments of animals’ movements and foraging behaviors. Second, bulk δ13C and δ15N and amino acid δ15N analyses were conducted on present-day pinnipeds of West Antarctica – crabeater, Weddell, and Ross seals – to thoroughly investigate their foraging ecologies. Third, subfossil specimens of four pinnipeds – crabeater, Weddell, leopard, and southern elephant seals – were analyzed for bulk and amino acid isotope values to discern temporal changes in their foraging strategies and habitats during the Holocene.

We found significant spatial shifts in zooplankton bulk isotope values, which were likely driven by gradients in sea surface temperature and nutrient utilization. Our analyses of modern seals showed that Ross seals forage in a pelagic-based food web isolated from that of crabeater and Weddell seals. Although crabeater and Weddell seals are foraging within a similar food web, the former is likely following sea ice, while the latter targets the most productive areas. Our amino acid δ15N results revealed a higher trophic position for Ross seals, equivalent to that of Weddell seals, than expected given bulk δ15N data. Our study of subfossil seal specimens showed that crabeater seals had more diverse diets, incorporating more fish, earlier in the Holocene than in modern times. This suggests the species can show greater flexibility in foraging than might be apparent from modern observations, which may allow them adapt to a changing environment. Furthermore, we found that part of the Ross Sea, habitat for Weddell seals and some southern elephant seals, likely experienced a productivity drop in the recent past, perhaps responding to increasing landfast and sea ice conditions.

As humanity embarks on a global experiment in climate warming associated with increased levels of atmospheric greenhouse gases, we require a thorough understanding of the mechanisms, dynamics, and spatial extent of current and past environmental change on a range of timescales. In the past 1.5 million years (Pleistocene and Holocene), glacial-interglacial cycles emerge as the dominant pattern of orbital-scale global temperature change with millennial-scale oscillations superimposed. The ~100-ka glacial cycles are especially well recognized in the oceanographic and geologic records, though the climate-ocean dynamics and feedback mechanisms responsible for these glacial cycles are often a source of debate. Past sea-surface temperature (SST) is an especially useful indicator of past environmental conditions and a multitude of paleotemperature indicators exist. I make use of a number of geochemical signals for SST including the magnesium-calcium ratio of biogenic calcite, oxygen isotopes, and the alkenone unsaturation index from lipid ketones in order to better understand the mechanisms and dynamics of the current and past climate system.

The California Current and the tropical Pacific are two of the major features that influence climate in California, the tropics, and across the globe through direct effects (e.g., upwelling, sea surface temperature changes) and atmospheric teleconnections. This dissertation examines past oceanic and atmospheric change in these two critical regions and linkages with high-latitude climate, insolation, and radiative greenhouse gas forcing. The coastal California chapter addresses questions regarding the regional and local strength of the California Current, upwelling intensity, and precipitation variability in the Holocene. Tropical Pacific chapters deal with the spatial distribution of tropical Pacific sea-surface temperatures as a reflection of oceanographic change and a driver of global climate. Each of these regions offers lessons for understanding climate variability from the late Pleistocene to the present and future climates.

Coyotes (Canis latrans) have an expanding North and Central American range and have also been shown to benefit from marine subsidies. Identifying the past and present role coyotes play in linking land and sea, and whether those links are lost or gained through time, will have important implications for the future management of this expanding species. The goals of my dissertation were to: (1) characterize the extent, magnitude and importance of a marine subsidy to modern coyotes on the central California coast; (2) determine whether Holocene coyotes on the central California Coast had an equivalent dietary niche; and (3) begin to evaluate (via predation and competition) the impact of this modern marine subsidy (where it occurs) on key terrestrial species.

To address these goals, I seasonally collected scats along coast-to-inland transects at three modern coastal sites around Monterey Bay over a span of two years. I used discriminant function analysis on a set of scat samples DNA-verified to species to show that morphological traits of gray fox, bobcat and coyote scats are not diagnostic of species; predictive models based on morphology have misclassification rates of ~35%. These results suggest that DNA-verification of scats is required in studies using scat to make claims about diet, abundance or habitat use by any of these animals in localities where they are sympatric. I characterized modern coyote diets using traditional scat analysis techniques in tandem with stable isotope analyses of scats themselves. I established a diet-to-feces discrimination factor for coyotes by analyzing multiple tissues from road kill carcasses and validated scat stable isotope dietary predictions by carefully comparing scat stable isotope values with isotopes measured in prey remains sourced from the scats.

For the investigation of Holocene coyote dietary ecology I selected six archaeological sites around Monterey Bay with a range of occupation periods spanning from ~3000 - 700 BP. This allowed for establishment of a Holocene baseline with which to compare modern coyote ecology over millennial timescales. My data point to both the existence of a marine subsidy to modern coyotes, and to a positive impact on coyote abundance. Sub-fossil isotope data suggest that Holocene coyotes did not consume marine-derived foods, despite the nearby presence of a mainland seal rookery. These data suggest that the use of marine resources by contemporary coyotes is a new behavior relative to their recent ancestors, perhaps enabled by reduced competition with either humans or other, now-absent consumers (e.g., grizzly bears, Ursus arctos californicus).

Oxygen isotope ratios of fish biominerals reflect environmental growth conditions - specifically, the temperature and δ¹⁸O values of water. In Holocene ocean sediments, phosphate δ¹⁸O (δ¹⁸O_P) values of small pelagic fish bones and scales can be coupled with abundance data to study connections between past climate and population dynamics. This requires the detection of decadal scale climate variability via precise isotope measurements. To accomplish this, isotope data is best corrected by multiple regression methods that facilitate both instrumental monitoring and correction model optimization. Our measurements of δ¹⁸O values from bones, scales, and otoliths indicated that all three materials provide similar information about growth conditions, provided that each material's unique allometry is considered. For sardines cultured at controlled temperatures, δ¹⁸O_P values of scales were consistent with the fractionation equation proposed by Longinelli and Nuti (1973). These results support the use of δ¹⁸O_P to investigate the paleoecology of small pelagic fish.

Patterns of species interactions are both the cause and consequence of ecosystem dy- namics. Understanding the origin and function of specific interaction patterns at the ecosystem scale has been a long-term goal in ecology. These efforts are often limited by the enormous size of biological systems, the temporal transience of ecological inter- actions, difficulties in obtaining reliable measurements [3], knowing what is important to measure in the first place, and the time-scale over which observations are made. In the following chapters, I first introduce a probabilistic framework to incorporate field- measured (rather than experimental) strengths of interactions between species using stable isotope data. This framework provides a means to examine whether different variance structures are predictive of specific interaction patterns, such as nestedness and modularity. Secondly, to assess the impact of global climatic perturbations on mammalian communities over long time scales, I use stable isotope ratios of predators and prey to examine six independent paleontological communities ranging from Europe to Beringia and spanning the Last Glacial Maximum. Both the temporal and spatial evolution of species-specific relationships, as well as community-scale structures, are investigated to understand how changes in climate and prey abundance [99] influenced trophic interactions in the late Pleistocene. Although Chapters 1 and 2 concern large- scale emergent properties of food-webs, I introduce in Chapter 3 a process-based model designed to investigate the effects of mechanical constraints on the foraging strategies of anthropoid primates, and early hominins in particular. Although this model serves primarily as a predictive tool, towards the end of Chapter 3 I discuss how it can be used instead to inform independent estimates of diet, which may be particularly useful in a paleontological context where data are limited. Finally, in Chapter 4, I extend upon this reasoning and introduce a method by which resource availability data and mixing space geometry can be used to update estimates of trophic interactions from Bayesian isotope mixing models, and demonstrate its utility using data from a New Zealand intertidal community. The four chapters presented here introduce techniques and frameworks by which stable isotopes, statistical mechanics of networks, and process-based models can be used to investigate both the formation and time evolution of the patterns of species interactions in ecological communities.