Dietary practice during the transition from Early Intermediate Period (200 BC-AD 600) to the Middle Horizon (AD 600-1000) is crucial to understanding Pre-Hispanic life on the southern coast of Peru. The Cerro Del Oro material was excavated in 1925 by Alfred Kroeber and since been biochemically unstudied for almost ninety years; left dormant at The Field Museum in Chicago. Through bioarchaeological reconstruction of diet and health at the site of Cerro Del Oro from a cemetery sample (N=35) in the Cañete Valley, the effects of demographic and subsistence changes can be examined through a combined analysis of osteological and light isotopic data. Stable carbon (13C/12C, or δ13C) and oxygen (18O/16O, or δ18O) isotopic values from tooth enamel carbonate are utilized to reconstruct diet during early childhood of each individual. Results indicate that the majority of the population were consuming a moderately variable terrestrial protein or C3 diet. This is significant due to the close proximity to marine resources.

This study utilizes stable isotope and dental microwear analyses to elucidate diet and subsistence practices of indigenous Muchik peoples interred at two sites in the Lambayeque region of northern Peru: La Capilla Santa María Magdalena De Eten (CSMME) (n=17) and La Capilla Del Niño Serranito (CNS) (n=18). Burials at CNS date to the Early Colonial Period (A.D. 1533-1620), while burials at CSMME date to the Mid- to Late-Colonial Period (A.D. 1625-1760). Dental microwear and stable isotope investigations reveal a highly correlated dietary profile across both sites, which suggests consistent subsistence practices across the Colonial Period, insofar as can be measured using these techniques. However, there is significant differences between CNS and CSMME in dental microwear features indicating the foods consumed by all members at each site—since sex and age are not significantly different between the two sites—is perhaps attributable to the influence of Spanish colonial rule to the degree to which these dental microwear features capture larger patterns in these two populations. Although samples sizes are limited, at CNS, the frequency of fine scratches and small pits increase with age and coarse scratches decrease between childhood and adolescence, indicative of transitions in diet or the use of the teeth during the maturation. Further, statistical inquiry found no significant dental microwear differences between site, age, or sex in the studied populations.

Historically, terrestrial food web research has focused on describing the structure of aboveground grazing webs, and determining how interactions among plants, herbivores and higher trophic levels influence primary productivity. Detrital food webs however, play a significant role in regulation of ecosystem dynamics through direct impacts on decomposition. Unraveling the complex nature of detrital food web structure is critical to developing a better understanding of ecosystem function. Therefore the primary objective of this research was to describe the structure of the leaf-litter food web in a temperate deciduous forest, with emphasis on interactions between a community of generalist predators, the forest-floor spiders, and arthropod prey. Elucidating occurrence of trophic interactions in the forest-floor food web was a formidable task due to the high diversity, small body sizes and cryptic habits of many litter-dwelling arthropods. Analysis of natural variation in consumer stable isotope ratios (δ13C and δ15N) formed the crux of this research because it simultaneously permitted quantification of the trophic positions of litterdwelling arthropods and identification of spider resources, including prey subsidies from the grazing web. A monoclonal antibody-based ELISA was employed to analyze the gut contents of spiders to quantify predation on a major arthropod taxon, the forest-floor flies. Surveys of spider distributions and prey availability in the litter layer also provided fundamental knowledge of community structure. Stable isotope analyses suggested that most spiders exhibited strong trophic connections to the detrital web, but weak links to herbivorous prey. Several lines of evidence supported a strong trophic link between large, litterdwelling collembolans (Tomoceridae) and cursorial spiders, including correlation between spider and tomocerid densities on the forest-floor, similarities in spider and tomocerid carbon signatures, and nitrogen enrichment of tomocerids relative to other prey types. Conversely, this research provided conflicting evidence regarding spider consumption of flies. Gut content assays indicated consistent predation on flies by cursorial spiders, while stable isotope models suggested that flies are likely of little importance in the spiders’ diets. This project yielded valuable insights into the role of spiders in the forest-floor food web and the potential importance of species-specific variation in prey consumption for detrital food web dynamics.

Dispersal is a fundamental process that shapes many aspects of population ecology and evolution. Dramatic local population declines brought about by anthropogenic-driven changes to ecological processes are unfortunately becoming ubiquitous and increasing the urgency to understand dispersal behaviour in many species. For species where direct methods of tracking movement and dispersal are unsuitable, other indirect methods need to be employed to understand and characterise these behaviours. The steep population decline, due to predation, at the largest EU population of Leach’s storm-petrels Oceanodroma leucorhoa (St Kilda, Scotland), and the potential part immigrant birds have in buffering this threat, highlighted the need to understand dispersal and connectivity of widely spaced colonies in this species. The implications for the persistence of local colonies and the wider population of Leach’s storm-petrels could then be assessed. A population genetic analysis of 9 colonies across the North Pacific and Atlantic distribution, using two DNA markers (mtDNA control region and microsatellites), revealed ocean basin differentiation (Global ST = 0.32 P <0.0001, Global FST = 0.04, P <0.0001) but also identified a migrant individual in the Pacific population (STRUCTURE migrant assignment). The Atlantic population was found to be genetically homogenous, with patterns of historical and contemporary gene flow, indicating that long-distance effective dispersal is prevalent in Leach’s storm-petrels within the ocean basin. Bayesian stable isotope analysis of carbon and nitrogen (13C & 15N) provides evidence for natal dispersal as an important dispersal mechanism, and reveals movement of immature birds between colonies during the breeding season as a likely mechanism to promote inter-colony exchange and gene flow. Stable isotope comparison also identified mixing on wintering grounds as another possible influence on dispersal. The potential for immigrant birds to offset the loss caused by predation at the St Kilda colony is supported by these studies, and will likely help the persistence of the colony in the short-term. However, future viability is debateable considering the evidence for both avian and mammalian predation. This research provides a better understanding of the extent and mechanism of dispersal in the Leach’s storm-petrel, which is important to predict the potential impact of environmental change and, where possible, implement effective population management for this species.

The brown trout, Salmo trutta L., displays one of the most variable and polymorphic life-history strategies of all the salmonids. In some populations, individuals spend their whole life-cycle in the river (freshwater-resident) whereas in others, a varying proportion migrates to sea for variable amounts of time to better feeding conditions before returning to spawn (anadromous). The ‘decision’ if an individual will migrate or not will be determined by the balance of the costs and benefits of following a particular life-history strategy. The balance of these, which do not affect males and females equally, will determine the future success (measured by fitness) of each strategy. This research addresses the influences of parental contribution, mainly maternal effect, of anadromous and freshwater-resident brown trout on offspring performance and subsequent life-history. A partial migratory population of brown trout was studied in the Tadnoll Brook, one of the seven major tributaries on the River Frome. The tributary is classified as a circum-neutral chalk stream, 9.9 km long with a catchment approximately 50 km2. Carbon and nitrogen stable isotope analysis (SIA) was used to quantify maternal reproductive contribution of anadromous and freshwater-resident brown trout to offspring and determine the future success (measured by fitness) in terms of size and time of emergence. A panel of 12 microsatellite loci was used to assign parentage to 0+ parr. Using field data collected over 1.5 years on individual fish, this study tested parental influence on offspring performance in terms of size and growth rate and calculate the reproductive contribution of maternal/paternal anadromous and freshwater-residents. Adult life-history strategy was identified using a combination of results from SIA, PIT tag data and ecological data (body size, temperature). Parr life-history strategy (1+) was inferred using PIT tag detection data. The results of the SIA indicated fry of anadromous females emerged earlier and at a larger size than fry of freshwater-resident females. Parentage assignment of parr was low (28 %), with 8 parr assigned to both parents and 43 assigned to only a single parent. There was no detectable effect of parental life-history on parr size and growth rate, however the raw data may suggest offspring of anadromous parents have an early size advantage but a slower growth compared to offspring of freshwater-resident parents during the first year of the parr stage. Twenty-four percent of the offspring were identified as putative smolts at 2+ and both forms interbred and could produce offspring of each life-history. Estimates of reproductive contribution (SIA and growth) show a higher proportion of anadromous females and males (growth only) contributed to offspring production. The results of this research indicate that the maternal anadromous contribution is higher in the Tadnoll Brook population, affording fitness benefits to their offspring during early ontogeny such as size advantages and emerging at a more profitable time to establish feeding territories. Adult life-history does not appear to influence juvenile (0+ parr) life-history but may have an effect on offspring performance. The presence of both forms in the population suggests the anadromous fitness benefits to offspring may only have an affect during ontogeny and early stages of growth. Then after juveniles reach a size threshold environmental factors influence offspring life-history, resulting in the largest parr with the fastest growth adopting an anadromous life-history.

Stable isotope analysis (SIA) is a valuable tool in ecotoxicology because δ13C and δ15N may provide insights into the trophic transfer of contaminants in a food web. The relationship between a species’ trophic position (TP, determined from δ15N) and internal concentration of biomagnifying contaminants can be established and used for regulatory purposes. However, the exposure of organisms to xenobiotics incurs physiological costs, and the stable isotope signature of a consumer reflects not only diet but also a physiological state. The latter raises questions regarding the interpretation of stable isotope signatures in contaminated areas. Therefore, the aim of this Thesis was to evaluate the behaviour of consumers’ stable isotope signatures in stressed systems, with a primary focus on the effects of environmental contaminants. In paper I, the physiological costs of chemical exposure were found to alter incorporation rates of dietary nitrogen and carbon in a consumer by influencing both growth and metabolic turnover, with resulting changes in isotope signatures relative to a control system. In paper II, the diet-consumer discrimination factors for 15N and 13C were confirmed to increase under chemical exposure mediated via increased metabolic costs. However, the physiological response was low and translated into only minor shifts in the δ13C and δ15N. The predictability of exposure effects on the stable isotope signature was demonstrated in paper III, in which animals exposed to a chemical with a known mode of action presented expected effects on elemental composition, body size, biomarkers of oxidative stress and the stable isotope signatures. Moreover, consumers’ oxidative balance was found to be related to their δ15N values, thus providing evidence of the kinetic isotope effect on the oxidative status. However, despite the alterations in stable isotope signatures observed in laboratory settings (papers I-III), the effect of xenobiotics on the TP estimates was nil or minor in the field-collected animals. Moreover, the TP values were not significantly different between the animals in the contaminated and the reference habitats because of the high overall uncertainties in the TP estimates (paper IV). Also, the TP estimates based on δ15N in bulk material were more similar between the contaminated and the reference systems than TP estimates based on δ15N values in amino acids. Therefore, the latter method appears more sensitive towards xenobiotics (and, possibly, other environmental stressors) and thus less suitable for TP assessment in contaminated areas. This Thesis improved the overall understanding of the applicability of SIA in stressed systems by establishing relationships between various exposure regimes, physiological responses and the stable isotope signatures in consumers. In model species at low trophic levels, the exposure to xenobiotics was found to significantly affect δ13C and δ15N values, which can be expected whenever physiological responses are detected. However, because of the overall high uncertainty in TP estimates, no significant differences between contaminated and control systems were detected, although the estimated TP were consistently higher in the contaminated systems. Future research should focus on higher trophic levels, in which effects of a greater magnitude can be expected. Moreover, the effects in entire food webs should be addressed rather than single prey–consumer relationships as well as other environmental variables that may contribute to the stable isotope variability in and among systems under various environmental pressures. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Master of Science / Department of Agronomy / Eduardo Alvarez Santos / Isotope analysis combined with micrometeorological techniques can bring new insights into the mechanisms governing biogeochemical cycles in ecosystems. New field-deployable optical sensors that have recently become available can provide accurate trace gas concentration measurements at sampling rates suitable for micrometeorological measurements. These instruments could help enhance current carbon cycling research efforts. This research will bring new insights into understanding the biophysical processes governing the carbon cycle at the ecosystem scale, which will be crucial for enhancing our future climate change scenario predictions. The impact that land use management has on the carbon cycle components of an ecosystem is an important issue that could be addressed with this new approach. More notably, research is needed to identify how management practices affect the abundance of C₃ and C₄ plant communities in grasslands and to identify how shifts in plant community composition can modify the net ecosystem exchange of CO₂. Chapter 1 of this thesis provides a literature review on the carbon cycle in grasslands, stable isotope analysis in environmental mediums, and the combination of isotope analysis with micrometeorological methods to study carbon exchange at the ecosystem scale. In Chapter 2, we describe the evaluation of the performance for a multi-port sampling system’s measurements of vertical concentration gradients of stable isotopes of CO₂. The results of these analyzes show that the sampling system was suitable to measure vertical gradients of concentration under field conditions. Chapter 3 describes how the sampling system was used to study the isotope exchange in two watersheds at the Konza Prairie Biological station under distinct management conditions. Gradients of isotopes were measured in two adjacent watersheds (K2A and C3SA). The K2A watershed is burned every other year, while the C3SA watershed is in a patch-burn grazing system and is burned every three years. Results show that the sampling system’s performance is adequate for our study. The sampling system was able to detect clear differences in the isotopic composition of nighttime NEE between the watersheds, which is believed to be greatly influenced by C₃ and C₄ plant community composition. Further research is needed to examine the role that other environmental conditions played on altering the isotopic signals of the NEE in each watershed. Additionally, other management practices should be examined using this sampling system to determine their impact on biophysical drivers in the ecosystem, which could subsequently impact the plant community abundance and diversity.

An efficient methodology for separation of magnesium from different geomaterials was developed in order to determinate their isotopic composition. This methodology with 100% yield is suitable for high precision analysis of Mg isotopes by multi collector inductively coupled plasma mass spectrometry (MC-ICP-MS). Three separate stages of ion-exchange chromatography were carried out in ultra-trace laboratory equipped with laminar flowbox using cation exchange resin, AG50W-X12 and chemicals of ultrapure quality. Variations in samples 26 Mg/24 Mg and 25 Mg/24 Mg ratios are expressed as δ26 Mg and δ25 Mg units, which are deviations in parts per 103 from the same ratio in DSM3 Mg standard. The robustness of the technique was assessed by replicate analyses of magnesium standards Cambridge 1 versus DSM3. The long term repeatability of the Mg isotope ratio measurements of Cambridge 1 against DSM3 using this technique is -2.577 ± 0.10‰ on δ26 Mg and -1.328 ± 0.06‰ on δ25 Mg at 95% of confidence (2σ). Delta 26 Mg in five natural standard samples was measured in order to validate a quality of measurement in two different laboratories: Czech Geological Survey, Prague, Czech Republic and GFS Potsdam, Research centre for geoscientist, Potsdam, Germany. The results measured in this study (laboratory of CGS) are...

This Ph.D. Thesis is focused on the effect of submerged vegetation on the structure of lake ecosystem and trophic relationships among fishes. Succession of submerged vegetation is a dynamic process and the vegetation community may change dramatically even during a year. Many environmental factors have impact on the succession of submerged vegetation and consequently the presence of the vegetation has substantial impact on the aquatic ecosystem. Nutrient level (mainly nitrogen and phosphorus) plays a key role in the succession of freshwater ecosystems. Further, herbivory significantly influences species composition and biomass of macrophytes and macroalgae. Herbivory of fish is a foraging strategy that is dependent on temperature. Foraging preferences of fish may suppress the palatable species. The rate of herbivory affects plant growth patterns and thus inpalatable species may be advantaged in the competition among plants. In aquatic ecosystems, herbivory is often performed by omnivorous species. The diet preferences of omnivorous fish differ among aquatic ecosystems and submerged vegetation can shape their trophic niches substantially.

The niche concept provides a tractable measure of the ecological roles and requirements of organisms, which can inform our understanding of the patterns of biodiversity, and subsequently, direct conservation policy. Although niche is most commonly considered for species, variation nested within lower hierarchies of biological organization (i.e., phenotypes, genotypes) also contributes to maintaining biodiversity. Herein I examine spatial and dietary niche variation among and within species in a consumer–resource system where resources and competition are structured by a heterogeneous environment. An underlying theme of this dissertation was developing research through a community-engaged approach that not only contributed to conceptual advancements in niche theory but also to applied conservation priorities. The marine archipelago of the central coast of British Columbia, Canada structures salmon (Oncorhynchus spp.) resources and the inter- and intraspecific competitive context for coastal grizzly (Ursus arctos) and black bears (Ursus americanus). This assembly of ursids represents nested levels of biological organization (i.e., species, phenotypes (white vs black-coated morphs of black bears) and genotypes (dominant homozygote black-coated black bears, heterozygote black-coated black bears, recessive homozygote white-coated ‘Spirit’ black bears)), which allows for investigation into niche variation across and within species. I investigated niche variation using a suite of non-invasive methods. Local and Traditional Ecological Knowledge (LEK/TEK) provided complementary information to genetic and stable isotope (13C and 15N) data from hair samples. First, I investigated changes in the spatial niche of coastal grizzly bears. By combining western scientific approaches with TEK/LEK interviews I found the range of coastal grizzly bears has expanded westward onto several coastal islands. The economic, cultural, and ecological impacts of this shift in spatial niche are not yet understood. Second, I tested hypotheses related to variation in the foraging niche of black bears in response to the competitive environment and salmon resource availability. I found that grizzly bear presence reduced the proportion of salmon in black bear diets by ~40%. I also found that salmon species diversity, and not biomass abundance, was positively correlated to salmon in black bear diets. This highlights the importance of resource diversity to consumers beyond the consideration of abundance. Third, I explored spatial niche patterns of Spirt bears in relation to protected areas. I found that landscape-level Spirit bear allele frequency and population estimates were lower than previously reported. Approximately ~50% of Spirit bear allele hotspots corresponded to protected areas. This finding suggests Spirit bears are rarer and less protected than previously assumed. Finally, I tested hypotheses related to niche variation between phenotype and genotypes of Spirit bear populations. I found both phenotypes and genotypes diverged in foraging niche, with Spirit bears and black-coated heterozygotes having elevated stable isotope signatures compared to black-coated homozygotes. This result supports the role of ‘multi-niche’ mechanisms in maintaining this rare polymorphism. Results from all chapters contributed to land- and marine-use stewardship efforts of collaborating First Nations. Collectively, this dissertation offers novel contributions towards understanding how niche variation at multiple levels of biological organization can contribute to conservation planning. / Graduate / 2020-04-04