Accelerating biodiversity change is a defining characteristic of the Anthropocene, and evidence accumulated from almost 30 years of research is often invoked to suggest that these changes will have catastrophic effects on ecosystems and the services they provide to humanity. In this thesis I use theory, empirical analysis and their combination to address key remaining issues surrounding the relationship between biodiversity, ecosystem function and ecosystem services. First, while the asymptotic relationship between biodiversity and ecosystem function is substantiated from experiments that randomly assemble plant communities, the response of ecosystems to directional biodiversity loss is highly variable. In the first two chapters I investigate how species level attributes (vulnerabilities, functional contributions) and community dynamics (compensation, non-random extinction) scale to affect individual and multiple ecosystem functions simultaneously. Second, a narrow set of plant-based ecosystem functions have come to dominate the field, and with few exceptions, linking these to the ecosystem services that directly affect human well-being has been challenging. Inland fisheries provide millions of people with their primary source of essential nutrients (e.g., protein, omega-3 fatty acids, iron, zinc), but are threatened by hydropower development, overfishing and climate change. The last three chapters explore how fish biodiversity both responds to these threats, influences fisheries production and affects nutritional security in the Amazon, Earth’s largest and most productive river basin. Additionally, I evaluate how alternative strategies to ameliorate fisheries declines that hinge on substituting wild fish with farmed animals can meet nutritional goals. By combining theoretical and empirical approaches and integrating concepts from ecology, fisheries, nutrition and economics, this body of work illuminates key drivers surrounding the variation observed in how ecosystems respond to biodiversity change, and the implications of these changes for the sustainability of aquatic food systems. Compensation can maintain biomass production, but incur strong changes in community composition. Differences in species vulnerabilities as well as in their functional contributions can predict the degree to which these compositional changes affect ecosystem functions. When considering critical ecosystems services, such as the contribution of inland fisheries to human nutrition, declining biodiversity always comes at the cost of increasing nutritional risk. This risk cannot be minimized by substituting wild fish with poultry or aquaculture species. Thus, investment in managing biomass production together with biodiversity, such as through protecting key habitats, maintaining riverine connectivity and enacting temporary closures, will maximize the long-term contribution of wild fisheries to human nutrition. Additionally, diversifying farmed animal production by interspersing high valued species with highly nutritious species can deliver both economic and food security benefits. More broadly, by illuminating how biodiversity contributes to the sustainability of food systems, this thesis provides new basic and applied dimensions to the field of biodiversity and ecosystem function. Further, the findings presented here demonstrate how an interdisciplinary approach can shed light on the intertwined relationships between biodiversity, ecological dynamics and Earth’s ongoing sustainability.

Genome-wide neutral diversity levels are shaped by both positive and purifying selection on linked sites. In humans like most species, the relative importance of these types of selection in shaping patterns of neutral diversity remains an open question. We can infer their relative contribution from observed patterns of neutral diversity by using information about recombination rates and targets of natural selection. To this end, I fit a joint model of the effects of positive selection (selective sweeps) and purifying selection (background selection) to genetic polymorphism data from the 1000 Genomes Project. I show that a model of the effects of background selection provides a good fit to patterns in diversity data and that incorporating the effects of selective sweeps does not improve the fit. Using my approach, the effects of background selection explain up to 60% of the variation in neutral diversity levels on the 1Mb scale and account for patterns in the data for which positive selection via selective sweeps had been invoked as explanations. I find that over 80% of the selected regions affecting neutral diversity levels are located outside of exons and that phylogenetic conservation is the best predictor of the source of selection in these regions. My results show that the genome-wide effects of background selection are pervasive, with measurable reductions in neutral diversity throughout almost the entirety of the autosomes. I provide maps of the effects of background selection and software for making similar inferences, which should provide important tools for future research that relies on interpreting patterns in neutral diversity levels.

The early Pliocene Gray Fossil Site (GFS) is a biodiverse site with a unique faunal assemblage that represents one of few sites of its age in eastern North America. A community structure analysis of the mammals at GFS was done to characterize species and better understand the paleoenvironment. Data and was gathered from twenty modern communities and five late Neogene sites to compare with GFS. Species from these 26 sites were categorized by body size, locomotor mode, cheek tooth crown height, and diet to characterize niches occupied. Descriptive statistics contrasted proportions of species within categories across communities. Discriminant function analyses (DFA) determined characteristics that best differentiate communities and classified fossil site habitat types. DFA results indicate that the GFS paleoenvironment was a habitat most similar to modern temperate forest regions in the eastern U.S. and China. Characteristics of GFS are dissimilar from other late Neogene sites examined in this study.

Plants species interactions via pollinators are a model system to understand the mechanisms that generate plant diversity in nature. However, most studies have focused on plant-plant interactions via pollinator attraction while ignoring the role of plant-plant interactions via pollen transfer. Heterospecific pollen transfer (henceforth HP) can be common and have negative fitness effects. Negative HP fitness effects may prompt the evolution of adaptive strategies to minimize them. However, the extent of spatial variation in HP load size within and among populations, a tenet for natural selection, remains unexplored. Such knowledge would hence constitute a first step in advancing our understanding of the importance of HP transfer as an evolutionary force promoting plant diversification. For instance, the opportunity for natural selection would only be expected under strong among population variation in HP load size. In this study we aim to answer the following specific questions: Is there variation in the amount and diversity of HP load in Lobelia siphilitica? How is the variation partitioned across different levels of organization (populations, individuals, and flowers among an individual)? Greater among-population variance would suggest that community attributes, such as plant density and diversity are the major drivers of HP load size. Greater among-plant variance would indicate plant traits that affect pollinator foraging behavior may play an important role. Greater variance among flowers within an individual plant, would suggest stochastic events may underlie variation in HP load size and diversity. In order to test these hypotheses, samples of the native perennial Lobelia siphilitica were taken from 10 populations in the Northeast Tennessee region (500 total). The styles were processed in the lab and pollen grains counted separating them into two categories, heterospecific and conspecific pollen. There was variation in the amount and diversity of HP load received. Populations are expected to have the largest variation among them due to different environments (disturbance levels, pollinators, plant communities, etc.) Since populations are expected to have the largest variation in HP received, they are also expected to have the greatest opportunity for natural selection to act. Looking at HP receipt within-species is important for identifying the mechanisms that can generate diversity in plant communities.

Yunnan, southwestern China, represents a modern biodiversity center for Rubus (Rosaceae). The history for this high modern diversity remains poorly known due to the lack of fossil evidence. In this report, fossil pyrenes of Rubus are taxonomically studied from the late Pliocene (Piacenzian) of Lanping County, northwestern Yunnan. These pyrenes show a greater morphological variation than that of extant Rubus pyrenes within the same species, indicating that they belong to different taxa of Rubus. Based on comparisons with both modern and other fossil species, our fossil pyrenes are assigned to five taxa, including a newly established one, Rubus lanpingensis nov. sp. These fossils suggest a somewhat high species diversity of Rubus in Lanping, a small area in northwestern Yunnan, during the late Pliocene. This provides the first fossil perspective for an understanding of the historical background of the modern Rubus diversity in a limited geographic area of Yunnan. The inferred palaeobiodiversity is probably associated with a large environmental heterogeneity in a limited area of Yunnan at that time.

No description available.

Global biodiversity is in decline as a result of unprecedented human alterations to the earth’s land cover. Understanding the ecological mechanisms of these large-scale changes in biodiversity is imperative in furthering our knowledge on the effects these alterations may have on animal behaviour and consequently on populations, allowing researchers and managers to effectively conserve species. During the last decade, there have been reports of moose populations both increasing and decreasing in North America due to a variety of factors (e.g., climate change, habitat disturbance, disease, etc.). Within British Columbia, wildlife managers have reported moose population declines of up to 50 – 70%, while other areas have remained stable. These changes have coincided, spatially and temporally, with the largest recorded mountain pine beetle (Dendroctonus ponderosae) outbreak. The outbreak resulted in extensive logging and road building in attempts to recover economic value from the beetle killed trees, resulting in drastic changes to the landscape. Understanding the effects that a highly disturbed landscape has on a species is critical for effective management and conservation. To investigate this, I examined the seasonal response of female moose to landscape change caused by the Mountain Pine Beetle outbreak and attendant salvage logging infrastructure in the Interior of British Columbia on the Bonaparte Plateau. First, I used a cluster analysis framework to develop biologically relevant seasons for female moose using individual movement and habitat use. I then used this temporal framework to develop seasonal home ranges for each individual moose. Second, I modeled the seasonal habitat selection of female moose to examine how moose respond to salvage logging infrastructure (i.e., dense road network and extensive cutblocks) using resource selection functions in an information-theoretic framework. We tested whether predation risk, forage availability or the cumulative effects of salvage logging best predicted moose space-use. Moose movement data clustered into five biologically relevant seasons, which were consistent with our biological and ecological knowledge of moose in the study area; however, these seasons and the size of the range differed from other seasons defined using alternative methods in the region. Across all seasons, the cumulative effects of forage availability and risk best predicted female moose distribution. In the calving and fall seasons, the top risk model best predicted moose habitat selection while the top forage availability model better explained moose habitat selection in spring, summer, and winter. Our results identified the importance of defining biological seasons using empirical data and how these seasons can differ from arbitrarily defined seasons, as well as the implications these can have in subsequent analysis and management. Additionally, we found that moose are seasonally trading the benefits of foraging for predation risk in these highly disturbed landscapes, using some aspects of salvage logging. My results bring perspective on how moose are using a highly disturbed landscape at the seasonal scale and a nuanced approach to landscape management. / Graduate

The overall objective of this study was to quantify the effects of dominant grass propagule source (i.e., cultivar vs. non-cultivar) and seeded diversity of propagules on community structure and ecosystem function during prairie restoration. Two field experiments, and two chronosequences were used to investigate this main objective. The two field experiments were established at the same latitude separated by 620 km (corresponding to a precipitation gradient from eastern Kansas to western Illinois), and consisted of a split plot design, with dominant grass source as the whole-plot factor (2 levels) and seeded dominance of grasses as the subplot factor (5 levels). Percent cover of each species in each treatment combination was quantified during the first five years of restoration. Total plant species richness and diversity were not adversely affected by cultivars in Kansas or Illinois. The effect of the dominant grass population source on the cover of focal grasses, planted species, and volunteer species were contingent upon location. By the fifth year of restoration, diversity and richness were greatest, and cover of volunteer species was lowest in the low grass dominance (i.e., high diversity) treatment. ANPP, as well as total, microbial, and mineralizable pools of C and N were measured to quantify ecosystem function in these two field experiments. Changes in ecosystem function in Kansas and Illinois were primarily driven by time and regional abiotic differences, not propagule source or seeded diversity. The effect of plant species diversity on ecosystem function was further investigated at a landscape scale by developing and sampling two chronosequences of high (HDC; n=20) and low diversity (LDC; n=15) prairies spanning over two decades of restoration in northwestern Illinois. In general most metrics of ecosystem function in both chronosequences moved towards levels measured in remnant prairies. While the constituent prairies of the HDC had higher species richness, diversity, and more rapidly increasing root biomass than the fields of the LDC, recovery of other important ecosystem functions including aboveground net primary productivity, total, microbial, and mineralizable soil C, and soil aggregate mean weighted diameter were achieved equally well with either high or low diversity prairie plantings.

Subterranean arthropod communities are important components of North American ecosystems, contributing numerous ecosystem services and essential food-web functions. Despite this, fundamental information about species diversity in these communities remains unknown, and their taxonomic composition and ecological diversity have scarcely been assessed. Subterranean pitfall traps are a commonly used method for sampling endogean and hypogean soil habitats in Europe but have never been widely implemented in North America. Here, I employed this method to sample subterranean arthropod communities in the Ridge and Valley and Blue Ridge ecoregions of Virginia, USA in the winter and spring. In total, 2,260 arthropod specimens were collected constituting 319 distinct species. I extracted and purified DNA and amplified the mitochondrial gene: cytochrome C oxidase subunit I (COI) from each recovered morphospecies and derived a unique COI barcode for each species sequenced. Objective sequence clustering was used to establish molecular operational taxonomic units (mOTUs) for downstream diversity analyses and establishment of dynamic identification resources. Total species richness and average species richness per site were assessed and compared for both regions and seasons. The Shannon-Wiener diversity index, Hutcheson's t-test, and effective numbers of species (ENS) were employed to compare regional subterranean arthropod diversity. The richness, Shannon-Wiener, and ENS comparisons indicated that both ecoregions encompass highly diverse subterranean arthropod communities with those of the Ridge and Valley being significantly more diverse than those of the Blue Ridge. / Master of Science in Life Sciences / Arthropods are invertebrate animals with hard exoskeletons, segmented bodies, and jointed paired appendages, and include insects, arachnids, crustaceans, and myriapods. Arthropods make up the majority of animal species on the planet and are important parts of ecosystems, making it important for researchers to study them. While we know a fair amount about North American arthropods that live above-ground, relatively little is known about those that live deep within the soil and underlying rock substrate. Subterranean pitfall traps are a common method used for collecting arthropods from subterranean habitats in various regions of the world but have rarely been used in the USA. As a result, much of the life beneath our feet may be unknown. I used these traps to collect subterranean arthropods in the Ridge and Valley and Blue Ridge regions of the Appalachian Mountains. A total of 2,260 individual arthropods were collected, belonging to 319 different species. I used DNA sequencing to establish a unique fingerprint-like "barcode" for each species. These barcodes serve as helpful identification resources, and will help name new species in the future. They also allowed me to measure the number of species (diversity) of subterranean arthropods collected from each region, and compare the two to determine which region is more diverse. I used common statistical metrics of diversity including species richness (number of species) and the Shannon-Wiener diversity index to compare regional subterranean arthropod diversity. My results show that both the Ridge and Valley and Blue Ridge regions of Virginia, USA are home to highly diverse subterranean arthropod communities and those of the Ridge and Valley are significantly more diverse than those of the Blue Ridge.

No description available.