Doctor of Philosophy / Department of Division of Biology / John Blair / The feasibility of restoration, which traditionally targets historical conditions, is questionable in the context of global change. To address this, my dissertation investigated (Chapter 2) the patterns of restoration establishment along a chronosequence of restored prairies with respect to nearby remnant prairies, (Chapters 3-4) responses of plant communities in restorations initiated using different methods (levels of species richness and sowing density) to drought, which is projected to increase in frequency, and (Chapters 5-6) the effects of propagule source and variation (mixing among sources) on restoration establishment and the generality of restoration outcomes across variable environments using reciprocal common gardens of multi-species restoration seedings. Chapter 2, published in Restoration Ecology, showed that restoration led to the recovery of desirable characteristics within several years, but restorations utilizing primarily fall-collected seeds likely diminished the representation of early phenology species, so biodiversity may be further enhanced by including early phenology species in seeding mixes. Chapters 3 and 4, published respectively in Ecological Applications and Applied Vegetation Science, examined the establishment of native plant communities after seeding and their responses to experimentally imposed drought. Both high seed mixture richness and high density seeding resulted in greater establishment of native, seeded species compared to low richness and low density treatments, and exotic species were less prevalent in high richness and high density treatments. However, we found little evidence of differential drought resistance, recovery, and resilience among treatments. This result coupled with increases in exotic species following drought suggest that other forms of active management may be needed to produce restored plant communities that are robust to climate change. Chapter 5 (published in Ecosphere) iii and Chapter 6 found that seed source affects individual species establishment, community structure, and productivity. However, there was no consistent advantage for any source, including local sources, across sites or species. This suggests that source effects on single species or effects observed at single locations should not be broadly generalized. Together, this dissertation shows that restoration can recover many characteristics of native prairies and that manipulation of seeding practices (seed mixture richness, seeding density, seed source) influence grassland establishment in terms of productivity, community structure, invasion, and the abundance and survival of individual species.

Doctor of Philosophy / Department of Biology / David C. Hartnett / Grazing and drought are instrumental in the development and maintenance of perennial grasslands. In this research I tested the belowground bud bank contribution to tallgrass prairie resistance and resilience when perturbed by grazing and drought. First, I tested the bud bank role in vegetation response to and recovery from severe drought (Chapter 2). I compared above- and belowground responses of experimentally droughted plots to ambient controls and irrigated plots during two years of severe drought and two years of recovery. I found that although aboveground net primary productivity declined 30-60% during drought, bud bank density and demography were insensitive to drought. These results suggest that grassland resistance and resilience when perturbed by drought may be mediated by stability of belowground bud banks. Second, I investigated vegetation and soil nutrient legacies following release from long-term grazing (Chapter 3). I documented a relatively rapid shift in aboveground vegetation within four years of grazer exclusion, with productivity, stem density, and diversity becoming relatively more similar to ungrazed than grazed prairie. The density and composition of the belowground bud bank and soil seed bank shifted more slowly, remaining more similar to grazed than ungrazed prairie. Responses of soil nutrients to removal of grazers varied, and in some cases was affected by recent fire history. These results demonstrate the contribution of belowground propagules to the maintenance of a diverse plant community both during grazing and after grazers are removed. Finally, I examined short-term vegetation responses to both drought and grazing (Chapter 4). Despite extreme drought and simulated grazing that reduced productivity and increased mortality of individual stems, the dominant C4 grasses maintained a stable bud bank. Aboveground net primary productivity and bud bank density of sedges and forbs, however, were reduced by both drought and grazing. This differential response of species to extreme drought and grazing led to shifts in community composition and species diversity over one growing season. Across drought and grazing treatments, live rhizome biomass was highly correlated with bud bank density and may be a useful, more easily measured index of bud bank density.

Doctor of Philosophy / Division of Biology / Walter K. Dodds / Tallgrass prairie evolved with fire-grazer interactions. Fire and grazing are vital processes for maintaining grasslands and cattle production, and therefore will be continued as land management schemes. The effects of fire and grazers on prairie streams are understudied, but may significantly influence stream ecology. This dissertation examined how prescribed burning, bison grazing, and patch-burn grazing (by cattle) influence water quality, stream biota, and riparian amphibians and reptiles at Konza Prairie, Kansas, or Osage Prairie, Missouri. Using Global Positioning System, we monitored bison and cattle distribution throughout watersheds. The immediate effects of prescribed burning were examined at both Konza and Osage Prairies. The impacts of bison on water quality were determined by using a long-term dataset from Konza Prairie and compared watersheds with and without bison. Amphibian and reptile assemblages were monitored for two years at Osage, and assemblage data were analyzed using redundancy analysis, permuted analysis of variance, and occupancy modeling. A patch-burn grazing experiment occurred for 5 years at Osage (2 years pretreatment data and 3 years of treatments) and was analyzed using a before-after, control-impact design. Prescribed burning had minimal effects on water chemistry. At Konza Prairie, bison did not alter water quality likely because they spent negligible time (<5%) in streams. Contrarily, cattle at Osage Prairie significantly increased stream concentrations of total suspended solids, nutrients, Escherichia coli bacteria, algal biomass, and primary production. Unlike bison, cattle spent significant time (~21%) in streams if allowed access to riparian zones. In watersheds with cattle excluded from streams by riparian fencing, water quality contaminant concentrations increased significantly, but not to the magnitude of unfenced streams. Amphibian abundance and richness were not different among patch types; instead, they were restricted to specific basins. However, reptiles displayed preference for certain patch-types, and had the highest abundance and richness in watersheds with fire and grazing. These results have implications for natural resource management. Riparian fencing of cattle may be a useful practice in areas where water resource protection is the priority. However, overland flow may alter water quality in watersheds with grazers despite fencing. Land managers will need to define management objectives and accept trade-offs in water quality, amphibian and reptile habitat, and cattle production.

Master of Science / Department of Biology / David C. Hartnett / Invasive plants pose a global threat by changing natural communities and ecosystems in ways that may be irreversible. Marrubium vulgare L. (horehound), native to Eurasia, is an invasive exotic plant found throughout the United States. Little is known about M. vulgare in the U.S. and this study aimed to understand the basic biology, habitat, and population dynamics of M. vulgare in its invasive habitat as well as the role of disturbance in the invasions. Wind Cave National Park (WCNP), an area comprising ponderosa pine and mixed grass prairie vegetation types, was used as the site for this study. In a GPS and GIS mapping study, M. vulgare was found to be significantly associated with prairie dog towns, an Aristida purpurea - Dyssodia papposa (threeawn and fetid marigold) vegetation community (a vegetation type found exclusively on prairie dog towns), and certain types of loamy soils. M. vulgare was rarely found off of prairie dog towns and then only in other disturbed areas such as bison trails or tree falls. Population studies showed M. vulgare populations were mostly stable or slightly decreasing in density (though not significantly) from 2010 to 2011; however, a few of the populations did increase dramatically in density from 2010 to 2011. M. vulgare populations existed in high densities (78.3-322.9 ramets/m2) and in low densities (0.1-2.2 genets/m2) throughout WCNP. Disturbances including prairie dog burrows, bison trails, prairie dog and bison presence, mowing, and percent cover of bare ground were measured in relation to population dynamics. While M. vulgare populations were disturbance dependent, there was no clear relationship between disturbances and population dynamics. Examination of M. vulgare life history traits found that while M. vulgare had relatively low biomass allocation to reproduction as compared to native perennial prairie species, M. vulgare produced an extremely high number of small seeds (estimated 1487/plant). Seedling establishment rates were also high. While not quantified, M. vulgare appears to be effectively dispersed through bison epizoochory. These results help to inform management of M. vulgare populations: minimizing disturbance, decreasing propagule supply, and minimizing dispersal may help to reduce M. vulgare invasions.

Master of Science / Department of Biology / Brett K. Sandercock / The migratory period is a critical time for birds. Population declines in long-distance migratory birds have been associated with trophic mismatches among climate change, timing of food availability, and timing of migratory movements. Studies on migratory songbirds have been limited to eastern North America and Europe, and migration strategies of birds may differ along the Pacific flyway. We evaluated the stopover ecology of five species of migratory songbirds at a coastal site in northern California. We found variation in changes in timing of spring migration, but consistent changes in timing of autumn migration over a 22-year period. Timing of spring migration advanced for Swainson’s Thrushes (Catharus ustulatus) and Yellow Warblers (Setophaga petechia), was compressed for Pacific-slope Flycatchers (Empidonax difficilis) and Wilson’s Warblers (Cardellina pusilla), but was protracted for Orange-crowned Warblers (Oreothlypis celata). In contrast, timing of autumn migration was delayed for Pacific-slope Flycatchers, Orange-crowned Warblers, and Yellow Warblers, but was protracted for Wilson’s Warblers. Warm, wet conditions were associated with advanced spring migration, and warm, dry conditions were associated with delayed autumn migration. Changes in timing of migration related to climate conditions were strongest for Pacific-slope Flycatchers and Orange-crowned Warblers. Stopover duration of our five study species was longer than songbirds in eastern flyways, and on average, was longer in spring than autumn. Pacific-slope Flycatchers and Yellow Warblers had longer stopovers in spring, whereas Swainson’s Thrushes and Wilson’s Warblers stopped had longer stopovers in autumn. Birds captured at low body mass had longer stopovers in spring and autumn. Migratory birds in western North America may have different migration strategies because of differences in climate and geography, but more study is needed to discover migratory routes and compare our results to other stopover sites along the Pacific flyway. Understanding differences in migration strategies of different populations of the same species are important in directing conservation efforts, especially in light of ongoing climate change.

Doctor of Philosophy / Department of Statistics / Gary L. Gadbury / Since their commercial introduction in 2005, DNA sequencing technologies have become widely available and are now cost-effective tools for determining the genetic characteristics of organisms. While the biomedical applications of DNA sequencing are apparent, these technologies have been applied to many other research areas. One such area is community ecology, in which DNA sequence data are used to identify the presence and abundance of microscopic organisms that inhabit an environment. This is currently an active area of research, since it is generally believed that a change in the composition of microscopic species in a geographic area may signal a change in the overall health of the environment. An overview of DNA pyrosequencing, as implemented by the Roche/Life Science 454 platform, is presented and aspects of the process that can introduce variability in data are identified. Four ecological data sets that were generated by the 454 platform are used for illustration. Characteristics of these data include high dimensionality, a large proportion of zeros (usually in excess of 90%), and nonzero values that are strongly right-skewed. A nonparametric method to standardize these data is presented and effects of standardization on outliers and skewness are examined. Traditional statistical methods for analyzing macroscopic species abundance data are discussed, and the applicability of these methods to microscopic species data is examined. One objective that receives focus is the classification of microscopic species as either rare or common species. This is an important distinction since there is much evidence to suggest that the biological and environmental mechanisms that govern common species are distinctly different than the mechanisms that govern rare species. This indicates that the abundance patterns for common and rare species may follow different probability models, and the suitability of the Pareto distribution for rare species is examined. Techniques for classifying macroscopic species are shown to be ill-suited for microscopic species, and an alternative technique is presented. Recognizing that the structure of the data is similar to that of financial applications (such as insurance claims and the distribution of wealth), the Gini index and other statistics based on the Lorenz curve are explored as potential test statistics for distinguishing rare versus common species.

Master of Science / Division of Biology / Samantha M. Wisely / Range-wide estimates of shorebird (Aves: Charadriiformes) populations suggest sharp declines in population sizes across a range of species. Efforts to accurately assess the conservation status of wild populations are becoming increasingly vital to species management. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant which winters in southeastern South America and breeds in the arctic. To establish an updated conservation status for Buff-breasted Sandpipers, we conducted a molecular survey of wild populations on spatial and temporal scales. We analyzed patterns of global population structure, demographic trends, and phylogeography using nine polymorphic microsatellites and two mitochondrial DNA (mtDNA) markers, cytochrome b and the control region, among 477 individuals across their distributional range. To empirically assess the impact of population declines on genetic diversity, we also surveyed segments of the same two mtDNA markers from 220 museum specimens collected across a 135-year period. Contemporary microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are admixed on a global scale, with effective population size estimates ranging from 2,657 to 16,400 birds and no signal of a recent genetic bottleneck. Contemporary mtDNA analyses suggested a pattern of haplotype diversity consistent with a historic radiation from a single refugium which we estimated to have occurred between 8,000−45,000 years before present. Using five measures of mtDNA diversity (haplotype and nucleotide diversity, trend analyses of haplotype richness, Watterson’s estimate of theta, and phi-statistics), as well as a Bayesian Skyline reconstruction of demographic trends in effective population size (N[subscript]e[subscript]f), we concluded that substantial mtDNA diversity and N[subscript]e[subscript]f had not been lost as a result of the population declines in this species. While genetic diversity did not appear to have been lost due to population losses, management efforts must focus on preventing future losses in order for wild populations to remain viable. Our results suggested that the global population of Buff-breasted Sandpipers should be treated as a single, panmictic conservation unit and that successful management must focus on preventing further declines and habitat fragmentation.

Master of Science / Department of Biology / John M. Briggs / Woody encroachment has altered the vegetative structure of grasslands worldwide and represents a potentially irreversible shift in grassland dynamics and biodiversity. Clonal woody species appear to be one of the greatest contributors to the shift from graminoid to woody dominance in the tallgrass prairie. Part of the high success rate of clonal species may be attributed to an ability to circumvent recruitment filters through the integration of environmental heterogeneity and acropetal translocation of resources from mother to daughter ramets. The clonal shrub Cornus drummondii persists in a tension zone of the graminoid-dominated tallgrass prairie, where the dominance structure is primarily maintained through the direct and indirect effects of fire. The competitive displacement of native herbaceous vegetation associated with the establishment and expansion of C. drummondii causes a major alteration in the fuel dynamics responsible for the propagation and sustainment of fire, potentially contributing to biofeedback mechanisms that facilitate shrub expansion. The goal of this research was to quantify fire behavior parameters (temperature, intensity, rate of spread, and heat flux) in relation to C. drummondii invasions and to test physiological integration as a mechanism driving encroachment, using manipulation experiments at the Konza Prairie Biological Station. We observed a significant decrease in fireline intensity associated with the encroachment of C. drummondii, which was amplified by the effects of stem density and shrub island area. This alteration in fire behavior also led to reduced heat flux at stems within shrub islands, reducing the likelihood of tissue necrosis and top-kill. With additional fuel, temperatures and fire intensities were higher, similar to open grasslands. In severing rhizomes, and effectively severing the integration of clonal ramets, we observed a higher risk of mortality of daughter ramets. These rhizome severed ramets were more water stressed, had lower photosynthetic rates, and lower woody and foliar biomass production. These results indicate that C. drummondii significantly alters fire behavior, releasing ramets from the fire trap of successive top-killing, while the integration of intraclonal ramets allows daughter ramets to survive mid-summer drought and increases the likelihood of successful establishment and further clonal reproduction.

Non-indigenous species can profoundly alter the ecosystems they invade and impact local economies. Growth and body condition declines of commercially fished Great Lakes lake whitefish coincide with the establishment of non-native dreissenid mussels and the cladoceran Bythotrephes longimanus. Declines in lake herring abundance—a key prey item for other commercially important species—have also been reported. Though additional stressors such as climate change may have contributed to changes in coregonid populations, they have not been thoroughly evaluated. Here, I present data that condition and contaminant declines in coregonids are associated with increasing density or warming climate, but growth declines in lake whitefish are likely due to ecosystem changes associated with dreissenids and Bythotrephes. In South Bay, Lake Huron, changes in lake whitefish diet composition and stable isotope signatures were consistent with increased reliance on nearshore resources after dreissenid establishment; lake whitefish occupied shallower habitats and experienced declines in mean diet energy densities post-dreissenid invasion. Growth of South Bay lake whitefish declined after environmental effects were statistically removed, whereas condition declines were explained best by changes in lake whitefish density. Among four lake whitefish populations, growth declined after dreissenids established, but not in uninvaded reference populations. Growth also declined among four lake whitefish populations after the establishment of Bythotrephes relative to reference populations. In contrast with growth, condition of lake whitefish did not change as a result of dreissenid or Bythotrephes invasion. Bioenergetic models revealed that activity rates increased and conversion efficiencies decreased in lake whitefish populations exposed to dreissenids, despite higher consumption rates in populations with dreissenids present. Condition declines among many lake whitefish and lake herring populations (and declines in mercury among herring populations) reflected regional differences and were not related to the presence of Bythotrephes or Mysis relicta. Declines in condition were more pronounced in northwest Ontario populations where climate has changed more dramatically than in southern Ontario. This work suggests that projected range expansions of dreissenid mussels and Bythotrephes will likely affect native fisheries, and their effect on these fisheries may be exacerbated by declining fish condition associated with climate change.

I compared changes in offshore Lake Ontario major species-group biomass, production and diets before (1987-1991) and after (2001-2005) invasion-induced ecological change. I synthesized the observations into carbon-based mass-balanced food webs linking two pathways of energy flow; the grazing chain (phytoplankton-zooplankton-fish) and the microbial loop (autotrophic bacteria-heterotrophic protozoans) and determined how the structure and function of the food web changed between time-periods. I use the food web descriptions to simulate the reestablishment of native deepwater bloater. I developed empirical models describing spatial variation in temperature and applied them to investigate predator temperature distributions, bioenergetic consequences of alewife diet and distribution shifts, and zooplankton productivity. Primary production declined as did the biomass and production of all species-groups except Chinook salmon. Total zooplankton production declined by approximately half with cyclopoid copepod production declining proportionately more. Zooplankton species richness and diversity were unaffected. Alewife adapted to low zooplankton production by consuming more Mysis, increasing their trophic level. The increased prey-size and exploitation of spatial heterogeneity in resource patches and temperature may have allowed alewife to maintain their growth efficiency. The trophic level also increased for smelt, adult sculpin, adult alewife and Chinook salmon. Phytoplankton grazing rates declined and predation pressure increased on Mysis, adult smelt and alewife, and decreased on protozoans. Resource to consumer trophic transfer efficiencies changed; increasing for protozoans, Mysis, Chinook salmon and other salmonines and decreasing for zooplankton, prey-fish and benthos. The changes suggest both bottom-up and top-down influences on food web structure. The direct trophic influences of invasive species on the offshore Lake Ontario food web were minor. Carbon flows to Mysis indicated an important, and changing ecological role for this species and we hypothesize that Mysis may have contributed to Diporeia declines. Simulations suggest that only a small reestablished bloater population, limited by Diporeia production, could be sustained.