Invasion patterns of emerald ash borer and European earthworms in forested ecosystems

Invasive and exotic species present a serious threat to the health and sustainability of natural ecosystems. These species often benefit from anthropogenic activities that aid their introduction and dispersal. This dissertation focuses on invasion dynamics of the emerald ash borer, native to Asia, and European earthworms. These species have shown detrimental impacts in invaded forest ecosystems across the Great Lakes region, and continue to spread via human-assisted long distance dispersal and by natural modes of dispersal into interior forests from areas of introduction. Successful forest management requires that the impact and effect of invasive species be considered and incorporated into management plans. Understanding patterns and constraints of introduction, establishment, and spread will aid in this effort. To assist in efforts to locate introduction points of emerald ash borer, a multicriteria risk model was developed to predict the highest risk areas. Important parameters in the model were road proximity, land cover type, and campground proximity. The model correctly predicted 85% of known emerald ash borer invasion sites to be at high risk. The model’s predictions across northern Michigan can be used to focus and guide future monitoring efforts. Similar modeling efforts were applied to the prediction of European earthworm invasion in northern Michigan forests. Field sampling provided a means to improve upon modeling efforts for earthworms to create current and future predictions of earthworm invasion. Those sites with high soil pH and high basal area of earthworm preferred overstory species (such as basswood and maples) had the highest likelihood of European earthworm invasion. Expanding beyond Michigan into the Upper Great Lakes region, earthworm populations were sampled across six National Wildlife Refuges to identify potential correlates and deduce specific drivers and constraints of earthworm invasion. Earthworm communities across all refuges were influenced by patterns of anthropogenic activity both within refuges and in surrounding ecoregions of study. Forest composition, soil pH, soil organic matter, anthropogenic cover, and agriculture proximity also proved to be important drivers of earthworm abundance and community composition. While there are few management options to remove either emerald ash borer or European earthworms from forests after they have become well established, prevention and early detection are important and can be beneficial. An improved understanding the factors controlling the distribution and invasion patterns of exotic species across the landscape will aid efforts to determine their consequences and generate appropriate forest management solutions to sustain ecosystem health in the presence of these invaders.

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

Carbon in the Peatlands in the Great Lakes Region

Peatlands cover only ~3% of the global land area, but store ~30% of the worlds' soil carbon. There are many different peat types that store different amounts of carbon. Most inventories of carbon storage in northern peatlands have been conducted in the expansive Sphagnum dominated peatlands. Although, northern white cedar peatlands (NW cedar, Thuja occidentalis L.) are also one of the most common peatland types in the Great Lakes Region, occupying more than 2 million hectares. NW cedar swamps are understudied, due in part to the difficulties in collection methods. General lack of rapid and consistent sampling methods has also contributed in a lack of carbon stock quantification for many peatlands. The main objective of this thesis is to quantify: 1) to evaluate peat sampling methods 2) the amount of C-stored and the rates of long-term carbon accumulation in NW cedar peatlands. We sampled 38 peatlands separated into four categories (black ash, NW cedar swamp, sedge, and Sphagnum) during the summers of 2011/2012 across northern MN and the Upper Peninsula of MI. Basal dates of peat indicate that cedar peatlands were between 1970-7790 years old. Cedar peatlands are generally shallower than Sphagnum peat, but due to their higher bulk density, hold similar amounts of carbon with our sites averaging ~800 MgC ha-1. We estimate that NW cedar peatlands store over 1.7 Gt of carbon in the Great Lakes Region. Each of the six methods evaluated had a different level of accuracy and requires varying levels of effort and resources. The depth only method and intermittent sampling method were the most accurate methods of peatland sampling.