Master of Arts / Department of Geography / J. M. Shawn Hutchinson / Military installations are important assets for the proper training of armed forces. To ensure the continued viability of training lands, management practices need to be implemented to sustain the necessary environmental conditions for safe and effective training. For this study two analyses were done, a contemporary burn history and a time series analysis. The study area is Smoky Hill Air National Guard Range (ANGR), an Impact Area (within the range) and a non-military Comparison Site. Landsat 5 TM / 7 ETM+ imagery was used to create an 11 year composite burn history image. NDVI values were derived from MODIS imagery for the time series analysis using the statistical package BFAST. Results from both studies were combined to make conclusions about training impacts at Smoky Hill ANGR and determine if BFAST is a viable environmental management tool. Based on this study the training within Smoky Hill ANGR does not seem to be having a negative effect on the overall vegetation condition. It was also discovered that BFAST was able to accurately detect known vegetation disturbances. BFAST is a viable environmental management tool if the limitations are understood.

Master of Arts / Department of Geography / J. M. Shawn Hutchinson / Grasslands of the Flint Hills are often burned as a land management practice. Remote sensing can be used to help better manage prairie landscapes by providing useful information about the long-term trends in grassland vegetation greenness and helping to quantify regional differences in vegetation development. Using MODIS 16-day NDVI composite imagery between the years 2001-10 for the entire Flint Hills ecoregion, BFAST was used to determine trend, seasonal, and noise components of the image time series. To explain the trend, 4 factors were considered including hydrologic soil group, burn frequency, and precipitation deviation from the 30 year normal. In addition, the time series data was processed using TIMESAT to extract eight different phenometrics: Growing season length, start of season, end of season, middle of season, maximum value, small integral, left derivative, and right derivative. Phenometrics were produced for each year of the study and an ANOVA was performed on the means of all eight phenometrics to assess if significant differences existed across the study area. A K-means cluster analysis was also performed by aggregating pixel-level phenometrics at the county level to identify administrative divisions exhibiting similar vegetation development. For the study period, the area of negatively and positively trending grassland were similar (41-43%). Logistic regression showed that the log odds of a pixel experiencing a negative trend were higher in sites with clay soils and higher burning frequencies and lower for pixels having higher than normal precipitation and loam soils. Significant differences existed for all phenometrics when considering the ecoregion as a whole. On a phenometric-by-phenometric basis, unexpected groupings of counties often showed statistically similar values. Similarly, when considering all phenometrics at the same time, counties clustered in surprising patterns. Results suggest that long-term trends in grassland conditions warrant further attention and may rival other sources of grassland change (e.g., conversion, transition to savannah) in importance. Analyses of phenometrics indicates that factors other than natural gradients in temperature and precipitation play a significant role in the annual cycle of grassland vegetation development. Unanticipated, and sometimes geographically disparate, groups of counties were shown to be similar in the context of specific phenology metrics and this may prove useful in future implementations of smoke management plans within the Flint Hills.

Land use / land cover (LULC) change assessment is getting more consideration by global environmental change studies as land use change is exposing dryland environments for transitions and higher rates of resource depletion. The semiarid regions of northwestern Ethiopia are not different as land use transition is the major problem of the region. However, there is no satisfactory study to quantify the change process of the region up to now. Hence, spatiotemporal change analysis is vital for understanding and identification of major threats and solicit solutions for sustainable management of the ecosystem. LULC change studies focus on understanding the patterns, processes and dynamics of land use transitions and driving forces of change. The change processes in dryland ecosystems can be either seasonal, gradual or abrupt changes of random or systematic change processes that result in a pattern or permanent transition in land use. Identification of these processes of change and their type supports adoption of monitoring options and indicate possible measures to be taken to safeguard this dynamic ecosystem. This study examines the spatiotemporal patterns of LULC change, temporal trends in climate variables and the insights of the communities on change patterns of ecosystems. Landsat imagery, MODIS NDVI, CRU temperature, TAMSAT rainfall and socio-ecological field data were used in order to identify change processes. LULC transformation was monitored using support vector machine (SVM) algorithm. A cross-tabulation matrix assessment was implemented in order to assess the total change of land use categories based on net change and swap change. In addition, the pattern of change was identified based on expected gain and loss under a random process of gain and loss, respectively. Breaks For Additive Seasonal and Trend (BFAST) analysis was employed for determining the time, direction and magnitude of seasonal, abrupt and trend changes within the time series datasets. In addition, Man Kendall test statistic and Sen’s slope estimator were used for assessing long term trends on detrended time series data components. Distributed lag (DL) model was also adopted in order to determine the time lag response of vegetation to the current and past rainfall distribution. Over the study period of 1972- 2014, there is a significant change in LULC as evidenced by a significant increase in size of cropland of about 53% and a net loss of over 61% of woodland area. The period 2000-2014 has shown a sharp increase of cropland and a sharp decline of woodland areas. Proximate causes include agricultural expansion and excessive wood harvesting; and underlying causes of demographic factor, economic factors and policy contributed the most to an overuse of existing natural resources. In both the observed and expected proportion of random process of change and of systematic changes, woodland has shown the highest loss compared to other land use types. The observed transition and expected transition under random process of gain of woodland to cropland is 1.7%, implies that cropland systematically gains to replace woodland. The comparison of the difference between observed and expected loss under random process of loss also showed that when woodland loses cropland systematically replaces it. The assessment of magnitude and time of breakpoints on climate data and NDVI showed different results. Accordingly, NDVI analysis demonstrated the existence of breakpoints that are statistically significant on the seasonal and long term trends. There is a positive trend, but no breakpoints on the long term precipitation data during the study period. The maximum temperature also showed a positive trend with two breakpoints which are not statistically significant. On the other hand, there is no seasonal and trend breakpoints in minimum temperature, though there is an overall positive trend along the study period. The Man-Kendall test statistic for long term average Tmin and Tmax showed significant variation where as there is no significant trend within the long term rainfall distribution. The lag regression between NDVI and precipitation indicated a lag of up to forty days. This proves that the vegetation growth in this area is not primarily determined by the current precipitation rather with the previous forty days rainfall. The combined analysis showed declining vegetation productivity and a loss of vegetation cover that contributed for an easy movement of dust clouds during the dry period of the year. This affects the land condition of the region, resulting in long term degradation of the environment

Land use / land cover (LULC) change assessment is getting more consideration by global environmental change studies as land use change is exposing dryland environments for transitions and higher rates of resource depletion. The semiarid regions of northwestern Ethiopia are not different as land use transition is the major problem of the region. However, there is no satisfactory study to quantify the change process of the region up to now. Hence, spatiotemporal change analysis is vital for understanding and identification of major threats and solicit solutions for sustainable management of the ecosystem. LULC change studies focus on understanding the patterns, processes and dynamics of land use transitions and driving forces of change. The change processes in dryland ecosystems can be either seasonal, gradual or abrupt changes of random or systematic change processes that result in a pattern or permanent transition in land use. Identification of these processes of change and their type supports adoption of monitoring options and indicate possible measures to be taken to safeguard this dynamic ecosystem. This study examines the spatiotemporal patterns of LULC change, temporal trends in climate variables and the insights of the communities on change patterns of ecosystems. Landsat imagery, MODIS NDVI, CRU temperature, TAMSAT rainfall and socio-ecological field data were used in order to identify change processes. LULC transformation was monitored using support vector machine (SVM) algorithm. A cross-tabulation matrix assessment was implemented in order to assess the total change of land use categories based on net change and swap change. In addition, the pattern of change was identified based on expected gain and loss under a random process of gain and loss, respectively. Breaks For Additive Seasonal and Trend (BFAST) analysis was employed for determining the time, direction and magnitude of seasonal, abrupt and trend changes within the time series datasets. In addition, Man Kendall test statistic and Sen’s slope estimator were used for assessing long term trends on detrended time series data components. Distributed lag (DL) model was also adopted in order to determine the time lag response of vegetation to the current and past rainfall distribution. Over the study period of 1972- 2014, there is a significant change in LULC as evidenced by a significant increase in size of cropland of about 53% and a net loss of over 61% of woodland area. The period 2000-2014 has shown a sharp increase of cropland and a sharp decline of woodland areas. Proximate causes include agricultural expansion and excessive wood harvesting; and underlying causes of demographic factor, economic factors and policy contributed the most to an overuse of existing natural resources. In both the observed and expected proportion of random process of change and of systematic changes, woodland has shown the highest loss compared to other land use types. The observed transition and expected transition under random process of gain of woodland to cropland is 1.7%, implies that cropland systematically gains to replace woodland. The comparison of the difference between observed and expected loss under random process of loss also showed that when woodland loses cropland systematically replaces it. The assessment of magnitude and time of breakpoints on climate data and NDVI showed different results. Accordingly, NDVI analysis demonstrated the existence of breakpoints that are statistically significant on the seasonal and long term trends. There is a positive trend, but no breakpoints on the long term precipitation data during the study period. The maximum temperature also showed a positive trend with two breakpoints which are not statistically significant. On the other hand, there is no seasonal and trend breakpoints in minimum temperature, though there is an overall positive trend along the study period. The Man-Kendall test statistic for long term average Tmin and Tmax showed significant variation where as there is no significant trend within the long term rainfall distribution. The lag regression between NDVI and precipitation indicated a lag of up to forty days. This proves that the vegetation growth in this area is not primarily determined by the current precipitation rather with the previous forty days rainfall. The combined analysis showed declining vegetation productivity and a loss of vegetation cover that contributed for an easy movement of dust clouds during the dry period of the year. This affects the land condition of the region, resulting in long term degradation of the environment

Epigenetics are stable heritable traits that are not a result of the DNA sequence. Epigenetic modification of DNA cytosine plays a role in development and disease. The covalent bonding of a methyl group or a hydroxymethyl group to the 5-carbon of cytosine epigenetically modifies cytosine to 5-methylcytosine or 5-hydroxymethylcytosine. Upon PCR amplification, the bisulfite treatment of DNA converts unmethylated cytosine to thymine, while 5-methylcytosine, 5-hydroxymethylcytosine, and other bases remain unchanged. The resulting sequences can be mapped to a reference genome; however, this can be challenging due to sequencing technology complexity, low sequence complexity, and biases and errors introduced with bisulfite treatment. Once the short read is mapped, the identity of 5-methylcytosine or 5-hydroxymethylcytosine can be determined by comparing the mapped read to the aligned reference genome. Bisulfite DNA read mapping is characterized by mapping performance as low as 40%. This research improves bisulfite short read mapping quality. First, reads generated from the bisulfite hairpin PCR protocol are used to study mapping failure and solutions. A read may not map to the genome; it may map uniquely, or it may map to multiple locations. Sequence complexity correlates with these mapping categories. The hairpin protocol allows for a recovery, in some cases, of the original untreated read, and mapping this read with the regular read mapper Bowtie2 improved mapper performance by 10%. New bisulfite read mapping software called BisPin was created that calls BFAST (BLAT-like Fast Accurate Search Tool) for mapping. BisPin resolves ambiguously mapped reads with a rescoring strategy, which yields a statistically significant improvement. BFAST-Gap for Ion Torrent reads was developed, since Ion Torrent machines are less expensive than Illumina machines and since Ion Torrent reads are longer. There are few mappers for Ion Torrent data. BFAST-Gap uses homopolymer run length for contextual gap penalty functions, since homopolymer runs cause errors in Ion Torrent reads. In conjunction with BisPin, this software performed well on real and simulated bisulfite Ion Torrent data and Illumina data. InfoTrim, a read trimmer with an entropy term, was developed with competitive results. / Ph. D. / DNA, deoxyribonucleic acid, is a large molecule comprised of four molecular bases: adenine, cytosine, thymine, and guanine, and it determines heritable traits in living organisms. Sequencing DNA determines the sequential arrangement of bases. A read is a small sequence of DNA bases. Epigenetics are stable heritable traits that are not a result of the DNA sequence. Chemical groups called methyl and hydroxymethyl can be attached to cytosine. These groups are an epigenetic modification of cytosine, and they play a role in disease and development. The chemical bisulfite is used to discover these chemical groups. The bisulfite sequencing of DNA is a process where bisulfite is introduced to DNA, and then the DNA is sequenced. Bisulfite treatment converts cytosines without the methyl and hydroxymethyl chemical groups into thymine. Software is then used to align and match the resulting DNA strands to a large reference DNA strand called a reference genome to distinguish between cytosines that have these chemical groups. This process is called mapping or alignment, and its performance can be as low as 40% for bisulfite data. This research improves this performance. The hairpin protocol is a known bisulfite sequencing method that sequences two opposing DNA strands, where the original untreated strand can sometimes be recovered. Mapping the recovered strands improved performance by 10%. Using hairpin data, sequence complexity, a measure of DNA sequence randomness, correlated with mapping performance. BisPin mapping software was created that implements the hairpin recovery approach. BisPin rescores DNA strands that map to multiple locations on the reference genome, and it supports multiple sequencing technologies. BFAST-Gap, a modified mapping program callable by BisPin, uses a context sensitive function to better align Ion Torrent reads, which tend to have errors in regions of repeated bases. BFAST-Gap was developed, since Ion Torrent sequencing machines are less expensive than Illumina machines and since Ion Torrent reads tend to be longer and have more information. The read trimmer InfoTrim was developed to trim the lengths of short DNA sequences to improve the quality of alignments. These programs were validated on real and simulated DNA data and performed well.