When analyzing ecological data, one considers traditional multivariate techniques to be unsuitable. The use of dissimilarity coefficients and distance matrices is a way, how to solve this problem. In this work we present some of these coefficients and distance-based tests: Mantel test, several versions of ANOSIM and MRPP tests and distance-based test for homogeneity of multivariate dispersions. We focus on relationships among these tests and illustrate the use with an example. We also discuss the difficulties of interpretation of the results of these tests.

For the last 9,000-10,000 years the Central Hardwood Region (CHR) has been primarily composed of a mosaic of mesophytic communities in climax and communities of successional forest types dominated by oak (Quercus Linnaeus) and hickory (Carya Nuttall). Shade intolerant oak/hickory dominated forest types have been maintained by natural disturbance processes in synergy with anthropogenic causes, resulting in a large composition of communities which are neither at climatic nor edaphic climax. Reduction in fire events, thinning, forest grazing, and other disturbance processes over the last 80-100 years have coincided with decreased regeneration of shade intolerant species due to lack of adequate light availability and recruitment of shade tolerant species of communities dominated by American beech (Fagus grandifolia L.) and maple (Acer saccharum L.) into the overstory of forests typically dominated by oak/hickory. Forest inventory data at Trail of Tears State Forest was analyzed across two separate time events (1980 and 2014) to determine compositional and structural changes which have occurred. Density, basal area, and community patterns via ordination were compared across six Ecological Land Types (ELTs) to determine topography’s effect on composition. Community trends were analyzed via NMS Ordination and between ELTs by a Mantel Test. A Multi-Response Permutation Procedures (MRRP) was also used as a nonparametric method for assessing differences between ELTs examined in the NMS. Density and basal area between years for species, ELT, and species*ELT interactions were compared. Across all ELTs, between 1980 and 2014, overstory density decreased from 218 trees/ac in 1980 to 180 trees/ac in 2014 and basal area increased from 98 ft2/ac in 1980 to 106 ft2/ac in 2014. Maple basal area increased from 5 ft2/ac to 12 ft2/ac while beech increased from 1 ft2/ac to 8ft2/ac, signifying progression of these species from the understory up into the canopy. The component of soft masting species within the forest has also decreased sharply in the last 34 years. MRPP analysis of overstory compositional gradients reported distinct species compositions between ELTs, however the trend was weak (MRPP: p < 0.001, A = 0.038). NMDS ordination graphs confirmed MRPP showing little separation among ELTs. The final stress was 18.71146 and instability was < 0.01 after 212 iterations (Table 6). Our research at TTSF is a clear example of oak/hickory succession to beech maple on an upland site among species community types as delineated by topographic moisture gradient (ELTs) within the CHR. Expansion of beech and maple onto xeric ELTs suggests a breakdown of edaphic barriers that have previously been thought to be resistant to encroachment from mesophytic species. Currently oak decline induced by lack of management is likely the number one forest health issue resulting in loss of oak/hickory and other soft masting species.

In human microbiome analysis, sequencing of bacterial 16S rRNA genes has revealed a role for the gut microbiota in maintaining health and contributing to various pathologies. Novel community analysis techniques must be evaluated in terms of bias, sensitivity, and reproducibility and compared to existing techniques to be effectively implemented. Next- generation sequencing technologies offer many advantages over traditional fingerprinting methods, but this extensive evaluation required for the most efficacious use of data has not been performed previously. Illumina libraries were generated from the V3 region of the 16S rRNA gene of samples taken from 12 unique sites within the gastrointestinal tract for each of 4 individuals. Fingerprint data were generated from these samples and prominent bands were sequenced. Sequenced bands were matched with OTUs within their respective libraries. The results demonstrate that denaturing gradient gel electrophoresis (DGGE) represents relatively abundant bacterial taxa (>0.1%) beta-diversity of all samples was compared using Principal Coordinates Analysis (PCoA) of UniFrac distances and Multi-Response Permutation Procedure (MRPP) was applied to measure sample cluster strength and significance; indicator species analysis of fingerprint bands and Illumina OTUs were also compared. The results demonstrate overall similarities between community profiling methods but also indicate that sequence data were not subject to the same limitations observed with the DGGE method (i.e., only abundant taxa bands are resolved, unable to distinguish disparate samples). In addition, the effect of stochastic fluctuations in ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? differ for DGGE and next-generation sequencing. I compared pooled and individual reactions for samples of high and low template concentration for both Illumina and DGGE using the combined V3-V4 region of the 16S rRNA gene, and demonstrated that template concentration has a greater impact on reproducibility than pooling. This research shows congruity between two disparate molecular methods, identifies sources of bias, and establishes new guidelines for minimizing bias in microbial community analyses.

State and Federal agencies have created sanctuaries and speed zones to help reduce manatee mortality while incorporating the recreational and commercial resource needs of these same habitats for humans. Specific habitat resources are considered necessary to increase manatee survivorship. We have only recently begun to address how manatees use some of these resources based on physiological or reproductive strategies. In this study, I quantified patterns of habitat use during seasonal and diel periods for different sex and reproductive manatee classes using data from a radio-telemetry study conducted by the Florida Fish and Wildlife Conservation Commission during 1991-1996. I used five environmental geographic data layers: bathymetry, distance to seagrass, distance to shoreline, distance to warm water refuge sites, and distance to fresh water sources, to discriminate seasonal and diel habitat use patterns for different manatee classes: males (M), females with calves (FWC), and females without calves (FNC). Mean occupancy values were calculated for environmental variable locations and seasonal, diel, and manatee class differences were tested using a Multi-Response Permutation Procedure (MRPP). Nonmetric Multidimensional Scaling (NMS) was used to visualize the ordination patterns of the manatee classes and to assess importance of correlated environmental variables. Significant differences in habitat use were noted between summer and winter based on distances to warm water, seagrass, and fresh water sources but similar habitat use patterns were exhibited within summer diel periods among manatee classes. All manatee classes appeared to have used a higher proportion of locations closer in proximity to seagrass at night than day in winter indicating a disproportionate difference in feeding bouts between diel periods. These differences may be attributed to adjusting feeding strategies to reduce thermoregulatory costs or to decrease human interactions. Differences in patterns were exhibited for the winter diel periods specifically for the FWC manatee classes during winter days. FWC had a higher proportion of locations within the warm water refuges during the day indicating a possible trade off situation between food consumption and thermal exposure. This study demonstrates coarse and fine scale patterns of variation in habitat use for manatees both seasonally and daily within winter. It also suggests that during winter months, manatees were not just utilizing their habitat but they appeared to have preferences and selection for certain habitat types. Recovery of a species is greatly enhanced when patterns of habitat use within the species' environment has been clearly defined. Understanding more specifically what types of habitats manatees choose might allow management to adjust strategies for protection of key habitats while encouraging further recovery of this species.

No description available.

Nitrogen-fixing bacteria in soybean nodules convert atmospheric nitrogen to plant-available forms in exchange for carbon from the plant, but other non-nitrogen-fixing bacteria also reside in nodules, and their role in the nodule is not well understood. This study was conducted to determine the effect of three non-nitrogen-fixing Pseudomonas spp. strains isolated from nodules on soybean, and we hypothesized these strains benefit soybean. A greenhouse study in which two cultivars of soybean (Asgrow AG46X6 and Pioneer P48A60X) were treated with three fluorescent Pseudomonas spp. strains (referred to in this study as Bullseye, Pancake, and Starfish) and an uninoculated control. Soybeans were harvested at two time points: the R2/R3 growth stage and the R6 growth stage. Following each harvest, measures of growth, yield, and nitrogen fixation were taken, and data were analyzed using two non-parametric, multivariate analyses: multiple response permutation procedure (MRPP) and permutational multivariate analysis of variance (PERMANOVA). Both analyses showed soybeans of both cultivars treated with Pancake differed from controls following the first harvest but not the second. When analyzed individually, most metrics for growth, yield, and nitrogen fixation following the first harvest were not significantly different between Pancake and control treatments, but Pancake treatment means were still generally higher than controls. If metrics are considered collectively in conjunction with the results of the multivariate analyses, the results show Pancake generally increased soybean growth and nitrogen fixation. These findings support the hypothesis that non-nitrogen-fixing bacteria from nodules benefit plants, and such bacteria have the potential to serve as biofertilizers. / Master of Science in Life Sciences / Soybeans are one of the most commonly grown crops in the world, and nitrogen-fixing bacteria colonize the roots of soybeans and initiate the formation of spherical nodules attached to the roots. Inside the nodules, these bacteria convert atmospheric nitrogen to plant-available forms in exchange for sugar from the plant, and such bacteria reduce the need to add nitrogen fertilizer to agricultural fields. Other non-nitrogen-fixing bacteria also reside in nodules, but their role in the nodule is not well understood. If these bacteria benefit soybeans, they have the potential to serve as biofertilizers (microbial inoculants that promote plant growth). This study was conducted to determine whether non-nitrogen-fixing bacteria isolated from nodules benefit soybean. A greenhouse study in which two cultivars of soybean (Asgrow AG46X6 and Pioneer P48A60X) were grown in soil and were either left uninoculated or were inoculated with one of three strains of bacteria from the genus, Pseudomonas (referred to in this study as Bullseye, Pancake, and Starfish). Following harvest, measures of growth, yield, and nitrogen fixation were taken, and data showed the bacteria generally benefited the soybean plants. Although, these results showed the bacteria benefitted the plants, field trials and further testing in the greenhouse should be conducted before using these bacteria as commercial biofertilizers. Additionally, the effects of other non-nitrogen-fixing nodule bacteria on soybeans should also be tested to identify other beneficial strains, and the cost of production should be compared to the potential gains of using such bacteria before they are developed into biofertilizers.

No description available.