Paronychia virginica Spreng. (Caryophyllaceae) is a perennial evergreen herb of exposed, relatively xeric habitats. Approximately 10 mid-Appalachian populations remain in Virginia, West Virginia, and Maryland and are disjunct from populations located primarily in Texas, Oklahoma, and Arkansas. A study was conducted to test the hypothesis that eastern and western populations differ significantly and, therefore, represent at least two distinct taxa. Statistical analyses of 8 qualitative and 24 quantitative morphological characters indicated very highly significant (P < 0.001) variation between eastern and western populations of P. virginica. Characters differing most significantly included sepal pubescence, awn length, awn pubescence, awn curvature, length-width ratio of leaves, and shape of leaf apices. Starch gel electrophoresis was performed and six enzyme systems/nine loci (EST-2, EST-3, LAP, MDH-1, MDH-2, PGI, PGM-1, PGM-2, and SKDH) were identified as being consistently scorable and informative. Although gene flow between populations of P. virginica was shown to be restricted (mean FST = 0.353), populations are maintaining relatively high levels of genetic diversity. Genetic variability was quantified for each population and mean values for number of alleles per locus (A), percent loci polymorphic (P), and expected heterozygosity (HEXP) were found to be 1.95, 47.22%, and 0.204, respectively, exceeding those values reported for seed plants, widespread species, and endemic species. Hierarchical F statistics suggest higher levels of genetic variability within individual populations than among populations, regardless of geographic location. All statistically significant (P < 0.05) deviations from Hardy-Weinberg equilibrium indicated a deficiency in heterozygotes at the respective loci. Considering results from both the morphometric and allozyme analyses, the current author suggests recognizing two distinct subspecies, P. virginica subsp. virginica in the eastern U.S. and P. virginica subsp. scoparia in the south-central U.S. Conservation efforts should be focused on the maintenance of existing populations in both eastern and western regions of the U.S. in order to preserve the genetic and evolutionary potential of these taxa. / Master of Science

As invasive species are so prominent, the influence of wildfire intensity on fuel loading, invasives, species richness, diversity, and evenness were studied at Shenandoah National Park. Most National Parks identify invasive species as the biggest threat to their goal of maintaining native ecosystems. Eight study sites were stratified into three burn classes (high intensity, low intensity, and control), and three transects were randomly located so that nested plots and fuel transects were measured at a distance of 50 ft (15 m), 150 ft (45 m), and 250 ft (75 m) from a road or trail. Field sampling was conducted between May 15, 2004 and June 30, 2004. A subsample of these plots were used to determine specific gravity and quadratic mean diameter for each size class of fuel and to determine the bulk density of the duff and litter layers. High intensity wildfires initially reduced species diversity and evenness in the tree and herbaceous strata, but after 14 years tree species diversity and evenness returned to levels found in unburned areas, while herbaceous strata diversity was not associated with time since burn. Low intensity wildfires resulted in the greatest impacts in the shrub stratum. Presence of invasive species was associated with more even and diverse vegetation in all strata, perhaps because invasive species were relatively sparse. Fuel loadings were reduced initially by high intensity wildfires, but quickly returned to the same level as unburned areas. Although these initial findings indicate that invasive species will not persist after wildfire disturbance, continual monitoring by National Parks would be prudent. / Master of Science

The Clinch Dace Chrosomus sp. cf. saylori is a species of minnow known from only two counties in Virginia. Prior surveys established the species' presence in just eight tributaries to the upper Clinch River. A management plan, which should include both population monitoring and habitat restoration, is still lacking for the species. Population monitoring must balance high detection probability with low risk of injury to captured individuals. I sampled 98 sites in 2014 and 2015 within the putative range of Clinch Dace to refine estimates of its distribution. I sampled 70 of the 98 sites with multiple gears and replication in an occupancy modeling framework. Clinch Dace occupied low-gradient headwater streams with relatively low conductivity in forested watersheds. My surveys uncovered two new tributaries occupied by Clinch Dace, and I was unable to find Clinch Dace in two historically occupied streams. Species detection probability was higher with backpack electrofishing than minnow trapping. N-mixture models suggest that Clinch Dace are more abundant in watersheds with high forest cover although forest cover is highly correlated spatially in the nested stream network. Density estimates from mark-recapture sampling suggest that Clinch Dace occur at low densities in approximately 31.5 km of headwater streams. The mean estimate of global population size was 6,706 individuals. Some populations could be affected by low genetic diversity. I conclude by developing a prioritization framework for restoration and protection of 15 candidate conservation areas. Managers should work with private landowners to implement best management practices in high priority watersheds. / Master of Science

The Reticulated Flatwoods Salamander, Ambystoma bishopi, is an inhabitant of longleaf pine forests in the southeastern United States. Historically distributed across southern Alabama, Georgia, and the Florida panhandle west of the Apalachicola-Flint Rivers, the range of this species has been drastically reduced. It is currently listed as federally endangered under the Endangered Species Act (ESA). Population viability analyses (PVAs) represent a key component of many recovery plans for threatened and endangered species. Here we use 10 years of mark recapture data collected from two breeding populations of A. bishopi to construct a demographic model that can be used to evaluate future extinction risk. In chapter one, we quantify population sizes through time, and estimate the impact of annual variability in numbers on genetic viability. This species exists in small (< 500) breeding populations and exhibit annual fluctuations in abundance characteristic of pond-breeding amphibians. In chapter 2, we adopt a modified version of the von Bertalanffy equation to construct size-at-age curves for A. bishopi that include the metamorphic transition. Individuals exhibit rapid growth in the larval stage such that they emerge as metamorphs at 60% of their final body size. In chapter 3, we employ a Cormack-Jolly-Seber model, modified to include continuous covariates, to generate size-dependent survival curves. Survival of A bishopi exhibits dramatic annual and seasonal variability, but is always positively correlated with body size. Lastly, in chapter 4, we combine the elements of all previous chapters to construct an Integral Projection Model (IPM). Given the prevalence of complete recruitment failure in these populations, and their relatively small size, extinction probabilities under a business-as-usual model were high. Increasing the frequency of successful recruitment drastically reduces extinction risk; however, adult survival exerts the greatest influence on long-term population growth. To assure the recovery of A. bishopi, management must consider all elements of the life-history when allocating resources and effort. More generally, both aquatic and terrestrial habitats must be protected for amphibian conservation to be effective, making them ideal candidates for 'umbrella species' status. Amphibian conservation would also benefit from an increase in systematic, long-term data collection. / Doctor of Philosophy / The southeastern United States is the global salamander hotspot, representing a crucible for diversity. Longleaf pine forests, the predominant ecosystem in the southeast, have been reduced to 3% of their former range, with dire consequences for the animals that inhabit them. The Reticulated Flatwoods Salamander, Ambystoma bishopi, is endemic to the region, and currently listed as federally endangered owing to recent population declines. A recovery plan for the species therefore, is required by law, under the Endangered Species Act (ESA). A salient component of modern recovery plans are population forecasts that evaluate future extinction risk. Such forecasts can then be used to assess alternative management strategies proposed to improve the species' long-term prospects. By studying two of the last remaining populations of A. bishopi from 2010-2019, we were able to collect the data required to construct a demographic model that can be used to run population projections. In some regards, A. bishopi is a typical amphibian, in that their populations show dramatic fluctuations in numbers through time, and they exhibit rapid growth in the aquatic larval stage, achieving 60% of their maximum body size in the first three months of life. Flatwoods salamanders breed in ephemeral wetlands, that often dry before successful metamorphosis can occur. The frequency of pond-drying results in a high probability of extinction for a single population, but survival of breeding individuals was equally important when considering long-term persistence. To assure the recovery of A. bishopi, management must consider all elements of the life-history when allocating resources and effort. More generally, both aquatic and terrestrial habitats must be protected for amphibian conservation to be effective, making them ideal candidates for 'umbrella species' status.

Habitat destruction/alteration and non-native species are widely considered the two most serious threats to biodiversity within freshwater ecosystems, which are among the most threatened in the world. I examined the effects of these factors, specifically focusing on land use and non-native species as drivers of abundance patterns of native fishes in the highly invaded and anthropogenically impacted New River basin (NRB) in the Appalachian region of the United States. In chapter 2, I examine current native and non-native species abundance patterns related to the highly variable land-use mosaic present across the NRB, with specific focus on the species-specific effects of intensive land-use practices (agriculture and urbanization) at varying spatial extents (upstream watershed, upstream riparian, and local riparian). In chapter 3, I investigate historical context of basin-wide and site-level abundance spread and decline of natives and non-natives in the upper and middle New River basin (UMNR) over the past 60+ years. Finally, in chapter 4, I partition the variation in native species abundance explained separately by land use and non-native species to determine which factor might be most influential in describing abundance distributions of UMNR native fishes over the past 20+ years. My results indicate widely varying responses of native species to various combinations of intensive land use and non-native species across contributing watersheds and widespread biotic homogenization and native species declines over the past 60+ years. These declines include reductions in unique communities and endemic species provided little consideration or protection under current conservation law. I suggest potential avenues for improvement of conservation actions to help preserve these unique species and communities based on their responses to various land-use and non-native species stressors. My study framework should be broadly applicable to other drainages and should provide opportunities for early identification of potential native species declines and the stressors that may be contributing to them. / Master of Science / Freshwater fishes are experiencing world-wide declines that have the potential to cause major negative ecological and economic impacts. Two of the biggest contributors to fish declines are habitat destruction and non-native species introductions. I examined populations of numerous fish species in the New River basin (NRB) in the Appalachian region of the United States to identify declining native species and determine how intensive land use (one type of habitat destruction) and non-native species may be contributing to these trends. My results suggest that nearly half of the native species occurring in the NRB may be experiencing widespread reductions in abundance. As a result of these declines and the spread of a few common native and non-native species, fish communities across the NRB are becoming less unique over time. Land-use changes, such as agricultural and road development near streams, which contribute to increased soil erosion and run-off of silt and sand into streams, could be causing broad habitat changes that lead to diminished populations of sensitive species and overall local and regional fish diversity. While no single non-native species may be held responsible for all native fish species declines in the NRB, complex interactions, such as competition and predation, between many natives and non-natives altogether could be contributing to many native fish declines. Farmers and other landowners can help to prevent future fish declines by re-establishing natural vegetation, such as trees, along streambanks and implementing other practices, such as cattle fencing, that reduce the streambank and soil erosion that harms fish habitat. Other stakeholders, such as anglers, can help prevent future native fish declines by limiting introductions of additional non-native species. For example, these stakeholders could avoid releasing aquatic pets and live bait into NRB streams. These practices would help limit future negative impacts caused by non-native species.

Yes / There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence. / This study was supported by the Research Foundation Flanders (grant 11A0618N), the Flanders Innovation and Entrepreneurship Agency (grants IWT-SB 141198 and IWT/50052), and the University of Antwerp (grant FFB150344).

Aquatic nuisance plants (ANS), like watershield (Brasenia schreberi), negatively affect water chemistry, ecosystem ecology, and human uses of waterbodies if not properly managed. Understanding ecological predictors as well as efficient control strategies is needed for successful control of ANS. This research assessed 1) potential environmental and ecological predictors of watershield prevalence along with 2) submersed injections of flumioxazin herbicide for watershield control. Twenty-one lakes in the state of Mississippi were surveyed for watershield presence. Watershield prevalence was not correlated to water clarity or plant diversity suggesting these are not drivers of watershield prevalence. A series of mesocosm and field trials were conducted to assess flumioxazin rate reductions for watershield control. In the mesocosm study, 100 ppb flumioxazin injections reduced water shield biomass to >70% 8 weeks after treatment (WAT). This was validated on a field population (>88% reduction) and provides a new control measure for Mississippi resource managers and landowners.

A study was initiated to adapt the REGEN regeneration prediction model to the Appalachians of Virginia and West Virginia. REGEN generates predictions via expert created REGEN knowledge bases (RKBs) that contain competitive rankings and stochastic parameters for selected species and size classes of advance reproduction. We developed RKBs for four site productivity classes (xeric, subxeric, submesic, mesic), and tested two (subxeric and submesic) using field collected inventory data in this study. To test the model we collected data from 48 paired sites which contained a mature stand and an adjacent regenerating stand (clearcut) of similar site productivity harvested within the past 20 years. Across all 48 sites, model predictions were within 5% of measured values on average, and explained 32% (R2 = 0.32) of the variation in species composition in regenerating stands. The species compositions of 41 of the paired stands on the Appalachian Plateau in West Virginia were further analyzed to compare species composition. Species composition was compared between the mature and regenerating stands in the subxeric and submesic site classes. A comparison of the upper canopy (dominant and codominant) species composition in regenerating stands to that of all stems ≥ 1.5 in dbh in the mature stands was conducted as well. Our results suggest that the future species composition of stands regenerating following clearcut harvests will likely differ from previous rotations with mesophytic, shade intolerant species being more numerous. Oaks will likely assume a smaller role as the clearcuts mature, particularly on the submesic sites. / Master of Science

Eight study sites were established in mid-elevation, south aspect, mixed-oak forests in the Ridge and Valley and Allegheny Mountain physiographic provinces of Southwestern Virginia and West Virginia to address questions concerning the variability in species composition, richness, and relative abundance of vascular plant species in those communities. All forest strata were sampled using a nested plot design. Variability in species richness and species composition was found to be high. Total species richness values ranged from 84 to 273, and Sorrenson's Coefficient of Similarity index values indicated that approximately 46, 38, and 51 percent of the species in the overstory, mid-story, and herb stratum were the same among sites, respectively. However, despite differences in composition and richness, K-S tests revealed significant differences in the distribution of ranked relative abundance only in the mid-story at two sites. Differences did occur in the relative abundance of twelve growth form categories. While tree seedlings and perennial herbs dominated, on average, woody vines and fern species represented substantial coverage on sites in the Allegheny Mountains. Correlations among forest strata were weak. The greatest amount of variation in species richness was attributiable to the standard deviation of a forest site quality index (FSQI), which was thought to represent the variation in microtopography across each site. The lack of correlation and high variability in plant species richness and composition, despite similarities in topographic characteristics, reinforce the inherent weaknesses involved with using the chronosequence approach to studying ecological responses in the Southern Appalachian mixed-oak region. Future remeasurement and long term monitoring of these study sites, following the implementation of silvicultural manipulations, will provide the information needed to make inference on the effects of forest management practices on Southern Appalachian mixed-oak forests. / Master of Science

The conservation of biodiversity and endemism in South Africa’s freshwater aquatic ecosystems is a high priority, particularly in the Cape Floristic Region. However, the perception that South Africa lacks suitable fish species for recreational angling, aquaculture and biological control, led to the widespread introduction and use of alien fish species. As a result, formal stocking programs have seen the introduction of five of the world’s top 100 invasive species into South Africa (Dudgeon et al. 2006). According to Dudgeon et al. (2006) freshwater ecosystems are the most endangered ecosystem in the world. The threats to freshwater biodiversity, according to Dudgeon et al. (2006), can be grouped into five categories that interact with one another: overexploitation, water pollution, flow modifications, destruction of habitat and invasion by exotic species. This PhD study took place in the Amatola region of the Eastern Cape Province, South Africa. The Amatola region is a rural area with no large-scale mining or industrial developments, only localised settlements. These developments are mainly situated around impoundments, because of the resources such as water and food that they provide. Thus the dams within the Amatola region should theoretically have no major industrial stressors on them. The three impoundments studied were Binfield Park, Sandile and Wriggleswade Dams. Binfield Park Dam is a 260ha impoundment. It impounds the Tyume River and is used by both subsistence anglers from the local communities and occasionally by recreational bass anglers. Sandile Dam is a 146ha impoundment and is the smallest of the three dams in this study. It impounds the Wolf and Keiskamma Rivers. Wriggleswade Dam is a 1000ha impoundment used extensively by recreational bass and carp anglers, and impounds the Kubusi River. There is a paucity of information regarding the health of the indigenous and alien fish species from the study region, as well as on the parasite diversity of these various fish species. In order to fill the gaps in the information the following hypothesis was proposed. That the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa. In order to achieve this hypothesis the main aim of this study will be to use the necropsy- and histology- based fish health assessment to determine the health status of the fish species in these impoundments as well as to understand the potential threat of water pollution and fish parasites. Fish were sampled with the aid of gill nets, fyke nets and by angling from each of the three impoundments over three surveys in July 2011, and March and August 2012. Following capture fish were transported to a field laboratory in aerated containers. At the field laboratory the fish were examined and dissected using the methods recommended by Adams et al. (1993) for a necropsy-based fish health assessment. Gills, livers, kidneys and gonads samples were also collected for histological analysis. Macroscopic and histology-based fish health assessment index was used, as well the analysis of muscle tissue of Micropterus salmoides and surface water and sediment from Binfield Park, Sandile and Wriggleswade Dams. It was shown that, according to the macroscopic fish health assessment index, M. salmoides in Wriggleswade Dam had a higher FHAI score compared to those in Binfield Park and Sandile Dam, there were no significant differences between the FHAI scores. However, the cause of the higher FHAI in the Wriggleswade Dam was because of the external skin damage caused by the presence of the alien parasite Lernaea cyprinacea. The histology-based fish health assessment index, however, showed that M. salmoides from Binfield Park had significantly higher histology Fish Index (IFISH) scores compared to those in Sandile and Wriggleswade Dams. The main contributors to the high IFISH score of Binfield Park were the significantly high Liver Index (IL) and Kidney Index (IK). The increased severity of the alterations observed in the liver and kidney tissue of the Binfield Park M. salmoides samples may have been as a result of the high concentration of mercury found in the muscle tissue of M. salmoides. The water quality and metals detected in the water of Binfield Park, Sandile and Wriggleswade Dams were all below the target water quality guideline values, as well as below those of previous research into the nutrients and presence of metals in these impoundments. The sediment metal analysis showed that the levels of Co, Mn and Ni were above the target guideline levels for Binfield Park, Sandile and Wriggleswade Dams, Cu was above target guidelines levels for Sandile Dam, and uranium was above the target guideline concentrations for Wriggleswade Dam. Binfield Park Dam had significantly high levels of mercury in the muscle tissue of M. salmoides, while Sandile Dam had significantly high levels of zinc in the muscle tissue of M. salmoides. It was shown that M. salmoides from each of the three impoundments are in a healthy state according to the parameters assessed. However, the presence of heavy metals, particularly mercury, uranium and zinc, do indicate the presence of human activities. The indigenous parasites of Anguilla mossambica have been well documented including the gastrointestinal nematode Paraquimperia africana, and the stomach nematode Heliconema africanum. Indigenous parasites such as the swimbladder nematode Anguillicola papernai had no effect on the condition factor of infected and uninfected eels. However, the damage caused by the alien parasites were evident, including the first documented effects of the alien gill monogenean Pseudodactylogyrus anguillae on indigenous wild populations of the longin fin eel A. mossambica from the Eastern Cape, South Africa. Histological observations indicated that an alien gill monogenean caused hyperplasia, increase in mucous cells, rupture of pillar cells as well as telangiectasia. This alien parasite has invaded the Keiskamma and Kei River systems in the Eastern Cape, South Africa. According to the macroscopic fish health assessment index, A. mossambica from Binfield Park, Sandile and Wriggleswade Dams are in a healthy state. However, the histology-based health assessment highlighted that the effects on P. anguillae have a severe negative impact on the health of A. mossambica. Using the macroscopic and histology-based fish health assessment, a comprehensive investigation into the fish health status of Mugil cephalus and Myxus capensis from Binfield Park Dam revealed that human effects and parasites are not the only threats to freshwater fish. Nephrocalcinosis is a non-infectious kidney disease which is characterised by abnormal calcium deposition in the kidneys of humans and some fish species. According to the macroscopic and histology-based fish health assessment, the M. cephalus and M. capensis are not in a healthy condition. The macroscopic and histology-based fish assessment indices are not stressor-specific, and therefore the cause of the poor health state of these two fish species could not be determined. A possible suggestion for the poor health of these two species is the age of the species. Because the two mullet species were stocked into Binfield Park Dam, Ellender et al. (2012) could successfully age them accurately to ten years of age, which is the upper limit of the life span for these species. Macroscopic and histology-based fish heath assessments were conducted on Labeo umbratus from Sandile Dam in order to determine the health of this species. Macroscopic and histology-based fish health assessment indicated that its L. umbratus are in a healthy state. The March 2012 survey specimens had a significantly higher macroscopic FHAI score than those from the July 2011 survey. The increased FHAI score was because of parasite infections, as well as discoloured livers and increased total blood plasma protein levels, which are indicators of nutritional state. However, the presence of the anchor worm parasite Lernaea barnimiana in low numbers had no significant impact on the health of L. umbratus. The effect of the alien anchor worm parasite Lernaea cyprinacea was shown on the transloacted small mouth yellowfish Labeobarbus aeneus. It was also shown that L. aeneus are, according the macroscopic FHAI and the histology-based fish health assessment index, in a healthy state. However, the high scores observed in the macroscopic fish health assessment index were primarily as a result of the presence of the alien parasite L. cyprinacea and its associated affects on the fish host. Because of the significant impact of this alien parasite species on the translocated host species, it can be assumed that this alien parasite species will have a negative effect on the health of indigenous fish species in the Great Kei River. It is clear from the results presented in this study that the necropsy based and histology based fish health assessment can be successfully implemented as tools to assess the effects of heavy metal pollution and alien fish parasites in freshwater fish from selected impoundments in the Amatola region, Eastern Cape Province, South Africa, thus the original hypothesis of this thesis is accepted. Based on work done in this research the gaps in research have been identified. Due to the high levels of mercury indentified in the muscle tissue of M. salmoides from Binfield Park Dam. A human health assessment and edibility should be conducted in order to determine if the fish from Binfield Park Dam is safe for human consumption. In order to conserve South Africa’s Freshwater fish biodiversity, country wide surveys of indigenous fish species must be undertaken so that the health and the parasite diversity can be evaluated. / PhD (Zoology), North-West University, Potchefstroom Campus, 2015