It is generally assumed that when natural habitat is converted to human-dominated cover such area is “lost” to its native species. Extinctions will ensue. The literature generally assumes that species are extirpated as natural area is reduced, following the well-known species-area relationship (SAR). However, SARs have consistently over-estimated species losses resulting from conversion of natural habitat to human-dominated land covers. We hypothesize that the overestimation occurs because these area-based models assume that converted habitat is “lost”, eliminating all species. However, in the real world, conversion of natural land cover to human-dominated cover frequently produces new land covers, different from the original habitat, but not necessarily completely inhospitable to biodiversity. We evaluated the responses of total avian richness, forest bird richness and open habitat bird richness to remaining natural area within 991 quadrats, each 100 km2, across southern Ontario. Total bird species richness does not follow SAR predictions; rather, the number of bird species peaks at roughly 50% natural land cover. The richness of forest birds does follow the usual SAR power-law as a function of forested area. In contrast, richness of birds that prefer open-habitat does not increase monotonically with either natural- or human-dominated land cover. However, we can partition human-dominated land cover into an “available human-dominated” component and “lost” habitat. Richness of open-habitat species relates to the amount of available human-dominated cover. Distinguishing three habitat types (natural, available human-dominated, and lost) permits accurate predictions of species losses in response to natural habitat conversion.

Dung beetles is a group of coprophagous beetles in the family Scarabaeidae. Dung beetles have an important function by improving nutrient circulation and biological control of parasites. Dung is a short-lived resource, making dung beetles tied to habitats continuously grazed. Decline in pasture combined with shorter grazing seasons has resulted in a decrease in available dung. Other reasons can be the use of chemicals to control internal parasites on the grazing animals. This has contributed to the fact that half of the dung beetles in Sweden are endangered. The aim of the present study was to analyze data on dung beetles from the County Administration Board in Östergötland and see if species communities have changed between 2001-2019. In addition, the effect of sand as soil type was studied by comparing the species richness between pastures with and without sand. Analysis whether there was any variation among species richness and species communities depending of grazing animals was also performed. Results showed that the number of species had increased over time and that changes in species communities had occurred. Pastures with sand had more species, however, the amount of sand in the nearest surroundings was of less importance. Dung beetles were found to have a preference when choosing dung-type. Pastures with dung from multiple species of grazing animals were found having the highest species richness. Studies on this would clarify even further what seems to favor dung beetles, this could then be applied to other areas to counteract the loss of species.

Understanding the health of rare and at-risk plant species is crucial for the conservation of biodiversity. Rare and at-risk species are often specialists with very specific requirements for growth and reproductive success. Some parameters associated with growth and reproductive success of rare aquatic species may include biotic and abiotic factors such as herbivory, competition, water depth, pH, and other factors associated with habitat quality. In this thesis, the population health of the rare and at-risk aquatic species Plantago cordata in Southern Illinois streams is assessed in relation to stream quality of sites containing Plantago cordata and sites without Plantago cordata.The objectives of this study were to (1) Determine if there is a relationship between population size structure and biotic habitat factors among populations and sites, and (2) Determine if there is a relationship between population size structure and abiotic habitat factors among populations and sites. Hypotheses were constructed using the hierarchy-of hypotheses method and most narrow alternative hypotheses are as follows: (1) There will be significant relationships between biotic and abiotic factors and Plantago cordata growth and reproductive success. (2) Levels of herbivory will have significant relationships with growth and reproductive success of Plantago cordata. (3) The abundance of co-occurring species individually and considered in functional groups (graminoid, herb, woody) will have significant relationships with growth and reproductive success of Plantago cordata. (4) Stream depth will have a unimodal relationship with growth and reproductive success of Plantago cordata, with maximum performance at an intermediate stream depth. (5) Stream pH will have a unimodal relationship with growth and reproductive success of Plantago cordata. (6) Stream quality (as outlined by the QHEI assessment) will have significant relationships with growth and reproductive success of Plantago cordata. General trends in herbivory suggest that Plantago cordata could be at greatest risk of herbivory during warmest average temperatures of the study season. There is evidence to suggest that flowering individuals could have a greater threat of herbivory than other growth stages based on Kendal correlation results. A Wilcox test determined that there were no statistical differences in species richness for plots with versus without Plantago cordata. There were relatively low values for percent cover of co-occurring species when considered in functional groups and there was overall relatively low species richness across all communities. Despite this, non-metric multidimensional scaling (NMDS) of community data provided evidence to suggest that there were statistical differences in the species composition of co-occurring individual riparian species among P. cordata populations. A significant negative correlation for water depth and flowering individuals and a significant positive correlation with water depth and pH occurred. A significant positive correlation for stream pH with the numbers of seedlings and dehiscing individuals was also found. One-way analyses of variance (ANOVAs) showed that some populations containing Plantago cordata were found to have stream pH values statistically different from nearby IEPA control streams without Plantago cordata. One population of Plantago cordata was found to be significantly different than two other populations in regards to stream pH using a linear mixed model. A principal components analysis (PCA) of stream Qualitative Habitat Evaluation Index (QHEI) assessments demonstrated distinct clustering of Plantago cordata streams and control IEPA streams without Plantago cordata. These findings provide partial evidence to suggest that growth and reproductive success of Plantago cordata could potentially be impacted by the abiotic and biotic parameters explored in this thesis.

Three wetland restoration methods: seeding, seeding + hay mulch, and seeding + hay mulch + vegetation plugs were compared via the plant community within a formerly cropped wetland in southeastern North Dakota. Arrangement of plugs were also compared to assess the success of native species establishment. Mean relative cover for native species and introduced species were recorded and analyzed to compare the restoration methods and plug arrangement. Three herbicide treatments were studied on upland prairie sites with and without prescribed burning to test effects on leafy spurge (Euphorbia esula) control and seeded native establishment. There is no difference native species richness between the restoration methods six years post restoration, and no difference in plant cover in the different arrangement of plugs. Quinclorac significantly reduced leafy spurge cover; however, glyphosate treatments had higher cover of seeded native species.

The objective of this study was to characterize the mitochondrial genomes of the species within the genus Ceratocystis and investigate the evolutionary process of the ribosomal RNA cistron found within these fungi. Ceratocystis incorporates a number of pathogenic species affecting a variety of hosts, making the study of these fungi economically significant. The fortuitous identification of a Ceratocystis species, C. manginecans, which contained two different internally transcribed spacer sequence types within the ribosomal rRNA cistron, enabled a study of concerted evolution in this fungus. Using this non-model organism we were able to show empirical evidence for unequal crossing over and gene conversion as the ultimate forces acting on this gene region dictating a concerted evolutionary effect. We suggest that this process is true for all eukaryotes. Using the knowledge drawn from previously characterized and annotated mitochondrial genomes of other eukaryotes, the genomes of three Ceratocystis species, namely Ceratocystis fimbriata, Ceratocystis albifundus and Ceratocystis moniliformis were fully assembled and annotated for comparative analysis. This comparative study addressed the genome size, gene content, tRNA presence as well as intron types and their homing endonucleases found among these three mitochondrial genomes. An interspecies characterization was then undertaken using the mitochondrial genomes of six different C. albifundus isolates from different geographical locations in Africa. Genetic variation and similarities among these isolates supports the previous hypothesis that the origin of this fungus is Southern Africa. It is hoped that the research presented in this thesis will contribute to the improved understanding of the mitochondrial genomes in Ceratocystis species. / Thesis (PhD)--University of Pretoria, 2013. / gm2013 / Genetics / Unrestricted

Greening disease in South Africa is associated with a phloem-limited member of the Alphaproteobacteria known as ‘Candidatus Liberibacter africanus’ (Laf). Spread of this bacterium is assisted by the flight and feeding activities of its triozid vector, Trioza erytreae. In addition to Laf, ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC) has been described from this country. LafC is widely associated with Calodendrum capense, an indigenous Rutaceous species. This dissertation aims to determine (i) whether reservoir hosts exist for Laf amongst indigenous rutaceous species that also act as native hosts to T. erytreae and (ii) whether LafC can be transmitted vertically through Ca. capense seeds. To achieve the first aim, a total of 234 Clausena anisata, 289 Vepris lanceolata and 231 Zanthoxylum capense specimens were assessed for the presence of Liberibacter by making use of a Liberibacter generic real-time PCR assay. Positive samples were further characterized by using a multi-gene phylgenetic approach based on the nucleotide sequences for the 16S, rplJ and omp genes, which respectively encode the 16S ribosomal RNA (rRNA) subunit, 50S ribosomal subunit protein L10 and the outer membrane protein. The tree host species from which Liberibacter sequences were obtained were DNA barcoded using standard procedures. Of the trees tested, 33 Cl. anisata, 17 V. lanceolata, 9 Z. capense and 1 Zanthoxylum davyi, tested positive for Liberibacter. Phylogenetic analysis of the rplJ and omp gene regions, revealed unique Liberibacter clusters associated with each tree species. Phylogenetic analysis of 16S data indicated that the strains detected in V. lanceolata and Cl. anisata were grouped with LafC, while those from Zanthoxylum species grouped separately. The presence of these bacteria in indigenous Rutaceous species should be further investigated to determine whether they are capable of being transmitted to and causing disease on commercial citrus species. To address the second aim of the study, seeds of Ca. capense were collected from two mother trees with known LafC infection. Following total DNA extraction from the midribs of leafs grown from these seeds, a LafC directed real-time PCR system was used to detect the bacterium. However, none of the samples had Ct values <35, the positive/negative threshold. From this study, no indication of seed-transmission was obtained within the limited number of samples which could be tested. The lack of vertical transmission of both Laf and LafC is seeminly a characteristic shared amongst African Liberibacter species. / Dissertation (MSc)--University of Pretoria, 2013. / gm2014 / Microbiology and Plant Pathology / unrestricted

The study evaluated the extent and threat of bark harvesting of plant species for medicinal purposes in the Venda region and investigated possibilities of the sustainability of these practices. Approximately 30% of the woody plant species in Venda were found to have medicinal properties in their bark, but only about 12% of these species are commonly traded in muthi shops in the region. Fifty-eight medicinal plant species are commonly harvested for medicinal properties in their bark and found in muthi shops in the region. These 58 species were scored for the possible threat of bark harvesting to the species’ survival using 20 ecologically relevant plant population traits. The most vulnerable species were Adansonia digitata, Adenia spinosa, Albizia adianthifolia, Albizia versicolor, Brackenridgea zanguebarica, Croton megalobotrys, and Warburgia salutaris. Of these species Brackenridgea zanguebarica and Warburgia salutaris are amongst the ten most traded medicinal plant species in Venda region. Elaeodendron transvaalense and Brackenridgea zanguebarica, the two species investigated in detail in this study, were amongst the most commonly traded medicinal plant species in Venda region. Analysis of size class distributions showed that both species had growing and healthy populations, exhibiting J-shaped population curves, centroids left-skewed from the midpoint of the size class distribution, and a fine-grained status. However, size-class distributions in both species revealed certain classes that needed monitoring since they were negatively affected by bark harvesting. Adult individuals of B. zanguebarica showed a high degree of bark regeneration as a response to bark removal from medicine men. The crown health status of E. transvaalense was generally good although some individuals, contributing 9% of the sample, had dead crowns. A linear relationship was noticed between areas harvested and stem circumference, which is understandable considering the large surface area of harvestable bark on bigger individuals. Matrix modeling of E. transvaalense revealed that the vegetative stage should be targeted for management action. An assessment of the adequacy of the Brackenridgea Nature Reserve, an initiative aimed at protecting Brackenridgea zanguebarica, revealed that the reserve size is not enough for conservation of a viable population. The method flagged out potential growth habitat for B. zanguebarica around the current reserve, which could be incorporated to enlarge the conservation area, which could be incorporated to enlarge the conservation area. Four different scenarios were analysed on how best to conserve the species. Assuming a 50% reduction in human-related activities, such as cultivation, harvesting and livestock grazing, it is recommended that the reserve be enlarged from its current 110 ha to 366 ha to maintain a viable population into the future. Finally, the study recommended the adoption of an integrated approach to achieve sustainability of bark harvesting in the Venda region. Only by selecting best practices from both indigenous and conventional conservation techniques will the conservation of natural resources that are of important to local communities, be successful. An action plan that will involve the formation of an association by all stakeholders interested in the sustainable utilization of natural resources must be developed. The association must be governed by a constitution with a clear mission statement and the harvesting of natural resources should be done in line with a collection policy. / Thesis (PhD)--University of Pretoria, 2012. / Plant Science / unrestricted

Originally endemic to South America, the nine-banded armadillo (Dasypus novemcinctus) has recently expanded its range northward to Illinois. With this range expansion comes concern from both wildlife managers and the general public regarding potential incoming pathogens and unknown impacts on native wildlife. My research, conducted during 2018-2020 in southern Illinois, addressed the following 3 objectives intended to provide information regarding this novel species: (1) test for the presence of Trypanosoma cruzi and Mycobacterium leprae, (2) model the potential distribution of armadillos, and (3) attempt several different armadillo capture methods. For Objective 1, I tested roadkilled specimens for T. cruzi and M. leprae, 2 pathogens known to infect humans, using PCR and ELISA, respectively. All 81 samples tested for T. cruzi and all 25 samples tested for M. leprae were negative. The latter case is consistent with the enemy release hypothesis, suggesting armadillos have evaded parasites present in their native environment due to geographical distance. The absence of T. cruzi in the sampled individuals implies dispersing individuals are more robust than those at the center of their range. For Objective 2, I used MAXENT to model potential armadillo distribution in 51 counties in southern Illinois using 39 presence locations. Modeling identified low-intensity development to be the most important predictor of armadillo presence. For Objective 3, I attempted to capture armadillos using spotlighting on roads, staking out burrows, unbaited single-door cage traps, and unbaited double-door cage traps. Based on trap nights per capture, I found the use of double-door cage traps to be the most efficient method. My study will aid in managing colonizing armadillo populations by presenting information regarding dynamics of disease transmission, predicting areas of armadillo presence, and capture methods.

Thesis (M.A. Agriculture. (Plant Production)) -- University of Limpopo, 2021 / Root-knot (Meloidogyne species) nematodes are host to most plant species, with the success of most crops being dependent upon proper nematode management tactics. Sweet potato (Ipomoea batatas L.) is highly susceptible to root-knot nematodes, with physical damage being visible on roots. The withdrawal of highly effective fumigant synthetic nematicides from the agrochemical markets resulted in a need to investigate alternative strategies for managing high nematode population densities, with the use of nematode resistance being the most preferred strategy. The objectives of this study were (1) to establish whether sweet potato cv. 'Blesbok' would be resistant to M. javanica under greenhouse conditions, (2) to investigate whether cucurbitacin containing phytonematicides would be comparable to Velum synthetic nematicide in suppressing Meloidogyne species. For Objective 1, treatments comprised 0, 5, 25, 125, 625, 3125 and 15625 eggs and second-stage juveniles (J2), had six replications and validated in time. Uniform sweet potato cuttings were transplanted in 20-cm diameter plastic pots, filled with steam pasteurised (300°C for 1 hour) loam soil. At 56 days after inoculation, plant growth, plant nutrient and nematode variables were assessed using analysis of variance and subjected to lines of the best fit. Treatments had significant (P ≤ 0.05) effects on eggs and highly significant (P ≤ 0.01) effects on J2, final nematode population densities (Pf) and the reproductive factor (RF), contributing 39, 45, 42 and 92% in total treatment variation (TTV) of the respective variables. Treatments did not have significant effects on plant variables. Calcium, K, Mg and Fe versus M. javanica levels each exhibited negative quadratic relations, with the models being explained by associations from 59 to 96%. In contrast, Zn versus M. javanica levels exhibited positive quadratic relation, with the model being explained by 80 and 98% association and optimised at 125 M. javanica units. For Objective 2, four treatments, namely, untreated control, Nemarioc-AL phytonematicide, Nemafric-BL phytonematicide and Velum had 10 replications and also validated in time. The plantlets with well-developed root system were transplanted under field conditions. Data for Object 2 did not comply with the requirements for ANOVA and were therefore subjected to Principal Component Analysis (PCA). Nemafric-BL phytonematicide treatment in both experiments reduced eggs, J2 in roots and J2 in soil and RP of Meloidogyne species, with the results being comparable to those of Velum synthetic nematicide. Nemarioc-AL phytonematicide reduced J2 in roots and in soil of Meloidogyne species, without affecting eggs in roots and RP. Nemafric-BL phytonematicide and Velum each increased plant growth variables in Experiment 1 and Experiment 2, whereas Nemarioc-AL phytonematicide did not have significant effects on plant growth variables. Velum chemical nematicide stimulated the accumulation of most essential nutrient elements in leaf tissues of the test cultivar, followed by Nemafric-BL phytonematicide, whereas Nemarioc-AL phytonematicide had no significant effects on the accumulation of essential nutrient elements. The study had two major outcomes, namely, (1) that the efficacy of Nemafric-BL phytonematicide was comparable to that of Velum chemical nematicide in suppression of population densities of Meloidogyne species in cv. ′Blesbok′ under field conditions and (2) that cv. ′Blesbok′ was tolerant to M. javanica and therefore, it was not necessary to investigate the mechanisms of nematode resistance. / Agricultural Research Council (ARC) and National Research Foundation (NRF)

A large database now exists for tardigrades in the Great Smoky Mountains National Park (GSMNP) consisting of 780 samples, 15,618 specimens, and 80 species including 14 new to science. We found 43 species of tardigrades in 150 soil/leaf litter samples. We calculated the Chao 1 species richness estimate with the species accumulation curve for the GSMNP and confirmed that our species list is virtually complete. Compared with soil data from mt. Fuji, Japan, estimated species richness in GSMNP was significantly higher. In our comparison of previous studies of soil/leaf litter tardigrades in other geographic areas, only the Kanagawa prefecture of Japan reported a higher number of species (47) than the GSMNP. Species richness estimators are valuable tools for comparing diversity in different habitats, even when sampling effort varies between studies.