Understanding demographic and disease processes in wildlife populations tends to be hampered by incomplete observations which can include significant errors. Models provide useful insights into the potential impacts of key processes and the value of such models greatly improves through integration with available data in a way that includes all sources of stochasticity and error. To date, the impact on disease of spatial and social structures observed in wildlife populations has not been widely addressed in modelling. I model the joint effects of differential fecundity and spatial heterogeneity on demography and disease dynamics, using a stochastic description of births, deaths, social-geographic migration, and disease transmission. A small set of rules governs the rates of births and movements in an environment where individuals compete for improved fecundity. This results in realistic population structures which, depending on the mode of disease transmission can have a profound effect on disease persistence and therefore has an impact on disease control strategies in wildlife populations. I also apply a simple model with births, deaths and disease events to the long-term observations of TB (Mycobacterium bovis) in badgers in Woodchester Park. The model is a continuous time, discrete state space Markov chain and is fitted to the data using an implementation of Bayesian parameter inference with an event-based likelihood. This provides a flexible framework to combine data with expert knowledge (in terms of model structure and prior distributions of parameters) and allows us to quantify the model parameters and their uncertainties. Ecological observations tend to be restricted in terms of scope and spatial temporal coverage and estimates are also affected by trapping efficiency and disease test sensitivity. My method accounts for such limitations as well as the stochastic nature of the processes. I extend the likelihood function by including an error term that depends on the difference between observed and inferred state space variables. I also demonstrate that the estimates improve by increasing observation frequency, combining the likelihood of more than one group and including variation of parameter values through the application of hierarchical priors.

South Africa produces an average of 154 million broilers (Gallus gallus domesticus) annually, arising to an estimated 886 million kg of broiler litter. The largest population of broilers are reared in the North West province. Various applications for this largely underexploited resource have been published, including forming part of ruminant diets and direct land application. This however has several disadvantages, as it could lead to eutrophication of fresh water sources and faecal contamination of produce. Windrow composting of broiler litter has previously been studied, and found to deliver a stabilized product free of pathogenic and phytotoxic effects, therefore making it an excellent soil conditioner. This study aimed to characterize the microbial community present during the windrow composting of broiler litter. Four different formulations of substrate were tested; these being broiler litter (Windrow 1), Windrow 1 with previously composted material (Windrow 2), Windrow 2 amended with woodchips (Windrow 3) and Windrow 3 with an additional 12.5% (w/w) zeolite (Windrow 4). Broiler litter used in this experiment had a C:N ration of 10.3:1, whilst the blue gum woodchips added as an amendment had a C:N ratio of 172:1. Windrow and environmental temperatures were monitored on a regular basis. Windrow 1 largely mimicked environmental temperature, and could not sustain a true thermophilic phase during the experimental period. Windrow 2 did achieve a short lived thermophilic phase during the first few days of the composting process, however could not sustain its temperature over the whole period. In contrast Windrows 3 and 4 sustained temperature above 40°C for the largest part of the experimental period, regardless of environmental temperature. No significant difference (p < 0.05) could be observed between average moisture levels in the 4 windrows. Internal moisture profiles were however found to differ significantly, especially on the surface of the windrows. Moisture was also lost faster in Windrows 1 and 2 compared to Windrows 3 and 4. Chemical analysis showed differences between the four windrows constructed. A higher amount of nitrogen was lost in Windrows 1 and 2, mostly due to a sub-optimal initial C:N ratio in these windrows. Windrow 2 contained the highest values for plant nutrients P, Mg, Ca, Mn and Cu. Microbial population dynamics were observed using PCR-DGGE of samples collected throughout the composting of various treatments. Various commercial DNA extraction kits where tested in a previous study for their ability to remove PCR inhibitory substances, such as humic acids. The Machery-Nagel Soil DNA isolation kit was used as it gave amplifiable DNA from all samples. Samples were amplified using a nested PCR approach primer sets 27f-1492r \ 341f(GC)-907r and EF3-EF4 \ EF4(GC)-fung5 (where “GC” indicates a GC-rich clamp) for prokaryotic and eukaryotic species respectively. The PCR products were analyzed by agarose gel electrophoresis, and equal amounts of product were subjected to denaturing gradient gel electrophoresis (DGGE). Bands obtained from these polyacrylamide gels where then re-amplified using the same secondary primer sets (without the GC-clamp), and sequenced. A total of 454 prokaryotic bands in 55 distinct rf-positions were observed. Seven distinct rf-positions were observed in eukaryotic DGGE profiles. Prokaryotic profiles were aligned and the microbial diversity was analyzed by means of Ward’s clustering algorithm and the dice coefficient of similarity, as well as Simpson’s reciprocal, Shannon-Weaver and Species richness indices. Canonical correspondence analysis (CCA) was also performed on both the banding patterns as well as the bands present, together with the physico-chemical results obtained. Several bands were successfully identified as being influenced by physico-chemical parameters. Temperature, C:N ratio, ash, and moisture showed a correlation on CCA bi-plots. Sixteen bands were sequence identified. These sequences were compared to two different databases. The 16S rRNA database for Bacteria and Archaea gave identities to genus level, however maximum identity scores were low. Of the 16 sequences, 12 sequences were identified as uncultured bacteria when compared to the nucleotide collection database. In comparing the sequences with sequences collected in the nucleotide collection database, 12 were either first described in composts and soils, or animal manures. Results indicated mostly members of the genus Bacillus and Paenibacillus. The addition of a carbon source greatly affected the microbial metabolism, resulting in a thermophilic phase being achieved in amended windrows. As no thermophilic phase was observed in windrows that were not amended with woodchips, it could be concluded that the use of a carbon source is irremissible when composting broiler litter. A zeolite amendment is also strongly advised, as this further increased temperatures within the windrow. / Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013.

South Africa produces an average of 154 million broilers (Gallus gallus domesticus) annually, arising to an estimated 886 million kg of broiler litter. The largest population of broilers are reared in the North West province. Various applications for this largely underexploited resource have been published, including forming part of ruminant diets and direct land application. This however has several disadvantages, as it could lead to eutrophication of fresh water sources and faecal contamination of produce. Windrow composting of broiler litter has previously been studied, and found to deliver a stabilized product free of pathogenic and phytotoxic effects, therefore making it an excellent soil conditioner. This study aimed to characterize the microbial community present during the windrow composting of broiler litter. Four different formulations of substrate were tested; these being broiler litter (Windrow 1), Windrow 1 with previously composted material (Windrow 2), Windrow 2 amended with woodchips (Windrow 3) and Windrow 3 with an additional 12.5% (w/w) zeolite (Windrow 4). Broiler litter used in this experiment had a C:N ration of 10.3:1, whilst the blue gum woodchips added as an amendment had a C:N ratio of 172:1. Windrow and environmental temperatures were monitored on a regular basis. Windrow 1 largely mimicked environmental temperature, and could not sustain a true thermophilic phase during the experimental period. Windrow 2 did achieve a short lived thermophilic phase during the first few days of the composting process, however could not sustain its temperature over the whole period. In contrast Windrows 3 and 4 sustained temperature above 40°C for the largest part of the experimental period, regardless of environmental temperature. No significant difference (p < 0.05) could be observed between average moisture levels in the 4 windrows. Internal moisture profiles were however found to differ significantly, especially on the surface of the windrows. Moisture was also lost faster in Windrows 1 and 2 compared to Windrows 3 and 4. Chemical analysis showed differences between the four windrows constructed. A higher amount of nitrogen was lost in Windrows 1 and 2, mostly due to a sub-optimal initial C:N ratio in these windrows. Windrow 2 contained the highest values for plant nutrients P, Mg, Ca, Mn and Cu. Microbial population dynamics were observed using PCR-DGGE of samples collected throughout the composting of various treatments. Various commercial DNA extraction kits where tested in a previous study for their ability to remove PCR inhibitory substances, such as humic acids. The Machery-Nagel Soil DNA isolation kit was used as it gave amplifiable DNA from all samples. Samples were amplified using a nested PCR approach primer sets 27f-1492r \ 341f(GC)-907r and EF3-EF4 \ EF4(GC)-fung5 (where “GC” indicates a GC-rich clamp) for prokaryotic and eukaryotic species respectively. The PCR products were analyzed by agarose gel electrophoresis, and equal amounts of product were subjected to denaturing gradient gel electrophoresis (DGGE). Bands obtained from these polyacrylamide gels where then re-amplified using the same secondary primer sets (without the GC-clamp), and sequenced. A total of 454 prokaryotic bands in 55 distinct rf-positions were observed. Seven distinct rf-positions were observed in eukaryotic DGGE profiles. Prokaryotic profiles were aligned and the microbial diversity was analyzed by means of Ward’s clustering algorithm and the dice coefficient of similarity, as well as Simpson’s reciprocal, Shannon-Weaver and Species richness indices. Canonical correspondence analysis (CCA) was also performed on both the banding patterns as well as the bands present, together with the physico-chemical results obtained. Several bands were successfully identified as being influenced by physico-chemical parameters. Temperature, C:N ratio, ash, and moisture showed a correlation on CCA bi-plots. Sixteen bands were sequence identified. These sequences were compared to two different databases. The 16S rRNA database for Bacteria and Archaea gave identities to genus level, however maximum identity scores were low. Of the 16 sequences, 12 sequences were identified as uncultured bacteria when compared to the nucleotide collection database. In comparing the sequences with sequences collected in the nucleotide collection database, 12 were either first described in composts and soils, or animal manures. Results indicated mostly members of the genus Bacillus and Paenibacillus. The addition of a carbon source greatly affected the microbial metabolism, resulting in a thermophilic phase being achieved in amended windrows. As no thermophilic phase was observed in windrows that were not amended with woodchips, it could be concluded that the use of a carbon source is irremissible when composting broiler litter. A zeolite amendment is also strongly advised, as this further increased temperatures within the windrow. / Thesis (MSc (Environmental Sciences))--North-West University, Potchefstroom Campus, 2013.

Africanized honey bees (AHB) are a hybrid between African and European honey bees (EHB). Compared to the EHB, AHB exhibit more intense, defensive behaviors but nevertheless provide the same important ecosystem service--pollination. AHB have been found in Tucson, AZ. since 1993. It is important to understand the population ecology of AHB for several reasons. Most directly, the behavioral traits retained from African bees present public safety and health risk. AHB are easily agitated; even slight disturbances (e.g., human movements) can provoke attacks. Several hybridized bee traits (e.g., higher colony growth rates, reproduction at a smaller colony size, nesting in a wider range of cavity materials, etc.) also make them more adapted to urban landscapes. The overlap of habitats and resource-using of AHB with human significantly raise the risk of stinging incidents, especially in the areas of bee aggregation. Although the presence of AHB in urban environments may present a public safety and health risk, they do contribute to urban ecosystems substantially through pollination. The fact that AHB is a part of the urban ecosystem suggests a need for a better understanding of the relationship among climate factors, urban landscape characteristics, and AHB population dynamics. The goal of my dissertation was to understand population dynamics of AHB in urban environments using removal records of AHB colonies in water meter boxes. I have demonstrated useful methods and repeatable procedures to process, extract, and synthesize water meter box data which were not collected or sampled specifically for any ecological research. I also examined the spatio-temporal distributions of AHB colony removals in water meter boxes, and evaluated the effects of variations of temperature and precipitation on observed patterns. Then, I investigated the linkage between spatial patterns of AHB colonies and urban landscape characteristics by evaluating densities of water meter boxes, AHB colony abundance, and colony occupancy among different land cover/land use types. Lastly, a conceptual model and quantitative models were developed to illustrate AHB population dynamics, particularly and the interactions among water meter boxes, alternative cavities, and honey bee colonies. Overall, the probabilities of AHB colonies selecting nesting sites can be influenced by: (1) the ratio of water meter boxes and alternative cavities; (2) the difference of vegetative attributes among locations associated with the preference of AHB in selecting new nesting sites. Seasonal variations of precipitation and temperature can affect the development and productivity of AHB population.

Recent genetic studies have confirmed that there was admixture between African early modern humans and archaic populations throughout the Old World. In this dissertation, I examine European early modern human dental morphology to assess the evidence for Neandertal-human admixture. The focus of this study is not on the question of taxonomic designations of Late Pleistocene Homo, but rather on the interactions of these populations in Europe. This focus on gene flow itself redefines the Neandertal question. Rather than asking if Neandertals are a different species from H. sapiens, I focus on the nature of the interactions between archaic and modern populations, which is essential to understanding the history of modern H. sapiens regardless of species definitions. I recorded dental metric measurements and morphology observations on 85 fossil Neandertals and early modern humans and a recent modern human comparative sample of 330 Native Americans and Spaniards. I examined each trait distribution individually and through the use of Mahalanobis D2, mean measure of divergence, principle components analysis, discriminant function analysis, k-means cluster analysis, and a population genetics program, structure. Through these methods, I found evidence of admixture in the dental trait distributions of European early modern humans. However, it is not evident in traditional distance measures or cluster analyses. The earliest European modern humans do not follow the trend of dental reduction found throughout the Pleistocene and into the Holocene and do not uniformly classify with any fossil population in discriminant function analysis of metric traits. The non-metric trait sample size is too small to make any definitive conclusions, but a mosaic pattern of trait frequencies also suggests admixture. The recent modern human sample shows that while increased variation and a mosaic of non-metric traits persist through many generations after admixture has ceased, traditional methods of distance analysis cannot detect low levels of admixture within 200 years. The program structure is effective in finding patterns of variation within and among populations using morphological data. It will be useful for future analyses of dental traits and other fossil data, given the ability to use it with an incomplete data set.

Most animals grow substantially during their lifetime and change in competitive ability, predatory capacity and their susceptibility to predation as they grow. This thesis addresses the implications of this on regulation and dynamics within populations as well as between population interactions. In size-structured populations either reproduction or maturation may be more limiting. If juveniles are competitively superior, the competitive bottleneck will be in the adults and reproduction will be limiting. Mortality will in this case result in overcompensation in juvenile biomass through increased reproduction. Compensation in biomass was demonstrated in Daphnia pulex populations subjected to size-independent mortality, where juvenile biomass did not decrease when a substantial harvest was imposed due to increase per capita fecundity. This supported that juveniles were superior competitors and that population cycles seen in Daphnia are juvenile-driven. Compensatory responses in biomass may lead to that predators facilitate eachothers existence by feeding on a common prey, a phenomenon coined emergent facilitation. In an experimental test of the mechanism behind emergent facilitation it was demonstrated that the invertebrate predator Bythotrephes longimanus was favoured by thinning of its prey Holopedium gibberum. The thinning mimicked fish predation and targeted large individuals while Bythotrephes preferrs small prey. Size dependent predation also occurs within populations, i.e. cannibalism, were large individuals feed on smaller conspecifics. Two populations of the common guppy (Poecilia reticulata) originating from different environments were demonstrated to differ in cannibalistic degree. Cannibalism was also affected by the presence of refuges and females and juveniles from one population were better adapted to structural complexity than the other. The effects of these differences in cannibalism on population regulation and dynamics were studied in long term population experiments. Both populations were regulated by cannibalism in the absence of refuges, and displayed cannibal-driven cycles with suppression of recruitment and high population variability. The presence of refuges decreased density dependence and population variability and harvesting of large females in the absence of refuges led to population extinctions in the more cannibalistic population. The less cannibalistic population had higher population biomass and stronger density-dependence in the presence of refuges. When refuges were present, cohort competition increased and cycles with short periodicity were seen. Large individuals were not only cannibals, but could successfully prey on other species. Small and large guppies were allowed to invade resident populations of Heterandria formosa. Small invaders failed while large invaders succeeded as predation from large invaders broke up the competitive bottleneck that the resident population imposed on juveniles of the invader.

Centaurea tchihatcheffii Fisch. &amp / Mey. is a critically endangered annual plant species with a narrow distribution in G&ouml / lbaSi, Ankara. The aim of this study is to understand the population dynamics of the species to help find the best way to conserve species for long term viability. The two healthiest subpopulations containing more than 1.5 million individuals were studied to estimate demographic parameters i.e. survival and reproduction rates by monitoring marked individuals, to identify pollinators, dispersers and pollen &amp / seed predators and to investigate population status, natural threats and their effects. The species is considered a weed in cereal plantations, showing adaptations of ruderal habit: High population densities (~18.5-63.2 individuals/0.5 m2), persistent seed bank with many viable seeds (~20,000/m2), rapid growth matching favorable weather conditions (almost 15 weeks from rosette to flowering), high survival with premature deaths making up only 2-20% of natural deaths mostly at rosette stage, no density dependent mortality, seed production by selfing and crossing via generalist pollinators, high reproduction rates (1200-7000 seeds/m2) and promotion of growth on aerated soil whereas inhibition with herbicides. Insect and avian predators do not cause an important damage to population. Absence of mutualists aiding in pollination (honeybee) and dispersal (ants) is out of question. There is no natural limitation on population persistence. The major threats are anthropogenic, i.e. cereal cultivation, construction and collection of individuals from natural populations. Conservation of remaining subpopulations as a reserve and alternative methods in cereal cultivation like reduced or no herbicide application should be considered as high priority conservation strategies.

The Indiana Bat (Myotis sodalis) population had decreased by 56% between 1967 and 2006. In summer 2006, a mysterious disease called White Nose Syndrome was first identified. Since then, the disease killed almost one million bats in North America. Many Biologists believe that both the population decrease before the appearance of the disease and WNS are associated with climate. In a joined effort with Yellowstone Ecological Research Center (YERC), US Fish and Wildlife Service (USFWS) and NASA Terrestrial Observation and Prediction System (TOPS), our study is a partial population viability analysis which aims to establish a link between bat population dynamic and climate before the appearance of WNS. / Biostatistics

Experiments were conducted in the greenhouse, field and growth chambers to evaluate effects of soil type, soil moisture regimes, and porosity on selected aspects of the dynamics of the Kona coffee root-knot nematode, Meloidogyne konaensis. First, the reproduction and damage potential of M. konaensis on resistant and susceptible rootstocks of coffee in four soils under two moisture regimes representative of areas where coffee is grown in Hawaii were assessed in greenhouse experiments. M. konaensis suppressed growth of coffee in all four soils. Nematode reproduction occurred readily in all soil types. Reproduction was lowest in the Hydric Dystrandept soil where the nematode holotype was found. In contrast, root galling was greatest in this soil. Greater galling occurred under constant moisture (33kPa) than under fluctuating moisture conditions in this soil. A field experiment in Kainaliu, Hawaii was conducted to determine the influence of irrigation, plant age, cultivar and nematode on coffee growth and yield. The population densities of the nematode in the soil varied according to plant age and irrigation treatment. Soil populations under irrigated conditions were greater during the months of May to July which normally follows the greatest annual precipitation and a period of active plant growth. Nematode reproduction was greater on coffee transplanted as 6-month-old seedlings than on coffee transplanted at 12- month ofage. Soil water tension varied by season and experimental treatment. Trees from 12-month-old transplants exhibited greater water tension fluctuation with greatest water tension occurring from January to April. Trees transplanted as 6-month-old seedlings into M. konaensis infested soil and irrigated yielded greater coffee fruit than the same aged trees treatment without irrigation. Crop loss and reduction of growth and yield were also more evident from 6-month-old seedlings without supplemental irrigation treatment. In contrast, yield from plots in treatments including irrigation, nematode and 12-month-old transplants yielded poorly. Overall highest yields were obtained from trees free of nematode and with supplemental irrigation. Yield reductions from nematode-infected plants ranged from 30-60% which is economically significant. Penetration, development and reproduction of M. Iwnaensis was determined on tomato as model plant at 0.77 and 0.65 porosity. The rate of root penetration and post-embryonic developmental rates occurred slightly faster the porosity treatment of 0.77 than in the more densely packed soil (porosity of 0.65). Development in the 0.65 porosity progressed slower than at 0.77. Even though the nematodes matured faster and began laying eggs sooner on plants growing at porosity of 0.77, much greater numbers of eggs were laid by 30 days after inoculation at the 0.65 porosity treatment than those at the 0.77 porosity. The finding from this research illustrates the primary role of the Kona coffee root-knot nematode in the Coffee Decline. The soil environment and host suitability are conducive factors for the coffee decline disease. Proper soil moisture management combined with sources of genetic resistance could minimize the damage enabling the coffee industry to remain profitable.

Bibliography: p. 269-279. / viii, 279 p. : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Applied Mathematics, 1995