Paddlefish (Polyodon spathula) is a commercially and recreationally important species, with a native range that extends over 22 US states. This is a large, long-lived, highly mobile riverine species that has been negatively impacted by habitat fragmentation, historic overharvest, and hatchery supplementation. Dams are the primary cause of habitat fragmentation, blocking migration routes, flooding spawning grounds, and isolating populations. A common management action to mitigate the impacts of habitat fragmentation and maintain harvestable populations is hatchery propagation and stocking. Reduction in stock size, isolation of populations, and stocking can all negatively impact the genetic integrity of Paddlefish. I evaluated the impacts of isolation and hatchery supplementation on the effective population size (Ne) of Paddlefish as well as the range-wide genetic structure of Paddlefish.

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Geographic profiling (GP) was originally developed to solve the problem of information overload when dealing with cases of serial crime. In criminology, the model uses spatial data relating to the locations of connected crimes to prioritise the search for the criminal's anchor point (usually a home or workplace), and is extremely successful in this field. Previous work has shown how the same approach can be adapted to biological data, but to date the model has assumed a spatially homogenous landscape, and has made no attempt to integrate more complex spatial information (eg, altitude, land use). It is this issue that I address here. In addition, I show for the first time how the model can be applied to conservation data and - taking the model back to its origins in criminology - to wildlife crime. In Chapter 2, I use the Dirichlet Process Mixture (DPM) model of geographic profiling to locate sleep trees for tarsiers in dense jungle in Indonesia, using as input the locations at which calls were recorded, demonstrating how the model can be applied to locating the nests, dens or roosts of other elusive animals and potentially improving estimates of population size, with important implications for management of both species and habitats. In Chapter 3, I show how spatial information in the form of citizen science could be used to improve a study of invasive mink in the Hebrides. In Chapter 4, I turn to the issue of 'commuter crime' in a study of poaching in Savé Valley Conservancy (SVC) in Zimbabwe, in which although poaching occurs inside SVC the majority of poachers live outside, showing how the model can be adjusted to reflect a simple binary classification of the landscape (inside or outside SVC). Finally, in Chapter 5, I combine more complex land use information (estimates of farm density) with the GP model to improve predictions of human-wildlife conflict.

Malaria is a deadly disease that causes nearly one million deaths each year. Understanding the demographic history of the malaria parasite Plasmodium falciparum and the genetic basis of its adaptations to antimalarial treatments and the human immune system is important for developing methods to control and eradicate malaria. To study the long-term demographic history and recent effective size of the population in order to identify genes under selection more efficiently and predict the effectiveness of selection, in Chapter 2 we sequenced the complete genomes of 25 cultured P. falciparum isolates from Senegal. In addition, in Chapter 3 we estimated temporal allele frequencies in 24 loci among 528 strains from the same population across six years. Based on genetic diversity of the genome sequences, we estimate the long-term effective population size to be approximately 100,000, and a major population expansion of the parasite population approximately 20,000-40,000 years ago. Based on temporal changes in allele frequencies, however, the recent effective size is estimated to be less than 100 from 2007-2011. The discrepancy may reflect recent aggressive efforts to control malaria in Senegal or migration between populations.

The critically endangered Kemp's ridley sea turtle experienced a dramatic decline in population size (demographic bottleneck) between 1947 and 1987 from 160,000 mature individuals to less than 5000. Demographic bottlenecks can cause genetic bottlenecks where significant losses of genetic diversity occur through genetic drift. The loss of genetic diversity can lower fitness through the random loss of adaptive alleles and through an increase in the expression of deleterious alleles. Molecular genetic studies on endangered species require collecting tissue using non-invasive or minimally invasive techniques. Such sampling techniques are well developed for birds and mammals, but not for sea turtles. The first objective was to explore the relative success of several minimally invasive tissue-sampling methods as source of DNA from Kemp's ridley sea turtles. Tissue sampling techniques included; blood, cheek swabs, cloacal swabs, carapace scrapings, and a minimally invasive tissue biopsy of the hind flipper. Single copy nuclear DNA loci were PCR amplified with turtle-specific primers. Blood tissue provided the best DNA extractions. Additionally, archival plasma samples are shown to be good sources of DNA. However, when dealing with hatchlings or very small individuals in field situations, the tissue biopsy of the hind flipper is the preferred method. This study's main focus was to evaluate whether the Kemp's ridley sea turtle sustained a measurable loss of genetic variation resulting from the demographic bottleneck. To achieve this goal, three alternative approaches were used to detect a reduction in Kemp's ridley's effective population size (Ne) from microsatellite data. These approaches were 1) Temporal change in allele frequencies, 2)An excess of heterozygotes in progeny, and 3)A mean ratio (M) of the number of alleles (k) to the range of allele size (r). DNA samples were obtained from Kemp's ridleys caught in the wild. PCR was used to amplify eight microsatellite loci and allele frequencies were determined. Data from only four microsatellites could be used. Although the reduced number of loci was a limiting factor in this study, the results of all three approaches suggest that Kemp's ridley sustained a measurable loss of genetic variation due to the demographic bottleneck.

Pulsatilla vernalis is one of several endangered plant species that benefit from wildfires and small scale disturbance events that repel competing vegetation and create open patches in the vegetation cover. Previous studies argue that Pulsatilla vernalis is decreasing in numbers due to vegetation changes associated with the decrease in wildfires, forest grazing and changes in forest management. In this study, 17 populations of P. vernalis were inventoried in order to examine if soil and/or vegetation structures affect the population structure of P. vernalis (i.e. population size, presence of flowering individuals, density of juveniles) and if performed conservation attempts in the populations have been positive for P. vernalis. This was done by counting the number of vegetative, flowering and juvenile individuals and examining soil and vegetation structure in the populations. The population sizes were then compared with estimates of population sizes from earlier inventories of P. vernalis at the same localities. The study also presents specific recommendations for an improved conservation management of P. vernalis. The results of this study show that mechanical conservation management had a positive effect on the population size and that open areas in the vegetation cover provided better conditions for viable populations of P. vernalis. To prevent the trend of decreasing population sizes of P. vernalis, conservation measures must be carried out to repel competing vegetation and to restore or maintain open patches in existing populations.

Identifying the diversity of contexts that can lead to hybridization is important for understanding its prevalence and dynamics in natural populations. Despite the potential of ecological succession to dramatically alter species co-occurrence and abundances, it is unknown whether it directly promotes hybridization and, if so, has long-lasting consequences. Here, we summarize 30 years of survey data across 10 populations to show that in western and mountain bluebirds, heterospecific pairing occurs during repeatable and transient colonization events at the early stages of species turnover. Despite mixed pairing occurring only during early succession, genetic data showed presence of hybrids at both early and late successional stages. Moreover, hybrids showed novel patterns of variation in morphology and behavior, emphasizing that even ephemeral contexts for hybridization can have important evolutionary consequences. Our results suggest that because ecological succession often brings together closely related competitors in disparate numbers but lasts for only a brief period of time, it may be a widespread but underappreciated context for hybridization.

Barriers to fish movement can cause aquatic habitat fragmentation by reducing the amount of available habitat. The primary goal of my research was to investigate applications of population genetic analysis tools as indicators of barrier effects on brook trout populations in fragmented subwatersheds. In chapter1, I tested the hypothesis that brook trout population genetic differentiation (FST) above and below barriers will differ in relation to barrier height and gradient. I also tested the hypothesis that average gene diversity per locus (H) and the numbers of alleles (A) differed between samples below and above each barrier. There was no significant difference in average number of alleles (A) or average gene diversity per locus (H) between the above- and below-barrier samples, but linear regression identified a statistically significant relationship between barrier height and FST values. Unrooted neighbor-joining consensus trees of Cavalli-Sforza and Edwards (1967) chord distances provided evidence of genetic differentiation between samples of resident brook trout above and below natural barriers. Additionally, average total allelic diversity (A), average gene diversity per locus (H), average number of private alleles per locus per sample, and total alleles per sample differed between Level III Ecoregions. In chapter 2 I tested the hypothesis that the presence of a barrier, total habitat potentially isolated above a barrier (km), road density, and percent forest cover within a subwatershed (USGS 6th-level Hydrologic Units) were significant habitat fragmentation factors affecting the effective population size (Ne) of brook trout in the Blue Ridge Level III Ecoregion. Multivariable linear regression indicated that total habitat above the barrier (km) and road density were significant variables retained in the model to predict Ne. In chapter 3, the objective of the study was to infer relationships between barriers and family structure in brook trout populations. Maximum likelihood analysis of pairwise kinship relationships between above- and below-barrier individuals indicated the presence of parent-offspring relationships between above- and below-barrier individuals at six sites in the Blue Ridge Level III Ecoregion and five sites in the Northern Lakes and Forests Level III Ecoregion, which indicated movement of individuals between the above- and below-barrier locations. / Ph. D.

Population structure in five African beef cattle breeds in South Africa was investigated, to assess the effect of animal recording in management of genetic diversity and genetic improvement. Pedigree records of 247,173 Afrikaner, 57,561 Boran, 198,557 Drakensberger, 256,692 Nguni and 55,309 Tuli breed were analysed using the online POPREP software system. Pedigree completeness over six generations varied with the lowest completeness in the Boran and the highest in the Afrikaner.The average generation interval ranged between 6.0 to 6.4 years. The rates of inbreeding per year were 0.03%, 0.04%, 0.06%, 0.07% and 0.08% in Boran, Nguni, Afrikaner, Drakensberger and Tuli respectively. Effective population sizes were 89, 107, 122, 191 and 364 in Tuli, Afrikaner, Drakensberger, Nguni and Boran respectively. Inbreeding and effective population size for the Boran was not a true reflection due to poor pedigree recording. These results indicate that none of the breeds are in critical limits of endangerment. Breeding values were regressed on birth year of each breed for weight traits; Kleiber ratio and scrotal circumference from 1986 to 2012. Genetic trends were stable for birth weights except the Afrikaner and Tuli. Genetic progress has been made in weaning and post weaning weights for all the breeds except for limited progress in the Nguni. Kleiber ratio and scrotal circumference in all measured breeds have shown good progress. The results of this study confirmed that recording of pedigree and performance records are effective in maintenance of genetic diversity and genetic improvement through selection based on EBVs of recorded traits. / Dissertation (MScAgric)--University of Pretoria, 2014. / tm2015 / Animal and Wildlife Sciences / MScAgric / Unrestricted

Approximately 40% of the world’s flowering plants are categorized as rare and of conservation priority. Carnivorous plants in particular are threatened and sensitive to environmental changes and hence can play a key ecological role in ecosystems, however, remain largely understudied. Drosera rotundifolia is classified as rare throughout North America, particularly in Southern Appalachia with only four known populations in Tennessee. Surprisingly, information on this species’ life history, survival and reproductive strategies is lacking, which limits conservation action. This project aims to fill these knowledge gaps by evaluating spatial variation, and in particular the effect of population size, in determining D. rotundifolia’s survival and reproductive strategies. This information is urgently needed to aid in the preservation of this species. I evaluated variation in germination rate, plant size, prey capture rate, flowering phenology, and mating strategies of D. rotundifolia across eight populations in Southern Appalachia and how this may be affected by population size and elevation. We recorded flower production, prey capture per individual, and plant size for all individuals in up to12 plots per population. We evaluated the degree of selfing, outcrossing and autonomous self-pollination for each population under greenhouse conditions. Approximately 3050 individual plants were observed across all sites with an average size of 26.29 mm ± 9.71mm but with large differences across populations (6.2 mm – 45.84 mm). Average daily prey capture rate was 9.88 insects across all populations but range between 0 insects – 90 insects observed per visit. Elevation seems to have no effect on flowering phenology (time of peak flowering). We found a significant effect of population size on prey capture rate, but it did not affect peak flowering or plant size. Plant size did not affect prey capture rate. Evaluation of reproductive strategies is ongoing. It has been shown that population size plays a key role in mediating reproductive success and genetic diversity within plant populations. Our results however suggest that population size may also play a key role in nutrient acquisition in Carnivorous species, which is key for their survival. Population size and elevation however did not affect flowering phenology or plant size. Larger plants were also no more successful at obtaining prey compared to smaller plants suggesting other important mechanisms are at play. Our results, although preliminary, can have important practical applications for conservation and management efforts in this species.