This study has focused on genetic variability and structure in Chaerephon atsinanana, a newly-described molossid bat found in the mid to southern region of the eastern watershed of Madagascar. As these bats are strong fliers, and are able to traverse the riverine and mountain barriers within the landscape, it was hypothesized that they would show relatively low levels of intraspecific genetic structure, consistent with patterns shown for other Molossidae on Madagascar (Mormopterus jugularis, Mops midas, Mops leucostigma, and C. lecuogaster. Phylogenetic (neighbor-joining, parsimony and Bayesian inference) and population genetic analyses of maternally-inherited mitochondrial control region sequences revealed the presence of 6 distinct haplotype groups separated by genetic distances of up to 8.14% (mean 4.95%). There were high levels of genetic structure among the haplotype groups (overall FST= 0.994). Thus the hypothesis of low levels of genetic structure was rejected. Bayesian skyline analyses and significantly ragged mismatch distributions were consistent with ancient stable C. atsinanana populations which were of constant size during the last two major Pleistocene glacial periods. This made retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure. An alternative hypothesis is that C. atsinanana haplotype groups are spatially structured as a result of philopatry. As mitochondria are maternally-inherited, this data is consistent with the existence of female philopatry in C. atsinanana. The second aim of this study was to examine the genetic structure of C. atsinanana with nuclear sequence markers, which are biparentally-inherited, in order to provide information on the male contribution to gene flow and the possible presence of male philopatry in this molossid bat species. The initial objective was to amplify and sequence candidate nuclear markers in order to identify those which were variable among C. atsinanana samples. I attempted to amplify and sequence a set of 12 nuclear markers, identified from the literature, which had been reported to show high levels of variability, or which were untested and showed the potential for high levels of variability. Of these, the intron markers PNPO-3, SLC38A7-8, CARHSP1-1, GAD2-1, OSTA-5 had not previously been used in phylogenetic analyses while FES, GHR, RHO1 CHRNA1, STAT5, PRKC1 and THY had been. I was not able to amplify and/or sequence SLC38A7-8, CARHSP1-1, GAD2-1, OSTA-5, CHRNA1, STAT5 and THY across the range of the C. atsinanana samples. PNPO-3, FES, GHR, RHO1 and PRKC1were successfully amplified and sequenced, but showed no variability and very little polymorphism, and were therefore unsuitable for testing hypotheses related to genetic variability of C. atsinanana populations. These five nuclear sequence markers were further used to investigate phylogenetic relationships among 5 genera (Chaerephon, Mops, Mormopterus, Otomops and Sauromys) and 13 species of Afro-Malagasy molossid bats, and to provide a nuclear phylogenetic perspective on the newly-described C. atsinanana. PNPO-3 is a novel nuclear intron marker, previously unused in phylogenetic studies. This intron provides resolution primarily at the genus level, and is less informative at interspecific level. These five nuclear markers were combined with already existing mitochondrial cytochrome b (Cyt b) and nuclear Rag2 data retrieved from GenBank. This study provides strong support for the monophyly of the Chaerephon and Mops taxa included, with the exception of C. jobimena, which was weakly associated with this group. There was no support for the generic affiliation of C. jobimena or for the monophyly of either of the genera Chaerephon or Mops individually. This leads to the suggestion that Mops and Chaerephon be combined into a single genus, with crown age of 14.82 (6.44-25.54) MYA, or 21.97 (12.16-33.44) MYA if C. jobimena is included. Otomops forms a strongly supported clade consistent with its generic status, comprising two subclades corresponding to the recognised sister species O. martiensseni and O. madagascariensis, which last shared a common ancestor 8.35 (2.87-17.47) MYA. This study provides good nuclear support for the mitochondrially-defined subclades of O. martiensseni, which last shared a common ancestor 4.18 (1.08-9.96) MYA. It would appear appropriate to name the clade from north east Africa and Arabia as a new species of Otomops, as the clade from southern and western Africa includes the type locality. This study provides weak support based on individual gene regions for associations of Sauromys with Otomops and Mormopterus, although these do not stand up in the concatenated datasets which offer better resolving power, indicating that Sauromys is not phylogenetically associated with Chaerephon/Mops, Otomops and Mormopterus. These results provide some support for the membership of Mormopterus in the proposed Old World Molossid tribe, Tadarini, but also support Mormopterus as a basal genus within the Molossidae, consistent with its designation as a separate tribe, Mormopterini. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2013.

Chaerephon pumilus, the little free-tailed bat, (family: Molossidae) has a distribution throughout most of sub-Saharan Africa and the eastern region of Madagascar. The vast geographical distribution of this species is accompanied by considerable phenotypic variation, which may conceal cryptic species. The cytochrome b (845 nucleotides) and D-loop (314 nucleotides) regions of the mitochondrial DNA were sequenced to assess phylogenetic relationships within C. pumilus (southern Africa) and in relation to Chaerephon species from Madagascar (C. pumilus, C. leucogaster). Samples were obtained from KwaZulu-Natal, South Africa, and localities in Swaziland. The cytochrome b sample (n = 11) comprised four haplotypes, with a haplotype diversity of 0.6727, whilst the D-loop (n = 34) dataset comprised 13 haplotypes with a haplotype diversity of 0.8342. Neighbour joining, maximum parsimony and Bayesian analyses revealed congruent tree structures for both mtDNA regions. All Chaerephon taxa in this study formed a monophyletic clade with respect to the outgroup Mops midas. Chaerephon pumilus from the eastern side of Madagascar formed a well-supported monophyletic group, sister to a clade comprising C. pumilus (southern Africa) and C. leucogaster, and is suggested to comprise a separate species. Southern African C. pumilus formed two paraphyletic clades, A and B, separated by a genetic distance of 0.9 %. Chaerephon leucogaster formed a monophyletic group nested within southern African C. pumilus, suggesting conspecificity. However, the well-characterized morphology of C. leucogaster lends support to its specific status, and suggests the possible existence of cryptic species among southern African C. pumilus. Population genetic analysis suggests that two C. pumilus (southern African) clades have been expanding, one for between 2432 and 4639 years, and the other for the 11156 to 21280 years. A combined cytochrome b analysis, trimmed to 343 nucleotides, was carried out on the data from this study and that of Jacobs et al. (2004), also on southern African C. pumilus. Haplotypes from the Jacobs et al. (2004) study, which also identified two 0.9 % divergent clades (light- and dark-winged) were found to be identical or very similar to haplotypes from this study and were interspersed among southern African C. pumilus haplotypes in phylogenetic analyses. Chaerephon pumilus haplotypes from Zambia and Tanzania were found to be more closely related to those from southern Africa and to C. leucogaster than to C. pumilus (Madagascar), further indicating that this may be a separate species. Haplotypes from the light-winged clade of Jacobs et al. (2004) were identical to those of dark-winged samples from this study, suggesting that wing shade may not be diagnostic of the two clades. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2008.

The overall objective of this thesis is to provide an enhanced understanding of the epidemiology of Mycobacterium bovis in the Greater Riding Mountain Ecosystem (GRME) and provide a scientific basis for disease management from a systems perspective now and into the future. M. bovis prevalence has been consistently higher in elk compared to white-tailed deer, and higher within a defined Core area compared to areas outside. Prevalence in both species declined significantly between 2003 and 2013. Only one infected elk was detected in 2013; the last infected white-tailed deer was detected in 2009 and the last infected cattle herd was detected in 2008. Parallel interpretation of three blood-based assays resulted in effective selective culling of elk within Riding Mountain National Park (RMNP) with predictive value negative of 100%. A lymphocyte stimulation test (LST) was the most sensitive single blood-based assay, but was difficult to perform under field conditions. Combinations of humoral antibody tests and cell-mediated tests performed better than any single test, likely detecting the broad spectrum of host pathology present. Seven of 14 risk factors were identified for wild cervids testing culture positive with the three being most strongly associated with culture positivity being geographical location (within core area), elk density and year category (sampling phase). Age, sex, and surveillance method were also significant factors, but species was not. A rapid decline in elk density in combination with fencing of hay storage yard and non-selective culling were likely key factors resulting in the M. bovis prevalence decline observed in elk, and an overall decline in prevalence from 1997 for both species. Elk were the primary reservoir species in this episystem, but are now considered a spillover host, while white-tailed deer have always been a spillover host due to lower densities and shorter life expectancy. Very limited strain diversity exists within the GRME with one spoligotype restricted to cattle and associated with a limited outbreak in five herds in the early 1990’s, and three other shared strains between cattle and wildlife. A single monomorphic type was present in white-tailed deer. Significant spatial overlap of wildlife and cattle isolates delineated a core area where management activities are now focused. The relative simplicity of this episystem has allowed significant progress on control and management to be achieved, despite being located within a national park. Wildlife surveillance will need to continue until at least 2022 in order to achieve a 95% probability of freedom using three different surveillance streams. Latent cases are likely to be extremely rare in future and unlikely to result in ongoing transmission as the factors that created this wildlife reservoir no longer exist. Wild cervids should not be considered ideal maintenance hosts for M. bovis in North America but rather facultative hosts; acting either as a reservoir or spillover host dependent on regional/local density and presence/absence of baiting and feeding.

Ecological patterns and processes influence ecosystem function at scales from nanometres to global scales depending on the organisms involved. Predicting the presence and abundance of species, at scales appropriate to the organisms and the underlying processes, is central to ecology. Models of species’ distributions can provide important insights into pattern-process-scale relationships including the relative importance of various environmental factors and their interactions that influence habitat selection at the individual and population levels. Mapping current and potential distributions informs the conservation of threatened species by providing spatial information on where a species is likely to occur and the identification of habitat elements and their spatial configurations which influence occupancy and persistence. The aim of this thesis was to incorporate the principles of pattern, process and scale in the identification of habitat associations for threatened species within a species’ distribution modelling framework. Accurate modelling of species’ distributions depends on robust sampling designs, reliable data input and appropriate statistical methodologies that align with the ecological model. I applied a range of innovative statistical methods to various sources of data to identify important habitat associations for a threatened species at different scales and tested the discriminative ability of the resultant models. I integrated the results from extensive field sampling and expert elicitation to build connectivity networks using graph theory algorithms to identify important conservation priorities for threatened species. The threatened brush-tailed rock-wallaby (Petrogale penicillata) was chosen as a suitable study species for quantifying habitat relationships at multiple spatial scales using species’ distribution modelling. The distribution of brush-tailed rock-wallabies is restricted to a set of suitable habitat characteristics related to rocky terrain supporting cliffs and boulder piles that occur infrequently across a landscape. At the site scale, they require suitable resting and refuge sites provided by rocky habitats, while at a landscape scale their dispersal is dependent on the connectivity of suitable habitats. The species is listed as threatened throughout eastern Australia and endangered in some states. Information about its current distribution and occupancy status is essential to support habitat conservation and threat management. The first chapter provides a broad view of the literature on modelling of species’ distributions and the thesis aims and structure. In chapter 2, I assess the ecological scale relevant to habitat modelling for the brush-tailed rock-wallaby. In chapter 3 I test whether habitat models from one region can be extrapolated to neighbouring regions. I use a novel approach and elicitation tool in chapter 4 to collect expert knowledge and assess it with a comprehensive set of field data in a Bayesian framework. In chapter 5 I assess whether landscape connectivity is a determinant of site occupancy by using graph theory algorithms to identify important habitat patches and dispersal pathways for rock-wallaby movement in fragmented landscapes. The final chapter synthesises the individual chapters’ findings within the context of species’ distribution modelling. Management implications are discussed for the conservation of the brush-tailed rock-wallaby and its habitat network. Wider implications are also suggested for other rock-wallaby species and species living in similar environments. The results of the thesis showed the habitat of the brush-tailed rock-wallaby was affected by site-scale and landscape-scale factors, supporting the need for a multi-scale approach when investigating species-environment associations. I found that models performed well within a region at both scales. Extrapolating the models to neighbouring regions resulted in good predictive performance at the site scale but substantially poorer predictive performance at the landscape scale. When there is insufficient field data to build robust data models, management bodies would benefit from incorporating expert knowledge. The study demonstrates the potential errors in using experts with knowledge gained from outside the area of interest. Finally, I highlight the importance of accounting for the landscape connectivity between patches from the perspective of the individual animal. Least cost analysis, using graph theory algorithms, provides a cost-efficient and effective framework for identifying landscape connectivity patterns and key paths and patches to help inform suitable land management strategies for conservation of threatened species. There is much pressure from conservation and management agencies to produce models of species’ distributions that could be potentially be used in other regions or with similar species. The thesis combines ecological theory with rigorous statistical methodology to test different modelling techniques for species distribution modelling. It demonstrates how a combination of expert knowledge, extensive field data and landscape connectivity measures successfully predicts ecological relationships at a number of scales. Species’ distribution models can benefit from applying a robust sampling design and suitable modelling techniques to various data sources to generate ecologically-based information to improve our understanding of species-habitat associations and provide a reliable component to incorporate into conservation planning. This thesis therefore provides important advances to spatial ecology and ecological modelling of species distributions and management of threatened species.

Thesis (M.S.)--University of Wisconsin--Stevens Point, 2007. / Includes bibliographical references (leaves 93-98).

Zugl.: Karlsruhe, University, Diss., 2006.

Thesis (M.S.)--Michigan State University. Dept. of Agricultural Economics, 2006. / Title from PDF t.p. (viewed on June 19, 2009) Includes bibliographical references (p. 92-96). Also issued in print.

Thesis (M. S.)--Michigan State University. Dept. of Fisheries and Wildlife, 2006. / Title from PDF t.p. (viewed on June 19, 2009) Includes bibliographical references. Also issued in print.

Thesis (MMedVet. (Wildlife Diseases))--University of Pretoria, 2007. / Includes bibliographical references.

Thesis (M.S.)--Wildlife and Fisheries Sciences Dept., South Dakota State University, 2009. / Includes bibliographical references. Also available via the World Wide Web.