Thesis (MTech (Nature Conservation))--Cape Peninsula University of Technology, 2016. / Lions are threatened across their natural range. The Kgalagadi Transfrontier Park (KTP), comprising the Kalahari Gemsbok National Park (KGNP; South Africa) and Gemsbok National Park (GNP; Botswana), is a stronghold for the species. Population size and demography of lions in the KGNP has been addressed in four historic studies. Studies in mid-1970 and 1990 reported a female biased population whereas in 2010 the sex structure was skewed towards males (56%). The bias in sex ratios towards males was first observed in cubs and sub-adults in 2001 and later, in 2010, throughout the population. Furthermore, in the 2010 assessment of the lion population, a smaller proportion of cubs (< 2 yrs) were observed in comparisons to the preceding studies (10% vs. ≥ 23%). The skew in age and sex structures that were observed in the KGNP led to concerns over the long-term sustainability of the greater KTP lion population. The lion population carries further risks associated with the stochastic, arid environment, in which the KTP lion population persists. Human-lion conflict on the borders of the KTP and anthropogenic alterations of the environment further threaten lion demographic stability.

Made available in DSpace on 2015-03-04T18:51:00Z (GMT). No. of bitstreams: 1 Tese-anariodoce.pdf: 2089941 bytes, checksum: e12d7ae40046ae6cfc796af142908753 (MD5) Previous issue date: 2008-05-19 / Fundação Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio de Janeiro / Most marine benthic invertebrates have a complex life cycle in which the adult phase is preceded by a planktonic larval phase. The passive nature of larval dispersal of these species results in a larval transport governed by hydrodynamic processes like advection and eddy diffusion. The recruitment depends on a variety of physical and biological factors, which include spawning, larval dispersal and survival, larval settlement, metamorphosis, post-settlement events, inter-specific and intra-specific competitions. In order to assess interactions between oceanographic and biological processes that determine the population dynamics of marine organisms with a sessile adult phase restricted to the coastline and a planktonic larval phase, we develop a stage-structured finite element model for the barnacle Balanus glandula that inhabits the rocky intertidal zone of central California, USA. As the larval dispersal depends on knowing the flow pattern, we also develop a numerical procedure to couple physical and biological models in a very simple way when the velocity flow field is known of some discrete points of the domain of interest and at a given time. We investigate the effects of different flow patterns and velocity speeds on the abundance and the distribution of this organism as well as the influence of other abiotic interactions such as temperature and habitat quality. The interplay of different intra- and inter-specific competitions is also addressed. / A maioria das espécies marinhas possui um ciclo de vida complexo em que a fase adulta é precedida por uma fase larval pelágica. Os adultos produzem larvas que são soltas na coluna d'água onde elas são influenciadas por processos hidrodinâmicos como advecção e difusão turbulenta. Para os organismos que na maturidade são fixos a um substrato, como as cracas em particular, estudos mostram que estes processos podem afetar diretamente o assentamento das larvas e a dinâmica das populações de adultos. Neste trabalho apresentamos um modelo em Elementos Finitos que permite estudar as interações entre os processos biológicos e oceanográficos na dinâmica de um organismo marinho (craca Balanus glandula) com uma fase adulta séssil restrita à linha costeira e uma fase larval planctônica. Alguns cenários são investigados no estudo da variação, ao longo do tempo e do espaço, do número de indivíduos e da distribuição desta população, com o objetivo de entender, explicar e predizer como os fatores abióticos e bióticos afetam tais variações. O modelo considerou a dinâmica da população estágio-estruturada tanto de uma única espécie quanto de duas espécies, diferentes padrões idealizados de correntes marinhas, qualidade do habitat, influência da temperatura e reconstrução do campo de velocidades a partir de dados locais.

Os objetivos foram definidos com base no cromossomo 5: 1) caracterizar genotipicamente as populações CTCT e TCTC, 2) construir o mapa consenso e 3) mapear simultaneamente QTLs associados às características de desempenho e carcaça. Foram obtidos dados fenotípicos para vinte e quatro características de desempenho e carcaça em 906 animais F2 (356 CTCT e 550 TCTC) oriundos de cruzamentos recíprocos entre uma linhagem de postura (CC) e outra de corte (TT). As quatro famílias CTCT e as seis famílias TCTC, que apresentaram maior grau de informatividade, tiveram seus F2 genotipados para 11 e sete marcadores microssatélites, respectivamente. A caracterização das gerações parentais, F1 e F2 foi realizada através da estimação dos parâmetros genotípicos conteúdo de informação polimórfica (PIC), heterozigosidades observada (Hetobs) e esperada (Hetesp) e número de alelos por loco (A) empregando o programa Cervus 3.0. Os cruzamentos recíprocos entre as duas linhagens (PIC = 0,07-0,78; Hetobs = 0,07-0,79; A = 2,0-7,0) possibilitaram um incremento no nível de informatividade dos locos tanto nas gerações F1 (PIC = 0,43- 0,76; Hetobs = 0,52-1,00; A = 3,0-6,0) quanto nas F2 (PIC = 0,44-0,71; Hetobs = 0,48-1,00; A = 3,0-6,0). Portanto, as populações CTCT e TCTC são apropriadas para a construção do mapa de ligação e mapeamento de QTLs. Mapas de ligação para cada população e o consenso (CTCT/TCTC) foram obtidos através da estimação das ordens e distâncias entre os locos pelo programa CRI-MAP. Os mapas apresentaram (intervalo médio entre marcadores, em cM) 148,0 cM (24,6) em TCTC, 174,7 cM (17,4) em CTCT e 163,8 cM (16,3) no consenso. Os mapas CTCT e o consenso foram mais semelhantes devido ao maior número de locos avaliados na região alvo e não foram constatadas inversões. O mapeamento simultâneo de QTLs empregou o mapeamento por intervalo combinado à modelagem fenotípica através de modelo misto (efeito de incubação aleatório) e as análises foram implementadas pelos programas SAS, QTL Express e R. Foram mapeados 12 QTLs (11 sugestivos e 1 significativo), dos quais seis ainda não foram descritos (peso dos pés, asas, fígado, peso vivo 42 dias, eficiência alimentar 35-41 dias e colesterol). Foi constatado efeito da interação QTL x população para o peso da gordura abdominal, cujos alelos para incremento dessa característica tiveram origem em fêmeas da linhagem de corte da população CTCT. Quatro possíveis genes candidatos (FGF4, FGF19, ALX4 e FMN1) foram selecionados através do mapeamento de QTLs. Futuramente, polimorfismos associados a estes genes poderão ser identificados e validados em populações comerciais. Dessa forma, a seleção assistida por marcadores em associação com a seleção fenotípica em programas de melhoramento genético poderá ser efetivamente implementada na galinha doméstica. / The aims were defined based on the chromosome 5: 1) to describe genotypically CTCT and TCTC populations, 2) to construct consensus linkage map and 3) to map jointly QTL associated with performance and carcass traits. Phenotypic data were obtained for twenty-four performance and carcass traits from 906 F2 animals (356 CTCT and 550 TCTC) generated from reciprocal crosses between a layer line (CC) and a broiler line (TT). The four families CTCT and the six families TCTC, which showed the highest degree of informativeness, had their F2 offsprings genotyped using 11 and seven microsatellite markers, respectively. Parental, F1 and F2 generations were genotypically characterized by estimation of the genotypic parameters polymorphic information content (PIC), observed heterozygosity (Hetobs) and expected heterozygosity (Hetesp) and number of alleles per locus (A) using Cervus 3.0 software. Reciprocal crosses between two lines (PIC = 0.07 to 0.78; Hetobs = 0.07 to 0.79, A = 2.0 to 7.0) increased the level of informativeness of the loci in both generations F1 (PIC = 0.43 to 0.76; Hetobs = 0.52 to 1.00, A = 3.0 to 6.0) and F2 (PIC = 0.44 to 0.71; Hetobs = 0.48 to 1.00, A = 3.0 to 6.0). Therefore, CTCT and TCTC populations are suitable for constructing the linkage map and QTL mapping. Linkage maps for each population and the consensus (CTCT / TCTC) were obtained by estimation of orders and distances between loci using CRI-MAP software. The maps presented (average interval between markers in cM) 148.0 cM (24.6) in TCTC, 174.7 cM (17.4) in CTCT and 163.8 cM (16.3) in consensus. CTCT and consensus maps were more similar due to high number of loci evaluated in the target region. No inversion was detected. Joint mapping of QTL was accomplished using interval mapping combined with phenotypic modeling via mixed model (random effect of hatch) and analyses were implemented in SAS, QTL Express and R softwares. Twelve QTL were mapped (11 suggestive and one significant). Out of these, six were not previously described (weights of legs, wings and liver, body weight at 42 days, feed efficiency 35-41 days and cholesterol). QTL x population interaction was evidenced for abdominal fat weight, indicating that the alleles that increased this trait came from the female broiler line of the population CTCT. Four putative candidate genes (FGF4, FGF19, ALX4 and FMN1) were selected by QTL mapping. In future, polymorphisms associated with these genes can be identified and validated in commercial populations. Thus, marker-assisted selection in combination with phenotypic selection in breeding programs will be effectively implemented in poultry.

Os objetivos foram definidos com base no cromossomo 5: 1) caracterizar genotipicamente as populações CTCT e TCTC, 2) construir o mapa consenso e 3) mapear simultaneamente QTLs associados às características de desempenho e carcaça. Foram obtidos dados fenotípicos para vinte e quatro características de desempenho e carcaça em 906 animais F2 (356 CTCT e 550 TCTC) oriundos de cruzamentos recíprocos entre uma linhagem de postura (CC) e outra de corte (TT). As quatro famílias CTCT e as seis famílias TCTC, que apresentaram maior grau de informatividade, tiveram seus F2 genotipados para 11 e sete marcadores microssatélites, respectivamente. A caracterização das gerações parentais, F1 e F2 foi realizada através da estimação dos parâmetros genotípicos conteúdo de informação polimórfica (PIC), heterozigosidades observada (Hetobs) e esperada (Hetesp) e número de alelos por loco (A) empregando o programa Cervus 3.0. Os cruzamentos recíprocos entre as duas linhagens (PIC = 0,07-0,78; Hetobs = 0,07-0,79; A = 2,0-7,0) possibilitaram um incremento no nível de informatividade dos locos tanto nas gerações F1 (PIC = 0,43- 0,76; Hetobs = 0,52-1,00; A = 3,0-6,0) quanto nas F2 (PIC = 0,44-0,71; Hetobs = 0,48-1,00; A = 3,0-6,0). Portanto, as populações CTCT e TCTC são apropriadas para a construção do mapa de ligação e mapeamento de QTLs. Mapas de ligação para cada população e o consenso (CTCT/TCTC) foram obtidos através da estimação das ordens e distâncias entre os locos pelo programa CRI-MAP. Os mapas apresentaram (intervalo médio entre marcadores, em cM) 148,0 cM (24,6) em TCTC, 174,7 cM (17,4) em CTCT e 163,8 cM (16,3) no consenso. Os mapas CTCT e o consenso foram mais semelhantes devido ao maior número de locos avaliados na região alvo e não foram constatadas inversões. O mapeamento simultâneo de QTLs empregou o mapeamento por intervalo combinado à modelagem fenotípica através de modelo misto (efeito de incubação aleatório) e as análises foram implementadas pelos programas SAS, QTL Express e R. Foram mapeados 12 QTLs (11 sugestivos e 1 significativo), dos quais seis ainda não foram descritos (peso dos pés, asas, fígado, peso vivo 42 dias, eficiência alimentar 35-41 dias e colesterol). Foi constatado efeito da interação QTL x população para o peso da gordura abdominal, cujos alelos para incremento dessa característica tiveram origem em fêmeas da linhagem de corte da população CTCT. Quatro possíveis genes candidatos (FGF4, FGF19, ALX4 e FMN1) foram selecionados através do mapeamento de QTLs. Futuramente, polimorfismos associados a estes genes poderão ser identificados e validados em populações comerciais. Dessa forma, a seleção assistida por marcadores em associação com a seleção fenotípica em programas de melhoramento genético poderá ser efetivamente implementada na galinha doméstica. / The aims were defined based on the chromosome 5: 1) to describe genotypically CTCT and TCTC populations, 2) to construct consensus linkage map and 3) to map jointly QTL associated with performance and carcass traits. Phenotypic data were obtained for twenty-four performance and carcass traits from 906 F2 animals (356 CTCT and 550 TCTC) generated from reciprocal crosses between a layer line (CC) and a broiler line (TT). The four families CTCT and the six families TCTC, which showed the highest degree of informativeness, had their F2 offsprings genotyped using 11 and seven microsatellite markers, respectively. Parental, F1 and F2 generations were genotypically characterized by estimation of the genotypic parameters polymorphic information content (PIC), observed heterozygosity (Hetobs) and expected heterozygosity (Hetesp) and number of alleles per locus (A) using Cervus 3.0 software. Reciprocal crosses between two lines (PIC = 0.07 to 0.78; Hetobs = 0.07 to 0.79, A = 2.0 to 7.0) increased the level of informativeness of the loci in both generations F1 (PIC = 0.43 to 0.76; Hetobs = 0.52 to 1.00, A = 3.0 to 6.0) and F2 (PIC = 0.44 to 0.71; Hetobs = 0.48 to 1.00, A = 3.0 to 6.0). Therefore, CTCT and TCTC populations are suitable for constructing the linkage map and QTL mapping. Linkage maps for each population and the consensus (CTCT / TCTC) were obtained by estimation of orders and distances between loci using CRI-MAP software. The maps presented (average interval between markers in cM) 148.0 cM (24.6) in TCTC, 174.7 cM (17.4) in CTCT and 163.8 cM (16.3) in consensus. CTCT and consensus maps were more similar due to high number of loci evaluated in the target region. No inversion was detected. Joint mapping of QTL was accomplished using interval mapping combined with phenotypic modeling via mixed model (random effect of hatch) and analyses were implemented in SAS, QTL Express and R softwares. Twelve QTL were mapped (11 suggestive and one significant). Out of these, six were not previously described (weights of legs, wings and liver, body weight at 42 days, feed efficiency 35-41 days and cholesterol). QTL x population interaction was evidenced for abdominal fat weight, indicating that the alleles that increased this trait came from the female broiler line of the population CTCT. Four putative candidate genes (FGF4, FGF19, ALX4 and FMN1) were selected by QTL mapping. In future, polymorphisms associated with these genes can be identified and validated in commercial populations. Thus, marker-assisted selection in combination with phenotypic selection in breeding programs will be effectively implemented in poultry.

This thesis investigated the autecology of the dacine species, Bactrocera cacuminata (Hering) (Diptera: Tephritidae: Dacinae). I specifically focused on the adult phase of the life cycle and resources believed to be significant to this life stage. The prevailing paradigm in dacine ecology predicts that the larval host plant serves as the centre of dacine activity, a state mediated by mutualistic associations with fruit fly-type bacteria. Contrary to predictions, an explicit test of this hypothesis found that the host plant of B. cacuminata, Solanum mauritianum Scopoli, acted almost exclusively as a site for oviposition and larval development. Other key adult behaviours, most notably feeding and mating, were rare at the host plant. Even in disturbed habitats, the paucity of key adult behaviours such as mating was striking. Adult flies of this species were therefore hypothesized to be utilizing other components of their habitat, i.e. resources vital to their life history requirements. Some of the resources that B. cacuminata are known to respond to include sugar, protein, methyl eugenol and the host plant. The latter three resources are believed to be critical in the reproductive success of dacine flies in general. I assessed the physiological status of flies arriving at these resources to determine if flies of different status foraged for resources differently. In dacines, the internal reproductive structures of the male and female flies have been used as predictors of physiological status. I quantified expansion of the male ejaculatory apodeme in B. cacuminata with age of fly and found that there is a threshold apodeme size that is strongly correlated Abstract with sexual maturity. Maturity of female flies could be accurately predicted by ovarian development. Using these methods to assess the physiological and nutritional status of flies arriving at resources (larval host plant, protein and methyl eugenol) in the field, I discovered that only sexually mature and mated females were responding to the host plant, while the males at the host plant were sexually immature. This confirmed the hypothesis that the host plant primarily served as an oviposition site. Additionally, this study revealed that sexually mature males with high nutritional reserves were most commonly collected at methyl eugenol (a plant-derived chemical that elicits a strong response in males of many dacine species) at dusk, the time of peak sexual activity in this species. This indicated that methyl eugenol was perhaps a significant resource in the context of the reproductive behaviour of this species. Methyl eugenol (ME) is one of group of phenyl propanoids to which males of certain species of Dacinae respond. The current hypothesis of the role of these phenyl propanoids is that they function as pheromone precursor chemicals. Response to these chemicals is hypothesized to be a trait under sexual selection. In Bactrocera dorsalis (Hendel), this effect is so strong that a single feeding on ME results in a strong mating advantage up to a month after males feed on the chemical. Bactrocera cacuminata fed on multiple occasions on ME in a laboratory bioassay. After a single 24-hour exposure to ME, investigations of mating competitiveness did not reveal any obvious advantage for ME-fed males over unfed males. However, ME-fed males did enjoy a higher mating success 16 and 32 days after exposure to the chemical, suggesting that some physiological benefits unrelated to the pheromone synthesis was driving this delayed advantage. Investigation of the physiological consequences of feeding on ME revealed no enhancement of nutritional or energetic reserves, suggesting that the delayed mating advantage observed was more likely a chance event. An alternate hypothesis about the proximate function of ME, proposed by Robert Metcalf, is that it serves as a mate rendezvous site. As mating behaviour was notably absent at the host plant, I tested Metcalf’s hypothesis. A field-cage experiment, spatially separating adult resources (host plant, methyl eugenol, sugar and protein) clearly demonstrated that methyl eugenol was functioning as a mate rendezvous stimulus for B. cacuminata. This is the first direct support for Metcalf’s hypothesis. A synthesis of the literature revealed that significantly greater ecological and evolutionary information was required to understand the basis of dacine response to phenyl propanoids. Different dacine species may be utilizing these chemicals differently, even if their evolutionary origin may have been as a plant based kairomone. My studies show that generalizations on the ecology and behaviour of Dacinae, often extrapolated from research on a few pest species, do not hold up in the case of B. cacuminata. This suggests that a more autecological, species-specific approach is required in dacine research, before any predictive generalizations can be made.

Obtaining accurate estimates of animal abundance is made difficult by the fact that most animal species are detected imperfectly. Early attempts at building likelihood models that account for unknown detection probability impose a simplifying assumption unrealistic for many populations, however: no births, deaths, migration or emigration can occur in the population throughout the study (i.e., population closure). In this dissertation, I develop likelihood models that account for unknown detection and do not require assuming population closure. In fact, the proposed models yield a statistical test for population closure. The basic idea utilizes a procedure in three steps: (1) condition the probability of the observed data on the (unobserved) period- specific abundances; (2) multiply this conditional probability by the (prior) likelihood for the period abundances; and (3) remove (via summation) the period- specific abundances from the joint likelihood, leaving the marginal likelihood of the observed data. The utility of this procedure is two-fold: step (1) allows detection probability to be more accurately estimated, and step (2) allows population dynamics such as entering migration rate and survival probability to be modeled. The main difficulty of this procedure arises in the summation in step (3), although it is greatly simplified by assuming abundances in one period depend only the most previous period (i.e., abundances have the Markov property). I apply this procedure to form abundance and site occupancy rate estimators for both the setting where observed point counts are available and the setting where only the presence or absence of an animal species is ob- served. Although the two settings yield very different likelihood models and estimators, the basic procedure forming these estimators is constant in both. / Graduation date: 2012

No abstract available. / Thesis (M.Env.Dev.)-University of Natal, Pietermaritzburg, 2003.

Thesis (M.S.)--University of Tennessee, Knoxville, 2008. / Title from title page screen (viewed on Sept. 23, 2009). Thesis advisor: Frank T. van Manen. Vita. Includes bibliographical references.

Thesis (M.Sc.(Zoology))--University of Pretoria, 2000. / Abstract in English. Includes bibliographical references.

The development of conservation and management programs for an animal population relies on a knowledge of the number of individuals in an area. In order to achieve reliable estimates, precise and accurate techniques for estimating population densities are needed. This study compared the use of direct and indirect methods of estimating kudu (Trage/aphus strepsiceras), bush buck (Trage/aphus scriptus), common duiker (Sy/vicapra grimmia), and blue duiker (Philantamba manticala) densities on Shamwari Game Reserve in the Eastern Cape Province, South Africa. These species prefer habitats of dense forest and bush for concealment and are therefore not easily counted in open areas. Herein direct observation counts were compared to indirect sampling via pellet group counts (clearance plots, line transects, variable-width transects, and strip transects). Clearance plots were examined every 2 weeks, while all other methods were conducted seasonally, from August 2002 until August 2003. The strip transect method provided the lowest density estimates (animals per hal ranging from 0.001 for bushbuck to 0.025 for common duiker, while direct observations yielded the highest estimates, ranging from 0.804 for bush buck to 4.692 for kudu. Also, a validation of methods was performed against a known population of kudu during which the DISTANCE method yielded the most accurate results, with an estimated density of 0.261 that was within the actual density of 0.246 to 0.282. In addition, the DISTANCE method was compared to helicopter counts ofkudu and its estimates were found to be approximately 2.6 times greater than the helicopter count results. When the assessment of the methods was made, the cost, manpower and effort requirements, coefficient of variation, and performance against a known population for each method were taken into consideration. Overall, the DISTANCE method performed the best with low cost, minimal manpower and effort requirements, and low coefficient of variation. On Shamwari Game Reserve, the DISTANCE method estimated 0.300 kudu, 0.108 bushbuck, 0.387 common duiker, and 0.028 blue duiker per ha, which, when extrapolated to the total number of animals present within subtropical thicket habitat, estimated 1973 kudu, 710 bush buck, 2545 common duiker, and 184 blue duiker.