Doctor of Philosophy / Department of Biology / Michael Herman / Soil nematode communities are important components of the micro fauna in grassland ecosystems and their interaction with soil microbes affects important ecological processes such as decomposition and nutrient recycling. To study genetic mechanisms underlying ecologically important traits involved in the response of nematode communities to soil microbes, we employed genomic tools available for the model nematode, Caenorhabditis elegans. Previous work identified 204 C. elegans genes that were differentially expressed in response to growth on four different bacteria: Bacillus megaterium, Pseudomonas sp., Micrococcus luteus and Escherichia coli. For many of the genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life-history traits in those environments. Mutations can have differential effects on fitness in variable environments, which can influence their maintenance in a population. Our fitness assays revealed that bacterial environments had varying magnitude of stress, defined as an environment in which the wild-type has a relatively low fitness. We performed fitness assays as part of a comprehensive analysis of life history traits on thirty five strains that contained mutations in genes involved in the C. elegans response to E. coli, B. megaterium, Pseudomonas sp. We found that many of the mutations had conditionally beneficial effects and led to increased fitness when nematodes bearing them were exposed to stressful bacteria. We compared the relative fitness of strains bearing these mutations across bacterial environments and found that the deleterious effects of many mutations were alleviated in the presence of stressful bacteria. Although transcriptional profiling studies can identify genes that are differentially regulated in response to environmental stimuli, how the expressed genes provide functional specificity to a particular environment remains largely unknown. We focused on defense and metabolism genes involved in C. elegans-bacterial interactions and measured the survivorship of loss-of-function mutants in these genes exposed to different bacteria. We found that genes had both bacteria-specific and bacteria-shared responses. We then analyzed double mutant strains and found bacteria-specific genetic interaction effects. Plasticity in gene interactions and their environment-specific modulation have important implications for host phenotypic differentiation and adaptation to changing environments.

No description available.

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The broad objective of this study was to identify single nucleotide polymorphisms (SNP) markers associated with tick resistance in South African Nguni cattle and it was addressed by three specific objectives. The first objective was to assess tick load and prevalence in Nguni cattle in different agro-climatic regions of South Africa using tick count data collected monthly from 586 Nguni cattle reared under natural grazing conditions, over two years. Tick counts were assessed under natural challenge at ARC Roodeplaat and Loskop farms (warm climate), and Mukhuthali Nguni Community and University of Fort Hare farms (cool climate). The second objective was to estimate genetic parameters for tick counts in Nguni cattle. The third objective was to identify SNPs associated with tick resistance in Nguni cattle. Counts for each tick species were conducted on each animal in the herd once a month on different body locations, including the head, ears, neck, back, legs, belly, perineum and tail. Distribution of counts was determined using the PROC FREQ (SAS, 2002 - 2010). The tick counts were then analysed with the PROC GLM procedure using the two fixed effect models. Genetic parameters for log-transformed counts were estimated from univariate animal and sire models and bivariate sire models using the ASREML program. Animals were genotyped using Illumina BovineSNP50K assay. After Quality Control (call rate >90%, minor allele frequency > 0.02), 40 436 SNPs were retained for analysis. Association analysis for tick resistance was carried out using two approaches: genome-wide association (GWA) analysis using the GenABEL package and a Regional Heritability Mapping (RHM) analysis. Six tick species were identified: Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) and Rhipicephalus simus (4%). Tick infestation was significantly affected by location, season, year, month of counting and age of the animal. Loskop farm, as the warmest location, had the highest tick counts and also showed the largest variation in tick loads. Higher tick counts were also observed in the hot-dry (September to November) and hot-wet (December to February) seasons compared to the other seasons. Amblyomma hebraeum was the dominant tick species across all four locations. Heritability estimates for tick count varied according to season and trait (body part or tick species) and ranged from 0.01±0.01 to 0.26±0.01. Genetic correlations ranged from -0.79±0.33 to 1.00±0.00 among counts for different body parts and 0.00±0.00 to 0.99±0.00 among tick species. Phenotypic correlations ranged from 0.06±0.01 to 0.72±0.01 among body parts and 0.01±0.02 to 0.44±0.01 for tick species. Whole body count was highly correlated to the perineum and the belly. These two traits appear to be the most suitable surrogates for whole body count. Several genomic regions of interest were identified for different traits by both the GWA and RHM approaches. Three genome-wide significant regions on chromosomes 7, 10 and 19 were identified for total tick count on the head, total A. hebraeum ticks and for total number of A. hebraeum in the perineum region. Suggestive significant regions were identified on chromosomes 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 and 26 for several of the tick traits analysed. The GWA approach identified more genomic regions than did the RHM approach. These findings provide information that would be useful in developing strategies for genetic improvement of tick resistance through selection. The chromosome regions identified as harbouring quantitative trait loci (QTL) underlying variation in tick burden form the basis for further analyses to identify specific candidate genes related to cattle tick resistance and provide the potential for marker-assisted selection in Nguni. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om enkel nukleotied polimorfismes (ENPs) merkers te identifiseer wat verwant is aan bosluisweerstand in Suid-Afrikaanse Nguni beeste; dit is aangespreek deur drie doelwitte. Die eerste doelwit was om bosluislading en -voorkoms van bosluise in Nguni beeste in verskillende landbou-klimaatstreke van Suid-Afrika te bepaal deur die gebruik van bosluistelling data wat maandeliks van 586 Nguni beeste, grootgemaak op natuurlike weiding, oor 'n tydperk van twee jaar versamel was. Die tweede doelwit van die studie, was om die genetiese parameters te bepaal vir die bosluistellings in die Nguni beesras. Om hierdie doelwit aan te spreek, is vier verskillende datastelle onderskei in die bosluistelling data wat oor die twee jaar periode versamel was. Genetiese parameters is derhalwe beraam vir die telling van bosluise om sodoende die beste seisoen te identifiseer vir die insameling van bosluistelling data om ten einde strategieë te ontwikkel vir die genetiese seleksie vir vehoogde weerstand teen bosluise. Die derde doelwit was om ENP streke te identifiseer wat verband hou met bosluisweerstand in Nguni beeste. Verskillende bosluisspesies was getel op elke dier in die kudde een keer per maand op verskillende plekke op die liggaam, insluitend die kop, ore, nek, rug, bene, maag, perineum en stert. Bosluistelling data is ontleed met behulp van die SAS program om bosluislading variasie te bepaal. Genetiese parameter skattings vir log getransformeerde bosluistellings data was bereken vanaf twee-veranderlike vaar modelle en een-veranderlike dier- en vaar modelle met behulp van die ASREML program. Om ‘n genomiese wye assosiasie studie (GWAS) uit te voer, is DNS geïsoleer en genotipering gedoen met behulp van die Illumina BovineSNP50K toets. Na kwaliteit kontrole (oproep frekwensie>90%, klein alleelfrekwensie>0.02) is 40.436 ENPs behou vir ontleding. Assosiasie analise vir bosluisweerstand is uitgevoer met behulp twee benaderings, d.i. 'n genoom-wye assosiasie (GWA) analise met behulp van die GenABEL pakket en 'n plaaslike oorerflikheid karterings (POK) analise. Ses bosluisspesies is geïdentifiseer, d.i. Amblyomma hebraeum (42%), Rhipicephalus evertsi evertsi (22%), Rhipicephalus (Boophilus) spp. (16%), Rhipicephalus appendiculatus (11%), Hyalomma marginatum (5%) en Rhipicephalus simus (4%). Bosluis besmetting was beduidend beïnvloed deur die plek, seisoen, jaar, maand tel en ouderdom van die dier. Loskop plaas het die warmste weer ervaar en het die hoogste bosluis tellings en ook die grootste variasie in bosluislading gehad. Hoër bosluistellings is ook waargeneem in die warm droë (September tot November) en warm nat (Desember-Februarie) seisoene in vergelyking met die ander seisoene. Amblyomma hebraeum is geïdentifiseer as die mees dominante bosluisspesies oor al vier lokaliteite. Die voorkeur aanhegtingsarea vir die bosluise was onder die stert, perineum en maag areas op die liggaam. Die oorerflikheid beraming vir bosluistelling, soos beïnvloed deur die seisoen en eienskap (d.i. deel van die liggaam of bosluisspesies), het gewissel van 0.01±0.01 tot 0.26±0.01. Genetiese korrelasies het gewissel van -0.79±0.33 tot 1.04±0.01 vir bosluistellings op verskillende liggaamsdele en tussen 0.00±0.00 en 0.99±0.19 vir bosluisspesies. Fenotipiese korrelasies was laag tot matig en het gewissel van 0.06±0.01 tot 0.72±0.01 vir liggaamsdele en 0.01±0.02 to 0.44±0.01 vir bosluisspesies. Die datastel D wat September-Januarie bosluistellings bevat het die hoogste genetiese variasie aangedui. Heel liggaam bosluistellings was hoogs gekorreleerd met bosluistellings rondom die perineum en maag. Hierdie twee lokaliteite blyk die mees geskikte plaasvervanger vir die heel liggaam bosluistelling te wees. Verskeie genoom gebiede van belang is geïdentifiseer vir die verskillende eienskappe van beide die GWA en RHM benaderings. Drie genoom-wye beduidende streke (op chromosome 7, 10 en 19) is geïdentifiseer vir die totale bosluistelling op die kop, totale A. hebraeum bosluise en vir die totale aantal A. hebraeum in die perineum streek. Aanbevelende beduidende streke is geïdentifiseer op chromosome 1, 3, 6, 7, 8, 10, 11, 12, 14, 15, 17, 19 en 26 vir 'n paar van die bosluis eienskappe wat ontleed was. Die GWA benadering identifiseer meer genoom gebiede as die POK benadering. Hierdie bevindinge bied nuttige inligting vir die ontwikkeling van strategieë vir die genetiese verbetering van bosluisweerstand deur seleksie. Die chromosome streke hier geïdentifiseer is skuiling kwantitatiewe eienskap loki (KEL) vir die onderliggende variasie in bosluislading en vorm die basis vir verdere ontledings vir spesifieke kandidaat gene te identifiseer wat verband hou met die vee bosluisweerstand en bied die potensiaal vir merkerbemiddelde seleksie in Nguni.

Caracteres complexos são aqueles determinados por muitos genes e que apresentam variação contínua. Em uma população, a variação herdável dos caracteres complexos não é independente, e pares de caracteres podem ser mais ou menos correlacionados entre si. O nível e o padrão da associação entre caracteres determina como o fenótipo da população se comporta perante os processos evolutivos. A associação entre caracteres pode tanto facilitar a evolução em algumas direções do espaço fenotípico quanto restringir a evolução em outras, pois caracteres mais associados entre si tendem a evoluir de forma conjunta. O padrão de associação entre caracteres pode ser representado pela matriz de covariância genética aditiva, que descreve o padrão variacional resultante da interação do mapa genótipo-fenótipo e de todos os processos de desenvolvimento que levam desde a informação contida no material genético até o indivíduo. Tanto o mapa genótipo-fenótipo quanto o padrão de covariação genético também apresentam variação herdável, e portanto podem ser alterados pelos processos evolutivos e mudar entre gerações. Esse processo estabelece uma interação de mão dupla entre evolução e covariação, na qual a covariação afeta o resultado dos processos evolutivos e os processos evolutivos afetam a covariação. Nesta tese, nós exploramos como os efeitos genéticos interagem para formar o padrão de covariação, e como esses efeitos e covariação evoluem sob seleção natural. Para isso, nós trabalhamos com três populações experimentais de camundongos que foram sujeitas a regimes de seleção artificial e, utilizando diferentes tipos de caracteres, procuramos entender como a covariação se estabelece e como ela é afetada pela seleção. No primeiro experimento, estudamos o padrão de covariação de caracteres cranianos em linhagens selecionadas para aumento e diminuição do tamanho corporal, e observamos que a seleção para tamanho altera os caracteres do crânio e a covariação entre eles. A seleção direcional diminui a variação total do crânio, mas também aumenta a proporção de variação na direção de seleção, potencialmente facilitando uma nova resposta seletiva na mesma direção. Esse resultado implica que a variação presente em uma população pode ser moldada pela sua história evolutiva de forma adaptativa. No segundo experimento utilizamos uma população intercruzada, criada a partir linhagens selecionadas para aumento e diminuição do tamanho corporal, para identificar regiões genômicas envolvidas na determinação da curva de crescimento. Utilizando estimativas dos efeitos genotípicos nos fenótipos de crescimento, nós pudemos prever os fenótipos das linhagens ancestrais utilizando apenas informação da população intercruzada, e também construir estimativas de qual seria a covariação entre os caracteres de crescimento para cada tipo de efeito genético. Além disso, relacionamos a distribuição dos efeitos genéticos com a história evolutiva da população, mostrando que tanto a seleção quanto restrições internas do desenvolvimento interagem para determinar a distribuição de efeitos genéticos e, portanto, a covariação. No terceiro experimento, utilizamos seis linhagens de camundongos, que haviam sido selecionadas para alterações na curva de crescimento, para formar uma população intercruzada. Essa população apresentava uma enorme variação na sua curva de crescimento, e, utilizando técnicas de mapeamento genético, nós identificamos regiões genômicas envolvidas na determinação dessa variação fenotípica. Também desenvolvemos, para criar uma expectativa para a distribuição de efeitos genéticos nessa população, um modelo de simulação computacional da evolução dos efeitos genotípicos sob seleção. Os efeitos genéticos na população intercruzada apresentam um padrão mais complexo que o das simulações, e encontramos uma combinação de efeitos genéticos com padrões diferentes que interagem para gerar a covariação genética presente na população. Por fim, apresentamos uma revisão sobre a evolução da covariação genética e discutimos as consequências macroevolutivas das questões abordadas nos outros capítulos / Complex traits are defined as traits that are determined by many genes and that show continuous variation. In a population, the heritable variation of complex traits is not independent, and pairs of traits might be more or less correlated. The level and pattern of the association between traits determine how the phenotype of the population behaves when faced with evolutionary forces, like natural selection and genetic drift. The association between traits can both facilitate evolutionary change in some directions of the phenotype space and hinder change in other directions because tightly associated traits tend to evolve together. The pattern of association among traits can be represented by the additive genetic covariance matrix. This matrix describes the variational pattern that is the result of the interplay between the genotype-phenotype map and development, which together lead from the genetic information to the formation of the individual. Both the genotype-phenotype map and the genetic covariation also show heritable variation, and so are able to evolve and change between generations. This process establishes a feedback between evolution and covariation, in which covariation affects the outcome of the evolutionary process and is also shaped by evolution. In this thesis, we explore how genetic effects interact to create patterns of covariation, and how these effects and covariation change under natural selection. In order to do this, we use three experimental mice populations that were subjected to artificial selection regimes, and, using several types of complex traits, we study how covariation is established and how it evolves. In the first experiment, we use the covariation pattern of cranial traits measured in mice strains selected for the increase and decrease of body size. In these strains, we see that size selection altered the means of the cranial traits and the covariation between them. Directional selection reduces the total amount of genetic information, but in a non-uniform way. Some directions in phenotype space lose more variation than others, and, counter-intuitively, the direction of selection loses less variation. This leads to an increase in the proportion of variation that is in the direction of selection, potentially facilitating future evolutionary change in the same direction. This result shows that the covariation pattern in a population is shaped by its evolutionary history and can be adaptive. In the second experiment, we use an intercross population, created with two inbred mouse strains that were selected for increase and decrease in weight, to identify genomic regions involved in determining the growth curve of the individuals. Using estimates of the genetic effects on the growth traits, we were able to predict the phenotypes of the ancestral strains using only information from the intercross. We were also able to partition the genetic covariation into the contributions due to different types of genetic effects. We interpret the distribution of genetic effects in light of the evolutionary history of the population and show that the distribution of genetic effects, and of genetic covariation, is a consequence of the interaction between selection and development. In the third experiment, we create an intercross using six inbred mice strains that had been selected for different changes in their growth curve. This intercross shows large variation in growth curves, and, using genetic mapping techniques, we identify genomic regions involved in producing this phenotypic variation. To create an expectation for the distribution of genetic effects in this population, we develop a computer simulation model for the evolution of genetic effects under directional selection. The genetic effects in the population are more complex than in the simulation model, and we find that the genetic covariation between growth traits is created by the interaction among several different kinds of genetic effects. Finally, we present a review on the evolution of genetic covariation and discuss the macroevolutionary consequences of the themes we explore in the other chapters

O alcance de altas produtividades em milho (Zea mays L.) depende do desenvolvimento de híbridos, o principal produto explorado nos programas de melhoramento. O sucesso na obtenção deste tipo de cultivar é conseguido com extensivo cruzamento de linhagens, seguido de avaliações para identificação das combinações de maior potencial. Geralmente, o melhorista tem à sua disponibilidade grande número de linhagens, possibilitando a realização de centenas a milhares de cruzamentos distintos, dos quais apenas uma pequena quantidade pode ser avaliada experimentalmente devido a limitação de tempo e recursos. Com o advento da Seleção Genômica (GS) tornou-se possível predizer o comportamento destes indivíduos não avaliados com base em seu genoma. No decorrer do processo de consolidação da GS várias metodologias foram propostas. A aptidão destas em predizer desempenhos fenotípicos é dependente da sua capacidade de acomodar a arquitetura genética das características e lidar com a multicolinearidade das matrizes genômicas. Neste sentido, métodos baseados em modelos mistos podem apresentar menor eficiência na predição de características oligogênicas devido à não capacidade de representar a distribuição real do efeito dos QTL. Além disso, a regularização das predições na presença de multicolinearidade é realizada por meio de um parâmetro de penalização (λ), o qual pode ser estimado de várias formas e consequentemente modificar a acurácia dos modelos. Além do aprimoramento dos métodos, outro aspecto importante é o procedimento de correção dos dados fenotípicos previamente à GS, o qual não é consenso na comunidade científica. Diante do exposto, este trabalho objetivou: verificar o efeito das formas de obtenção do λ (via REML na GS e pela herdabilidade da característica) e da correção do fenótipo (valor genotípico e média ajustada) na GS e avaliar a eficiência da modelagem diferencial de QTL de maior efeito na capacidade preditiva da metodologia G-BLUP, comparando-a ao LASSO Bayesiano, BayesB e G-BLUP convencional. Para isso foram utilizadas informações de híbridos simples de milho tropical avaliados em cinco locais para produtividade de grãos, altura de planta e espiga no ano de 2015. Os dados genômicos foram obtidos com a plataforma Affymetrix® Axiom® Maize Genotyping Array de 616.201 SNPs. Foram estudados diferentes cenários de GS considerando os fatores supracitados, sendo estes comparados entre si por suas capacidades preditivas e seletivas. Os resultados obtidos indicam que a correção do fenótipo e a forma de estimação de λ afetam a capacidade preditiva. O uso de valores genotípicos como correção dos fenótipos e estimação de λ via REML apresentaram os melhores resultados. Foi também observado que a modelagem de SNPs de maior efeito como fator fixo aumenta discretamente a capacidade preditiva da metodologia G-BLUP para as características oligogênicas avaliadas (altura de planta e espiga), sendo indicado o uso do G-BLUP convencional. Complementarmente, observou-se que a GS apresentou modesta eficiência na seleção de híbridos superiores sob intensidades moderadas. Entretanto, a sua alta capacidade de selecionar sob baixa intensidade pode ser amplamente explorada nos programas de melhoramento de milho visando a seleção precoce direta. / The achievement of high yield in maize (Zea mays L.) relies on the development of hybrids, which is the main product of breeding programs. The success in obtaining this kind of cultivar is achieved through extensive crossing of inbred lines followed by field trials to identify the combinations with greatest potential. Generally, breeders have a large number of inbred lines on their hands, being able to perform hundreds to thousands of different crosses, of which only a small portion can be experimentally evaluated due to time and resource limitations. Genomic Selection (GS) has made it possible to predict phenotypes of unevaluated individuals based on their genome. Throughout the establishment process of GS many approaches have been proposed. The ability of these approaches at predicting phenotypic performance depends on their capacity of accommodating the genetic architecture of the traits and dealing with the multicollinearity of the genomic matrices. Hence, methods based on mixed model equations may present lower prediction efficiency for oligogenic traits due to their inability of depicting the real distribution of the QTL effects. Moreover, the prediction regularization in the presence of multicollinearity is done by a shrinkage factor (λ), which can be estimated in a number of ways and may affect the accuracy of the models. In addition to the improvement of the models, the correction of the phenotype utilized in the predictions is also important, which is not a consensus among researchers. Based on these facts, this study aimed to assess the effect of estimation of λ (by REML in the GS model and by the heritability of the traits) and the correction of the phenotype (genotypic value and adjusted mean) on the GS. It also targeted to evaluate the effect of differential modeling of major makers on the prediction accuracy of G-BLUP, comparing it to Bayesian LASSO, BayesB and ordinary G-BLUP. To those ends, tropical maize single-crosses evaluated at five sites for grain yield, plant and ear height in 2015 were utilized. The genomic data was obtained with the Affymetrix® Axiom® Maize Genotyping Array of 616,201 SNPs. Distinct GS scenarios were studied considering the aforementioned factors which were compared by their prediction and selection accuracy. The results suggest that the correction of the phenotype and the way of estimation of λ do affect prediction accuracies. The use of genotypic values as the correction of phenotypes and the estimation of λ by REML showed best results. It was also observed that modeling major SNPs as fixed effect factors had little improvement on the prediction accuracy of G-BLUP for the oligogenic traits evaluated (plant and ear height). Thereby, ordinary G-BLUP should be the method of choice to predict these traits. Additionally, it was observed that GS presented modest efficiency for selecting superior hybrids under moderate intensities. However, its high effectiveness at selecting under low intensities might be exploited on maize breeding programs for early direct selection.

The pitcher plant mosquito Wyeomyia smithii maintains a broad geographic range from the Gulf of Mexico to central Canada, and throughout its range is genetically and phenotypically variable, though fully interfertile. Many of the traits that vary across the broad range of this mosquito owe their diversity to selection on populations, which maximize fitness in the unique environment in which each populations finds itself. While a diversity of traits vary by latitude and merit the interest of evolutionary biologists, including critical photoperiod, voltinism, and thermal tolerance, of interest in the following thesis is the variation in blood-feeding propensity within this single species of mosquito. In no other mosquito species are some populations obligate non-biters while in other populations willingly hematophagous. This thesis explores the evolutionary transition from biting to non-biting in the pitcher plant mosquito at multiple levels of biological integration, starting first by establishing a heritable basis for the transition, then moving to the fitness and life historical consequences of both the natural system and of a line artificially selected in the lab. The latter half of this thesis moves on to probe the genetic architecture underlying the shift in phenotype and ends after examining the transition to non-biting at the level of the gene using an RNA-sequencing experiment. The results stemming from this thesis are thoroughly discussed: in short, we find that fitness differs between biting and non-biting populations, that complex genetic architectures underlie the transition to non-biting in nature, but not under artificial selection, and finally, that many candidate loci are differentially regulated in biting populations relative to non-biting populations and that these loci most often cluster with metabolic biological pathways.

Doctor of Philosophy / The population size and range of giraffe Giraffa camelopardalis have been greatly reduced in Africa in the past century, resulting in geographical isolation of local populations and some herds surviving at the edge of the species’ preferred range. Numerous factors have contributed to these declines, but historical analysis indicates that habitat loss and fragmentation, human encroachment, disease and poaching are the main threatening processes. These processes can be expected to continue to impact on giraffe populations, particularly as human populations grow and needs for land and resources increase. This study used field data and laboratory analyses to investigate the taxonomy, behaviour and ecology of desert-dwelling giraffe Giraffa camelopardalis angolensis in the northern Namib Desert. This population resides at the extreme of the giraffe’s range. My research also complements the community-based natural resource management (CBNRM) program of the Namibian government, and provides baseline data on the current population status and structure of giraffe in the Kunene Region. The field data, genetic, habitat and forage samples used in this study were collected by myself and a number of research assistants over a period of two years (2001 to 2003), following preliminary research that I undertook between 1999 and 2001. Laboratory analysis of genetic samples was conducted by Dr R. Brenneman and his team at Henry Doorly Zoo, Omaha, NB., as well as by Mr D. Brown at UCLA, CA. Mr W. Gawa!nab and his team at the agricultural laboratory, Ministry of Agriculture, Water and Rural Affairs, Namibia, conducted chemical analyses on plant samples that form part of the giraffe’s diet. The genetic architecture of Namibian giraffe was investigated, including the samples from the desert-dwelling giraffe of the northern Namib Desert and giraffe from Etosha National Park. The results were compared with genetic profiles of giraffe subspecies throughout Africa, but in particular with G. c. giraffa which is the currently-accepted nomenclature of the Namibian giraffe. Results indicated that the Namibian giraffe has five unique haplotypes and is genetically distinct from G. c. giraffa or any other extant subspecies; it is considered here, tentatively, to represent G. c. angolensis. Furthermore, the Namibian Abstract iv giraffe has been separated from other populations for an extended period. Some gene flow has occurred between the desert-dwelling and Etosha NP giraffe population, and can be attributed to recent translocations between these regions. Within the study region, a sharing of haplotypes between three studied subpopulations indicated gene flow among giraffe throughout the northern Namib Desert, and this was confirmed by field-based monitoring. Taken together, these findings suggest that Namibian giraffe should be viewed as important for the conservation of overall genetic variation within Giraffa camelopardalis, although further investigation into the taxonomy of the Namibian form is warranted. Following these findings, I then investigated the behaviour and ecology of the desert-dwelling giraffe. As no previous study has been published on the ecology of G. c. angolensis, there is an information gap in our knowledge of this subspecies. One hundred and fifty six giraffe were identified individually using field-based identification methods and digital imagery. An assessment of the population structure and dynamics indicated marked variation in numbers, sex and age structure, herd structure and densities between three study areas. These variations possibly arose from differences in study area size, aridity, availability of forage and human impacts. I also investigated levels of associations between giraffe within the population using a simple ratio technique, and observed that increased association occurred in smaller populations; there appeared to be a matrilineal social structure. In one bull-biased population, a higher degree of association between bulls was observed compared to bulls in the other two populations. To gain further insight into the distribution and range of giraffe, I collected GPS locations from a combination of field-based monitoring and GPS satellite collars. The GPS satellite collars were the first trial of this technology on giraffe in Africa. Using Range Manager, a MapInfo animal location analysis extension program, I estimated 100% and 95% minimum convex polygon for daily, monthly and annual home range sizes of giraffe in the northern Namib Desert. Giraffe were observed to have large home ranges, with the largest individual range for a bull, Africa-wide, being recorded in this study. Large home ranges correlated with low population density, reduced diversity of forage and, in bulls, increased search areas for receptive cows. Giraffe movements occurred predominantly along riparian woodlands, although seasonal use of other habitats was recorded. Observations Abstract v Abstract vi and data from four GPS satellite-collared giraffe provided high-resolution data on daily movements, and indicated a pattern of highly biphasic movement behaviour that correlated with ambient temperatures. Diurnal activity budgets varied between the sexes, with cows spending more time feeding and resting, while bulls walked and ruminated more frequently. Juveniles rested more often than other giraffe. Seasonal variation in activity budgets was evident, perhaps reflecting use of an energy maximiser strategy for cows and an energy minimiser strategy for bulls. The establishment of artificial water points in the Hoanib River during the study period appeared to alter the seeming independence of giraffe on water in the northern Namib Desert, and also resulted in small-scale shifts in use of the riparian woodland by elephant. To investigate the diet of giraffe, I observed animals feeding in the field and also carried out laboratory analyses of the chemical content of preferred plant species. Seasonal changes in the abundance, moisture and protein content of available food plants correlated with shifts in the diet of giraffe. Giraffe impacted on their preferred forage source, Faidherbia albida, causing distinct structural changes in the individual plants and the F. albida population. This impact, combined with elephant damage and seasonal flood events, has resulted in a shift in the age structure and dynamics of the F. albida population over the past two decades. Finally, I present a brief overview on the history of conservation and management in the Kunene Region. The established CBNRM program provides a baseline for future wildlife conservation and management, of which the desert-dwelling giraffe could be an integral component for non-consumptive tourism. Long-term research on the population’s status, range, behaviour, social structure, habitat requirements, and ecology would help to provide a better understanding of the giraffe’s adaptation to the arid environment, while focussed legislation would enable increased control of communal lands and continue to benefit community-based conservancies.

<p>Evolution can be studied at many levels, from phenotypic to molecular, and from a variety of disciplines. An integrative approach can help provide a more complete understanding of the complexities of evolutionary change. This dissertation examines the ecology, genetics, and molecular mechanisms of the evolution of floral anthocyanin pigmentation in four species of <em>Mimulus</em> native to central Chile. Anthocyanins, which create red and purple colors in many plants, are a valuable model for studying evolutionary processes. They are ecologically important and highly variable both within and between species, and the underlying biosynthetic pathway is well characterized. The focus of this dissertation is dramatic diversification in anthocyanin coloration, in four taxa that are closely related to the genomic model system <em>M. guttatus</em>. I posed three primary questions: (1) Is floral diversification associated with pollinator divergence? (2) What is the genetic basis of the floral diversification? (3) What is the molecular mechanism of the increased production of anthocyanin pigment? The first question was addressed by evaluating patterns of pollinator visitation in natural populations of all four study taxa. The second question was explored using segregation analysis for a series of inter- and intraspecific crosses. One trait, increased petal anthocyanins in <em>M. cupreus</em>, was further dissected at the molecular level, using candidate gene testing and quantitative gene expression analysis. Pollinator studies showed little effect of flower color on pollinator behavior, implying that pollinator preference probably did not drive pigment evolution in this group. However, segregation analyses revealed that petal anthocyanin pigmentation has evolved three times independently in the study taxa, suggesting an adaptive origin. In addition to pollinator attraction, anthocyanins and their biochemical precursors protect against a variety of environmental stressors, and selection may have acted on these additional functions. Molecular analysis of petal anthocyanins in <em>M. cupreus</em> revealed that this single-locus trait maps to a transcription factor, <em>McAn1</em>, which is differentially expressed in high- versus low-pigmented flowers. Expression of the anthocyanin structural genes is tightly correlated with <em>McAn1</em> expression. The results suggest that <em>M. cupreus</em> pigmentation evolved by a mutation cis to <em>McAn1</em> that alters the intensity of anthocyanin biosynthesis.</p> / Dissertation

Most common diseases have substantial heritable components but are characterized by complex inheritance patterns implicating numerous genetic and environmental factors. A longstanding goal of human genetics research is to delineate the genetic architecture of these traits - the number, frequencies, and effect sizes of disease-causing alleles - to inform mapping studies, elucidate mechanisms of disease, and guide development of targeted clinical therapies and diagnostics. Although vast empirical genetic data has now been collected for common diseases, different and contradictory hypotheses have been advocated about features of genetic architecture (e.g., the contribution of rare vs. common variants). Here, we present a framework which combines multiple empirical datasets and simulation studies to enable systematic testing of hypotheses about both global and locus-specific complex trait architecture. We apply this to type 2 diabetes (T2D).

Doctor of Philosophy / The population size and range of giraffe Giraffa camelopardalis have been greatly reduced in Africa in the past century, resulting in geographical isolation of local populations and some herds surviving at the edge of the species’ preferred range. Numerous factors have contributed to these declines, but historical analysis indicates that habitat loss and fragmentation, human encroachment, disease and poaching are the main threatening processes. These processes can be expected to continue to impact on giraffe populations, particularly as human populations grow and needs for land and resources increase. This study used field data and laboratory analyses to investigate the taxonomy, behaviour and ecology of desert-dwelling giraffe Giraffa camelopardalis angolensis in the northern Namib Desert. This population resides at the extreme of the giraffe’s range. My research also complements the community-based natural resource management (CBNRM) program of the Namibian government, and provides baseline data on the current population status and structure of giraffe in the Kunene Region. The field data, genetic, habitat and forage samples used in this study were collected by myself and a number of research assistants over a period of two years (2001 to 2003), following preliminary research that I undertook between 1999 and 2001. Laboratory analysis of genetic samples was conducted by Dr R. Brenneman and his team at Henry Doorly Zoo, Omaha, NB., as well as by Mr D. Brown at UCLA, CA. Mr W. Gawa!nab and his team at the agricultural laboratory, Ministry of Agriculture, Water and Rural Affairs, Namibia, conducted chemical analyses on plant samples that form part of the giraffe’s diet. The genetic architecture of Namibian giraffe was investigated, including the samples from the desert-dwelling giraffe of the northern Namib Desert and giraffe from Etosha National Park. The results were compared with genetic profiles of giraffe subspecies throughout Africa, but in particular with G. c. giraffa which is the currently-accepted nomenclature of the Namibian giraffe. Results indicated that the Namibian giraffe has five unique haplotypes and is genetically distinct from G. c. giraffa or any other extant subspecies; it is considered here, tentatively, to represent G. c. angolensis. Furthermore, the Namibian Abstract iv giraffe has been separated from other populations for an extended period. Some gene flow has occurred between the desert-dwelling and Etosha NP giraffe population, and can be attributed to recent translocations between these regions. Within the study region, a sharing of haplotypes between three studied subpopulations indicated gene flow among giraffe throughout the northern Namib Desert, and this was confirmed by field-based monitoring. Taken together, these findings suggest that Namibian giraffe should be viewed as important for the conservation of overall genetic variation within Giraffa camelopardalis, although further investigation into the taxonomy of the Namibian form is warranted. Following these findings, I then investigated the behaviour and ecology of the desert-dwelling giraffe. As no previous study has been published on the ecology of G. c. angolensis, there is an information gap in our knowledge of this subspecies. One hundred and fifty six giraffe were identified individually using field-based identification methods and digital imagery. An assessment of the population structure and dynamics indicated marked variation in numbers, sex and age structure, herd structure and densities between three study areas. These variations possibly arose from differences in study area size, aridity, availability of forage and human impacts. I also investigated levels of associations between giraffe within the population using a simple ratio technique, and observed that increased association occurred in smaller populations; there appeared to be a matrilineal social structure. In one bull-biased population, a higher degree of association between bulls was observed compared to bulls in the other two populations. To gain further insight into the distribution and range of giraffe, I collected GPS locations from a combination of field-based monitoring and GPS satellite collars. The GPS satellite collars were the first trial of this technology on giraffe in Africa. Using Range Manager, a MapInfo animal location analysis extension program, I estimated 100% and 95% minimum convex polygon for daily, monthly and annual home range sizes of giraffe in the northern Namib Desert. Giraffe were observed to have large home ranges, with the largest individual range for a bull, Africa-wide, being recorded in this study. Large home ranges correlated with low population density, reduced diversity of forage and, in bulls, increased search areas for receptive cows. Giraffe movements occurred predominantly along riparian woodlands, although seasonal use of other habitats was recorded. Observations Abstract v Abstract vi and data from four GPS satellite-collared giraffe provided high-resolution data on daily movements, and indicated a pattern of highly biphasic movement behaviour that correlated with ambient temperatures. Diurnal activity budgets varied between the sexes, with cows spending more time feeding and resting, while bulls walked and ruminated more frequently. Juveniles rested more often than other giraffe. Seasonal variation in activity budgets was evident, perhaps reflecting use of an energy maximiser strategy for cows and an energy minimiser strategy for bulls. The establishment of artificial water points in the Hoanib River during the study period appeared to alter the seeming independence of giraffe on water in the northern Namib Desert, and also resulted in small-scale shifts in use of the riparian woodland by elephant. To investigate the diet of giraffe, I observed animals feeding in the field and also carried out laboratory analyses of the chemical content of preferred plant species. Seasonal changes in the abundance, moisture and protein content of available food plants correlated with shifts in the diet of giraffe. Giraffe impacted on their preferred forage source, Faidherbia albida, causing distinct structural changes in the individual plants and the F. albida population. This impact, combined with elephant damage and seasonal flood events, has resulted in a shift in the age structure and dynamics of the F. albida population over the past two decades. Finally, I present a brief overview on the history of conservation and management in the Kunene Region. The established CBNRM program provides a baseline for future wildlife conservation and management, of which the desert-dwelling giraffe could be an integral component for non-consumptive tourism. Long-term research on the population’s status, range, behaviour, social structure, habitat requirements, and ecology would help to provide a better understanding of the giraffe’s adaptation to the arid environment, while focussed legislation would enable increased control of communal lands and continue to benefit community-based conservancies.