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PhD, Faculty of Health Sciences, University of the Witwatersrand / The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter gatherers and cattle herders, respectively, who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. This project made use of mitochondrial DNA (mtDNA), Y-chromosome DNA and autosomal DNA markers to examine the population structure of various San and Khoe groups and to reconstruct their prehistory. The groups included in the study consists of six different Khoe-San groups (‡Khomani, Nama, Khwe, !Xun, /Gui + //Gana + Kgalagari and Ju\’hoansi), four different Coloured groups and five other population groups that were included in the comparative analysis. For the mtDNA study a minisequencing technique was successfully developed which allowed the assignment of mtDNA lineages into the 10 global mtDNA macro-haplogroups. Haplogroups were further resolved using control region sequence data obtained from both hypervariable regions (HVR I and HVR II). Using this approach 538 individuals (both males and females) were screened and their mtDNA types were resolved into 18 haplogroups encompassing 245 unique haplotypes. In addition, 353 males were examined for Ychromosome DNA variation using 46 bi-allelic Y-chromosome markers and 12 Y-STR markers. The Y-chromosomes in the sample were assigned into 29 haplogroups (using biallelic variation) following the nomenclature initially recommended by the Y-chromosome Consortium and resolved into 268 unique haplotypes (Y-STR variation). To assess the level of autosomal variation, 220 genome wide autosomal SNPs were typed in 352 individuals. These SNPs were combined in different datasets and analysed using two different approaches allowing for genotype and haplotype analyses. Data from these three marker systems were analysed using different analytical methods (distance based phylogenetic analysis, network analysis, dating of lineages, principal components analysis, phylogeographic analysis, AMOVA analysis, population structure analysis, and population genetic summary statistics) to asses the ancestral associations and the genetic affinities of the various San, Khoe and Coloured populations. The most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) and Y-chromosome haplogroups (haplogroups A and B) found in Khoe-San and Coloured groups. The sub-haplogroups were, however, differentially distributed in the different Khoe-San and Coloured groups which suggested different demographic histories. The current distribution of Khoe-San groups comprises a wide geographic region extending from southern Angola in the north to the Cape Province (South Africa) in the south. Linguistically Khoe-San groups are also divided into northern Khoisan-speaking groups (Ju division) and southern Khoisan-speaking groups (Tuu division) with an additional linguistic group (Khoe) associated with some Khoe-speaking San groups in Botswana and the Khoe herders of South Africa and Namibia (such as the Nama). For all three genetic marker systems, northern groups (Ju speaking - !Xun, Ju\’hoansi and Khoe-speaking San - /Gui + //Gana) grouped into one cluster and southern groups (historically Tuu speaking - ‡Khomani and Coloured groups) grouped into a second cluster with the Khoe group (Nama) clustering with the southern Khoe-San and Coloured groups. The Khwe genetic profile was very different from the other Khoe-San groups. Although high proportions of Bantu-speaking admixture were identified in the Khwe group, they also contained a unique distribution of other mtDNA and Y-chromosome lineages. A previously published theory suggested that, based on the presence of a specific E-M35 Ychromosome haplotype, the Khwe might be descendants of an east African pastoralist group that introduced the pastoralist culture to a region located in the present day northern Botswana. This pattern also mirrors what archaeologists have found with respect to the introduction of pastoralism to southern Africa. The theory was further supported and elaborated on in the present thesis. Considering the frequency and distribution of E-M35, the highest frequency (46%) was found in the Khwe with a present-day distribution in northern Botswana and southern Angola while a decrease in frequency is observed towards the south with low frequencies (<10%) in the Karoo Coloured groups. Conversely, none of the mtDNA (female) L0k and L0d lineages observed in the Khwe group were observed in the southern Khoe-San and Coloured groups. From these observations a theory was proposed that after introduction into the region of northern Botswana, the southwards spread of pastoralism was not a clear-cut demic or cultural diffusion. Rather some male individuals integrated with the southern tribes and took with them the pastoralist practice and likely also their Khoe-language. Altogether this thesis presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the Degree of Doctor of Philosophy. / Y chromosome DNA and mitochondrial DNA (mtDNA) variation were examined in Ugandans, Zambians, Biaka Pygmies and non-Pygmies from the Central African Republic. Y chromosome DNA variation was also examined in populations from the Democratic Republic of Congo. Data generated in this study were analysed together with published data to (1) clarify the understanding of the overall patterns of haploid genetic variation in Africa; (2) examine genetic affinities among central African and other African populations; (3) assess the concordance of haploid markers with different mutation rates in assessing population affinities; (4) compare male and female migration rates in African populations; and (5) refine theories regarding the prehistory of central Africa populations based on linguistics and archaeology. Sixteen biallelic and eight microsatellite Y-specific markers were examined in 369 central African individuals. Eleven Y chromosome haplogroups (HGs A, B*, B-M150, B-Ml 12, B- M211, E-M191, E-M2, E-M35, E-M40, FJ and R) and 174 compound haplotypes were identified. The mtDNA 9-bp deletion, 3592 Hpal and 10397 Alul restriction polymorphisms, and two hypervariable regions (HVRs) were examined in 397 individuals. A total of 246 mtDNA types were identified and classified into 19 mtDNA subhaplogroups. Using Y chromosome data, central African populations shared close genetic affinities with each other and with populations from west and southern Africa. Extensive unidirectional Y chromosome gene flow from non-Pygmy populations to Biaka Pygmies was observed. Using mtDNA data, central African non-Pygmy populations shared close genetic affinities with each other and with populations from west, east and southern Africa. MtDNA studies indicated almost complete maternal genetic isolation of Biaka. Overall, using both mtDNA and Y chromosome data, pan-African populations were best grouped by geographic rather than by linguistic criteria. Different mtDNA and Y chromosome data types revealed similar genetic relationships among African populations. Female migration rates appear to have exceeded male migration rates in non-Pygmy central African populations in this study, whilst the opposite was found in Biaka Pygmies. Data types at different levels of resolution suggested that male and female migration rates in Africa may have differed over time, and may not have been significantly different. This research has provided new insights into the complex demographic history that shaped the present-day genetic landscape of central African populations. / WHSLYP2016

Species extinction rates are causing alarm. Anthropogenic distortion of the climate system is rapidly altering the natural environment. Arabidopsis thaliana is a model species in molecular biology with widespread wild populations showing functional diversity however its ecology and evolution is poorly understood. Faced with a changing natural world, what is the adaptive potential of the model plant species Arabidopsis thaliana? This thesis focuses on the interactions of genotypes, phenotypes and environments to assess the current state of adaptation in this vagile species and to identify mechanisms for rapid adaptation to future stress, focusing on plant pathogens. Here I show that A. thaliana populations in England exhibit evidence of local adaptation and genetic structure. A large common garden experiment using genotypes gathered in natural habitats revealed functional fitness differences in genotype-by-environment interactions. Wild populations showed differential representation of RPM1 alleles suggesting non-random processes are responsible for the exhibited patterns. A further common garden experiment demonstrated ‘home site advantage’ through a correlation between fitness and home site climate, which suggests that local adaptation had occurred. Phenotypic plasticity and mechanisms for rapid adaptation could be essential for plant survival under predicted climate change. Using Xanthomonas spp. as xenopathogens, I show differing levels of pre-adaptation for pathogen response exists in wild UK populations of A. thaliana. By using a multi-generation study, I found some evidence that epigenetic modification enabled rapid adaptation to pathogen stress. Finally, I compared the metabolic expressions of phenotype among genotypes in two artificial environments. Environmental effects detected by this method are far greater than genetic ones, suggesting that metabolic plasticity can underpin environmental adaptation. Taken together, my results suggest that wild populations of A. thaliana contain a range of mechanisms for rapid adaptation to environmental change. If these capacities are general, my work offers a note of optimism about the fate of some wild plant species in the face of global climate change. Additionally, as A. thaliana is a model species in genomics, my findings may facilitate future exploitation of these traits by crop geneticists.

<p>Undersökningens syfte är att ta reda på vilka räknestrategier som elever i skolår 1 och 2 använder då de löser additionsuppgifter. Syftet är att undersöka vilken variation av lösningsstrategier, som kan visa sig i en och samma klass. I undersökningen har det sammanlagt genomförts 13 kvalitativa intervjuer med elever från en klass, som både består av elever i skolår 1 och 2. Vid analysen av deras svar, som skett utifrån fenomenografin och variationsteorin har variationer i elevernas räknestrategier framkommit. Den vanligaste strategin i både skolår 1 och 2 visade sig vara ett- och ett räkning och då ofta tillsammans med fingerräkning, som ett konkret hjälpmedel. Det framkom även flertalet andra räknestrategier och att det fanns en variation av lösningar både mellan eleverna, men även hos samma elev vid olika uppgifter.</p>

These studies compared giant hill strains of Russet Norkotah and Umatilla Russet to the parent varieties. Selections were initially based on late maturity and increased vine vigor. Subsequent evaluations emphasized yield and quality parameters in comparison to the parent varieties. Giant hills were collected from the Columbia Basin and Central Oregon in 1999. Seed was tested and increased in a greenhouse during the winter of 1999 and in the field in 2000. Clones were inspected for viruses and other diseases in both years. Replicated performance trials were conducted at the Hermiston Agricultural Research and Extension Center in the Columbia Basin and at the Central Oregon Agricultural Research Center, near Madras, in 2001. Trials were grown using commercial management practices common to the areas. Tubers from the Madras trial were retained for use in future plantings. Relative yields of Russet Norkotah strains differed drastically between sites even though the growing seasons were similar in length. Several Russet Norkotah strains preformed better than the parent variety at Madras when the strains achieved good vine growth and the parent variety did not. Vine growth was subnormal at Madras in 2001 primarily due to delayed emergence and the subsequent short growing season. Few performance differences and no advantages were evident when Russet Norkotah strains were grown in the Columbia Basin under conditions with less environmental stress than usual. All strains of Umatilla Russet grown under a long season in the Columbia Basin out-yielded the parent variety; however, many strains also produced a high percentage of malformed tubers. In general, Umatilla Russet strains failed to produce adequate yields and tubers of acceptable size when delayed emergence shortened the growing season at Madras. At Madras, strains of Umatilla Russet with high biomass tended to have lower yields while strains of Russet Norkotah with high biomass tended to have high yields. Some strains performed better than the parent varieties at the two trial sites. Superior strains have been submitted to the Oregon Potato Variety Development Program and Oregon Foundation Potato Seed Project for further evaluation. / Graduation date: 2002

I studied the occurrence of two sympatric morphs of arctic charr, Salvelinus alpinus (L.) in Vatnshlidarvatn, a small shallow lake in NW Iceland. The arctic charr were subjectively distinguished by colour and appearance as brown morph or silver morph, and measured for morphological and life history characters. The study revealed the presence of two growth forms represented by the two morphs that differed in age and size at sexual maturation, reproductive investment, and time and place of spawning. The morphs differed significantly in gill raker number and morphometric characters related to manoeuvrability and cruising ability. Morphological segregation was established early in life and is most readily explained as developmental heterochrony. Both morphs were benthivorous, but could be segregated as diet specialist and generalist, with diet segregation being important only when food (especially the benthic crustacean Eurycercus spp.) was scarce, The occurrence of one abundant food resource, and lack of interspecific competition (no other fish species are present) may explain the different feeding strategies. The presence of "empty" niche should induce variability and divergence in morphology and life history to occupy available niche space. / Graduation date: 1997

Undersökningens syfte är att ta reda på vilka räknestrategier som elever i skolår 1 och 2 använder då de löser additionsuppgifter. Syftet är att undersöka vilken variation av lösningsstrategier, som kan visa sig i en och samma klass. I undersökningen har det sammanlagt genomförts 13 kvalitativa intervjuer med elever från en klass, som både består av elever i skolår 1 och 2. Vid analysen av deras svar, som skett utifrån fenomenografin och variationsteorin har variationer i elevernas räknestrategier framkommit. Den vanligaste strategin i både skolår 1 och 2 visade sig vara ett- och ett räkning och då ofta tillsammans med fingerräkning, som ett konkret hjälpmedel. Det framkom även flertalet andra räknestrategier och att det fanns en variation av lösningar både mellan eleverna, men även hos samma elev vid olika uppgifter.

Denna studie undersöker hur pedagoger i skolans tidigare år uppfattar utomhuspedagogik. Tidigare forskning visar att pedagoger är eniga om att utomhuspedagogik kopplas till att vara en plats för lärandet där eleven upplever fenomen i sin rätta miljö. Utomhuspedagogik ses också som ett objekt då den tillåter individen att uppleva och erfara kunskaper med kroppen och material i naturen samt som en metod som tillåter variation i undervisningen. I utomhuspedagogiken läggs stort värde i förstahandserfarenheter då eleverna får uppleva och delta konkret i en växelverkan mellan teori och praktik. Utemiljön stimulerar elevernas fysiska aktiviteter och deras sinnen, vilket har en positiv inverkan på lärandet. Även sett ur ett hälsoperspektiv så har fysiska aktiviteter i utemiljöer även en positiv inverkan på individens hälsa då en kombination mellan att vistas ute och att röra på sig bland annat motverkar stress.Vår studie består av kvalitativa intervjuer som gjorts på sju pedagoger samt kvantitativa enkäter på sammanlagt 18 pedagoger. Resultatet visar att pedagoger har en positiv syn på utomhuspedagogik då den medför en variation och ett komplement till den vanliga undervisningen. Utomhuspedagogiken bidrar till rörelse, frisk luft, koncentrations- och motorikövning, samt att det blir ett verklighetsförankrat lärande där alla sinnena blir involverade.