Thesis (PhD (Agric.) -- Stellenbosch University, 1984. / INTRODUCTION: The study of seed dormancy and germination has for centuries occupied the minds of agronomists, physiologists, brewers, bakers and, more recently, weed scientists. The agronomist requires that the seed that he sows will germinate rapidly and uniformly and produce a vigorous healthy seedling .. The physiologist is interested in the understanding of the basic processes involved at the molecular level, and the geneticist in the inheritance of the quiescent character of the seed. Brewers seek a seed that will retain its viability at least until the following crop is harvested but which will also, on imbibition, rapidly set in motion those processes that will convert starch into sugar. The baker is concerned with the baking quality of the seed and, as far as he is concerned~ the more dormant the seed the better, as this eliminates the problem of pre-harvest sprouting which is very detrimental to baking quality. The weed scientist seeks to encourage all weed seeds present in the soil to germinate simultaneously so as to enable him to destroy the weed population with one application of herbicide or a single cultivation.

I assessed major factors influencing the interactions between the mestizo community and wildlife of the Impenetrable, in the Argentine Chaco, and the ways in which these interactions are influenced by the larger economic and political context. I used a mixed qualitative and quantitative methods approach, between 2001 and 2005. I found that wildlife represented an important food source, especially for the poorer rural households. The importance of wild meat varied across the community and region, in relation to the socioeconomic characteristics of households, village size, forest condition, season, species biology, and cultural preferences. Some species used by local people, primarily white-lipped and chacoan peccaries, and jaguar, were in decline and their range had been reduced by habitat destruction and overhunting, especially in the humid sub-region. These species persisted in areas of low human density, low hunting pressure and scarce development. Harvest of peccaries for food was unsustainable. Characteristics of the resource and of the community explained the lack of incentives for community-based management of peccaries. The resource was too large in relation to the local technology and the community's institutional capacities were scarcely developed. Changes in property right regimes also influenced people-wildlife interactions and were related with species mobility. Acquisition of land title by peasants did not reduce overexploitation of highly mobile resources such as peccaries, which continued to be hunted as open access resources. The national economic collapse of 2001 had a strong influence in the region. Hunting by villagers increased as a result of growing unemployment, whereas peasants reduced their hunting and turned to forest exploitation. Acquisition of land title by non-locals and intensification of ranching and forest exploitation subsequently increased, thereby affecting the livelihoods of local peasants by reducing grazing areas and affecting wildlife by reducing habitat. This study shows how people-wildlife interactions are complex and dynamic, and indicates that conservation measures are unlikely to succeed without considering the biological, cultural, socio-economic, and political factors involved. External factors require especial consideration. In this case, a national change in economic policy produced a local change in land use that is jeopardizing the peasants culture and the region's biodiversity.

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Roman epic authors extended, reinvented and created new wild animal representations that stood apart from traditional Greek epic renderings. The treatment of wild animals in seven Roman epics (Virgil’s Aeneid, Lucan’s Civil War, Ovid’s Metamorphoses, Statius’ Thebaid and Achilleid, Valerius’ Argonautica and Silius’ Punica) forms the basis of this thesis, but the extensive study of other relevant works such as Homer’s Iliad and Odyssey and Apollonius’ Argonautica allows greater insight into traditional Greek renderings and throws Roman developments into starker contrast. Initial stages of research involved collection and detailed examination of almost 900 epic references to wild animals. The findings from this preliminary research were analysed in the context of Pliny’s Natural History, Aristotle’s Historia Animalium, and other ancient works that reveal the Greeks’ and Romans’ views of wild animals. The accumulation of such a range of evidence made it possible for patterns of development to become evident. This thesis focuses on the epic representation of animals and considers a number of questions: 1) How Roman epic authors represented animals’ emotions and employed creatures’ thought processes. 2) How Roman epic authors examined the difference between wild and tame animals and manipulated the differences and similarities between humans and animals and culture and nature. 3) How wild animals were aligned with scientific and cultural beliefs that were particular to Roman society. 4) How animals were employed to signify foreign countries and how some epic animals came to be symbolic of nations. 5) How Roman epic authors represented particular aspects of animal behaviours with fresh insight, sometimes ignoring traditional representations and historiographic sources.

The purpose of this study was to investigate if Sweden should reintroduce wild forest reindeer (Rangifer tarandus fennicus Lönn) to the Swedish fauna and what conditions there were for a reintroduction to Vildmarksriket between Mora, Leksand and Vansbro. The purpose was also to investigate the impact of the reintroducement of the stakeholders in the area, such as forest owners, farmers, authorities, organizations and local residents. The methods used were a quantitative attitude survey which consisted of questionnaires and qualitative interviews. The interviews were strategically selected and semi-structured. The conclusion of this study was that stakeholders in the area Vildmarksriket have different opinions about the wild forest reindeer. The issue that concern stakeholders the most and that can create anxiety and conflict in Vildmarksriket is whether the wolves and the bears will be affected by wild forest reindeer and how forestry can be affected. Generally there is a positive attitude towards wild forest reindeer, but there is also a strong uncertainty. Wild forest reindeer can affect species and ecosystems in the region, but the effect seems to be small regardless of whether they are negative or positive. Vildmarksriket still has the potential to be a suitable area for wild forest reindeer to be reintroduced. According to the legislation that exists today, Sweden has no direct juridical obligation to reintroduce wild forest reindeer.

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A ( diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

Orientador: Sheila Canevese Rahal / Resumo: O objetivo do presente estudo foi avaliar radiograficamente os membros torácicos e pélvicos de um grupo de saguis mantidos em cativeiro, oriundos de apreensões realizadas para o combate do tráfico ilegal de animais. Foram utilizados 14 saguis, sendo 12 adultos e dois juvenis, oito machos e seis fêmeas, com massa corpórea entre 248 e 354 gramas, sendo um sagui-de-tufo-branco (Callithrix jacchus), oito saguis-de-tufo preto (Callithrix penicillata) e cinco saguis híbridos (Callithrix sp.). Com exceção de três saguis que estavam radiograficamente normais, todos os demais apresentaram alterações radiográficas dos membros, pélvicos e/ou torácicos. A despeito das alterações, a maioria dos animais conseguia se locomover sem grandes limitações no cativeiro. Dos 11 saguis com alterações no membro pélvico, cinco (45,45%) apresentavam estreitamento pélvico e desvio varo bilateral do fêmur, sendo um sugestivo de raquitismo e um de osteomalácia. Os demais apresentaram alterações, tais como má-consolidação de fratura acetabular com osteoartrite da cabeça femoral, amputação parcial de membro, antecurvato de ambas as tíbias, osteoartrite do joelho, entre outros. Seis saguis (54,54 %) mostraram alteração no membro torácico, tais como fratura do rádio, subluxação escápulo-umeral e incongruência da articulação úmero-radio-ulnar, entre outros. Foi possível concluir que 78,57% dos saguis avaliados tinham alterações ósseas e/ou articulares detectadas radiograficamente, que foram predominantes nos m... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: This study aimed to provide a radiographic evaluation of the fore- and hind limbs of marmosets in captivity, originated from capture carried out to combat illegal wildlife trade. A total of 14 marmosets, 12 adults and two juveniles, eight males and six females, weighing between 248 and 354 grams were used, including one common marmoset (Callithrix jacchus), eight black-pencilled marmoset (Callithrix penicillata) and five hybrid marmosets (Callithrix sp.). Except three marmosets radiographically normal, all the others showed radiographic changes of the forelimbs and/or hind limbs. Despite the changes, most primates were capable of moving without major limitations in captivity. Of the 11 marmosets with radiographic changes of the hind limbs, five (45.45%) had pelvic narrowing and bilateral varus deviation of the femur, which had one suggestive of rickets and one of osteomalacia. The other marmosets had changes such as malunion of acetabular fracture with hip osteoarthritis, transtíbial amputation, antecurvatum of both tibias, and knee osteoarthritis, among others. Six marmosets (54.54%) showed alterations in the forelimbs, such as radius fracture, scapulohumeral subluxation, and bilateral humeral-radio-ulnar joint incongruence, among others. In conclusion, 78.57% of the evaluated marmosets had bone and/or joint changes detected by plain radiograph, which were found predominantly in the hind limbs and without impediment to locomotion in captivity. / Mestre

As aves silvestres são consideradas importantes reservatórios de diversos vírus aviários que podem afetar aves comerciais. Dessa forma, o monitoramento das aves silvestres é fundamental para garantir a sanidade dos plantéis avícolas brasileiros. Nos últimos anos, o número de espécies de aves nas quais os coronavírus aviários foram encontrados aumentou vertiginosamente em diversos países. Contudo, poucos estudos envolvendo a detecção de coronavírus aviários em aves de cativeiro e aves silvestres ou sinantrópicas foram realizados no Brasil. Assim, o presente estudo teve como objetivo identificar a presença dos coronavírus aviários em aves silvestres no Brasil e caracterizá-los molecularmente. As amostras foram testadas através do teste de RRT-PCR para detecção do gene UTR do IBV, bem como uma nested-PCR para detecção do gene S1 dos coronavírus aviários. O sequenciamento de alto desempenho foi utilizado para caracterizar os vírus detectados. No total, foram testadas 300 amostras de aves silvestres (147 suabes orofaringeanos e 153 suabes cloacais). No total, 27 amostras foram positivas pelo teste RRT-PCR. Duas amostras de Anseriformes das amostras positivas no teste de RRT-PCR foram selecionadas para sequenciamento de alto desempenho. Em ambas as amostras sequenciadas foi constatada a co-infecção pelos vírus da bronquite infecciosa e vírus da doença de Newcastle. A análise das amostras demonstrou alta identidade com vírus vacinais, o que demonstra que estirpes vacinais utilizadas na imunização de aves de produção circulam em aves silvestres e de produção de subsistência. / Wild birds are an important reservoir of different viruses that can affect poultry. Viral surveillance in wild birds is, thus, extremely important to ensure the poultry heal in Brazil. In recent years, the number of species of birds in which avian coronaviruses have been found skyrocketed in several countries. However, few studies involving the detection of avian coronaviruses in captive wild birds or wild life birds were conducted in Brazil. Thus, the present study aimed to identify the presence of avian coronaviruses in Brazil and characterize them molecularly. Samples were tested by RRT-PCR test for detection of the UTR gene of IBV, as well as a nested-PCR for detection of S1 gene. In total, 300 samples of wild birds (147 oropharyngeal swabs and 153 cloacal swabs) were tested. In total, 27 samples were positive in RT-PCR assay. Two positive samples in RRT-PCR assay were selected for Next-generation sequencing. In both sequenced samples, co-infection with infectious bronchitis virus and Newcastle disease virus was found. The analysis of samples showed identity with vaccinal strains used in immunization of commercial flocks circulate in wild birds and subsistence flocks.

As aves silvestres são importantes reservatórios de vírus que podem acometer as aves domésticas. O monitoramento da circulação viral em aves silvestres é de extrema importância para garantir a sanidade dos plantéis avícolas. O presente estudo teve como objetivo 1) comparar dois testes moleculares de RT-PCR para a detecção dos vírus da família Paramyxoviridae em aves silvestres e sinantrópicas; 2) caracterizar os vírus detectados nestas amostras. Dois testes de RT-PCR e testes específicos de RT-PCR em tempo real (RRT-PCR) para o vírus da doença de Newcastle (NDV) e o metapneumovírus aviário (aMPV) foram utilizados para comparar o limite de detecção entre as amostras. As amostras de aves silvestres foram testadas por dois testes de RT-PCR. Um pequeno fragmento da região do sítio de clivagem do gene F das amostras positivas foi sequenciado. Os testes de RT-PCR foram validados com sucesso, mas apresentaram diferenças entre os limites de detecção quando comparados aos testes específicos de RRT-PCR utilizando diferentes vírus. No total, 100 amostras de aves (suabes) foram testados pelo teste RT-PCR que apresentou um limite de detecção similar entre os diferentes agentes virais. O teste selecionado foi capaz de detectar duas amostras de aves silvestres que foram também detectadas pelo testes específico para NDV e relacionadas às amostras de NDV vacinais do genótipo II da classe II referentes aos vírus de NDV lentogênico (113RQGR ↓ L117). Nosso estudo demonstra a deficiência na biosseguridade adotada pelos sistemas avícolas por permitir a saída dos vírus vacinais para as aves silvestres / Wild birds are important reservoirs of viruses can affect poultry. Surveillance of circulating viruses in wild birds is of the most importance tool to ensure the poultry health. The present study aimed to 1) compare two molecular tests for detection of family Paramyxoviridae viruses in wild and feral birds; 2) characterize the detected viruses in those samples. Two RT-PCR techniques and specific real time RT-PCR (RRT-PCR) assays for detection of Newcastle disease virus (NDV) and avian metapneumovirus (aMPV) were used to compare the limit of detection among them. Wild bird samples were tested by using two RT-PCR tests. A small fragment of cleavage site region in F gene from positive samples was sequenced. The RT-PCR were successfully validated, however they had differences in the limit of detection when compared to specific RRT-PCR assays using different viruses. In total, 100 wild bird samples (swabs) were tested by the selected RT-PCR with similar limit of detection between tested viruses. Two samples were positive by this test and they were also detected by the specific RRT-PCR for NDV. These samples were closed related to vaccinal NDV strains belonging to genotype II class II. Deduced amino acid sequences of cleavage site region from detected samples were characterized as lentogenic NDV strains (113RQGR ↓ L117). Our study demonstrates the poor biosafety used by poultry industry allowing the vaccinal escape to wild bird species

It is well known that nucleotide diversity varies across the genomes of eukaryotic species in ways consistent with the effects of natural selection. However, the contribution of selection on advantageous and deleterious mutations to the observed variation is not well understood. In this thesis, I aim to disentangle the contribution of background selection and selective sweeps to patterns of genetic diversity in the mouse genome, thus furthering our understanding of natural selection in mammals. In chapter 1, I introduce core concepts in evolutionary genetics and describe how recombination and selection interact to shape patterns of genetic diversity. I will then describe three projects in which I examine aspects of molecular evolution in house mice. In the first of these, I estimate the landscape of recombination rate variation in wild mice using population genomic data. In the second, I estimate the distribution of fitness effects for new mutations, based on the site frequency spectrum, then analyse population genomic simulations parametrized using my estimates. In the third, I use a model of selective sweeps to estimate and compare the strength of selection in protein-coding and regulatory regions of the mouse genome. This thesis demonstrates that selective sweeps are responsible for a large amount of the variation in genetic diversity across the mouse genome.