Norway spruce (Picea abies (L.) Karst.) together with the sister species Siberian spruce (P. obovata Ledeb.) form a vast continuous distribution over Eurasia. The present distribution of P. abies in Europe was formed recently, after the last glacial maximum. Theories about the colonization routes and history of this species differ depending on the datasets examined to date. This thesis aims to investigate the genetic structure and diversity of P. abies and establish its glacial refugia and postglacial migration. A range-wide sampling was performed of both P. abies and P. obovata, and a genotyping-by-sequencing approach was used to obtain whole-genome single nucleotide polymorphism (SNP) data. Two major genetic lineages of P. abies were found; northern and central Europe. The northern lineage was further divided into a Scandinavian and a north-east European cluster; the Scandinavian cluster being more closely related to P. obovata and the north-east European cluster to the central European lineage. Introgression from P. obovata was detected far into northern Fennoscandia. The central European lineage was divided into an Alpine and a Carpathian cluster, originating from different glacial refugia. Genetic diversity was higher in the northern part of the range, which can be attributed to the relatively large refugium that recolonized this area, as well as introgression from P. obovata. Genetic diversity was also somewhat elevated where the two central European clusters meet, as is expected in areas where two previously isolated lineages admix. This study is the first range-wide investigation of P. abies using whole-genome SNP information, and shows how the genetic structure of the species has been shaped by the last glacial maximum and postglacial recolonization.

Abstract The amount and distribution of genetic diversity are likely to affect the evolutionary potential of a species. When feasible and cost-effective policies for management and monitoring of endangered populations or species are planned, knowledge of the spatial genetic structure and the type of population dynamics is of great concern. In this thesis the genetic diversity and population structures of two endangered arctic plant species was examined on different geographical scales in Northern Europe. The species were Siberian primrose (Primula nutans) and pendant grass (Arctophila fulva), which both grow in a seashore habitat and have similar distribution patterns on the shores of the Arctic Ocean and the Bothnian Bay. The goal of the present study was to provide basic population genetic information for the study species using microsatellite and AFLP markers. Both markers were used for the first time in these species, and species-specific microsatellite markers were developed during the study. A further aim was to interlink the population genetic processes of the species into distribution patterns at the regional and population levels and to compile a synthesis of the impact of hierarchical spatiotemporal processes and autocorrelation in genetic variation at different levels. The studies of this thesis provided new information on the diversity and population structure of the endangered study species and new markers that are useful in future genetic studies of primrose species. The diversity of Siberian primrose was low, and there was no dispersal between the study regions. In pendant grass, a relatively high amount of variation was found considering the evident clonal reproduction and gene flow that was detected between populations connected by waterways. The results suggested that both clonal and sexual reproduction are important in this species. On a local scale, pendant grass populations had characteristics of “stepping stone” and classical metapopulation models. The results indicated that on a long time scale, both species will continue to decline without efficient management efforts. Most critical for the persistence of the species is the conservation of suitable habitats. Translocations could be considered in order to enhance the diversity of existing populations and establish new populations. By examining the present day structure of Siberian primrose, it was possible to make inferences regarding the colonisation history of the species in the North European area. The current distribution of Siberian primrose seemed to result from a vicariant process that took place after the last ice-age, when the species colonised the area. It spread first to the White Sea area, probably from the east, and subsequently colonised the Bothnian Bay and the Barents Sea in the west. The isostatic land uplift after the retreat of the Eurasian ice sheet uncovered large areas of land from the Baltic Sea basin that previously were under water. These geological changes resulted in the current disjunct distribution of Siberian primrose.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Aeglidae is the only freshwater anomuran family. Fossil evidences relate a marine origin for aeglids. However, genus Aegla invaded the freshwater environment of southern South America, becoming endemic and widespread in that Neotropical region. Besides, the group is widely diversified, consisting of approximately 70 recognized species. Despite the species richness, aeglids have experienced progressive habitat loss and reduction in their populations due to the steam environments alterations. In order to enable future works on Aegla diversity, this study proposed to develop microsatellite markers for Aegla longirostri. Because of their high polymorphism, such molecular markers have been widely used for establishing genetic structure, dynamic and relationship within and among populations. A total of 42 true microsatellite loci was isolated from the library enriched for (CA)n repeats, besides 17 chimeric sequences attained from technical artifacts. The repeats ranged from 3 to more than forty units. However, primer pairs could be developed for thirteen sequences. Successful PCR amplifications were obtained for loci AlCA135 and AlGA138 up to the moment. This microsatellite loci have been screening in 15 individuals of a population from the central region of Rio Grande do Sul State, Brazil, where that species is endemic, in order to evaluate polymorphism. The other developed primer pairs are still undergoing optimization. These markers are promising for investigating population genetic structure for this species. Besides, they revealed cross-species amplification when tested with Aegla uruguayana. Chimeric PCR products attained in this study, which correspond to 29% of the captured sequences, were object of a deep study about artifacts in microsatellite isolation. Moreover, it was proposed a mechanism to explain their formation and implications. / Aeglidae é a única família de crustáceos anomuros cujos representantes vivos são habitantes exclusivos de água doce. A origem marinha do grupo é evidenciada pelos registros fósseis. Entretanto, o gênero Aegla conquistou o ambiente dulcícola na região temperada do sul da América do Sul onde é endêmico, amplamente distribuído e diversificado, constituindo-se de aproximadamente 70 espécies descritas. Apesar da riqueza de espécies, os eglídeos têm sido vítimas de progressiva perda de habitat e declínio populacional devido à degradação dos ecossistemas límnicos sul-americanos. Visando possibilitar trabalhos futuros voltados à avaliação da diversidade do gênero, este estudo propôs o desenvolvimento de marcadores microssatélites para Aegla longirostri. Devido ao seu alto grau de polimorfismo, estes marcadores têm sido amplamente utilizados para avaliação de estrutura populacional, dinâmica e relações entre e dentro de populações dos mais variados organismos. Foram obtidos 42 locos verdadeiros de microssatélites com a construção de uma biblioteca genômica enriquecida com microssatélites (CA)n para A. longirostri, além de 17 seqüências quiméricas oriundas de artefatos da técnica. As repetições encontradas variaram de três a mais de 40 unidades. Desse total, 13 permitiram a projeção de primers. Condições ideais de amplificação foram estabelecidas para os locos AlCA135 e AlGA138 até o momento, os quais estão sendo testados em 15 indivíduos de uma população da região central do estado do Rio Grande do Sul, onde esta espécie é endêmica, para avaliação do polimorfismo. Testes de amplificação seguem sendo feitos para os demais locos desenvolvidos. Estes marcadores são promissores para investigação de estruturação genética em populações desta espécie. Além disso, estes locos apresentaram amplificação cruzada positiva quando testados para a espécie Aegla uruguayana. Para as seqüências quiméricas obtidas, as quais correspondem a 29% do total capturado, sugeriu-se um mecanismo para explicar sua causa e avaliaramse as implicações deste evento em construções de biblioteca genômica enriquecida com microssatélites.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The Aeglidae are Decapoda crustaceans endemic from the neotropical region of South America. They are the only anomuran family entirely restricted to freshwater, occurring mainly in streams. Requirement for well conserved habitat has restricted the populations to springs, as an effect of the constant degradation of continental aquatic ecosystems. In the central region of Rio Grande do Sul state, the species Aegla longirostri, besides suffering the effects of habitat fragmentation, is subjected to a mountainous geographic barrier, which has been separating the basins of River Guaíba and River Uruguay for about 11 my. Microsatellite loci are molecular markers with high levels of heterozigosity which have been widely used in population genetics studies. Microsatellite markers previously isolated from A. longirostri genome were characterized and the levels of heterozigosity and allelic diversity were calculated for each locus. A total of seven polymorphic microsatellite loci were used to verify genetic variability among four different populations from central region of Rio Grande do Sul state concerned the two basins described above. Results show a great genetic differentiation among all populations and not only between populations isolated by the geographic barrier. Factors as lack of larval stage and low dispersion capacity are possibly contributing to such differentiation level. Anthropic actions, resulting in alteration of aquatic environments, can also be a more recent factor contributing to the genetic diversity among the populations studied, since aeglids are very strict in relation to the water quality. / Os aeglídeos são crustáceos decápodos endêmicos da região Neotropical da América do Sul. São os únicos anomuros de água doce, habitantes principalmente de cursos d água. A exigência por um habitat conservado tem restringido as populações de Aegla às nascentes, como efeito da constante degradação ambiental dos ecossistemas aquáticos continentais. Na região central do estado do Rio Grande do Sul destacamos a ocorrência de populações de Aegla longirostri, que além dos efeitos de fragmentação de habitat, estão expostas a uma barreira geográfica de formação montanhosa, que há cerca de 11 milhões de anos separa as bacias dos Rios Uruguai e Guaíba. Locos de microssatélites são marcadores que apresentam altos níveis de heterozigosidade e têm sido amplamente utilizados em estudos de genética de populações. Marcadores microssatélites previamente isolados do genoma de A. longirostri foram caracterizados determinando-se os níveis de heterozigosidade e a diversidade alélica para cada loco. Dos oito locos de microssatélites analisados, sete se mostraram polimórficos e foram empregados em indivíduos de quatro diferentes populações da região central do estado do Rio Grande do Sul para analisar a variabilidade genética entre as populações de A. longirostri em ambas as bacias. Os resultados mostram uma grande diferenciação genética entre todas as populações e não somente entre as populações isoladas pela barreira geográfica. Possivelmente, fatores como ausência de fase larval durante o desenvolvimento destes crustáceos, aliada a uma baixa capacidade de dispersão, podem estar contribuindo para esta diferenciação. A ação antrópica, resultando em degradação do ambiente aquático, também pode ser um fator recente a contribuir para a diferenciação genética entre as populações estudadas, visto que os aeglídeos são bem exigentes em relação à qualidade da água onde vivem.

The basking shark, Cetorhinus maximus, has historically been a target of international fisheries, leading to well-documented declines in parts of its global distribution. Currently, the basking shark is listed as globally ‘Vulnerable’ and regionally ‘Endangered’ (North Pacific and Northeast Atlantic) on the IUCN Red List of Threatened Species, rendering the species an international conservation priority. Here, we assessed the global matrilineal genetic population structure and evolutionary history of the basking shark by completing the first whole mitochondrial genome sequence level survey of animals sampled from three globally widespread geographic regions: the western North Atlantic (n = 11), the eastern North Atlantic (n = 11), and within New Zealand territorial waters (n = 12). Despite the relatively large amount of sequence data assessed (~16,669 bp per individual), whole mitogenome analyses showed no evidence of population differentiation (ΦST = -0.047, P > 0.05) and very low nucleotide diversity (π = 0.0014 ± 0.000) across a global seascape. The absence of population structure across large distances and even between ocean basins is indicative of long-dispersal by this species, including an ability to cross known biogeographic barriers known to differentiate populations of other highly vagile pelagic fishes. Notably, evolutionary analyses of the mitogenome sequences revealed two globally sympatric but evolutionary divergent lineages, with a Bayesian framework estimated coalescence time of ~2.46 million years ago. Coalescent-based Bayesian skyline analysis uncovered subtle evidence of Pleistocene demographic flux for this species, including a potential decline in female effective population size. Thus, historical population changes may be responsible for the occurrence of the two highly divergent, yet sympatric lineages, as population declines may have resulted in the loss of intermediate haplotypes and resulted in an overall loss of genetic diversity. This work supports the recognition of basking sharks as a single matrilineal global population, and as such requires the application of a cooperative multiagency and international approach to fisheries management to conserve this highly vulnerable and ecologically unique species.

Psora decipiens is a characteristic species of the terricolous lichen community Toninio-Psoretum decipientis distributed mostly on calcareous or basic substrates. The community consists in various modifications of lichens Placidium squamulosum, Toninia sedifolia, T. opuntioides, Fulgensia fulgens, F. bracteata and others. Photobionts of the lichen Psora decipiens were determined. Psora decipiens shared with Placidium sp. the single photobiont species, a common terrestrial alga Myrmecia israeliensis. Cloning of ITS rDNA revealed high intrathalline variability in M. israeliensis within a single lichen thallus. Several genotypes were often found in a thallus, uncovering either a high mutation rate of the algae or constant relichenization processes. Saxicolous Psora species (P. testacea, P. himalayana, P. valesiaca and P. rubiformis) had M. biatorellae as a photobiont, indicating a possible photobiont influence on substrate specifity of Psora lichens. Finally, the proper methodology used for identification of lichen photobionts is discussed. For a correct photobiont identification, morphological investigations of intrathaline diversity combined with coherent molecular techniques are needed. Such procedure was not applied in the former studies of Psora decipiens, resulting in a poor characterization of...

Early blight (Alternaria solani Sorauer)is a major foliar disease of potatoes in most growing regions of the world and is underestimated in South Africa. This project studies the epidemiology and control of the disease in South Africa. A decision support system (DSS) for early blight in South Africa was developed and evaluated in field trials. This early blight DSS is the first such system to be developed in South Africa and once incorporated with the late blight model, will represent innovative technology for use in the South African potato industry. Trends in weather variables and concentrations of airborne conidia of A. solani were monitored. Distinct seasonal variation was noted. Peaks in spore concentration coincided with periods favourable for spore formation and dispersal; most notable was diurnal periodicity and interrupted wetting periods. The results obtained from these measurements will be useful in improving early blight DSSs for southern Africa. Isolates of A. solani from various potato-growing regions in South Africa were characterized using virulence, vegetative compatibility (VC) and random amplified microsatellite (RAMS) primers. Neither the virulence assays nor VC tests sufficiently characterised the population. Analysis of RAMS profiles revealed 27% genetic diversity among the isolates. This value is similar to diversity values obtained by previous authors studying A. solani, however, it is relatively high for an asexually reproducing fungus. There was no evidence for geographical clustering of isolates, indicating that isolates are widespread across South Africa. A survey on control practices and grower perceptions of early blight in South Africa was conducted using a questionnaire. These questionnaires were distributed to growers from 10 potato-growing regions in South Africa. Results highlighted the most popular control methods and cultivars in the South African potato industry. The majority of respondents indicated that they would use an accurate, cost-effective early blight DSS, and that more research is necessary on early blight in South Africa. A survey on control practices and grower perceptions of early blight in South Africa was conducted using a questionnaire. These questionnaires were distributed to growers from 10 potato-growing regions in South Africa. Results highlighted the most popular control methods and cultivars in the South African potato industry. The majority of respondents indicated that they would use an accurate, cost-effective early blight DSS, and that more research is necessary on early blight in South Africa. Estimated crop losses ranged from 1% - 60%, with an average of approximately 20%. This is the first comprehensive epidemiological study to be conducted on early blight in South Africa and has highlighted the need for further research. / Thesis (DPhil (Plant Pathology))--University of Pretoria, 2006. / Microbiology and Plant Pathology / unrestricted

Please read the abstract in the section 00front of this document / Thesis (PhD (Microbiology))--University of Pretoria, 2006. / Microbiology and Plant Pathology / unrestricted

Embora os morcegos sejam hospedeiros de tripanossomas de vários subgêneros, o conhecimento sobre a diversidade genética, variedade de hospedeiros, vetores, ciclos de vida, distribuição geográfica e relações filogenéticas desses tripanossomas é muito limitado. Neste estudo, caracterizamos tripanossomas de morcegos do Brasil e de Moçambique (África). A diversidade morfológica, biológica e genética e o relacionamento filogenético de espécies de Schizotrypanum revelaram os clados T. dionisii e T. c. marinkellei (restritos a morcegos) e T. cruzi. Nossos resultados permitiram descrever um novo genótipo de T. cruzi e uma nova espécie desse subgênero em morcegos africanos. Confirmamos, com análises filogenéticas, a presença de T. rangeli em morcegos e caracterizamos uma nova espécie, tradicionalmente classificada como Megatrypanum, mas filogeneticamente não posicionada neste subgênero. Novas análises, visando melhor resolver as filogenias e estimar tempos de divergências, são necessárias para inferir a hipótese mais provável para a história evolutiva desses tripanossomas. / Although bats are hosts of trypanosomes from several subgenera, our knowledge regarding their genetic diversity, host-range, vectors, life-cycles, geographical distribution and phylogenetic relationships is very limited. Here, we characterized bat trypanosomes from Brazil and Mozambique (Africa). Morphological, biological and genetic diversity, and phylogenetic relationships of Schizotrypanum species disclosed T. dionisii, T. c. marinkellei (bat restricted) and T. cruzi clades. Our findings also enabled the description of a new genotype of T. cruzi and a new species of this subgenus infecting African bats. We also reported T. rangeli in bats confirmed by phylogenetic analysis and characterized a new species of bat trypanosome traditionally classified as Megatrypanum, but not phylogenetically supported in this subgenus. Further analyses aiming better-resolved phylogenies and reliable molecular-clock model to estimate divergence times are required to infer the most likely hypothesis for the evolutionary history of bat trypanosomes.

O conhecimento da associação entre plantas carnívoras e a comunidade bacteriana pode mostrar uma diversidade ainda não conhecida, além de proporcionar um melhor entendimento dos mecanismos envolvidos na interação de ambas. O objetivo deste trabalho foi avaliar a diversidade microbiana presente em utrículos de Utricularia foliosa através da análise de bibliotecas do gene 16S rRNA obtida por pirosequenciamento. Os resultados indicam que no ponto 1, Proteobacteria (58%), Firmicutes (11%), Cyanobacteria (11%), Acidobacteria (7%), Verrucomicrobia (5%), Actinobacteria (3%) Chlamidiae (2%) e Bacteroidetes (1%) foram os grupos dominantes. Já no ponto 2 houve uma maior presença de Eukaryota (51%), sendo que os grupos mais presentes foram Streptophyta (88%), Bacillariophyta (7%) e Chlorophyta (2%). A grande presença de algas encontradas pode estar relacionada à disponibilidade de nutrientes nos utrículos e gerar um acréscimo de carbono e nitrogênio à cadeia alimentar no interior da armadilha. / Knowledge of the association between carnivorous plants and the bacterial community can show a diversity not yet known, and provide a better understanding of the mechanisms involved in the interaction of both.The aim of this study was to evaluate the microbial diversity present in utricles of Utricularia foliosa and evaluate the effect of plant growth site in this diversity. For this the 16S rRNA gene library was sequenced by pyrosequencing (454-Roche). The results indicate that in point 1, the dominants groups were composed by Proteobacteria (58%), Firmicutes (11%), Cyanobacteria (11%), Acidobacteria (7%), Verrucomicrobia (5% ) Actinobacteria (3%) Chlamidiae (2%) and Bacteroidetes (1%), while in the point 2, Eukaryota (51%), such as Streptophyta (88%), Bacillariophyta (7%) and Chlorophyta (2%) were dominant. The large presence of algae inside the utricles may be related to the availability of nutrients and increase the Carbon and nitrogen level inside the traps, allowing the growth of the plant and also the microbial community in this structures.