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Current studies of koalas in the wild mainly rely on information gathered by traditional field methods, such as community sightings, spotlighting, radiotracking, animal trappings, ear tagging and faecal pellet incidence. Collection of faeces is potentially the most reliable source of non-invasively obtaining DNA samples, which can be used to identify specific individuals. This thesis demonstrated a simple, rapid and reproducible method of extracting DNA from Koala faecal pellets using a commercially available DNA extraction kit, shows the maximum age of pellets from which DNA can be reliably extracted and defines the conditions required for the long term storage of pellets before DNA extraction is carried out. Mitochondrial DNA PCR analysis provided a simple and rapid indication of the success of both the faecal DNA extraction and pellet collection process. The faecal DNA was successfully used for microsatellite analysis and the subsequent genetic profiling of individuals from within the Campbelltown Koala population. The study paves the way for the analysis of microsatellite loci in koala faecal pellet DAN to study populations, which are too sparsely distributed to allow the capture of individual koalas / Master of Science (M. Sc.) (Hons.)

This study reexamines the nuclear microsatellite analysis by Rooney et al. (1999a) of Bering-Chukchi-Beaufort Seas bowhead whales (Balaena mysticetus) to determine if this population underwent a genetic bottleneck as a result of 19th and early 20th Century commercial whaling. This investigation used more accurate laboratory techniques to score alleles, had a larger sample size that was divided into two groups (mainland Alaska and St. Lawrence Island (SLI)), and used a moderately different set of microsatellite loci which are more variable and thus, more informative. The results corroborate the findings of Rooney et al. (1999a) for mainland Alaska showing no evidence of a genetic bottleneck. However, the SLI data analyses provide conflicting conclusions. The Wilcoxon test is significant for a heterozygote excess (p = 0.042) suggesting that a genetic bottleneck has occurred. This is not substantiated by the exact tests of each locus or the table-wide sign test. There is a possibility that a bottleneck has occurred, but due to the small sample size this is not a definitive conclusion and warrants reanalysis with a larger sample size.

This study reexamines the nuclear microsatellite analysis by Rooney et al. (1999a) of Bering-Chukchi-Beaufort Seas bowhead whales (Balaena mysticetus) to determine if this population underwent a genetic bottleneck as a result of 19th and early 20th Century commercial whaling. This investigation used more accurate laboratory techniques to score alleles, had a larger sample size that was divided into two groups (mainland Alaska and St. Lawrence Island (SLI)), and used a moderately different set of microsatellite loci which are more variable and thus, more informative. The results corroborate the findings of Rooney et al. (1999a) for mainland Alaska showing no evidence of a genetic bottleneck. However, the SLI data analyses provide conflicting conclusions. The Wilcoxon test is significant for a heterozygote excess (p = 0.042) suggesting that a genetic bottleneck has occurred. This is not substantiated by the exact tests of each locus or the table-wide sign test. There is a possibility that a bottleneck has occurred, but due to the small sample size this is not a definitive conclusion and warrants reanalysis with a larger sample size.

Made available in DSpace on 2016-06-02T20:20:27Z (GMT). No. of bitstreams: 1 TeseROS.pdf: 3247175 bytes, checksum: 6643dcff7715f3477c5e183a77356a7e (MD5) Previous issue date: 2007-07-04 / Financiadora de Estudos e Projetos / Euglossine bees are important pollinators of many Neotropical plant species, particularly orchids which could present a species-specific bee-flower relationship, essential to the reproductive success of these plants. Orchids produce chemical compounds to attract males of Euglossine bees (the effective pollinators of the orchids), and these compounds were isolated and are being used to study the biology of the euglossine males. Allozymes markers, although their low polymorphism content, were widely applied in population analyses. In order to provide a powerful tool to be applied to nest and population genetics research, primers flanking microsatellite loci were developed for Eulaema nigrita and Euglossa cordata (13 loci each). The use of these markers in 483 euglossine males of Euglossa, Eufriesea, Eulaema and Exaerete species, sampled in several Brazilian biomes and areas, evidenced the presence of only two diploid males, one in Euglossa annectans and other in Euglossa mandibularis. These findings support the hypothesis that diploid males (usually unviable or sterile individuals) occur in low frequencies in Brazilian Euglossine bee populations, a fact that is according to previous studies using allozymes. The application of these markers to nest structure analyses revealed nest sharing among unrelated females of Eulaema nigrita (eight nests). For Euglossa cordata and Euglossa townsendi nests (11 and seven nests, respectively), analysis demonstrated that monogamy (one female mated with a single male) is the rule, although nest sharing among unrelated females could also occur in E. townsendi. These results give a new focus on the research about population genetics and nest sociogenetic structure of Euglossine bees, opening new insights on the Euglossini biology and genetics. / As abelhas Euglossini são polinizadores importantes de várias espécies Neotropicais e, particularmente, para as orquídeas, onde a relação espécie-específica abelha-flor pode ser decisiva no sucesso reprodutivo destas plantas. Os machos são os polinizadores efetivos das orquídeas, cujos compostos atrativos produzidos por estas foram isolados e têm sido utilizados em diversos estudos envolvendo os machos de Euglossini. Os marcadores alozímicos, mais comumente utilizados nos estudos do grupo, apresentam em geral, um baixo polimorfismo, o que limita de certa forma as análises populacionais. Visando analisar de uma maneira mais acurada a genética das populações e de ninhos destas espécies de abelhas foram desenhados primers flanqueando locos de microssatélites em Eulaema nigrita e Euglossa cordata (13 locos cada). O emprego destes marcadores em 483 machos de 23 espécies de Euglossini dos gêneros Euglossa, Eufriesea, Eulaema e Exaerete provenientes de diversas regiões do Brasil revelou a presença somente de dois machos diplóides, um em Euglossa annectans e outro em Euglossa mandibularis. Estes achados reforçam a proposição de que os machos diplóides (geralmente inviáveis ou estéreis) não são freqüentes em populações destas abelhas do Brasil, corroborando dados prévios obtidos por meio de análise alozímica. O emprego dessa metodologia na avaliação da estrutura nidal revelou ainda que em Eulaema nigrita (oito ninhos) ocorre o compartilhamento do ninho entre fêmeas não aparentadas. Para as espécies Euglossa cordata e Euglossa townsendi (11 e sete ninhos, respectivamente) os ninhos, via de regra, são formados por uma fêmea acasalada com um único macho, embora para E. townsendi também tenha sido observado o compartilhamento de ninho por fêmeas não aparentadas. Os dados aqui apresentados lançam um novo olhar sobre a genética das populações e a estrutura sociogenética nidal de Euglossini, sendo, certamente, uma contribuição importante para o avanço do conhecimento a respeito da biologia e genética deste grupo de abelhas.

Au cours des 60 dernières années le développement des infrastructures de transports (Autoroutes, Lignes Grandes Vitesse, Nationales doubles voies) a fragmenté l'habitat des cerfs élaphe (Cervus elaphus). D'après les observations naturalistes, cette anthropisation a causé la fragmentation de deux populations géographiques existantes en sept dans la partie Sud et d'une en trois dans la partie Nord. Afin d'évaluer l'impact de ces infrastructures sur la structuration génétique de ces populations de cerfs, nous avons échantillonné chacune de ces populations grâce à la coopération de trois fédérations de chasse. Le cours laps de temps écoulé depuis la construction de ces infrastructures nous a conduits à choisir comme marqueurs moléculaires les microsatellites, efficaces dans l'inférence d'évènements récents. Les nouvelles techniques de séquençages (NGS) permettent d'obtenir d'importants jeux de données rapidement, nous avons choisi d'utiliser ces méthodes de séquençage pour obtenir nos données. Aucun logiciel ne permettant de traiter les données de séquençage haut débit des microsatellites pour des espèces dont le génome n'est pas complètement séquencé, nous avons alors réalisé un programme, MicNeSs qui permet de génotyper rapidement et objectivement (sans intervention humaine) un grand nombre d'individus et de locus. Nous avons utilisé MicNeSs pour génotyper 345 individus pour 17 locus microsatellites. A partir de ce jeu de données, nous avons montré l'existence d'une structuration génétique des populations de cerfs élaphe en Île-de-France en liaison avec les infrastructures routières et ferroviaires. Nous avons mis en évidence un effet fort des jumelages autoroutes/LGV et une efficacité différentielle des passages grande faune de 2ème et 3ème génération sur les populations de cerfs élaphe en Île-de-France. / During the last 60 years, the development of urban areas, main roads, highways and railways in Île de France, has fragmented the habitat of the red deer (Cervus elaphus). According to naturalistic observations, it caused the fragmentation of the two existing putative populations in the South in to seven putative populations and one in three in the North.In order to estimate the impact of the infrastructure on the genetic structure of these populations we sampled each of the putative population with the help of three hunting societies. Due to the short time passed since the first highway construction we chose microsatellite loci as molecular markers, efficient in the inference of recent events. The next generation sequencing (NGS) enable to have quickly important data set, we chose to use this technic to obtain our data. No software permits to treat microsatellites data from NGS for the species without complete genome, we made one program, MicNeSs which genotypes quickly and objectively a lot of individuals and loci. We used MicNeSs to genotype 345 individuals for 17 microsatellite loci. With this data set we showed the presence of a genetic structure of the red deer populations in association with the road and rail infrastructure. We highlighted a strong impact of the paired of highway/railway and a differential efficiency of the wildlife passages of the second and third generation on the red deer populations in Île-de-France.

<p dir="ltr">The Blanding’s Turtle (<i>Emydoidea blandingii</i>) is a species of conservation needs that ranges across the U.S Midwest and Northeast, and Ontario/Nova Scotia, Canada. The species has experienced several range expansions and contractions due to glacial dynamics and industrial landscape changes, which have led to population isolation and bottlenecks. Understanding genetic variation and population structure across the species’ geographic range is essential for conservation efforts to maintain and restore populations. While several regional studies have evaluated genetic variation in <i>E. blandingii</i>, there has been little population sampling across Michigan and limited attempts to directly compare genetic variation across extensively sampled populations within both its main range and disjunct segments in the Northeast U.S. In this study, I utilized 12 microsatellite loci to directly compare the genetic diversity of <i>E. blandingii</i> across 153 localities in a portion of the Great Lakes and the Northeast of the range. Additionally, 13 microsatellite loci were used to assess genetic diversity across 92 localities in Indiana, Ohio, and Michigan, including further sampling within Michigan. My findings confirmed higher genetic diversity within the Great Lakes compared to the Northeast and revealed greater genetic differentiation in the Northeast than in the Great Lakes. Population structure in both regions was influenced by distance (IBD) and watersheds, with a more pronounced effect in the Northeast. Using four different genetic clustering approaches (PCA, sPCA, STRUCTURE, and TESS3r), I identified three range-wide clusters, three within the Northeast, and three within the Great Lakes. Within the Great Lakes, estimates of effective population size (<i>N</i>e) were high at both the population and watershed level, although influenced by sample size. The long lifespans of <i>E. blandingii</i> likely contribute to high levels of genetic diversity, while post-glacial gene flow across the landscape has resulted in low to moderate levels of differentiation within the regions. This study highlights poorly understood population structure and differences in genetic diversity between regions. Although Great Lakes populations are less isolated and more genetically diverse than those in the Northeast, this does not suggest that they are secure. Both regions face potential genetic loss over the next century, requiring further management implications to mitigate any further decline.</p>

Made available in DSpace on 2014-06-11T19:35:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-05-21Bitstream added on 2014-06-13T20:26:26Z : No. of bitstreams: 1 silva_jm_dr_ilha.pdf: 5229353 bytes, checksum: 26881a18397c496d59109ba02eed094d (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O Eucalyptus camaldulensis, espécie nativa da Austrália, é plantada com sucesso em vários países em função da sua superioridade na produção de madeira, em relação a outras espécies sob condições ambientais adversas, com destaque para tolerância ao déficit hídrico e à alta temperatura. Em abril de 1986 instalou-se uma população base de Eucalyptus camaldulensis, em Selvíria-MS, na Fazenda de Ensino e Pesquisa e Extensão - Faculdade de Engenharia de Ilha Solteira/UNESP, constituída por 25 matrizes, sendo 13 (Lote 14517) procedentes da região de Nott’s Crossing, Katherine River, Austrália, e as 12 restantes pertencentes ao lote 13923 da CSIRO. O objetivo principal deste trabalho foi investigar a variabilidade genética da população base e do teste de progênies, baseado na caracterização molecular (locos microssatélites) e quantitativa (caracteres quantitativos DAP, altura, forma do fuste, volume, brotação, densidade básica da madeira e resistência à penetração), para fins de conservação e melhoramento genético. Os caracteres quantitativos foram avaliados dos 20 aos 23 anos após a instalação da população base, sendo que aos 21 anos desbastou-se 83,33% da população base, baseado no índice multi-efeitos, transformando-se em uma população de melhoramento ou pomar de sementes. Em outubro de 2008 instalou-se um teste de progênies a partir de sementes de 136 árvores oriundas da população de melhoramento, e avaliou-se altura total de plantas aos seis meses após instalação do teste de progênies. A caracterização molecular ocorreu em 250 indivíduos da população de melhoramento e em 500 indivíduos do teste de progênies. A população base e o teste de progênies possuem alta variabilidade genética para os caracteres avaliados, mesmo após o desbaste seletivo. Existe seleção para heterozigotos... / Eucalyptus camaldulensis is Australian specie that is planted successfully in many countries in function of its superiority in production of wood in relation to other species in adverse environmental conditions, emphasis by tolerance to drought and high temperature. In April 1986 established a base population of Eucalyptus camaldulensis in Selvíria-MS in Experimental Research Station, Engineer School of Ilha Solteira, UNESP, with 25 seed-trees, 13 (lot 14517) coming from region of Nott´s Crossing, Katherine River, Australia, and 12 belong to the lot 13923 CSIRO. The main objective of this study was to investigate the genetic variability of the base population and the progeny test based on molecular characterization (microsatellite loci) and quantitative (quantitative traits DBH, height, stem shape, volume, sprouting, wood basic density and penetration resistance), for purposes of genetic conservation and breeding. The quantitative traits were evaluated from 20 to 23 years after installation of the base population, and logging up 83,33% of the base population with 21 years, based multi-effect index selection, turning into a breeding population or seed orchard. In October 2008 it was installed a test progeny from seed of 136 trees coming from the breeding population, and evaluated total height at six months after installation of the progeny test. There was a molecular characterization in 250 individuals of the improvement population and in 500 individuals from progeny test. The base population and progeny test are highly variable genetic traits, even after selective thinning. There is selection for the heterozygous between progeny and adult phase, and the species has a mixed mating system, producing seeds by a combination of crosses with self pollination, with a predominance of crosses. The improvement population is isolated in terms of gene... (Complete abstract click electronic access below)

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Orientador: Alexandre Magno Sebbenn / Resumo: Cariniana estrellensis e Cariniana legalis são uma das maiores árvores dos biomas florestais da Amazônia e Mata Atlântica, sendo atualmente vulneráveis à extinção devido ao intenso desmatamento desses biomas. Estratégias para conservação in situ e ex situ são urgentes e estudos de diversidade genética e fluxo de genes são chaves e para esses propósitos. Assim, investigamos a diversidade genética, a estrutura genética espacial (SGS) e o fluxo histórico de genes em populações fragmentadas de ambas as espécies, utilizando marcadores de microssatélites. Todas as árvores encontradas nas populações foram mapeadas, medidas para o diâmetro na altura do peito (DAP) e amostrado o cambio de casca. O índice de fixação (F), em alguns casos, foi significativamente maior em árvores com menor DAP, indicando que as árvores menores apresentam um maior parentesco do que as maiores. Foi detectada SGS significativa para populações de ambas as espécies (60-350 m), indicando um padrão de dispersão de genes de isolamento pela distância (IBD). Para ambas as espécies, foi observada alta imigração de semente (38,5-61,5%) e pólen (80,1-100%), mostrando que as populações não são isoladas geneticamente. Não foi detectada autofecundação, mas o cruzamento entre árvores relacionadas foi detectado nas espécies (8,9-12,5%), sugerindo uma seleção mais forte contra árvores de autofecundação do que se originou do cruzamento entre árvores relacionadas. A distância de dispersão de pólen e sementes em C. estrellensi... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Cariniana estrellensis and Cariniana legalis, two of the largest trees in the Amazon and Atlantic Forest biomes, are currently vulnerable to extinction due to the intense deforestation of these biomes. Strategies for in and ex situ conservation are urgent, and studies of genetic diversity and gene flow are key aspects needed to develop these strategeis. Thus, we investigate the genetic diversity, spatial genetic structure (SGS), and historical gene flow in fragmented populations of both species, using microsatellite markers. All trees found in the study populations were mapped, measured for diameter at breast height (DBH), and sampled for bark cambium. Our results show that in some cases, fixation index (F) was significantly higher in trees with lower DBH, indicating that smaller trees have higher levels of inbreeding than larger ones. Significant SGS was detected in populations of both species (60-350 m), indicating a gene dispersal pattern of isolation by distance (IBD). For both species, we found high seed (38.5-61.5%) and pollen (80.1-100%) immigration demonstrating that populations are not genetically isolated. No self-fertilization was detected, but we did find evidence of mating among related trees (8.9-12.5%), suggesting stronger selection against selfed individuals than those originated from mating among relatives. Pollen and seed dispersal distance for C. estrellensis reached longer distances (> 3 km) than for C. legalis (maximum of 385 m). However, pollen and seeds... (Complete abstract click electronic access below) / Doutor