Teses / dissertações: "Clonal and genetic diversity"

1

Weidow, Elliot D. "Genetic Diversity in an Invasive Clonal Plant? A Historical and Contemporary Perspective". ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/td/2522.

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Introduced populations of Eichhornia crassipes (Pontederiaceae) possess extremely low levels of genetic diversity due to severe bottleneck events and clonal reproduction. While populations elsewhere have been well studied, North American populations of E. crassipes remain understudied. We used Amplified Fragment Length Polymorphism markers to assess genetic diversity and population structure in North American E. crassipes populations. Patterns of diversity over the past fifty years were analyzed using herbarium specimens. Furthermore, we sampled populations across the Gulf Coast of the United States throughout a year to determine contemporary genetic diversity and assess potential seasonal effects. Genetic diversity was found to be scant in the United States without population structure, agreeing with previous studies from other regions. Genetic diversity has remained consistently low over the past fifty years despite significant changes in selection pressure. However, evidence for and against population structure between seasons was found and the consequences of this are discussed.

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2

Bullock, James Michael. "The maintenance of genotypic diversity in a clonal plant". Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.279711.

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3

McClintock, Katherine. "Genetic variability, clonal diversity and taxonomic comparisons of Carex lasiocarpa Ehrh. and Carex lanuginosa Michx. (Cyperaceae)". Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=61192.

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Enzyme electrophoresis, chromosome counts and self-incompatibility trials were used to compare genetic and clonal diversity in Carex lasiocarpa and C. lanuginosa, two closely-related wetland sedge species of north-temperate distribution. Genetic variation was similar in the two species, but C. lanuginosa was somewhat less diverse and had a higher coefficient of genetic differentiation among populations than C. lasiocarpa. Wright's fixation index indicated that both species are primarily outcrossing, although crossing experiments suggested that C. lanuginosa may be self-fertile. The haploid chromosome numbers were n = 38 for C. lasiocarpa and n = 40 or 41 for C. lanuginosa. Cluster analysis using genetic identities and principal components analysis of allele frequencies clearly grouped the two species, but the separation was less clear for morphological data. Clonal diversity was higher and clone size smaller in C. lasiocarpa than in C. lanuginosa, but C. lasiocarpa showed less clonal and genetic diversity at dry than at wet sites.

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4

Metzger, Genevieve. "CLONALITY AND GENETIC DIVERSITY IN POLYGONELLA MYRIOPHYLLA, A LAKE WALES RIDGE ENDEMIC PLANT". Master's thesis, University of Central Florida, 2010. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2103.

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Although capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I use microsatellite markers to investigate questions about clonal structure and genetic diversity in five populations of P. myriophylla and address some of the implications of my findings for conservation of this species: Overall, I find that 57% of sampled clusters of P. myriophylla are composed of a single genet (genetic individual) with multiple physiological units (ramets) while the remainder are made up of two or more genets. I found differences in both clonal reproduction and genetic diversity among populations. I also found evidence of limited gene flow even over small spatial scales (less than 10 km) and for at least 4 genetic clusters occurring within the species range. Despite high levels of genetic diversity overall, there is evidence of reduced genetic diversity in two populations My results suggest that high levels of clonality may be important in maintaining genetic diversity in P. myriophylla. I also provide evidence that dirt roadsides may not represent a refuge for this species.
M.S.
Department of Biology
Sciences
Biology MS

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5

Stokes, Richard L. "Pollination Ecology, Self-incompatibility and Genetic Diversity in the Herbaceous Eastern North American Spring Ephemeral, Erythronium americanum". University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1353089025.

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6

Solé, Magali. "Factors affecting the genotypic and genetic diversity of the dioecious clonal plant Cirsium arvense at the metapopulation level". [S.l.] : [s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=971596697.

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7

Maciel, Kelly de Jesus Silva. "Análise da diversidade e divergência genética em clones de Eucalyptus spp. potencialmente importantes para Goiás". Universidade Federal de Goiás, 2014. http://repositorio.bc.ufg.br/tede/handle/tede/6247.

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Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG
The success of the Brazilian forestry is due largely to the excellent adaptability of the Eucalyptus genus to our climate and soil conditions. The recent expansion of eucalypts to the North and Midwest regions of Brazil presents challenges such as the need for clones adapted to drought, high temperatures and nutrient deficient soils of Cerrado. Three clonal trials were installed in different regions of Goiás State to evaluate the adaptability and growth of 113 elite clones of Eucalyptus spp. The objective of this study was to estimate the genetic diversity and divergence among 90 of the clones used in three clonal trials installed in different regions of Goiás State. The clones were genotyped with nine microsatellite loci organized into four "multiplex" systems for PCR. The amplified fragments were separated on the ABI–3100 platform (Applied Biosystems). The genotyping was performed using the GeneMapper software (Applied Biosystems). Genetic diversity parameters were estimated using the GDA and Fstat programs. The parameters number of alleles (A), expected heterozygosity (He), observed heterozygosity (Ho), intrapopulation fixation index (f) and allelic richness were estimated for each microsatellite locus. The results showed that all loci used in this study were highly polymorphic, with an average of 16.78 alleles per locus. The EMBRA28 and EMBRA3 loci showed the highest number of alleles (24 and 22). In general, for most markers, the observed heterozygosity had similar estimates when compared to the expected heterozigosity under Hardy-Weinberg Equilibrium. As a result, the fixation index (f) did not differ significantly from zero. Analyses of genetic structure of the clones was performed using the software Structure (version 2.3.4), with K values ranging from 1 to 10, with 10 interactions each. Results indicated presence of three distinct genetic groups (K = 3). However, there was no clear relationship between the populations obtained and the different species of Eucalyptus used in the study. This result can be explained by the clone sample is originated from breeding programs where crosses may have admixed populations, disrupting some genetic structures. Most importantly, the molecular analyses indicate extraordinary genetic diversity within the clonal trials installed in Goiás. This genetic diversity can be exploited for breeding new genetic material adapted to the Cerrado conditions.
O sucesso do setor florestal brasileiro deve-se em grande parte à excelente adaptabilidade do gênero Eucalyptus ao nosso clima e condições do solo. A recente expansão do eucalipto para as regiões norte e central do Brasil requer pesquisas para que os clones se adaptem à seca, elevadas temperaturas e escassez de nutrientes nos solos do Cerrado. O objetivo deste estudo foi estimar a diversidade e divergência genética entre 90 dos clones utilizados em uma rede de testes clonais no estado de Goiás. Os clones foram genotipados com nove locos microssatélites organizados em quatro sistemas “multiplex” para PCR. Os fragmentos amplificados foram separados na plataforma ABI-3100 (Applied Biosystems). A genotipagem foi realizada utilizando o programa GeneMapper (Applied Biosystems). Os parâmetros de diversidade genética foram estimados usando os programas GDA e Fstat. Os parâmetros número de alelos (A), heterozigosidade esperada (He), heterozigosidade observada (Ho), índice de fixação intrapopulacional (f) e riqueza alélica foram estimados para cada loco microssatélite. Os resultados mostraram que todos os locos utilizados neste estudo foram altamente polimórficos, com média de 16,78 alelos por loco. A genotipagem dos locos EMBRA28 e EMBRA3 mostrou o maior número de alelos (24 e 22). De maneira geral, para a maioria dos locos estudados, a heterozigosidade observada apresentou estimativas semelhantes à heterozigosidade esperada dentro das condições do Equilíbrio de Hardy-Weimberg. Como resultado, o índice de fixação (f) não diferiu significativamente de zero. A análise da estrutura genética dos clones foi realizada utilizando o programa Structure (versão 2.3.4), com valores de K variando de 1 a 10, com 10 iterações cada. Os resultados indicaram a presença de três grupos genéticos distintos (K = 3). Entretanto, não foi observada uma clara relação entre as populações obtidas e as diferentes espécies de Eucalyptus utilizadas no estudo. Esse resultado pode ser explicado pelo fato da amostra de clone ser originada de programas de melhoramento, onde os cruzamentos recombinam o material genético das populações, desfazendo algumas estruturas genéticas. De forma mais importante, as análises moleculares indicaram grande diversidade genética dentre os clones que estão sendo avaliados em Goiás. Esta diversidade genética pode ser explorada em um programa de melhoramento para obtenção de novos materiais genéticos adaptados às condições do Cerrado.

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8

Starnes, John H. "CHARACTERIZATION AND DISTRIBUTION OF NOVEL NON-LTR RETROELEMENTS DRIVING HIGH TELOMERE RFLP DIVERSITY IN CLONAL LINES OF MAGNAPORTHE ORYZAE". UKnowledge, 2013. http://uknowledge.uky.edu/plantpath_etds/6.

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The filamentous ascomycete fungus Magnaporthe oryzae is a pathogen of over 50 genera of grasses. Two important diseases it can cause are gray leaf spot in Lolium perenne (perennial ryegrass) and blast in Oryza sativa (rice). The telomeres of M. oryzae isolates causing gray leaf spot are highly variable, and can spontaneously change during fungal culture. In this dissertation, it is shown that a rice-infecting isolate is much more stable at the telomeres than an isolate from gray leaf spot. To determine the molecular basis of telomere instability several gray leaf spot isolates telomeres were cloned, which revealed two non-LTR retrotransposons inserted into the telomere repeats. The elements have been termed Magnaporthe oryzae Telomeric Retrotransposons (MoTeRs). These elements do not have poly-A tails common to many other non-LTR retrotransposons, but instead have telomere like sequences at their 5’ end that allow them to insert into telomeres. Intact copies of MoTeRs were restricted to the telomeres of isolates causing gray leaf spot. Surveys for the presence of these elements in M. oryzae showed they were present in several host-specialized forms including gray leaf spot isolates, but were largely absent in the rice blast isolates. The absence of MoTeRs in rice blast isolates, which are relatively stable by comparison, suggested that the telomere instability in gray leaf spot isolates could be due to MoTeRs. Analyzing spontaneous alterations in telomere restriction fragment profiles of asexual progeny revealed that MoTeRs were involved. Expansion and contraction of MoTeR arrays were observed and account for some telomere restriction profile changes. New telomere formation in asexual progeny followed by MoTeR addition was also observed. Based on this evidence, MoTeRs are largely responsible for the high variability of telomere restriction profiles observed in GLS isolates.

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9

鳥丸, 猛., e Takeshi TORIMARU. "クローンを形成する雌雄異株低木ヒメモチにおけるクローン多様性と遺伝的変異". 名古屋大学農学部付属演習林, 2005. http://hdl.handle.net/2237/8623.

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10

Gu, Hongcang. "GENETIC DIVERSITY AND SYMPTOM SEVERITY DETERMINANTS OF BEAN POD MOTTLE VIRUS". UKnowledge, 2004. http://uknowledge.uky.edu/gradschool_diss/441.

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Bean pod mottle virus (BPMV), a member of the genus Comovirus in the family Comoviridae, is widespread in the major soybean-growing areas in the United States. Soybean yield losses of 10-40% have been reported as a consequence of BPMV infection. The complete nucleotide sequences of two strains, K-Ha1 and K-Ho1, were determined. Field isolates of BPMV were classified into two distinct subgroups (I and II) based on slot blot hybridization and sequence analyses. Full-length cDNA clones from which infectious transcripts can be produced were constructed for strains K-G7, K-Ho1 and K-Ha1. Whereas strains K-Ha1 and K-G7 induced mild or moderate symptoms in infected soybean plants, strain K-Ho1 produced very severe symptoms. Symptom severity was mapped to RNA1. Chimeric RNA1 constructs were generated by exchanging full or partial coding regions of the five RNA1-encoded mature proteins between the full-length cDNA clones of the three RNA1s and the resultant transcripts were inoculated onto soybean. The results showed that the coding regions of the protease co-factor (Co-pro) and the putative helicase (Hel) are determinants of symptom severity. Although symptom severity correlated well with accumulation of viral RNA, neither the Co-pro nor Hel protein could be demonstrated as a suppressor of RNA silencing. Furthermore, separate expression of the Co-pro or Hel proteins from a PVX vector induced necrosis on the inoculated leaves of Nicotiana benthamiana. Characterization of BPMV K-Ho1 indicated that it is a diploid reassortant, containing two distinct types of RNA1s and one type of RNA2. Examination of field isolates from various locations in the United States and Canada revealed that diploid reassortants are of frequent occurrence in natural populations of BPMV. The vary severe symptoms induced by BPMV K-Ho1 can be mimicked by inoculation of plants with a mixture of RNA1 transcripts from two distinct strain subgroups and RNA2 transcript from either subgroup. Plants inoculated with a mixture of transcripts containing two types of RNA1 from the same strain subgroup did not produce very severe symptoms. These are due to interactions between two distinct types of RNA1s. At present, no soybean cultivars with resistance to BPMV are commercially available. Therefore, the feasibility of cross protection as an alternative disease management strategy was studied. Two mild strains of BPMV (K-Da1 and K-Ha1), belonging to subgroup II, were tested for their ability to protect infected plants against a severe strain (K-Ho1). Inoculation of the soybean cultivar Essex on the primary leaves with either of the two mild strains conferred complete protection against challenge inoculation with the severe strain K-Ho1, regardless of the timing of challenge inoculation. Cross-protection was evident regardless of whether virions or BPMV-RNA were used as inocula. Cross protection was independent of the soybean cultivar used and method of virus inoculation, sap-inoculation or by the bean leaf beetle, vector of BPMV. Protection was complete and durable.

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11

Musa, Muawiya Abarshi. "Molecular diagnostics, genetic diversity and generating infectious clones for cassava brown streak viruses". Thesis, University of Greenwich, 2012. http://gala.gre.ac.uk/9092/.

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Cassava brown streak disease (CBSD) threatens cassava production in eastern and southern African countries. Diagnostic protocols currently available for the causal agents of CBSD, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV), were unreliable but were urgently needed. In this study, sampling procedures and diagnostic protocols were developed for accurate and reliable detection of both CBSV and CBSUV. The cetyltrimethylammonium bromide (CTAB) method of RNA extraction was optimized for sample preparation from infected cassava plants and compared with the commercial kit RNeasy (Qiagen) for sensitivity and reproducibility. Results showed that both protocols were reliable but CTAB was more cost-effective and ideal for resource-poor laboratories. Mixed infections of cassava mosaic begomoviruses (CMBs) that cause cassava mosaic disease (CMD), CBSV and CBSUV have become more common with the recent spread of CBSD at mid-altitudes. A multiplex PCR for the simultaneous detection of viruses that cause both diseases, the first of its kind for cassava, was therefore developed to detect CBSV and CBSUV along with the three commonly occurring CMBs (African cassava mosaic virus (ACMV)), East African cassava mosaic virus (EACMV), and East African cassava mosaic virus-Uganda (EACMVUG) in eastern Africa. Similarly, a duplex PCR was developed for the simultaneous detection of CBSV and CBSUV, both viruses being detected in field-collected samples from Tanzania and Kenya. The genetic diversity of more than 40 CBSD isolates from Kenya, Tanzania, Uganda, and Mozambique was further examined by sequencing the coat protein (CP) gene and partial HAM1 gene sequences. The phylogenetic tree clustered the CBSD isolates into two groups reflecting the two virus species causing CBSD. In this study, various strategies were carried out for generating infectious clones of CBSV; gateway cloning, in vivo and in vitro transcription methods, and amplification of the viral genome in three fragments. Although 3 overlapping CBSV fragments were successfully cloned, the presence of an unexpected mutation at one of the cloning sites unfortunately did not allow reassembling of the fragments to construct the full-length cDNA.

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12

Rosvall, Ola. "Enhancing gain from long-term forest tree breeding while conserving genetic diversity /". Umeå : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1999. http://epsilon.slu.se/avh/1999/91-576-5643-6.pdf.

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13

Lundqvist, Elisabeth. "Genetics and ecology of natural populations". Doctoral thesis, Umeå universitet, Molekylärbiologi (Teknat- och Medfak), 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-103815.

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I have studied the genetic variation of single species using morphological variation and enzyme electrophoresis. I have striven to understand the interaction between the breeding structure and the ecology of the species in relation to the community, in which it lives. The work was done in the county of Västerbotten, northern Sweden. In the Skeppsvik archipelago I have studied the population structure of Silene dioica: ecotypic variation in other populations. I have also studied the genetic diversity of Angelica archangelica, Bistorta vivipara, Viscaria alpina and the earthworm Eiseniella tetraedra along the free-flowing Vindel and Sävar Rivers and the regulated Urne River. The island populations of S. dioica are subdivided into several breeding units and levels of differentiation among subpopulations within islands were about twice as high as among islands. Restricted seed and pollen dispersal creates patches made up of related individuals that may diverge as a result of drift. Frequent seed and pollen dispersal occurs among islands and they will receive the same alleles. This may explain the pattern of differentiation observed. In contrast, the patches within islands may be founded by only a few individuals. * S. dioica exhibits morphological differentiation in vegetative and floral characters between serpentine, cold spring, rich forest and coastal habitats. There was no association between genetic and geographical distance or between genetic distance and habitat. Serpentine and cold spring, which represented the most extreme habitats were also most differentiated. Populations of S. dioica are subject to herbivory; predation may exert a selective pressure on vegetative characters. A number of selective forces such as pollinators and fungal parasites act on reproductive characters. Assuming that water dispersal is important I tested several hypotheses to explain patterns of genetic diversity expected to be exhibited by riparian organisms along free-flowing and regulated rivers. I show that dispersal, distribution and breeding structure are important determinants of the evolution of the riparian flora. Patterns of genetic diversity may be exhibited at many spatial scales, e.g. among entire rivers, and between types of riverbanks within a river reach. Populations must be sampled at a spatial scale relevant to the hypothesis to be tested.

Diss. (sammanfattning) Umeå : Umeå universitet, 2002, härtill 5 uppsatser.

digitalisering@umu

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14

Rigonato, Janaina. "Diversidade de cianobactérias em manguezais do Estado de São Paulo". Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-17092010-183527/.

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Os micro-organismos desempenham importante papel na reciclagem dos elementos em ecossistemas de manguezais, uma vez que como produtores primários podem controlar reações químicas. O grupo particular das cianobactérias atua promovendo a entrada de carbono e nitrogênio por meio da sua capacidade de realizar fotossíntese oxigênica e fixação de nitrogênio atmosférico. No Brasil, as florestas de manguezais ocupam uma área de aproximadamente 25.000 km2 e no Estado de São Paulo, 240 km2 da área total está coberta por este ecossistema. O objetivo deste trabalho foi avaliar a diversidade de cianobactérias que colonizam as folhas de Avicennia schaueriana, Rhizophora mangle e Laguncularia racemosa do manguezal da Ilha do Cardoso, um ambiente pristino, bem como acessar e comparar a população de cianobactérias dos solos dos manguezais da Ilha do Cardoso e de Bertioga, este último contaminado com óleo bruto. Para este propósito, as técnicas de DGGE e biblioteca de clone do gene RNAr 16S, ARISA e TRFLP do gene nifH foram utilizadas. Os resultados da filosfera evidenciaram uma sutil influência do gênero de árvore na colonização das cianobactérias, entretanto, um forte efeito da localização destas dentro do manguezal foi observado. As folhas das árvores do meio da área de manguezal apresentaram uma maior diversidade de gêneros de cianobactérias. No geral, foram identificados 19 gêneros e várias sequências de cianobactérias não cultiváveis. Uma predominância de sequências com alta similaridade com representantes das ordens Nostocales e Oscillatoriales foi observada. Sequências com identidade com o gênero Symphyonemopsis (ordem Stigonematales) foram recuperadas em maiores quantidade. Com relação à diversidade no solo, os resultados de DGGE e ARISA demonstraram que a população de cianobactérias é distinta entre os manguezais estudados, porém os perfis eletroforéticos das amostras coletadas próximo ao mar se agruparam, sugerindo que a colonização é influenciada pelas condições de inundação. O perfil mais diferente foi obtido no ponto próximo à floresta no manguezal de Bertioga, local mais afetado pela contaminação de óleo. As bibliotecas de clones claramente indicaram diferenças das sequências do gene RNAr 16S entre os pontos amostrados. Um total de 99 UTOs foi obtido, com 61 singletons. Na localidade próxima ao mar os gêneros Procholorococcus e Synechococcus foram dominantes em ambos os manguezais. A maioria das sequências de RNAr 16S encontradas nos outros pontos foram relacionadas com cianobactérias não cultiváveis. A diversidade alfa sugeriu que o local com menor diversidade foi o meio do manguezal de Bertioga, e o maior foi em Bertioga próximo à floresta, os demais pontos tiveram valores similares. Os maiores índices de riqueza foram encontrados nos pontos próximos à floresta, enquanto menores valores foram observados nos pontos próximos ao mar. A maioria das sequências de RNAr 16S obtidas em Bertioga no meio do manguezal e próximo à floresta tiveram identidades menores do que 90% com as disponíveis no GenBank. Estas sequências podem representar novos táxons ou cianobactérias conhecidas, porém ainda não sequenciadas. O TRFLP do gene nifH indicou que os locais próximos ao mar e meio do manguezal na Ilha do Cardoso abrigaram populações de diazotróficos semelhantes, enquanto que em Bertioga estes pontos apresentaram diferenças nos perfis de TRFLP. As maiores diferenças estavam nos locais próximos à floresta em ambos os manguezais.
Microorganisms play important role in the recycling of elements in mangrove ecosystems, since as primary producers they can control chemical reactions. The particular cyanobacteria group act promoting the input of carbon and nitrogen through their ability to realize oxygenic photosynthesis and fixing atmospheric nitrogen. In Brazil, the mangrove forests occupy an area of approximately 25.000 km2, and in the total area of São Paulo State, 240 km2 are covered by this ecosystem. The aim of this work was to evaluate the cyanobacterial diversity that colonize Avicennia schaueriana, Rhizophora mangle and Laguncularia racemosa leaves from Cardoso Island mangrove, a pristine site, as well as to assess and compare the soil cyanobacterial population from both Cardoso Island and Bertioga mangroves, this last one contaminated with crude oil. For this purpose, the techniques of DGGE and clone library of 16S rRNA gene, ARISA, and TRFLP of nifH gene were used. The phyllosphere results evidenced a subtle difference of the genus of tree on the colonization of cyanobacteria, however a strong effect from trees location within the mangrove was observed. The tree leaves from the middle of mangrove area showed a greater diversity of cyanobacterial genera. In geral, 19 genera and several uncultivated cyanobacteria were identified. A predominance of sequences with high similarities to representatives of the order Nostocales and Oscillatoriales were observed. Sequences with similarities to the genus Symphyonemopsis (order Stigonematales) were recovered in higher quantity. Regarding to the soil diversity, DGGE and ARISA results showed that the cyanobacterial population is distinct among both mangroves studied, however the electrophoretic profiles from samples collected near to the sea grouped together, suggesting that colonization is influenced by flood conditions. The most different profile was obtained in the site near to the forest in Bertioga mangrove, location more affected by the oil contamination. Clone libraries clearly showed 16S rRNA sequences differences among sites sampled. A total of 99 OTUs were obtained, with 61 singletons. In the site near to the sea the Procholorococcus and Synechococcus genera were dominant in both mangroves. The majority of 16S rRNA sequences found in the other sites were related to uncultured cyanobacteria. Alpha diversity suggested that the site with lowest diversity was middle of the Bertioga mangrove, and the highest was Bertioga near to the forest, the remainder sites had similar values. The highest richness indices were found in the sites near to the forest, while lower values were observed in the sites near to the sea. The majority of the 16S rRNA sequences obtained from the middle of the mangrove and near to the forest in Bertioga showed identities lower than 90% with that available in the GenBank. These sequences may represent novel cyanobacterial taxa or known cyanobacteria not yet sequenced. The TRFLP of nifH gene indicated that the sites near to the sea and middle of the Cardoso Island mangrove harbored similar diazotrophic populations, while in Bertioga these sites presented differences in TRFLP profiles. The greatest differences were in the sites near to the forest in both mangroves.

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15

Mitchell, Suzanne Elizabeth. "Clonal diversity and coexistence in Daphnia magna populations". Thesis, University of Hull, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389469.

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16

Mirza, Intisar Hussain. "Clonal diversity of the immune response of insulin". Thesis, University of Southampton, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253776.

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17

Vardo-Zalik, Anne. "Clonal Diversity of the Malaria Parasite Plasmodium Mexicanum: Diversity Over Time and Space, and Effects on the Parasite’s Transmission, Infection Dynamics and Virulence". ScholarWorks @ UVM, 2008. http://scholarworks.uvm.edu/graddis/234.

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The biology of malaria parasites, Plasmodium spp., may be influenced by the presence of genetically distinct conspecific clones within a single infection, resulting in competition for host resources and transmission, and increased virulence for the vertebrate host. The extent of within host diversity, however, may be limited because overall clonal diversity could be reduced by the transmission biology of Plasmodium and variation in local prevalence. I examined clonal diversity of a natural malaria parasitehost association, P. mexicanum in its hosts, the western fence lizard, Sceloporus occidentalis, and sandflies, Lutzomyia vexator and L. stewarti, at a site in California ("Hopland"). Using microsatellite markers I characterized for the parasite, I examined (i) diversity within and among infections over time and space, (ii) transmission success of clones into both vector and lizard, (iii) the effects of clonal diversity on the parasite's infection dynamics and virulence for the lizard. From 1996 to 2006, clonal diversity varied both temporally and spatially, with slightly more multiclonal infections detected during years of high vs. low parasite prevalence (88% vs. 78% for sites with the highest prevalence at Hopland). Spatially, low prevalence sites (< 1% of lizards infected) had fewer multiclone infections (50%). Thus, even when prevalence drops over time, or at sites with chronically low prevalence, clonal diversity of the parasite remains high. Using natural and induced infections in the lizard, I found that multiclonal infections are no more infectious to vectors than single-clone infections, and almost all clones transfer successfully when the insect takes a blood meal. A competition experiment demonstrated that infections block new genotypes from entering a lizard host. Thus, multiclone infections are likely to be established when vectors feed on a complex infection and transmit those parasite clones to an uninfected lizard. The transmission biology of Plasmodium thus allows for the maintenance of genetic diversity in the parasite population. Finally, I examined the effects of multiclonality on the parasite's infection dynamics and virulence to the lizard host. Induced infections harboring a single or multiple clones had similar overall growth rates and maximal parasitemia, but multiclonal infections had significantly higher investment in gametocytes, suggesting competition for transmission. In addition, variation in parasite growth and density was greater for multiclonal infections, with approximately 1/3 displaying high replication rates and final parasitemia. Virulence measures indicated that weight change and proportion of immature erythrocytes was consistent for infections with 1, 2, 3 or > 3 clones, but the highly diverse infections had greater blood hemoglobin and glucose and more rapid clotting rates. Compared with the noninfected control lizards, highly diverse infections (3+) had higher blood glucose levels but similar hemoglobin levels. I have found that genetic diversity of the malaria parasite Plasmodium mexicanum varies both temporally and spatially, although overall diversity remains high. The transmission dynamics of the parasite maintains high genetic diversity within infections. Additionally, diversity within hosts plays a significant role in variation of infection dynamics and virulence.

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Tsujimoto, Michiaki. "Clonal population structure and genetic variation of ramet-production traits in a clonal plant, Cardamine leucantha". Kyoto University, 2020. http://hdl.handle.net/2433/253122.

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19

Crona, Joakim. "Charting the Genetic Landscape and Clonal Architectures of Pheochromocytoma". Doctoral thesis, Uppsala universitet, Institutionen för kirurgiska vetenskaper, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-234285.

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Genotypic and phenotypic inter patient heterogeneity characterize pheochromocytoma and paraganglioma (PPGL). Up to 60% of PPGL are associated with either somatic or germline mutations in at least 14 established disease causing genes. Consequently, a comprehensive screening test for PPGL patients utilizing standard techniques is not feasible and in the diagnostic approach, multiple different phenotype guided gene prioritization protocols have been utilized. This may result in misdiagnosis, especially in patients with sporadic presentation. Diagnostic testing of somatic mutations in tumour material is not performed due to the lack of actionable results. The aims of this study were, (1) to investigate the use of novel sequencing techniques in a clinical application, (2) to discover novel PPGL disease causing loci using novel sequencing techniques, (3) to characterize a large cohort of PPGL for mutations in known disease causing genes and to analyse corresponding genotype-phenotype correlations, (4) to dissect the molecular and genetic landscape of MEN2 PPGL and (5) to determine the clonal architecture and heterogeneity within, and in-between matched PPGL. For these purposes we studied PPGL tumours from a total of 96 patients using targeted and/or whole exome enrichment, capillary and high throughput sequencing as well as genome wide array based genotyping. Novel bioinformatics pipelines were constructed for raw data processing and downstream interpretation. Quantitative PCR, western blot and immunohistochemistry were utilized in order to characterize molecular traits. Selected experimental findings were correlated to patient phenotype. We conclude that novel sequencing techniques could be utilized in clinical genetic screening of patients with PPGL. Somatic gain-of-function mutations in H-RAS are likely to contribute to disease pathogenesis. Analysing tumour DNA for somatic mutations in disease causing genes could provide relevant clinical information and have an impact on patient management. Concomitant mutations in PPGL may occur in exceptional cases and have a substantial impact on tumour biology and patient phenotype. And finally genetic heterogeneity is present between and within a majority of PPGL tumours.

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Bumgarner, Stacie L. "Mechanisms underlying cell-to-cell diversity in clonal populations of yeast". Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/45150.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references.
The FLO promoters are among the largest promoters in yeast and receive a complex combination of signals from upstream signaling pathways through their association with downstream DNA binding factors and chromatin remodelers. The genes regulated by these promoters encode cell-surface glycoproteins that mediate a range of cell-to-cell and cell-to-surface adhesions. Phenotypic diversity in clonal populations of yeast cells is mediated in part by epigenetic silencing of the FLO10 and FLO11 promoters. Silencing of the FLO promoters is heterogeneous, or variegated, within a clonal population of cells. The variegated transcription of FLO10 and FLO11 results in a population of yeast cells that exhibits cell-to-cell variability in flocculation, adhesion to and invasion of inert surfaces, and filamentous growth. In this thesis, I discuss chromatin modifying proteins that localize to the FLO10 and FLO11 promoters and act in trans to affect transcription and silencing at these promoters. I describe the results of genome-wide screens to identify additional trans-acting chromatin modifying factors that play roles in the transcriptional regulation and silencing of the FLO10 and FLO11 promoters. Some of the candidates identified in these screens had effects on FLO transcription that initially seemed paradoxical in light of contemporary theories regarding the role of chromatin structure in regulating transcription. Given that histone deacetylases generally repress transcriptional activity, we were particularly surprised to find that mutations in components of the Rpd3L histone deacetylase complex reduce FLO promoter activity, indicating that Rpd3L plays a role in transcriptional activation of FLO genes. Careful analysis of these mutants, their phenotypes, the transcription of FLO11, and most importantly, the noncoding transcripts that we have detected in the promoter region of FLO11, have revealed the basis for this apparent paradox.
by Stacie L. Bumgarner.
Ph.D.

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Reina, Castillón Judith 1989. "Detectable clonal mosaicism : underlying mechanisms, clinical implications and genetic counselling". Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/666707.

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Somatic genetic mosaicism can be present both in healthy individuals but also in subjects with certain conditions as ageing or cancer. Its detection by SNP array in blood can be used as biomarker of cancer risk improving patients’ management and survival in the future. Given the increased cancer risk in Fanconi anemia (FA) patients, we have evaluated the prevalence and evolution of mosaicism in them as well as its relationship with cancer and survival. We also have studied mosaic uniparental disomy (UPD) as a putative protective mechanism in hematologic cancer. Finally, we have explored FA knowledge and follow-up adherence of FA families. Our results suggest blood mosaicism detection as a good less invasive follow-up strategy for cancer prevention in FA and propose UPD as a possible rescue mechanism avoiding hematologic cancer development. Two opposite roles of mosaicism in cancer become evident from our data. FA knowledge and follow-up adherence is satisfactory in FA families thanks to genetic counsellors’ actions.
El mosaicisme genètic somàtic pot està present en individus sans i en altres amb certes condicions com edat avançada o càncer. La seva detecció en sang per array d’SNPs pot ser utilitzada com a biomarcador de risc tumoral millorant el tractament i la supervivència dels pacients en un futur. Donat el risc de càncer incrementat en pacients amb anèmia de Fanconi (AF), hem avaluat la prevalença i l’evolució del mosaicisme en ells i la seva relació amb càncer i supervivència. També hem estudiat la disomia uniparental (DUP) en mosaic com a possible mecanisme de protecció en front el càncer hematològic. Finalment, hem explorat el coneixement sobre l’AF i l’adherència al seguiment en famílies AF. Els nostres resultats suggereixen la detecció de mosaicisme en sang com a sistema adequat i menys invasiu de detecció precoç de càncer en AF i proposa la DUP com a possible mecanisme de rescat protector en front el càncer hematològic. Dos rols oposats del mosaicisme envers el càncer esdevenen evidents considerant les nostres dades. El coneixement sobre l’AF i l’adherència al seguiment són satisfactoris en famílies AF gràcies a les accions dels assessors genètics.

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Abdollahi, Nika. "B cell receptor repertoire analysis in clinical context : new approaches for clonal grouping, intra-clonal diversity studies, and repertoire visualization". Electronic Thesis or Diss., Sorbonne université, 2021. http://www.theses.fr/2021SORUS063.

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Le séquençage de nouvelle génération a permis aux chercheurs de réaliser des analyses approfondies du paysage du répertoire immunologique. Cependant, une préoccupation importante dans ces études est le coût informatique de l'analyse de millions de séquences avec une complexité, une variabilité et une capacité de mutation inhérentes, imposant des défis informatiques et nécessitant le développement de méthodes efficaces. Ce défi est encore plus évident dans le contexte clinique qui n'a pas nécessairement accès à des professionnels ayant des compétences informatiques ou des ressources informatiques robustes. Ainsi, l'objectif principal de cette thèse est de développer un ensemble d'outils dédiés qui seront utilisés dans l'environnement clinique, pour le diagnostic médical et les soins aux patients, et dans l'environnement de recherche, pour effectuer une analyse approfondie et à grande échelle du répertoire. Nous avons conçu et implémenté de multiples algorithmes et les avons rassemblés dans un pipeline interactif de visualisation du répertoire BCR afin de faciliter le processus d'intégration de l'analyse du répertoire BCR dans les pratiques médicales
Next-generation sequencing has enabled researchers to conduct in-depth analyses of the immunological repertoire landscape. However, a significant concern in these studies is the computational cost of analyzing millions of sequences with inherent complexity, variability, and mutational capacity, imposing computational challenges and necessitating the development of efficient methods. This challenge is even more evident in the clinical context that does not necessarily have access to professionals with computing skills or robust computational resources. Thus, the main goal of this thesis is to develop a set of dedicated and integrated tools to be used in the clinical environment, for medical diagnostic and patient care, and in the research environment, to perform large-scale and in-depth repertoire analysis. We have designed and implemented multiple algorithms and gathered them in a user-friendly interactive BCR repertoire visualization pipeline to facilitate the process of integrating BCR repertoire analysis into medical practices

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Quinton, Margaret. "Genetic diversity in selected populations". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0016/NQ47407.pdf.

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Barker, Gary L. A. "Genetic diversity in Emiliania huxleyi". Thesis, University of Bristol, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294614.

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Fitzcharles, Elaine M. "Genetic diversity of Antarctic fish". Thesis, University of St Andrews, 2015. http://hdl.handle.net/10023/6860.

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Correct species identification is fundamental to all areas of biology, but particularly the policy related areas of conservation and fisheries management. To enable guidelines to be developed for environmental management and conservation, such identifications need links to studies of the evolutionary history, biological factors and environmental influences driving species divergence and population dynamics for the target species. This study concerns two genera of gadiform fish, Muraenolepis and Macrourus, found in southern temperate and Antarctic waters, with a single species, Macrourus berglax, present in the North Atlantic. With similar distribution patterns to toothfish species, Dissostichus eleginoides and D. mawsoni, they are a major food source and by-catch of the toothfish fishery. Both are slow growing and long lived, with different evolutionary histories, life expectancies and strategies for reproduction. For both genera, the accuracy of morphological keys, number of described species and their distribution is under debate. This study has identified specimens to species level using both morphological and genetic techniques, redefining the range for morphological features and taxonomic keys. For Muraenolepis, this has clarified confusion over Mu. marmoratus and Mu. microps being a single species, confirmed some mis-identification from sexual dimorphism and provided genetic evidence for the recently described species Mu. evseenkoi. For Macrourus, this work has identified a new species, now named Ma. caml, and found that Ma. holotrachys and Ma. berglax are genetically identical, raising the question of bipolar distribution or recent divergence. The low level of genetic variation within both species suggests a recent evolution and expansion into Antarctic waters. Similar geographic species limits imply common processes influencing divergence, with the oceanographic fronts as potential barriers. Further investigation of niche overlap and fine scale population structure are required to fully understand the processes driving speciation and provide the underlying data required for fisheries management.

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Rynearson, Tatiana A. "Clonal diversity, population differentiation and bloom dynamics in the centric diatom, Ditylum brightwellii /". Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/10979.

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Tan, Chia Lock. "Tissue culture and genetic transformation of Theobroma cacao". Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310835.

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Cornils, Kerstin, Lars Thielecke, Doreen Winkelmann, Tim Aranyossy, Mathias Lesche, Andreas Dahl, Ingo Roeder, Boris Fehse e Ingmar Glauche. "Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion". Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-230481.

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Background: Clonal competition in cancer describes the process in which the progeny of a cell clone supersedes or succumbs to other competing clones due to differences in their functional characteristics, mostly based on subsequently acquired mutations. Even though the patterns of those mutations are well explored in many tumors, the dynamical process of clonal selection is underexposed. Methods: We studied the dynamics of clonal competition in a BcrAbl-induced leukemia using a γ-retroviral vector library encoding the oncogene in conjunction with genetic barcodes. To this end, we studied the growth dynamics of transduced cells on the clonal level both in vitro and in vivo in transplanted mice. Results: While we detected moderate changes in clonal abundancies in vitro, we observed monoclonal leukemias in 6/30 mice after transplantation, which intriguingly were caused by only two different BcrAbl clones. To analyze the success of these clones, we applied a mathematical model of hematopoietic tissue maintenance, which indicated that a differential engraftment capacity of these two dominant clones provides a possible explanation of our observations. These findings were further supported by additional transplantation experiments and increased BcrAbl transcript levels in both clones. Conclusion: Our findings show that clonal competition is not an absolute process based on mutations, but highly dependent on selection mechanisms in a given environmental context.

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Paul, Richard E. L. "The genetic diversity of Plasmodium falciparum". Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318788.

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Townsend, S. J. "Genetic diversity and domestication in sheep". Thesis, University of East Anglia, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368146.

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Williams, Louise Jane. "Recombinational mechanisms in human genetic diversity". Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342483.

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Rogers, Emma Jayne. "Haplotype evolution and human genetic diversity". Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342507.

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Ritz, Liliane R. "Genetic diversity in the tribe Bovini /". [S.l.] : [s.n.], 1997. http://www.ub.unibe.ch/content/bibliotheken_sammlungen/sondersammlungen/dissen_bestellformular/index_ger.html.

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Schmid, Marianne. "Genetic diversity in Swiss cattle breeds /". [S.l.] : [s.n.], 1998. http://www.stub.unibe.ch/html/haupt/datenbanken/diss/bestell.html.

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Cutler, Jenny L. "Clonal diversity in populations of the seagrass thalassia testudinum in rabbit key basin, Florida bay". FIU Digital Commons, 1998. http://digitalcommons.fiu.edu/etd/2702.

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Levels of clonal diversity within the seagrass Thalassia testudinum Banks ex Kӧnig have been predicted to be low. This species has historically been perceived as relying on vegetative propagation for growth and extension of meadows, the role of sexual reproduction has been poorly understood. The purpose of this study was to test the hypothesis that detectable levels of variation exist within large T. testudinum meadows. I employed a probability based hierarchical sampling design to insure a thorough spatial coverage of the area. This method also allowed me to investigate variation at three different spatial scales. Genetic variation was tested for using a microsatellite based DNA fingerprinting technique proposed by Zietkiewicz et al, 1994. Variation was detectable at all spatial scales studied. Comparison of genetic vs. spatial distance suggested a trend of isolation by distance. This study shows that sexual reproduction is more important within Thalassia testudinum than was previously thought.

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Gardner, Michelle. "Genetic diversity of " brain genes" across worldwide". Doctoral thesis, Universitat Pompeu Fabra, 2007. http://hdl.handle.net/10803/7169.

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El treball presentat en aquesta tesi és un estudi de la diversitat genètica en un conjunt de gens implicats en funcions neurològiques ("Gens cerebrals"). Hom ha examinat vint-i-dos gens implicats en els sistemes de neurotransmissió dopaminèrgic, serotoninèrgic i glutamatèrgic.
L'objectiu de l'estudi té dos vessants: per una banda l'anàlisi de la diversitat genètica en un conjunt de gens implicats en malaltia humana, en aquest cas en malaltia psiquiàtrica, en poblacions humanes mundials, amb la intenció d'assentar les bases per propers esforços de mapatge genètic; i per altra banda analitzar la diversitat genètica en aquest conjunt de gens per tal de descobrir evidències d'esdeveniments històrics, incloent possibles evidències de selecció.
The work presented in this thesis is a study of the genetic variation in a set of genes related to neurological function ('Brain genes'). Twenty two genes are examined, all of which are involved in either the Dopaminergic, Serotonergic or the Glutamatergic systems of neurotransmission.
The objective of the study has two aspects: on the one hand the analysis of genetic variation in a set of genes which are implicated in human disease, in this case psychiatric disease, across global human populations, towards the end of providing some new insight for gene mapping efforts, and on the other hand the study of genetic variation in this set of genes may reveal traces of the population history events undergone, including possible evidence for selection.

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Wilkinson, Samantha. "Genetic diversity and structure of livestock breeds". Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/6488.

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This thesis addresses the genetic characterisation of livestock breeds, a key aspect of the long-term future breed preservation and, thus, of primary interest for animal breeders and management in the industry. First, the genetic diversity and structure of breeds were investigated. The application of individual-based population genetic approaches at characterising genetic structure was assessed using the British pig breeds. All approaches, except for Principle Component Analysis (PCA), found that the breeds were distinct genetic populations. Bayesian genotypic clustering tools agreed that breeds had little individual genetic admixture. However, inconsistent results were observed between the Bayesian methods. Primarily, BAPS detected finer genetic differentiation than other approaches, producing biologically credible genetic populations. BAPS also detected substructure in the British Meishan, consistent with prior known population information. In contrast, STRUCTURE detected substructure in the British Saddleback breed that could not wholly be explained. Further analysis of the British Saddleback revealed that the genetic subdivision did not reflect its historical origin (union of Essex pig and Wessex Saddleback) but was associated with herds. The Rainbarrow appeared to be moderately differentiated from the other herds, and relatively lower allelic diversity and higher individual inbreeding, a possible result of certain breeding strategies. The genetic structure and diversity of the British traditional chicken breeds was also characterised. The breeds were found to be highly distinctive populations with moderately high levels of within-breed genetic diversity. However, majority of the breeds had an observed heterozygote deficit. Although individuals clustered to their origin for some of the breeds, genetic subdivision of individuals was observed in some breeds. For two breeds the inferred genetic subpopulations were associated with morphological varieties, but in others they were associated with flock supplier. As with the British Saddleback breed, gene flow between flocks within the chicken breeds should be enhanced to maintain current levels of genetic diversity. Second, the thesis focused on breed identification through the assignment of individuals to breed origin. Dense genome-wide assays provide an opportunity to develop tailor-made panels for food authentication, especially for verifying traditional breed-labelled products. In European cattle breeds, the prior selection of informative markers produced higher correct individual identification than panels of randomly selected markers. Selecting breed informative markers was more powerful using delta (allele frequency difference) and Wright's FST (allele frequency variation), than PCA. However, no further gain in power of assignment was achieved by sampling in excess of 200 markers. The power of assignment and number of markers required was dependent on the levels of breed genetic distinctiveness. Use of dense genome-wide assays and marker selection was further assessed in the British pig breeds. With delta, it was found that 96 informative SNP markers were sufficient for breed differentiation, with the exception of Landrace and Welsh pair. Assignment of individuals to breed origin was high and few individuals were falsely assigned, especially for the traditional breeds. The probability that a sample of a presumed origin actually originated from that breed was high in the traditional breeds. Validation of the 96-SNP panel using independent test samples of known origin and market samples revealed a high level of breed label conformity.

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Gustafson, Steven Matt. "An analysis of diversity in genetic programming". Thesis, University of Nottingham, 2004. http://eprints.nottingham.ac.uk/10057/.

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Genetic programming is a metaheuristic search method that uses a population of variable-length computer programs and a search strategy based on biological evolution. The idea of automatic programming has long been a goal of artificial intelligence, and genetic programming presents an intuitive method for automatically evolving programs. However, this method is not without some potential drawbacks. Search using procedural representations can be complex and inefficient. In addition, variable sized solutions can become unnecessarily large and difficult to interpret. The goal of this thesis is to understand the dynamics of genetic programming that encourages efficient and effective search. Toward this goal, the research focuses on an important property of genetic programming search: the population. The population is related to many key aspects of the genetic programming algorithm. In this programme of research, diversity is used to describe and analyse populations and their effect on search. A series of empirical investigations are carried out to better understand the genetic programming algorithm. The research begins by studying the relationship between diversity and search. The effect of increased population diversity and a metaphor of search are then examined. This is followed by an investigation into the phenomenon of increased solution size and problem difficulty. The research concludes by examining the role of diverse individuals, particularly the ability of diverse individuals to affect the search process and ways of improving the genetic programming algorithm. This thesis makes the following contributions: (1) An analysis shows the complexity of the issues of diversity and the relationship between diversity and fitness, (2) The genetic programming search process is characterised by using the concept of genetic lineages and the sampling of structures and behaviours, (3) A causal model of the varied rates of solution size increase is presented, (4) A new, tunable problem demonstrates the contribution of different population members during search, and (5) An island model is proposed to improve the search by speciating dissimilar individuals into better-suited environments. Currently, genetic programming is applied to a wide range of problems under many varied contexts. From artificial intelligence to operations research, the results presented in this thesis will benefit population-based search methods, methods based on the concepts of evolution and search methods using variable-length representations.

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Clarke, Stephen James. "Genetic diversity in nativeIrish oak and ash". Thesis, Queen's University Belfast, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397902.

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Mauricio, Isabel Larguinho. "Genetic diversity in the Leishmania donovani complex". Thesis, London School of Hygiene and Tropical Medicine (University of London), 2000. http://researchonline.lshtm.ac.uk/682281/.

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The Leishmania donovani complex comprises four described species: L. donovani, L. archibaldi, L. infantum and L. chagasi. L. chagasi is the only New World species and has been considered similar to L. infantum, although some authors insist on maintenance of its independent species status. L. donovani has at least two major epidemiological subgroups whose relationships are poorly understood. In this thesis, molecular biological techniques were used to investigate the taxonomy and phylogenetic relationships within the L. donovani complex, with isoenzyme analysis (lEA) as reference technique. Random amplification of polymorphic DNA (RAPD) was used to provide anonymous genetic markers which allowed overall comparisons of genomes. Selected target genes and intergenic regions were also amplified by the polymerase chain reaction (PCR), namely the major surface protease (msp or gp63), the mini-exon and the ribosomal internal transcribed spacer (ITS). PCR products of intergenic regions between msp genes (ITG/CS and ITG/L), mini-exon and ITS were analysed by restriction fragment length polymorphism (RFLP). Phylogenies generated from each of the methods were compared with that of IEA. L. infantum and L. chagasi were found to be synonymous, whilst L. donovani was found to be more polymorphic than L. infantum and a fourth possible species in the complex, L. archibaldi, was not supported. Six genetic groups of strains were identified in the L. donovani complex, based on all DNA based analyses, which agreed with IEA typing. Pooled data from RFLP and RAPD analyses generated robust phylogenies which were congruent with ITG/CS RFLP and msp DNA sequence based phylogenies, but not with lEA phylogenies. The evolutionary history of the L. donovani complex is analysed in the light of the present results. The diverse typing methods were also evaluated and genetic markers suggested, that are applicable to classification and typing of L. donovani species and strains.

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Soto, Esteban. "Genetic and virulence diversity of Flavobacterium columnare". Master's thesis, Mississippi State : Mississippi State University, 2007. http://library.msstate.edu/etd/show.asp?etd=etd-05292007-091752.

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Palo, Jukka. "Genetic diversity and phylogeography of landlocked seals". Helsinki : University of Helsinki, 2003. http://ethesis.helsinki.fi/julkaisut/mat/ekolo/vk/palo/.

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Ceccobelli, Simone. "Genetic diversity of mediterranean autochthonous chicken breeds". Doctoral thesis, Università degli studi di Padova, 2013. http://hdl.handle.net/11577/3422653.

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Local breeds can be considered a part of the history of some human populations as well as important materials from a scientific point of view. The characterisation and inventory of animal genetic resources and routine monitoring of population for variability are fundamental to breed improvement strategies and programmes and for conservation programmes. Molecular genetics provide us with very remarkable tools to analyse the variation between and within breeds. Different approaches have been developed to understand the different aspects that contribute to breed differentiation. The thesis is made up in three contributes. The objective of the first part (Chapter 3) was to investigate genetic variation and to analyze population structure in two Italian breeds (Ancona and Livorno) as potential valuable genetic variability source. Blood samples from 131 individuals were collected and genotyped through a thirty microsatellites-based analysis. All the observed descriptive statistical indexes suggested a heterozygosity deficiency and an inbreeding level (mean observed heterozygosity = 0.46, mean expected heterozygosity = 0.53, FIS in Ancona and Livorno = 0.251 and 0.086). The tree from inter-individual DAS distance using Neighbour-Joining algorithm and the FCA analysis showed a higher internal variability in Livorno than in Ancona. STRUCTURE analysis showed the genetic uniqueness of the breeds and the presence of sub-groups in Ancona originating from a possible genetic isolation. In Chapter 4, the genetic characterization of five Italian chicken breeds (Ancona, Livornese bianca, Modenese, Romagnola and Valdarnese bianca) was described, including their remote genetic origins, the differentiation among them and their present level of biodiversity. The first aim of this study is to investigate the maternal genetic origin of five Italian local chicken breeds based on mitochondrial DNA (mtDNA) information. The second topic was to assess the genetic diversity and population structure of these chicken breeds, and to quantify the genetic relationships among them by using 27 microsatellite markers. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and probably two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described previously to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from of the five Italian breeds were collected. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher inbreeding index (FIS = 0.08) when compared to commercial populations used as reference. Structure analysis showed a separation of the Italian breeds from these reference populations; a further sub-clustering allowed to discriminate between the five Italian breeds. Aim of the third study was to investigate the genetic diversity and relationship among sixteen Mediterranean chicken populations using sequencing mitochondrial DNA and a panel of 27 microsatellite markers (Chapter5). A 506 bp fragment of the mtDNA D-loop region was sequenced in 160 DNA samples. Twenty-five variable sites, that defined 21 haplotypes, were observed and assigned to three clades and probably three maternal lineages. The major haplotype (E1) was present in the Mediterranean populations, originates from the Indian subcontinent. Different sequences were included in haplogroup A and B that are distributed in South China and Japan. For the microsatellite analysis, 465 individual blood samples from of the sixteen Mediterranean chicken populations were collected. The results indicated that about 22% of the total variability originated from variation between the Mediterranean populations as previously reported in other European chicken breeds. Structure analysis exhibited extensive genetic admixture in many studied populations. In conclusion, suitable conservation measures should be implemented for these breeds in order to minimize inbreeding and uncontrolled crossbreeding. A special care is required for the conservation and preservation of these potentially vulnerable breeds.
Le razze locali possono essere considerate parte della storia di molte popolazioni umane, così come materiale importante dal punto di vista scientifico. La catalogazione, la caratterizzazione e il controllo di routine della variabilità delle risorse genetiche animali sono pratiche fondamentali nelle strategie di miglioramento genetico e nei programmi di conservazione. La genetica molecolare ci fornisce importanti strumenti per analizzare la variabilità genetica tra e all’interno delle razze. Numerosi approcci sono stati sviluppati e utilizzati per comprendere i diversi aspetti che contribuiscono alla differenziazione delle razze. Questa tesi è costituita da tre contributi scientifici. L’obiettivo del primo (Capitolo 3) è stato quello di studiare la variabilità e analizzare la struttura di popolazione di due razze avicole Italiane (Ancona e Livorno), poiché possono essere considerate una fonte preziosa di variabilità genetica. Sono stati raccolti campioni di sangue da 131 animali e genotipati mediante l’utilizzo di un panel di 30 marcatori microsatelliti. Gli indici genetici calcolati suggeriscono un deficit di eterozigosità e un certo livello di consanguineità (eterozigosità media osservata = 0,46; eterozigosità media attesa = 0,53; FIS in Ancona e Livorno = 0,251 e 0,086). L’albero delle distance inter-individuali DAS, elaborato mediante l’algoritmo Neighbour-Jouning, e l’analisi FCA, hanno evidenziato una elevata variabilità interna in Livorno rispetto alla razza Ancona. L’analisi mediante il software STRUCTURE ha evidenziato l’unicità genetica delle due razze oggetto di studio e la presenza di subgruppi nella razza Ancona, derivanti da un possibile isolamento genetico. Nel quarto capitolo, è descritta la caratterizzazione genetica di cinque razze avicole italiane (Ancona, Livornese bianca, Modenese, Romagnola e Valdarnese Bianca), incluse le loro origini, la loro differenziazione e il loro attuale livello di variabilità genetica. Il primo obiettivo di tale studio è di indagare l’origine genetica di queste cinque razze di pollo italiane sulla base delle informazioni provenienti dal DNA mitocondriale (mtDNA). Il secondo obiettivo è stato quello di valutare la variabilità genetica, la struttura di popolazione e le loro relazioni genetiche mediante l’utilizzo di 27 marcatori molecolari microsatelliti. Al fine di raggiungere tali obiettivi, è stato sequenziato un frammento di 506 bp della regione D-loop del DNA mitocondriale di 50 animali delle cinque razze avicole oggetto di studio. Sono stati individuati diciotto siti di variabilità che hanno definito 12 aplotipi. Questi ultimi sono stati assegnati a tre aplogruppi, probabilmente attribuiti a due linee materne. I risultati hanno mostrato che il 90% degli aplotipi ricade nell’aplogruppo E, originario del subcontinente Indiano come descritto in precedenza da altri autori. Per l’analisi microsatellitare, 137 singoli campioni di sangue sono stati raccolti nelle cinque razze italiane oggetto di studio. Un totale di 147 alleli è stato rilevato in 27 marcatori microsatelliti. Le cinque razze Italiane hanno mostrato un livello di consanguineità leggermente superiore (FIS = 0,08) rispetto alle popolazioni commerciali utilizzate come razze di riferimento. L’analisi con il software STRUCTURE ha rilevato una chiara separazione delle cinque razze Italiane da queste popolazioni riferimento; una seconda analisi delle sole razze oggetto di studio ha permesso di discriminare le singole razze italiane. Scopo del terzo studio è stato quello di descrivere la variabilità genetica e le relazioni tra sedici popolazioni avicole allevate nel bacino del Mediterraneo, mediante il sequenziamento della regione D-loop del DNA mitocondriale e l’utilizzo di un panel di 27 marcatori molecolari microsatelliti (Capitolo 5). Un frammento di 506 bp del D-loop mitocondriale è stato sequenziato in 160 campioni di DNA. Sono stati osservati 25 siti di variabilità e 21 aplotipi che definiscono tre aplogruppi e probabilmente tre linee materne. Il principale aplotipo, individuato nelle popolazioni del Mediterraneo, è rappresentato dall’E1 derivante dal subcontinente Indiano. Altre sequenze sono incluse negli aplogruppi A e B, i quali originano dal sud della Cina e dal Giappone. Per l’analisi microsatellitare, sono stai racconti 465 campioni di sangue. I risultati indicano che circa il 22% della variabilità totale origina da variazioni che intercorrono tra le popolazioni oggetto di studio. L’analisi di STRUCTURE ha rilevato un’ampia mescolanza genetica in molte delle popolazioni studiate. In conclusione, adeguate misure di conservazione dovrebbero essere attuate al fine di minimizzare fenomeni di consanguineità e d’incrocio incontrollato nelle razze studiate. Particolare attenzione, pertanto, è richiesta al fine di conservare e salvaguardare queste razze potenzialmente vulnerabili.

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SAITTA, CLAUDIA. "Predisposition to hematological malignancies in children and adults: from genetic profiling to clonal evolution". Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/365155.

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Recenti evidenze hanno dimostrato come la predisposizione rivesta un ruolo cruciale nel 5-10% dei tumori pediatrici. Ciò nonostante, è ancora un ambito nebuloso, che va ulteriormente investigato. Nell’adulto, l’evoluzione clonale agisce in modo simile: l’accumulo di mutazioni somatiche dovuto all’età, aumenta la prevalenza di neoplasie mieloidi tra gli individui più anziani. Come specifici pathway di co-occorrenza predispongano a tumori ematologici, è da indagare in modo più approfondito. In questo studio, ci siamo focalizzati sul ruolo della predisposizione genetica nei tumori ematologici del bambino e dell’adulto, allo scopo di migliorare le conoscenze riguardo alle alterazioni genetiche che agiscono nella fase pre-leucemica. Abbiamo realizzato il nostro studio attraverso diverse tasks, caratterizzate dall’obiettivo comune di scandagliare il ruolo della predisposizione genetica nel promuovere la trasformazione neoplastica. Innanzitutto, abbiamo sequenziato una corte di 120 diagnosi consecutive di pazienti pediatrici affetti da Leucemia Linfoblastica Acuta e casi sporadici con altri tumori ematologici, così come casi con ricorrenza familiare. Il profiling genetico ha confermato il ruolo cruciale di alcuni geni nella Leucemogenesi, come quelli appartenenti al pathway di RAS, sia in termini di incidenza, sia di patogenicità. Inoltre, ha fatto luce sulle mutazioni germinali nelle Coesine: queste alterazioni, solitamente associate a sindromi genetiche denominate Coesinopatie, non sono eventi sporadici, ma si presentano con una frequenza non trascurabile (6%) e degna di ulteriori approfondimenti. Considerando questa evidenza, ci siamo focalizzati sulle varianti germinali dei geni STAG1 e RAD21. I nostri risultati hanno dimostrato che queste alterazioni sono responsabili di una scarsa coesione cromatinica, promuovono quindi instabilità genetica spontanea e sono caratterizzati da meccanismi di riparo al danno del DNA difettivi. Pertanto, geni che non sono classicamente correlati alla fase conclamata delle neoplasie ematologiche pediatriche promuovono condizioni che predispongono al cancro, aggravando infatti il rischio di eventi somatici responsabili dell’insorgere della neoplasia. Al fine di valutare il contributo della predisposizione genetica considerando tutto l’arco della vita, abbiamo investigato il ruolo dell’Evoluzione Clonale nell’adulto. Nonostante sia considerato un fenomeno fisiologico nell’invecchiamento, è anche significativamente associato a malattie cardiovascolari, tumori solidi e neoplasie ematologiche. Lo screening mutazionale di 1794 individui anziani (oltre 80 anni) ha permesso di stabilire un modello basato su tre gruppi di rischio, in cui l’accumulo differenziale di mutazioni somatiche dipendente dall’età aumenta la prevalenza di neoplasie mieloidi o malattie associate all’infiammazione. Nello specifico, le mutazioni dei geni dello Splicing, di JAK2, o la presenza di mutazioni multiple (DNMT3A, TET2, ASXL1 con lesioni genetiche aggiuntive), nonché le varianti con frequenza allelica ≥ 0,096, hanno un valore predittivo positivo per le neoplasie mieloidi. Infine, abbiamo sottolineato il ruolo delle mutazioni dei geni dello Splicing non solo come eventi precoci nella patogenesi, ma anche in una fase precedente, figure chiave nel determinare l’insorgenza della malattia mielodisplasica. In conclusione, una migliore conoscenza e caratterizzazione di queste alterazioni può avere impatti clinici differenti. In primo luogo, può garantire una migliore comprensione del processo di tumorigenesi, aprendo nuovi scenari in merito al contributo della Predisposizione genetica e dell’Evoluzione Clonale nelle neoplasie ematologiche. Inoltre, può avere conseguenze significative sia nella terapia dei pazienti, sia nella consulenza genetica familiare: consentirebbe quindi strategie di sorveglianza mirate e aggiustamenti terapeutici paziente-specifici.
Despite genetic predisposition occurs in 5-10 % of pediatric cancer, it is still a nebulous field, that has to be better characterized. In the adult setting, clonal evolution acts similarly, and age-dependent accumulation of somatic mutations increases the prevalence of myeloid neoplasms among older individuals. How the specific co-occurrence of somatic events predisposes to hematological malignancies have to be further clarified. In the present project, we focused our attention in dissecting the role of genetic predisposition in both childhood and adult hematological malignancies, with the purpose of improving knowledge about genetic alterations that act in pre-leukemic phase. We planned and developed our study through several tasks, characterized by the joint purpose of investigating the contribution of genetic predisposition in promote tumor transformation. Firstly, we screened a cohort of 120 consecutive diagnosis of pediatric patients affected by Acute Lymphoblastic Leukemia and sporadic cases with other hematological malignancies, as well as cases with familiar recurrence. Genetic profiling confirmed the crucial role of some genes in Leukemogenesis, like those belonging to Ras pathway, both in term of incidence and pathogenicity. Moreover, it shed light on germline mutations in Cohesins: these alterations, usually associated to genetic syndromes called Cohesinopathies, are not random or sporadic events, but occur with a frequency (6%) that is not negligible and worthy of further study. Considering this evidence, we made a focus on STAG1 and RAD21 germline variants. Our results demonstrated that they lead to a poor chromosomal strength and promote spontaneous instability, resulting in a lowered response to exogenous and endogenous agents, as well as defective DNA repair mechanisms. So, genes that are not classically related to full-blown stage of hematological disease, promote cancer prone conditions in pediatric patients, aggravating the risk of somatic events that are responsible of the disease’ onset. In order to evaluate the contribution of genetic predisposition in cancer considering overall the time of life, we investigated the role of clonal evolution in the adult setting. Despite it is considered normal in aging, it is also significantly associated with cardiovascular disease, as well as solid tumors and hematological malignancies. The mutational screening of 1794 oldest-old individuals allowed to establish a model based on 3 risk groups, in which differential age-dependent accumulation of somatic mutations increases prevalence of myeloid malignancies or inflammatory-associated diseases. Specifically, mutations in Splicing genes, JAK2 or the presence of multiple mutations (DNMT3A, TET2, ASXL1 with additional genetic lesions), as well as variants with allele frequency ≥0.096, have a positive predictive value for myeloid neoplasms. Finally, we underlined the role of Splicing genes mutations not only as early events in pathogenesis, but also in a previous phase, as key players in determine the onset of myelodysplastic disease. Overall, a better knowledge and characterization of these alterations will have different impacts: it will improve the understanding of tumorigenesis, opening new scenarios regarding the contribution of genetic predisposition and clonal evolution to hematological malignancies. Moreover, it could have significative effects on both patients’ care and familial genetic counseling, enabling targeted surveillance strategies, and tailored therapeutical adjustments that include familiar screening in case of familiar donor in hematopoietic stem cell transplantation.

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Moody, Jonathan. "Genetic diversity in the processing and transcriptomic diversity in the targeting of microRNAs". Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/25409.

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MicroRNAs are short RNA molecules that are central to the regulation of many cellular and developmental pathways. They are processed in several stages from structured precursors in the nucleus, into mature microRNAs in the cytoplasm where they direct protein complexes to regulate gene expression through, often imperfect base-pairing with target messenger RNAs. The broad aim of this project is to better understand how polymorphisms and new mutations can disrupt microRNA processing and targeting, and ultimately define their contributions to human disease. I have taken two approaches towards this. The first approach is to comprehensively identify the microRNA targets by developing and applying a novel computational pipeline to identify microRNA binding events genome-wide in RNA-RNA interaction datasets. I use this to examine the transcriptomic diversity of microRNA binding, finding microRNA binding events along the full length of protein coding transcripts and with a variety of non-coding RNAs. This reveals enrichment for non-canonical microRNA binding at promoters and intronic regions around splice sites, and identifies highly spatially clustered binding sites within transcripts that may be acting as competitive endogenous RNAs to compete for microRNAs, effectively sequestering them. Using statistical models and new cell fractionated RNA-seq data, I rank the features of microRNAs and their binding sites which contribute to the strength and specificity of their interaction to provide a better understanding of the major determinants of microRNA targeting. The second approach is to directly identify DNA sequence changes in microRNA precursors that alter processing efficiency affecting mature microRNA abundance which are routinely overlooked in the search for disease or trait associated causal variants. I have systematically screened public datasets for both rare and common polymorphisms that overlap microRNA precursors and are correlated with mature microRNA levels as measured in short RNA sequencing. I use these eQTL SNPs to examine the most important microRNA precursor regions and sequence motifs. Several of these SNPs have been observed as risk factors in cancer or other clinically relevant traits, and correlated with microRNA processing efficiency. I demonstrate that a specific DNA change which is known to be important in the development of some cancers, is located in a microRNA precursor and affects the balance of its two products, miR-146a-3p and miR-146a-5p, that can be produced from that single precursor providing new insights into the mechanisms of microRNA production and the aspects of genetic mis-regulation that result in cancer. I find further examples of common human polymorphisms that appear to affect microRNA production from their precursors, several of these variants are independently implicated in human immune disease, cancer susceptibility and associated with other complex traits. As they exhibit a molecular phenotype and immediately lead to mechanistic hypotheses of trait causality that can be tested, these variants could provide a route into the frequently intractable problem of mechanistically linking non-coding genetic variation to human phenotypes. Applying similar studies to patient DNA has revealed rare and unique DNA changes that are now candidates for causing human disease that are being subject to follow-up experimental studies. Collectively this work has started to define which sequences changes in microRNAs are likely to disrupt their function and provides a paradigm for the analysis of microRNA sequence variants in human genetic disease.

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Graham, Elaine Brigid. "Genetic diversity and crossing relationships of Lycopersicon chilense /". For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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47

Larsson, Pär. "The genetic composition and diversity of Francisella tularensis". Doctoral thesis, Umeå University, Clinical Microbiology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1139.

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Francisella tularensis is the causative agent of the debilitating, sometimes fatal zoonotic disease tularemia. To date, little information has been available on the genetic makeup of this pathogen, its evolution, and the genetic differences which characterize subspecific lineages. These are the main areas addressed in this thesis.

The work indicated a high degree of genetic conservation of F. tularensis, both on the sequence level as determined by sequencing and on the compositional level, determined by array-based comparative genomic hybridizations (aCGH). One striking finding was that subsp. mediasiatica was most similar to subsp. tularensis, despite their natural confinement to Central Asia and North America, respectively. All genetic Regions of Difference RD found by aCGH distinguishing lineages were had resulted from repeat-mediated excision of DNA. This was used to identify additional RDs. Such data along with a multiple locus sequence analysis suggested an evolutionary scenario for F. tularensis.

Based on genomic information, a novel typing scheme for F. tularensis was furthermore devised and evaluated. This method provided increased robustness compared to previously used methods for F. tularensis typing, while retaining a capacity for high resolution.

Finally, the genomic sequence of the highly virulent F. tularensis strain SCHU S4 was determined and analysed. Evidenced by numerous pseudogenes and disrupted metabolic pathways, the bacterium appears to be undergoing a genome reduction process whereby a large proportion of the genetic capacity gradually is lost. It is likely that F. tularensis has irreversibly has evolved into an obligate host-dependent bacterium, incapable of a free-living existence. Unexpectedly, the bacterium was found to be devoid of common virulence mechanisms such as classic toxins, or type III and IV secretion systems. Instead, the virulence of this bacterium is probably largely the result of specific and unusual mechanisms.

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48

Uimaniemi, L. (Leena). "Maintenance of genetic diversity in four taiga specialists". Doctoral thesis, University of Oulu, 2004. http://urn.fi/urn:isbn:9514274105.

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Abstract Genetic diversity in three taiga specialists – the Siberian tit (Parus cinctus), the Siberian jay (Perisoreus infaustus) and the Siberian flying squirrel (Pteromys volans) – was assessed by comparing DNA sequence variation across the mitochondrial control region and allele frequencies of microsatellites from samples collected from Fennoscandia and Siberia. Population sizes of these species have declined in association with fragmentation and loss of suitable forest habitat due to modern forestry practices in Fennoscandia. The red squirrel (Sciurus vulgaris) served as a reference for the flying squirrel. Genetic differentiation among species studied ranged from a panmictic population in the Siberian tit to that of the strong differentiation of populations (θST = 53%) in the flying squirrel in Finland. MtDNA and microsatellite data, together with assignment studies, showed the Siberian jay population to be significantly genetically structured and supported the existence of a metapopulation like structuring in Fennoscandia. Division of genetic variation among flying squirrel populations along the ancient shoreline of the Littorina Lymnea Sea stage of the Baltic Sea (7000 BP) and two geographically associated branches in the minimum spanning network supported a two-way colonisation history for the species. The Finnish inland appears to have been colonised from the east in association with the arrival of Norway spruce. At the same time, Coastal Finland was colonised from the south-east through the Karelian Isthmus. Gene flow of the species appeared female biased and restricted. Species exhibiting more restrictive dispersal characteristics and habitat requirements possessed stronger population genetic structure than those with opposite characteristics. Growth or contractions in population size leave characteristic signatures in mtDNA that can be studied by comparing different sequence diversity estimates among populations. I applied this method to the species studied. Significant differences in nucleotide diversities indicated restrictions in gene flow among populations in all species studied. Half of the Siberian jay populations gave a signal of population size bottleneck. All the species studied showed differences in their population genetic structures across their entire distribution ranges consistent with the multirefugia model, most likely to be attributable to differences in their ecological characteristics and Pleistocene histories.

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49

Larsson, Pär. "The genetic composition and diversity of Francisella tularensis /". Umeå : Umeå universitet, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1139.

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50

Ismail, Mohamed. "Molecular genetic diversity among natural populations of Populus". Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/26273.

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Genetic diversity is a key factor in species survival, evolution, and adaptation. It also reveals species genetic structure and provides insights into how different demographic forces shape species genetic variability. Although, black cottonwood (Populus trichocarpa Torr. & Gray) is the first tree to have its genome completely sequenced; however, information regarding its natural genetic diversity and population structure is lacking. I have investigated the extent of genetic diversity within and among 38 natural populations of P. trichocarpa sampled across British Columbia using 10 nuclear (nuSSR) and 12 chloroplast microsatellite (cpSSR) markers. CpSSR represents two haplotypes, clustering as northern and southern groups; however, a Bayesian population structure analysis suggested the presence of three highly admixed groups supported by low population differentiation (low FST and RST). Monmonier’s spatial analysis suggested the presence of one genetic discontinuity dividing the studied area into northern and southern regions. These findings indicated that P. trichocarpa might have originated from two, northern and southern, glacial refugia that have experienced moderate contact through extensive gene flow. Nucleotide diversity for 10 candidate-gene loci involved in adaptive, defence, and housekeeping functions was abundant and varied across loci, with the majority showing neutral variations. Linkage disequilibrium (LD), decays rapidly to r² ≈ 0.18 within 700 base pairs (bp). Comparing the nucleotide diversity between P. trichocarpa and P. balsamifera L. to the Eurasian P. tremula L. indicated that the two North American species had lower diversity (θw range 0.002 to 0.004) than the Eurasian poplar (θw = 0.005). The estimated time of divergence between the two North American and the Eurasian species indicated that the latter was five- to six-fold older compared to the two former species. The substitution rate was lower in North American species (0.4 x 10-⁸ per year) compared to the Eurasian poplar (2 x 10-⁸). Different association genetics models produced strikingly different results after the inclusion or exclusion of population structure, highlighting the importance of proper model construction.

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Teses / dissertações sobre o tema "Clonal and genetic diversity"

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