Previous evidence has shown that the simple sequences microsatellites and poly-purine/poly-pyrimidine tracts (PPTs) could be both a cause, and an effect, of meiotic recombination. The causal link between simple sequences and recombination has not been much explored, however, probably because other evidence has cast doubt on its generality, though this evidence has never been conclusive. Several questions have remained unanswered in the literature, and I have addressed aspects of three of them in my thesis. First, what is the scale and magnitude of the association between simple sequences and recombination? I found that microsatellites and PPTs are strongly associated with meiotic double-strand break (DSB) hotspots in yeast, and that PPTs are generally more common in human recombination hotspots, particularly in close proximity to hotspot central regions, in which recombination events are markedly more frequent. I also showed that these associations can't be explained by coincidental mutual associations between simple sequences, recombination and other factors previously shown to correlate with both. A second question not conclusively answered in the literature is whether simple sequences, or their high levels of polymorphism, are an effect of recombination. I used three methods to address this question. Firstly, I investigated the distributions of two-copy tandem repeats and short PPTs in relation to yeast DSB hotspots in order to look for evidence of an involvement of recombination in simple sequence formation. I found no significant associations. Secondly, I compared the fraction of simple sequences containing polymorphic sites between human recombination hotspots and coldspots. The third method I used was generalized linear model analysis, with which I investigated the correlation between simple sequence variation and recombination rate, and the influence on the correlation of additional factors with potential relevance including GC-content and gene density. Both the direct comparison and correlation methods showed a very weak and inconsistent effect of recombination on simple sequence polymorphism in the human genome.Whether simple sequences are an important cause of recombination events is a third question that has received relatively little previous attention, and I have explored one aspect of it. Simple sequences of the types I studied have previously been shown to form non-B-DNA structures, which can be recombinagenic in model systems. Using a previously described sodium bisulphite modification assay, I tested for the presence of these structures in sequences amplified from the central regions of hotspots and cloned into supercoiled plasmids. I found significantly higher sensitivity to sodium bisulphite in humans in than in chimpanzees in three out of six genomic regions in which there is a hotspot in humans but none in chimpanzees. In the DNA2 hotspot, this correlated with a clear difference in numbers of molecules showing long contiguous strings of converted cytosines, which are present in previously described intramolecular quadruplex and triplex structures. Two out of the five other hotspots tested show evidence for secondary structure comparable to a known intramolecular triplex, though with similar patterns in humans and chimpanzees. In conclusion, my results clearly motivate further investigation of a functional link between simple sequences and meiotic recombination, including the putative role of non-B-DNA structures.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Enneacanthus chaetodon, the blackbanded sunfish, has become increasingly rare throughout its distribution in the Eastern United States. In Virginia, E. chaetodon maintains an endangered status and individuals persist in six populations. Mitochondrial DNA (mtDNA) and microsatellite data were assessed to determine the genetic characters and gene diversity of the Virginia populations. The results of these analyses were then compared to five additional populations; four from New Jersey and one from North Carolina that were known to have relatively good fitness and were not impacted severely by habitat alteration. The results of this study are relevant to selection of proper management techniques and strategies for this species. Mitochondrial DNA analyses detected no variation in the Virginia populations but significant (P F > 0.2) of inbreeding. The New Jersey and North Carolina populations demonstrated lower amounts of inbreeding than populations in Virginia. New Jersey displayed a significant (P < 0.05) amount of subdivision among populations compared to Virginia. Hypothesis testing supported the contention that the regions are significantly different from one another and that Virginia populations may have gone through one or more population bottlenecks in the past, explaining the low levels of diversity observed and significantly high inbreeding coefficients. Captive breeding programs could be implemented as a management measure to increase population numbers and restore fish into areas where they have been known to inhabit in the recent past. From a proper management perspective, habitat protection and maintenance are more important than supplementation to population survival. Success of either approach with Virginia populations would provide a useful model for managing small populations of blackbanded sunfish in other regions.This project was supported by a grant from the Virginia Department of Game and Inland Fisheries (VDGIF), grant #ED0817BB.

Elucidating patterns of connectivity for species of conservation concern is crucial in the design of networks of ecologically coherent marine protected areas, and therefore is considered in the design of such a network recently proposed to the UK Government. However, data concerning connectivity are deficient for most invertebrate sessile taxa. Therefore, this study used microsatellite panels developed de novo to assess the population genetic structure and genetic connectivity of two temperate octocorals in the North East Atlantic. Microsatellite panels for both species show evidence of cross-species transferability, and therefore in future may prove to be useful monitoring tools for the target species but also for congenerics further afield in Europe. Eunicella verrucosa (O. Alcyonacea: S.O.Holaxonia: F. Gorgoniidae), a threatened and IUCN red-listed sea fan, was sampled in the northerly extremes of its eastern Atlantic range in southern Portugal, Brittany, the South West UK and western Ireland. In this vicinity, connectivity appears to be defined at regional scales and localised cases of inbreeding and differentiation suggest that the population structure of this species is best described as a metapopulation. Alcyonium digitatum (O. Alcyonacea: S.O. Alcyoniina: F. Alcyoniidae), a soft coral, was sampled in the central portion of its range in Brittany, western Ireland, south west UK and the North Sea. This species exhibited very little population structure and apparent panmixia across the sampled range. However, high levels of heterozygote deficiencies and inbreeding in the majority of populations implies that the genetic structure of some populations of this species may be defined by self-seeding and rarer dispersal events that occur sufficiently often to offset divergence via genetic drift. Coalescent analyses indicate that in both species, migration between regions occurs asymmetrically. The presence of few duplicate genotypes in both datasets implies that sexual reproduction predominates in both species in the sampled area. Eunicella verrucosa is a charismatic species that is often used to promote marine conservation efforts in the UK and A. digitatum is a ubiquitous animal around western European coasts; the two species often occur together and both may suffer the damaging effects of mobile fishing gears. This research represents the first population genetic assessment of both species and the first time microsatellites have been used to assess population structure of octocorals in the North East Atlantic.

Seven families of XX and YY homozygous Oreochromis niloticus were produced by mitotic gynogenesis from XY neofemales and their genetic status was verified by multilocus DNA fingerprinting and progeny testing. Two of these gynogenetic families and their corresponding diploid controls were used with 64 AFLP primer combinations in different levels of screening (XX/YY grand pool; XX/YY family pool; XX/YY gynogenetics and XX/XY control individuals) to search for sex-linked or sex-specific markers. Grand pool screening did not reveal any sex-linked markers. Subsequent family pool and individual level screening identified four sex-linked AFLP markers from two primer combinations, three Y-linked (OniY425, OniY382, OniY227) and one X-linked (OniX420). Two of these (OniX420, OniY425) were shown to be allelic. Single locus PCR markers were developed for all of those markers. Linkage analysis of these markers and the sex locus within the source families revealed tight linkage, with estimated map distances of 13cM, 17cM and 20cM for OniY382, OniY227 and OniX420/OniY425 respectively. However, these sex-linked AFLP markers failed to consistently identify sex in unrelated individuals. To develop an effective system for parentage analysis in normal and gynogenetic progeny, AFLPs and multiplexed polymorphic microsatellite loci were investigated. Both were found to be effective, but microsatellites were more appropriate since they are codominant and some loci showed high gene-centromere recombination rates, suitable for discriminating meiotic from mitotic gynogenetics, while AFLPs are dominant markers. Spontaneous diploidization of the maternal chromosome set (SDM) was observed in gynogenetic progeny of one XY neofemale. Maternal inheritance and ploidy status were verified by multilocus DNA fingerprinting and chromosome karyotyping. Close genetic linkage between the red gene and an autosomal sex-reversal gene(s) in gynogenetic progeny and influences of autosomal sex-reversal gene(s) producing males in a fully inbred XX clonal line were previously reported in O. niloticus. To test if the same autosomal sex-reversal locus was responsible in both cases, a series of test crosses was carried out involving XX clonal neomale(s) and homozygous red females. The results indicated the involvement of more than one autosomal sex-reversal locus, one of which is linked to red body colour.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

The praying mantis (Mantis religiosa) is the only representative of the order Mantodea in central Europe. Within Czech Republic, this species is distributed mostly on xerothermic localities in southern Moravia. However, M. religiosa has been spreading more to the north not only in Czech Republic, but also in other Europian countries recently. The aim of this study was to reconstruct phylogeography based on genetic markers. It seems that studied species was distributed at least in three lineages in Europe, which could be connected with glacial refugias. First lineage was spread to the north probably from Pyrenean peninsula, second lineage from Crimea peninsula and third lineage from Balkan area. Nine microsatellite loci were tested and will be used for consequent sctudy of phylogeography and distribution of M. religiosa within Europe. Keywords: Mantis religiosa, mtDNA, microsatellite, expansion, phylogeography, phylogeny.

Master of Science / Division of Biology / Samantha M. Wisely / Range-wide estimates of shorebird (Aves: Charadriiformes) populations suggest sharp declines in population sizes across a range of species. Efforts to accurately assess the conservation status of wild populations are becoming increasingly vital to species management. One shorebird of conservation concern, the Buff-breasted Sandpiper (Tryngites subruficollis), is a New World migrant which winters in southeastern South America and breeds in the arctic. To establish an updated conservation status for Buff-breasted Sandpipers, we conducted a molecular survey of wild populations on spatial and temporal scales. We analyzed patterns of global population structure, demographic trends, and phylogeography using nine polymorphic microsatellites and two mitochondrial DNA (mtDNA) markers, cytochrome b and the control region, among 477 individuals across their distributional range. To empirically assess the impact of population declines on genetic diversity, we also surveyed segments of the same two mtDNA markers from 220 museum specimens collected across a 135-year period. Contemporary microsatellite and mtDNA analyses revealed that Buff-breasted Sandpipers are admixed on a global scale, with effective population size estimates ranging from 2,657 to 16,400 birds and no signal of a recent genetic bottleneck. Contemporary mtDNA analyses suggested a pattern of haplotype diversity consistent with a historic radiation from a single refugium which we estimated to have occurred between 8,000−45,000 years before present. Using five measures of mtDNA diversity (haplotype and nucleotide diversity, trend analyses of haplotype richness, Watterson’s estimate of theta, and phi-statistics), as well as a Bayesian Skyline reconstruction of demographic trends in effective population size (N[subscript]e[subscript]f), we concluded that substantial mtDNA diversity and N[subscript]e[subscript]f had not been lost as a result of the population declines in this species. While genetic diversity did not appear to have been lost due to population losses, management efforts must focus on preventing future losses in order for wild populations to remain viable. Our results suggested that the global population of Buff-breasted Sandpipers should be treated as a single, panmictic conservation unit and that successful management must focus on preventing further declines and habitat fragmentation.

The genetic status of the critically endangered Mississippi sandhill crane (Grus canadensis pulla) was analyzed using 2009 studbook data from the U.S. Fish and Wildlife Service managed captive breeding and release program. Microsatellite DNA data provided information on shared founder genotypes, allowing for refined analysis of genetic variation in the population, and informed breeding recommendations. The genetic variation observed in the Mississippi sandhill crane was contrasted with variation observed in the Florida sandhill crane (Grus canadensis pratensis). Results show far less variation in the Mississippi population. Results also suggest that while gene flow no longer occurs between the two populations, the introduction of cranes from the Florida population would help to increase the observed genetic diversity of the Mississippi sandhill crane population.

Anadenanthera é um gênero botânico pertencente à família Mimosaceae e endêmico da América Latina e Caribe. Compreende duas espécies arbóreas tropicais: Anadenanthera colubrina (Vell.) Brenan. (angico, angico vermelho, angico branco, curupay) e Anadenanthera peregrina (L.) Speg. (angico, angico preto, angico de casca, angico do cerrado, yopo ou cohoba). As duas espécies são de ocorrência frequente na paisagem da região de Ribeirão Preto, apresentando-se em aglomerados quase monoespecíficos popularmente conhecidos como angicais. Visando contribuir para futuras medidas conservacionistas, o objetivo deste trabalho foi investigar a diversidade genética, o sistema de reprodução, a estrutura genética espacial e o fluxo gênico contemporâneo de A. colubrina e A. peregrina em angicais da Região de Ribeirão Preto SP usando como ferramenta de análise um conjunto de marcadores moleculares microssatélites (SSR). Para isso, foram construídas duas bibliotecas enriquecidas para microssatélites usando a espécie A. colubrina que resultaram em 20 marcadores SSR testados para a espécie e subsequentemente transferidos para A. peregrina. Desses 20 marcadores, 14 foram polimórficos em cada uma das espécies. Através dessa ferramenta molecular, foi possível realizar os estudos de diversidade genética, endogamia e distribuição genética espacial em A. colubrina e A. peregrina na região de Ribeirão Preto, que acusaram de uma maneira geral, muitas semelhanças entre as duas espécies, bem como entre os angicais de uma mesma espécie. A diferença mais marcante encontrada entre elas foi com relação a estrutura genética espacial, pois todos os angicais de A. colubrina apresentaram forte estruturação, enquanto que os de A. peregrina demonstraram ter uma dispersão aleatória dos indivíduos. O sistema reprodutivo e o fluxo de pólen nas duas espécies foi acessado usando sete marcadores moleculares microssatélites. Para essas análises foram genotipados indivíduos juvenis e adultos (totalizando 352 de A. colubrina e 355 de A. peregrina) presentes nos angicais Acol/PB, Aper/SP255 e Aper/Faz. Através das análises constatou-se que ambas as espécies tem sistema de acasalamento misto, embora A. colubrina tenha apresentado uma proporção maior de autofecundação (tm Acol = 0,619; tm Aper= 0,905). Também foram encontrados elevados índices de cruzamento entre parentes (tm-ts Acol = 0,159; tm-ts Aper = 0,216) e parentesco (coancestria), o que resultou num baixo tamanho efetivo populacional para ambas as espécies. As estimativas das taxas de cruzamentos multilocos individuais apresentaram grande variação nas duas espécies, mostrando a flexibilidade do sistema reprodutivo no gênero Anadenanthera. O número efetivo de doadores de pólen foi muito baixo para um mesmo fruto (1,10 em A. colubrina e 1,24 em A. peregrina) e mais alto entre frutos de uma mesma árvore (2,61 em A. colubrina e 3,35 em A. peregrina), usando a estimativa indireta de correlação de paternidade. Análises de paternidade revelaram distâncias de dispersão de pólen em duas escalas para ambas as espécies. Dessa forma, ocorreram muitos cruzamentos locais, entre árvores próximas no mesmo angical, mas também foram encontradas grandes distâncias de dispersão de pólen. A média da distância de dispersão em A. colubrina foi de 299,88 m e de 214,369 m em A. peregrina. Alto fluxo de pólen oriundo de árvores externas aos angicais de ambas as espécies foi detectado, indicando que os grupos não são isolados reprodutivamente. Por outro lado, o fluxo gênico crítico foi também muito elevado nas estimativas, provavelmente devido ao baixo poder de exclusão que os locos apresentaram dentro dos angicias de ambas as espécies. / Anadenanthera is a genus of Mimosaceae that is endemic to Latin America and the West Indies and comprises two tropical tree species: Anadenanthera colubrina (Vell.) Brenan. (popularly known as angico, angico vermelho, angico branco or curupay) and Anadenanthera peregrina (L.) Speg. (angico, angico preto, angico de casca, angico do cerrado, yopo or cohoba). Both species are commonly found in the Ribeirão Preto region, usually as nearly monospecific agglomerates known as angicais. To aid future conservationist measures, this work investigated the genetic diversity, gene flow, spatial genetic structure and contemporary mating system of A. colubrina and A. peregrina in the angicais of Ribeirão Preto Region SP by analyzing a sample of simple sequence repeat markers (SSR). Two microsatellites libraries were created from A. colubrina, providing 20 SSR markers that were tested for that species and later applied to A. peregrina. Fourteen out of the 20 markers were polymorphic between the species, allowing an examination of the genetic diversity, endogamy and spatial genetic structure in A. colubrina and A. peregrina in the Ribeirão Preto region, which revealed several similarities between the two species, as well as among the angicais of a single species. The most remarkable difference between the species was related to the spatial genetic structure, as all angicais of A. colubrina presented strong structuration, whereas those of A. peregrina exhibited an aleatory dispersion of individuals. The mating system and pollen flow in both species were analyzed through seven SSR. Adults and juveniles from the angicais Acol/PB, Aper/SP255 and Aper/Faz were genotyped for those analyses (352 specimens of A. colubrina and 355 of A. peregrina), revealing that both species undergo a mixed mating system, although A. colubrina presented a higher percentage of self-mating (tm Acol = 0.619; tm Aper= 0.905). High indices of mating among relatives (tm-ts Acol = 0.159; tm-ts Aper = 0.216) and coancestry were also found, resulting in a low effective population size for both species. A wide range in the estimate of the mutilocus breeding rate was found for both species, reflecting the plasticity of the mating system in the genus Anadenanthera. The effective number of pollen donors was very low for a single fruit (1.10 in A. colubrina and 1.24 in A. peregrina) and higher between fruits from the same tree (2.61 in A. colubrina and 3.35 in A. peregrina), using an indirect estimate of the paternity correlation. Paternity analyses revealed the distance of pollen dispersion on two different scales: many local outcrossings (between close trees from the same angical) in addition to long-distance pollen dispersion. The average dispersion distance was 299.88 m in A. colubrina and 214.369 m in A. peregrina. A high pollen flux from trees outside the angicais of both species was observed, indicating a lack of reproductive isolation. However, the gene flow was also very high, likely due to the low power of exclusion presented by loci from both species inside the angicais.