Thesis (Ph. D.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 260-285). Also available on the World Wide Web.

Thesis (Ph. D.)--University of Alberta, 1997. / Includes bibliographical references.

Orientador: Paulo Eduardo Martins Ribolla / Banca: Virgilio E. do Rosário / Banca: Alexandre Afrânio / Banca: Marcelo Urbano / Banca: Maria Anice Mured Sallum / Resumo: A malária é uma das principais parasitoses humanas do mundo, causando mais de um milhão de mortes, e quase 500 milhões de casos agudos da doença por ano. No Brasil, esta doença continua sendo uma das mais importantes do país, tendo sido registrados no ano de 2009 mais de 300 mil casos. O mosquito Anopheles darlingi é o principal vetor desta doença no Brasil e outros países da América do Sul. Devido à sua importância como vetor da malária humana, estudos sobre a estrutura populacional de An. darlingi tem sido objeto de vários estudos. A sua distribuição na Região Amazônica é ampla e dados recentes mostram alto grau de heterogeneidade, tanto genética como de comportamento. Grande parte desta variabilidade observada em An. darlingi pode estar relacionada com estratégias adaptativas para explorar nichos ecológicos distintos enquanto que a estrutura populacional e a diferenciação pode ser explicada por diferenças no tamanho efetivo da população, padrões de fluxo gênico e acontecimentos históricos e de colonização recente. De igual modo, alterações ambientais efetuadas pelo homem podem ter um impacto significativo na dinâmica de populações de vetores e, consequentemente, na transmissão da malária. Este projeto utilizou a genotipagem de 10 microssatélites para o estudo populacional de Anopheles darlingi coletados em sete localidades ao longo da extensão das Hidrelétricas de Jirau e Santo Antônio, às margens do Rio Madeira, em Porto Velho - RO. Estes métodos foram aplicados na caracterização de amostras coletadas nestas regiões no 1º e 2° semestres de 2007. O objetivo do trabalho foi analisar a estrutura populacional de An. darlingi ao longo do Rio Madeira, na área de influência das Hidrelétricas de Jirau e Santo Antônio. Os resultados mostraram alto fluxo gênico entre as populações, mesmo distando de 70 km. Foram encontradas diferenças... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Malaria is the major human parasitic diseases in the world, causing more than a million deaths and almost 500 million acute cases of disease per year. In Brazil, this disease remains one of the most important, having been recorded in the year of 2009 more than 300.000 cases. The mosquito Anopheles darlingi is the principal malaria vector in Brazil and other countries in South America. Due to its importance as a vector of human malaria, population structure of Anopheles darlingi has been the subject of several studies. Its distribution in the Amazon region is large and recent data show a high degree of heterogeneity, regarding genetic and behavioral aspects. Much of this observed variability may be related to adaptive strategies to exploit different ecological niches, while the population structure and differentiation can be explained by differences in effective population size, patterns of gene flow and historical events and recent colonization. Similarly, environmental changes made by man can take a significant impact on population dynamics of vectors and hence the transmission of malaria. This project genotyping 10 microsatellites for population-based study of Anopheles darlingi collected at seven locations along Rio Madeira at Porto Velho - RO. These methods were applied in the characterization of samples collected in these regions in the 1st and 2nd semesters of 2007. The objective was to analyze the population structure of Anopheles darlingi along the Madeira River, the area of influence of Hydroelectric of Jirau and San Antonio. The results showed high gene flow among populations, even at 70 km apart. We found significant genetic differences among populations when samples were compared seasonally. The samples collected in the first half of the year showed effective population size 10x greater than those collected in the second half. These differences may represent differences... (Complete abstract click electronic access below) / Doutor

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.

Biodiversity in Southeast Asia has been decreasing as a result of human activities. The findings of the Millennium Ecosystem Assessment, reported in 2005, demonstrated that environmental change, such as deforestation, has resulted in recent major loss of biodiversity at the species level and increased rates of extinction; however, it is unknown whether a similar deficit has occurred at the level of genetic diversity within species. This study aims to understand how the past has shaped the current pattern of genetic diversity, the impact of recent forest loss on genetic diversity and how this information can be used to develop effective conservation strategy. To achieve this aim, microsatellites were developed by sequencing genomic libraries and from comparisons of database sequences. The utility of these markers for population genetics studies has been tested and confirmed for the three main study taxa and across a broad range of other squirrel species. These microsatellites and mitochondrial sequence data (cytochrome b gene) were utilized to determine the genetic diversity and population structure of three squirrel taxa with varying degrees of forest dependency on Thailand’s tropical forests. The most forest dependent taxon is Phayre’s flying squirrel (Hylopetes phayrei). The second taxon is the moderately forest-dependent tree squirrel, the Grey-bellied squirrel (Callosciurus caniceps). The third, and least forest dependent taxon, is the Indochinese ground squirrel, Menetes berdmorei. Our data revealed far more biodiversity in these taxa than previously recognized; there were three genetically distinct lineages in H. phayrei and M. berdmorei and two lineages in C. caniceps. This demonstrates that biodiversity in this region has been underestimated. In the two most forest dependent taxa lineage divergence dated to the Pleistocene indicating that this biodiversity was generated by isolation in allopatric forest refugia during the cool, dry periods of the Pleistocene. In H. phayrei, the most forest-dependent taxon, at least two of the lineages were distinct species occurring sympatrically in Thailand on the border with Myanmar. This taxon supported the biogeographical hypothesis developed in forest dependent mosquitoes of allopatric isolation in northwest and northeastern Pleistocene refugia. Callosciurus caniceps had evidence of a southern refugium in peninsular Thailand or Malaysia. The lower levels of structuring in the least forest dependent taxon M. berdmorei suggest a limited impact of Pleistocene environmental change. All three taxa had eastern lineages which may have been due to Pleistocene forest fragmentation in some of the species. These eastern populations typically had lower levels of microsatellite and mtDNA genetic diversity. This is likely due to the recent loss of genetic diversity as in recent decades these forests have been highly fragmented and reduced in size due to human activity. Our finding that the northern Thai-Myanmar border region is a suture zone in highly dependent forest species and has high within lineage/species diversity makes this region a priority for conservation. The distinct genetic lineages in the east and south should also be managed as separate conservation units. Further efforts are required to assess the impact of loss of genetic diversity in Thailand’s fragmented forests and how this may be remedied.

Cette thèse de doctorat est un projet franco-polonais en co-tutelle entre le Département du Fonctionnement des Ecosystèmes Marins (l'Université de Gdansk, Pologne) et le laboratoire DIMAR (l'Université de la Méditerranée, France). La variation physiologique et la structure génétique des populations d’une espèce lagunaire, le bivalve, Cerastoderma glaucum, ont été étudiées. C. glaucum est une espèce sessile avec une phase larvaire planctonique. Elle est présente surtout dans les bassins isolés ou semi-isolés sans marée, comme les lagunes, les estuaires, les baies et les lacs. Ces habitats sont extrêmes de par des changements de conditions environnementales à court terme plus importants que dans le milieu marin. Ils sont souvent isolés, le flux de gènes est limité et des adaptations locales sont attendues. C. glaucum a révélé une forte variabilité des paramètres morphométriques et physiologiques entre les 3 populations de la Mer Baltique, la Mer du Nord et la Méditerranée. Les coques de la Mer Baltique sont beaucoup plus petites que celles des autres populations et leur taux de respiration est le plus élevé, ce qui est probablement provoqué par le stress osmotique. Les populations de l’Europe du nord ont un pattern de la reproduction monocyclique, tandis que la population de la Méditerranée peut se reproduire tout au long de l’année. Les changements saisonniers dans la composition biochimique sont corrélés avec les changements de condition trophique et avec le cycle reproductif. / This PhD is a Polish-French project between the Department of Marine Ecosystems Functioning (University of Gdansk, Poland) and DIMAR laboratory (Université de la Méditerranée, France). Physiological variation and genetic structure of the populations of lagoon specialist, the bivalve, Cerastoderma glaucum, have been studied. C. glaucum is a sessile species with a planctonic larval stage. It inhabits mainly non-tidal areas, like lagoons or brackish lakes. Those habitats are extreme, because they are much more subject to short-term variations in environmental conditions than marine habitats. They are also often isolated and as a consequence the gene flow among populations is limited and local adaptations are expected. The lagoon cockle revealed a strong interpopulation variability of morphometric and physiological parameters among 3 populations studied: from the Baltic Sea, the North Sea, and the Mediterranean Sea. The cockles from the Baltic Sea were much smaller than those from other populations and they exhibited the highest respiration rate, probably due to osmotic stress. The populations from the northern Europe had a monocyclic reproductive pattern, whereas the Mediterranean population seemed to reproduce throughout the year. Seasonal changes in biochemical components contents appeared to be correlated with changes in trophic conditions and the reproductive cycle. High respiration rates in populations from the northern Europe in spring and autumn could have resulted from gamete development (in spring) and phytoplankton blooms (in spring and autumn).

Observing populations at different spatial scales gives greater insight into the specific processes driving genetic differentiation and population structure. Here we determined population connectivity across multiple spatial scales in the Red Sea to determine the population structures of two reef building corals Stylophora pistillata and Pocillopora verrucosa. The Red sea is a 2,250 km long body of water with extremely variable latitudinal environmental gradients. Mitochondrial and microsatellite markers were used to determine distinct lineages and to look for genetic differentiation among sampling sites. No distinctive population structure across the latitudinal gradient was discovered within this study suggesting a phenotypic plasticity of both these species to various environments. Stylophora pistillata displayed a heterogeneous distribution of three distinct genetic populations on both a fine and large scale. Fst, Gst, and Dest were all significant (p-value<0.05) and showed moderate genetic differentiation between all sampling sites. However this seems to be byproduct of the heterogeneous distribution, as no distinct genetic population breaks were found. Stylophora pistillata showed greater population structure on a fine scale suggesting genetic selection based on fine scale environmental variations. However, further environmental and oceanographic data is needed to make more inferences on this structure at small spatial scales. This study highlights the deficits of knowledge of both the Red Sea and coral plasticity in regards to local environmental conditions.

Malaria is the main cause of approximately one million deaths every year that mostly affect children in south of Sub-Saharan Africa. The Anopheles gambiae complex consists of seven morphologically indistinguishable sibling species. However, their behavior, ecological adaptations, vectorial capacity, and geographical distribution differ. Studying the phylogenetic relationships among the members of the complex is crucial to understanding the genomic changes that underlie evolving traits. These evolutionary changes can be related to the gain or loss of human blood choice or to other epidemiologically important traits. In order to understand the phylogenetic relationships and evolutionary history of the members of the An. gambiae complex, breakpoints of the 2Ro and 2Rp inversions in An. merus and their homologous sequence in the outgroup species were analyzed using fluorescent in situ hybridization (FISH), library screening, whole-genome mate-paired sequencing and bioinformatics analysis. Molecular phylogenies of breakpoint genes were constructed afterwards. In addition, multigene phylogenetic analyses of African malaria vectors were performed. Our findings revised the chromosomal phylogeny, and demonstrated the ancestry of 2Ro, 2R+p and 2La arrangements.  Our new chromosomal phylogeny strongly suggests that vectorial capacity evolved repeatedly in members of the An. gambiae complex, and the most important vector of malaria in the world, An. gambiae, is more closely related to ancestral species than was previously thought. Our molecular phylogeny data were in agreement with chromosomal phylogeny, indicating that the position of the genetic markers with respect to chromosomal inversion is important for interpretation of the  phylogenetic trees. Multigene phylogenetic analysis revealed that a malaria mosquito from humid savannah and degraded rainforest areas, An. nili, belongs to the basal clade and is more distantly related to other major African malaria vectors than was assumed previously. Finally, for the first time a physical map of 12 microsatellite markers for the Asian malaria vector An. stephensi was developed. Knowledge about the chromosomal position of microsatellites was shown to be important for a proper estimation of population genetic parameters. In conclusion, our study improved understanding of genetics and evolution of some of the major malaria vectors in Africa and Asia. / Ph. D.

Understanding whether groups of individuals represent a single panmictic gene pool, or multiple genetically structured populations across a species range should aid in predicting whether specific conservation strategies would be more or less effective for species preservation. Further, contrasting the population structures of multiple coexisting taxa could foster an even deeper understanding of evolutionary divergence among demes and potentially even suggest local adaptation in the form of tight coevolutionary relationships. Finally, the analysis of population dynamics within small and isolated populations could improve our understanding of the relative importance that different evolutionary mechanisms have in predicting population persistence in the wild. Using microsatellite markers I characterized the population genetic structure in the critically endangered Cyclura cychlura cychlura iguanas on Andros Island. I found significant differences between inferred and realized rates of gene flow. This finding demonstrates that evolutionarily independent populations can occur even with high rates of dispersal. In the second and third study I contrasted patterns of genetic variability in Cyclura cychlura cychlura iguanas, ticks in the genus Amblyomma parasitizing these iguanas, and Rickettsia spp., potential pathogens transmitted by these ticks. I determined that genetic differences among Rickettsia samples and Amblyomma samples are highly concordant with genetic divergence among iguana populations. This finding suggests largely vertical dispersal of ticks and their super-parasite, a high specificity of this reptile-tick interaction, and historically low rates of dispersal in iguanas. This finding also indicates that island populations of iguanas may be locally adapted due to tight coevolutionary relationships. Finally, I investigated the mechanisms that eliminate harmful mutations in small isolated and natural populations of the critically endangered Cyclura cychlura cychlura iguanas. Using molecular tools I found indirect evidence suggesting that small natural populations can maintain significant levels of genetic variation in spite of strong selection acting against harmful mutations. Under regimes of random mating, the buildup of harmful mutations in small populations may result in a large number of inviable young. However, harmful mutations may also be eliminated when exposed to natural selection through increased competition, as population density increases. However, quantification of the relative role of competition was not feasible in this study.

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