Genetic material of Lithuanian origin varieties, breeding lines and wild ecotypes representing P. pratense, P. bertolonii and P. phleoides species were studied for the most important agro-morphological and feeding value indicators as well as at the genetic level employing different biochemical–molecular markers. The water stress experiment clearly demonstrated the existence of different levels of water stress response in Phleum species, suggesting that P. phleoides might have evolved under conditions of limited water availability. “Blind” mapping by HRM was used successfully to map water stress response genes of timothy in the perennial ryegrass mapping population. In total, 12 putative water stress response genes were mapped in seven perennial ryegrass linkage groups. / Pasitelkus agromorfologinius, kokybės ir biocheminius – molekulinius metodus ištirtos lietuviškos kilmės pašarinių, žemaūgių bei stepinių motiejukų veislės, selekcinės linijos bei laukiniai ekotipai. Fiziologiniai sausros atsparumo tyrimų rezultatai įrodė, kad stepiniai motiejukai turi geriau išvystytą atsparumo sausrai mechanizmą. Pirmą kartą motiejukuose aptikti ekspresuojami atsparumo sausrai kandidatiniai genai HRM metodu sužymėti daugiametės svidrės genolapyje.

The aim of the present study was to evaluate the power of discrimination and genetic (diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categories / Niger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa).

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Social amoebae are eukaryotic organisms that inhabit soil of almost every climate zone. They are remarkable for their switch from unicellularity to multicellularity as an adaptation to starvation. When starved, millions of single cells aggregate and form a multicellular fruiting body, which contains reproductive spore cells and dead stalk cells, which help in spore dispersion. This costly behavior made social amoebae a model system for addressing major questions of the evolution of cooperation and multicellularity. In this study we look at three different aspects of social amoebae behavior; aggregation, non-aggregation and competition, and ask how they contribute to our understanding of cooperation in social amoebae and microbial systems in general.We explored the known but neglected observation that, upon starvation, not all cells aggregate and engage in multicellular development. We describe phenotypically and genetically non-aggregating cell proportion in D. discoideum species. Both aggregating and non-aggregating strategy are costly or beneficial depending on duration of starvation. With our computational model we propose that partitioning the population into unicellular and multicellular states is adaptive in fluctuating environments with unpredicted duration of starvation periods. Social amoebae may therefore lie at the intersection of cooperation and bet-hedging. In the second part, we provide a new framework for addressing the contrasting observations of high genetic diversity in natural populations of social amoebae and experimentally suggested low diversity-high relatedness required for cooperation. We propose that complex life cycle of social amoebae provides multiple competition points that can possibly play an important role in maintaining diversity and cooperation. We explore this experimentally and computationally by looking at competition over the whole life cycle between 6 natural isolates of D. discoideum. Our simulation model indicates that competition at different stages of the life cycle can lead to exclusion of "social winners". Though we failed to explain strain coexistence. Although preliminary, our results emphasize the importance of integrating species ecology in cooperative studies.Finally, we focus on a new aggregation dynamics in P. pallidum species observed in our lab. Aggregation is a population level process during which population gets divided into numerous subpopulations/aggregates that face selection independently. Such population partitioning can have strong evolutionary consequences on cooperation that have not yet been explored experimentally. We describe the population dynamics qualitatively and propose several quantitative measurements of population partitioning into aggregates. Our preliminary results suggest that there is a preference for aggregates of certain size, but there is no spatial organization of aggregates.

The aim of the present study was to evaluate the power of discrimination and genetic(diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categories; Niger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa).Buccal swabs were collected from unrelated males from Mwanza province (Sukuma),Mara (Kuria and Luo), Arusha (Maasai and Iraqw) and Dodoma province (Alagwa).Samples were typed using ABI 377 Genetic Analyser (Applied Biosystem) followed by analysis using softwares Gelprocessor, GeneScan 3.0.0 (Applied Biosystems) and Genotyper 3.7 (Applied Biosystems). The data obtained were analysed by GenePop 4.0,Arlequin 3.11 and Genetix v.4.05.2 software packages. Analyses such as AMOVA, Fst population pairwise comparison, Factorial component Analysis were used to obtain Allele frequency, haplotype frequency, gene diversities among various loci and levels of gene flow between populations.For the overall individuals, the highest Gene Diversity value was 0.8251 (DYS385) and the lowest was 0.2723 (DYS392). The overall Haplotype Diversity was 0.9984 and Discrimination capacity resulted 84.27%. A total of 225 distinct haplotypes were identified in 267 individuals, 28 were shared, the most frequent haplotype was present in 5 individuals. The levels of genetic diversity for the haplotypes per group as revealed by haplotype diversities confirmed that the most diverse group being Sukuma, Kuria,Iraqw, Maasai, Luo and Alagwa being the least diverse. The Discrimination capacity of these set of markers showed the highest value in Sukuma population (100%) subsequently followed by Iraqw, Luo, Maasai, Kuria and Alagwa (78.38%) being the lowest. Analysis of Molecular Variance showed a significant differentiation among populations, 93.96% of variance was found within population and 6.04% among population. Population pairwise results between all population pairs (except Sukuma and kuria and Alagwa and Luo) showed significant results (P < 0.05). Genetic heterogeneity that was found among Tanzanian populations could not be attributed to language barriers but was largely being contributed by a limited level of gene flow between these populations due to different ethnical, social, cultural and historical backgrounds between them. All Y chromosome extended haplotype loci used in this study (except DYS392 and DYS391 which showed the lowest level of polymorphism) were found to be likely useful for forensic application in Tanzania. Furthermore the extended haplotype markers used in this study may be useful in the establishment of the National DNA database following the enactment of the Human DNA Legislation in Tanzania (http://www.parliament.go.tz). / Magister Scientiae - MSc

La presente tesis, titulada “Genes, peoples and languages in Central Africa”, examina los patrones de diversidad genética en poblaciones del oeste de Africa central, más específicamente, poblaciones Bantús y Pigmeas de Gabon y Camerún, dos zonas vitales para la comprensión de la expansión Bantú. Se han analizado más de 800 muestras a nivel del cromosoma Y con el fin de caracterizar genéticamente a estas poblaciones, y establecer la relación genética entre ellas. Los resultados han demostrado que la expansión Bantú homogeneizó el acervo genético de las poblaciones Bantús, eliminando la diversidad pre-Bantú, mientras que diversificó aquel de las poblaciones Pigmeas, introduciendo linajes Bantus. Además, se ha visto que el flujo de linajes paternos parece haber tenido una única dirección: de Bantus a Pigmeos. Estos resultados contrastan con aquellos obtenidos para linajes maternos (DNA mitocondrial) en estas zonas, donde se ha observado un considerable flujo genético de Pigmeos a Bantus, sugiriendo un posible sesgo sexual en la tasa de mestizaje entre poblaciones Bantus y Pigmeas. Un hallazgo interesante es la presencia de un linaje no-africano en estas poblaciones de África subsahariana. / The present thesis titled “ Genes, peoples and languages in Central Africa” examines the genetic diversity patterns in populations from west central Africa, more specifically, in Bantu and Pygmy populations from Gabon and Cameroon, two key areas in the understanding of the Bantu expansion. More than 800 samples have been analysed at the Y chromosome level in order to genetically characterise these populations and establish the genetic relationship between them. The results have shown that the Bantu expansion largely homogenised the gene pool of Bantu populations, erasing the pre-Bantu diversity, while it diversified that of Pygmy groups, introducing Bantu lineages into their gene pool. Furthermore, gene flow of paternal lineages seems to have taken place mainly in one direction; from Bantus to Pygmies. These results contrast with those found in studies of maternal (mtDNA) lineages in these areas, where considerable gene flow from Pygmy to Bantu populations have been observed, suggesting possible sex-biased admixtures rates between Bantu and Pygmy populations. An interesting finding, is the significant presence of a non-African lineage in these sub-Saharan populations.

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Avian cholera, caused by infection with Pasteurella multocida, is an important infectious disease of wild birds in North America Since it was first confirmed in 2005, annual outbreaks of avian cholera have had a dramatic effect on common eiders on East Bay Island, Nunavut, one of the largest breeding colonies of northern common eiders (Somateria mollissima borealis) in the eastern Arctic. I investigated potential avian and environmental reservoirs of P. multocida on East Bay Island and other locations in the eastern Canadian Arctic by collecting cloacal and oral swabs from live or harvested, apparently healthy, common eiders, lesser snow geese, Ross’s geese, king eiders, herring gulls, and snow buntings. Water and sediment from ponds on East Bay Island were sampled before and during outbreaks. Avian and environmental samples were tested using a real-time polymerase chain reaction (PCR) assay to detect P. multocida. PCR positive birds were found in every species except for snow buntings, and PCR positive common eiders were found in most locations, supporting the hypothesis that apparently healthy wild birds can act as a reservoir for avian cholera. In all years, P. multocida DNA was detected in ponds both before and after the avian cholera outbreak began each year, suggesting that the environment also plays a role in outbreak dynamics. Contrary to our expectations, model results revealed that ponds were generally more likely to be positive earlier in the season, before the outbreaks began. Whereas average air temperature at the beginning of the breeding season was not an important predictor for detecting P. multocida in ponds, eiders were more likely to be PCR positive under cooler conditions, pointing to an important link between disease and weather. Potential origins of P. multocida causing avian cholera in Arctic eider colonies were investigated by comparing eastern Arctic isolates of P. multocida to isolates from wild birds across Canada, and the central flyway in the United States. Using repetitive extragenic palindromic-PCR (REP-PCR) and multi-locus sequence typing (MLST), we detected a low degree of genetic diversity among isolates, and P. multocida genotypes were correlated with somatic serotype. Isolates from East Bay Island were distinct from P. multocida from eider colonies in the St. Lawrence Estuary, Quebec, however, East Bay Island isolates were indistinguishable from isolates collected from a 2007 pelagic avian cholera outbreak on the east coast of Canada. Isolates from East Bay Island and Nunavik shared sequence types, indicating possible transmission of isolates among eider colonies in the eastern Arctic. Previously, feather corticosterone in eiders was found to be significantly associated with environmental temperature during the moulting period. In my study, path analysis revealed that environmental conditions experienced during the moulting period had direct impacts on arrival date and pre-breeding body condition of common eiders during the subsequent breeding period on East Bay Island, with indirect impacts on both reproductive success and survival. Higher temperatures experienced during the fall moulting period appear to impose significant costs to eiders, with subsequent carry-over effects on both survival and reproduction many months later during avian cholera outbreaks. This thesis describes several important features of the host, agent and environmental dynamics of avian cholera in North America with a particular focus on the disease in the eastern Canadian Arctic. Continued exploration of infectious wildlife disease dynamics is needed to better predict, detect, manage, and mitigate disease emergence that can threaten human and animal health and species conservation.

Submitted by Ronildo Prado (ronisp@ufscar.br) on 2017-08-01T19:59:42Z No. of bitstreams: 1 DissPAAB.pdf: 4100356 bytes, checksum: 348f90d1cf3911093faeec744c33f884 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-08-01T19:59:54Z (GMT) No. of bitstreams: 1 DissPAAB.pdf: 4100356 bytes, checksum: 348f90d1cf3911093faeec744c33f884 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-08-01T20:00:00Z (GMT) No. of bitstreams: 1 DissPAAB.pdf: 4100356 bytes, checksum: 348f90d1cf3911093faeec744c33f884 (MD5) / Made available in DSpace on 2017-08-01T20:00:08Z (GMT). No. of bitstreams: 1 DissPAAB.pdf: 4100356 bytes, checksum: 348f90d1cf3911093faeec744c33f884 (MD5) Previous issue date: 2015-06-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The main goal of any captive breeding program consists is maximizing the conservation of genetic diversity. Groups kept in captivity are particularly susceptible to the loss of genetic diversity, inbreeding depression and adaptation to captivity, due to their small size. The genetic characterization of wild and captive populations is an important tool both to minimize these impacts and for the conservation of these species, since it enables the development of management strategies aimed at maintenance of genetic diversity. In this context, the main objective of the study was to evaluate genetic variability and paternity for animals of black lion tamarin from Centro de Primatología do Rio de Janeiro, Fundacão Parque Zoológico de Sao Paulo, Parque Ecológico de Sao Carlos and 14 specimen belonging to the Durrell Conservation Trust in England using 15 microsatellite loci. The results of the allelic richness and expected heterozygosity showed similar values of alleles numbers and heterozygosity when compared with other species of Callitrichidae. Factorial correspondence analysis (FCA) showed greater homogeneity among captive animals than wild animals from Capão Bonito. The captive groups showed no differentiation among them and high differentiation from the wild Capão Bonito population. The data obtained herein are fundamental to increase the knowledge in genetic aspects of tamarins and support breeding programs to prevent loss of genetic diversity and inbreeding. / Maximizar a conservação da diversidade genética é um dos principais objetivos de qualquer programa de reprodução em cativeiro. Por serem de pequeno tamanho, grupos mantidos em cativeiro são particularmente suscetíveis à perda de diversidade genética, depressão endogâmica e adaptação ao cativeiro. Na tentativa de minimizar tais impactos, a caracterização genética de populações de vida livre e de cativeiro, torna-se uma importante ferramenta para a conservação destas espécies, uma vez que possibilita o desenvolvimento de estratégias de manejo que visem à manutenção de níveis adequados de diversidade genética. Neste contexto o objetivo principal deste trabalho foi avaliar através de 15 loci microssatélites, os níveis de variabilidade genética e paternidade dos animais mantidos em cativeiro no Brasil, no Centro de Primatologia do Rio de Janeiro, Fundação Parque Zoológico de São Paulo, Parque Ecológico de São Carlos e 14 espécimenes que faziam parte do Durrell Conservation Trust na Inglaterra. Os resultados referentes à riqueza alélica e heterozigosidade esperada mostraram que há uma representação similar nos valores de alelos e heterozigosidade quando comparado com outras espécies de Calitriquídeos. A análise de correspondência fatorial (FCA) mostrou que os grupos em cativeiro do Brasil apresentaram maior homogeneidade, quando comparados a um grupo de vida livre proveniente da região de Capão Bonito (São Paulo) e aos 14 indivíduos que representam ao grupo em cativeiro do zoológico de Durrell. O alto grau de parentesco entre os animais em cativeiro evidencia baixa diferenciação entre os grupos pertencentes às diferentes instituições brasileiras estudadas. Os grupos de cativeiro do Brasil, no entanto, mostraram-se divergentes dos animais de Capão Bonito. As informações obtidas neste trabalho são fundamentais para aumentar o conhecimento sob aspectos genéticos dos micos-leões-pretos e subsidiar planos de reprodução assistida que visem minimizar a perda de diversidade genética e a endogamia.

Entre as doenças que trazem preocupações e podem causar prejuízos no setor canavieiro em todo o Brasil, destaca-se a ferrugem marrom, causada pelo fungo Puccinia melanocephala H. & P. Sydow. Essa doença ocorre em todas as regiões canavieiras do mundo, desde a Ásia e a África, de onde o complexo \"Sacharum spp.\" é originário, até as Américas e Oceania. No Brasil, a ferrugem foi detectada, pela primeira vez em 1986, no município de Capivari-SP e logo em seguida em Pernambuco e Alagoas. Desde o primeiro surgimento no Brasil, a ferrugem tem sido mantida sob controle, com grande parte das cultivares apresentando resistência. O conhecimento acerca da estrutura populacional de P. melanocephala é necessário para desenvolver estratégias satisfatórias no controle desta doença e no desenvolvimento de cultivares resistentes. A variabilidade genética entre isolados pode ser avaliada por meio de marcador molecular microssatélite e os dados podem ser usados para monitorar as populações do patógeno. Este trabalho teve como objetivo avaliar, por meio do desenvolvimento de uma biblioteca enriquecida em locos de microssatélites, a variabilidade genética entre isolados de P. melanocephala bem como avaliar a patogenicidade de isolados de diferentes regiões produtoras de cana-de-açúcar. Primeiramente, os 44 isolados de ferrugem da cana foram identificados por microscopia utilizando estruturas morfológicas dos urediniósporos. Desse total, 34 foram identificadas como P. melanocephala e 10 como Puccinia kuehnni. Por meio da construção da biblioteca enriquecida com locos microssatélites foram desenvolvidos 21 locos para ferrugem marrom, e desse total, 16 apresentaram amplificações satisfatórias e somente quatro foram polimórficos. A variabilidade genética dos isolados de P. melanocephala foi relativamente alta (HT = 0,650). A análise de agrupamento não permitiu a separação dos isolados de P. melanocephala de acordo com sua região de origem. Os índices de diversidade (DST = -0,039) e divergência (GST = -0,061) genética observados sugerem que a variabilidade genética está igualmente distribuída nas regiões estudadas, ocorrendo uma única população heterogênea. As regiões de origem dos isolados utilizadas para avaliação de patogenicidade não apresentaram variações significativas na agressividade. Os resultados obtidos no presente trabalho evidenciam que o melhoramento genético da cana-de-açúcar para resistência a ferrugem marrom deve ser conduzido em locais com clima favorável a ocorrência do patógeno, que possivelmente representam a diversidade genética presente em diferentes regiões de cultivo / Among the diseases that bring concerns and can cause losses in the sugarcane industry in Brazil, stands out the brown rust, caused by the fungus Puccinia melanocephala H. & P. Sydow. This disease occurs in all sugarcane regions of the world, from Asia and Africa, where the complex \"Sacharum spp.\" originates, to the Americas and Oceania. In Brazil, the rust was detected for the first time in 1986 in the region of Capivari-SP and soon after in the Pernambuco and Alagoas. Since the first appearance in Brazil, the rust has been brought under control, with most of the cultivars showing resistance. The knowledge about the population structure of P. melanocephala is necessary to develop suitable strategies to control this disease and the development of resistant cultivars. The genetic variability between isolates can be assessed by means of microsatellite molecular markers and data can be used to monitor populations of the pathogen. The aim of this work was to develop a library enriched for microsatellite loci in P. melanocephala and assessment of pathogenicity of isolates from three different sugarcane regions producing. First, the 44 sugarcane rust isolates were identified by microscopy using morphological structures of urediniospores. Of this total, 34 were identified as P. melanocephala and 10 as P. kuehnni. Through the construction of the library enriched with microsatellite loci were developed 21 loci brown rust of those, 16 had satisfactory PCR amplifications and only four were polymorphic. The genetic variability of isolates of P. melanocephala was relatively high (HT = 0.650). The cluster analysis did not allow the separation of isolates of P. melanocephala according to their region of origin. The index of the genetic diversity (DST = -0.039) and genetic divergence (GST = -0.061) suggest that genetic variability is equally distributed in the regions studied, occurring only a heterogeneous population. The regions of origin of isolates used for pathogenicity assessment did not show significant variations in aggressiveness. The results obtained in this work show that the genetic improvement of sugarcane for resistance to brown rust should be conducted in areas with favorable weather for the occurrence of the pathogen, which may represent the genetic diversity present in different sugarcane regions