Submitted by Renata Lopes (renatasil82@gmail.com) on 2016-10-13T19:51:52Z No. of bitstreams: 1 ceciliafonsecapoggian.pdf: 268787 bytes, checksum: 5898d68297ebccdcc7f27145276525da (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2016-10-22T13:01:59Z (GMT) No. of bitstreams: 1 ceciliafonsecapoggian.pdf: 268787 bytes, checksum: 5898d68297ebccdcc7f27145276525da (MD5) / Made available in DSpace on 2016-10-22T13:01:59Z (GMT). No. of bitstreams: 1 ceciliafonsecapoggian.pdf: 268787 bytes, checksum: 5898d68297ebccdcc7f27145276525da (MD5) Previous issue date: 2008-02-26 / CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico / FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais / Os animais da raça Guzerá, bem adaptados às condições tropicais do Brasil, têm sido utilizados para produção de leite e carne. Em função da redução do tamanho efetivo da população, a probabilidade de endogamia e deriva genética na raça tem aumentado. Em 1994, iniciou-se o Programa Nacional de Melhoramento da Raça para leite por meio do teste de progênie e do núcleo MOET de seleção. O sucesso deste programa pode ser comprometido pelo aumento do coeficiente de endogamia (F) e perda de diversidade genética na raça, pois os animais de maior valor genético são mais utilizados para reprodução. O objetivo deste trabalho foi examinar a diversidade genética da população Guzerá selecionada para leite no Brasil, calcular a endogamia na raça e avaliar seus efeitos sobre características produtivas e reprodutivas, visando monitorar a variabilidade genética e orientar acasalamentos. Dados genealógicos de 10.051 animais nascidos até 2007 foram usados para estimação dos parâmetros populacionais. O coeficiente médio de endogamia dos animais endogâmicos foi 0,025, e o aumento esperado da endogamia, devido à contribuição não balanceada dos fundadores, foi 0,16%. O coeficiente de relação médio entre os indivíduos da população foi estimado em 1,06%, e o intervalo de gerações, em 7,48 anos. A média do tamanho efetivo populacional por geração foi 77, o número efetivo de fundadores, 318, o número efetivo de ancestrais, 101, e o efeito gargalo, 3,15. Dos 2.106 ancestrais, 47 foram responsáveis por 50% da diversidade genética da população referência. As características produção total de leite, produção de leite aos 305 dias de lactação, produção total de gordura, produção total de proteína e idade ao primeiro parto foram afetadas negativamente (p<0,05) pelo aumento do coeficiente de endogamia. Os valores médios de F, até o momento, são baixos, porém, o reduzido tamanho efetivo da população indica riscos de endogamia e perda de variabilidade genética na raça Guzerá selecionada para leite no Brasil. / Animals of the Guzerat breed have strongly fitted to tropical conditions of Brazil, and have been used for milk and beef production. The probability of inbreeding and genetic drift increases due to reduction in the effective population size. In 1994, a selection program for milk production traits was initiated in some purebred herds, using progeny test and MOET nucleus. Its success, otherwise, can be endangered by increase in inbreeding coefficient (F) and loss of genetic diversity, since animals with high genetic value have more chance to reproduce. This study was undertaken to evaluate the evolution and the current genetic status of the Guzerat cattle under milk selection, aiming to monitor the genetic variability and guide matings. Genealogical data of 10,051 animals born until 2007 were used to estimate population parameters. The average F for all inbred animals included in this data set was 0.025 and the increase of inbreeding by unbalancing of founders contribution was 0.16%. The average relationship coefficient was 1.06% and the generation interval was 7.48 years. The mean effective population size by generation was 77, the effective number of founders and effective number of ancestors for the reference population were, respectively, 318 and 101. The bottleneck effect was 3.15. Of 2,106 ancestors, 47 contributed to 50% of the reference population. Total milk production, milk production at 305 days of lactation, total fat production, total protein production and age at first calving was negatively affected (p<0.05) by the increase in F. Average F values and regression coefficients are still low, but the reduced effective population parameters indicates risk of inbreeding, genetic drift and, consequently, loss of variability in the Guzerat breed under milk selection in Brazil.

O presente estudo teve como objetivo avaliar a estrutura populacional, estimar parâmetros (coeficientes de herdabilidade e correlações) e determinar as tendências genéticas e fenotípicas de características de crescimento e adaptação em bovinos da raça Nelore, linhagem Lemgruber. O banco de dados utilizado nas análises constituiu-se de 39.290 animais no arquivo de pedigree e de 24.353 animais no arquivo de produção. Os parâmetros populacionais foram obtidos por meio dos softwares POPREP (GROENEVELD et al., 2009) e ENDOG v 3.2 (GUTIÉRREZ e GOYACHE, 2005). As estatísticas descritivas e os parâmetros genéticos para cada característica estudada foram estimadas por meio de quatro análises hepta-característica utilizando o programa VCE-6 (KOVAC & GROENEVELD, 2003) sob modelo animal completo. As tendências genéticas e fenotípicas foram obtidas pela regressão dos valores genéticos e fenotípicos respectivamente sobre o ano de nascimento dos animais e os coeficientes da regressão foram estimados por meio do método de quadrados mínimos. Apesar da endogamia média do rebanho ser considerada moderada verificou-se alta porcentagem de indivíduos endogâmicos e reduzido tamanho efetivo populacional. Além disso, o incremento contínuo de endogamia ao longo dos anos demonstra a necessidade de intervenção na seleção dos indivíduos para reprodução, de modo que, problemas futuros possam ser evitados. Os coeficientes de herdabilidade direta foram estimados em 0,24, 0,31, 0,31, 0,21, 0,19, 0,30, 0,41, 0,19 e 0,17 respectivamente para peso ao nascimento (PN), peso aos 120 dias de idade (P120), peso à desmama (PD), peso ao ano (PES12), ganho de peso pós desmama, de 205 aos 550 dias (GP345), ganho de peso na prova à pasto da ABCZ, em 224 dias (GP224), perímetro escrotal (PE), temperamento (TEMP), e repelência (REP) e indicam que a variabilidade genética aditiva existente é suficiente para a obtenção do ganho genético em resposta à seleção desde que sejam realizados ajustes, tanto nas estratégias de seleção adotadas para a obtenção de maiores ganhos nos valores genéticos, como também nos fatores ambientais que possam possibilitar ao máximo, a expressão do potencial genético dos animais. / The present study had as objective to evaluate the population structure, to estimate parameters (coefficients of heritability and correlation) and to determine the phenotypic and genetic trends for growth and adaptability traits in Nellore cattle, Lemgruber line. The database used in the analysis consisted of 39,290 animals in the pedigree and 24,353 animals in the production file. The population parameters were obtained from the software POPREP (Groeneveld et al., 2009) and ENDOG v 3.2 (Gutierrez and GOYACHE, 2005). The descriptive statistics and genetic parameters for each characteristic studied were estimated by four seven-traits analysis using the program VCE-6 (Kovac & GROENEVELD, 2003) which uses the animal model. The phenotypic and genetic trends were obtained by means of phenotypic and genetic values respectively on the year of birth of the animals and the regression coefficients were estimated by the method of least squares. Although the average inbreeding of the herd being considered moderate, there was high percentage of inbred individuals and small effective population size. Furthermore, the continuous increase in inbreeding over the years demonstrates the need for intervention in the selection of individuals for reproduction, so that future problems can be avoided. Direct heritability coefficients were estimated as 0.24, 0.31, 0.31, 0.21, 0.19, 0.30, 0.41, 0.19 and 0.17 respectively for birth weight (PN), weight 120 days of age (P120), weaning weight (PD), weight at 12 months of age (PES12), weight gain after weaning from 205 to 550 days (GP345), weight gain during the pasture test of ABCZ in 224 days (GP224), scrotal circumference (PE), docility (TEMP) and repellency (REP) and indicate that the additive genetic variability is sufficient to obtain genetic gain in response to selection as far as adjustments in selection strategies are adopted to achieve larger gains in breeding values, and environmental factors that may allow the expression of the genetic potential of the animals.

Individuals vary from each other in their genetic content. Genetic diversity is at the core of the evolutionary theory. Rooted in a solid theoretical framework developed as early as the 1930s, current empirical observations of genomic diversity became possible due to technological advances. These measurements, originally based on a few gene sequences from several individuals, are becoming possible at the genome scale for entire populations. We can now explore how evolutionary forces shape diversity levels along different parts of the genome. In this thesis, I focus on the variation in levels of diversity within genomes using avian systems and in particular that of the collared flycatcher (Ficedula albicollis). First, I describe the variation in genetic diversity along the genome of the collared flycatcher and compare it to the amount of variation in diversity across individuals within the population. I provide guidelines on how a small number of makers can capture the extent of variability in a population. Second, I investigate the stability of the local levels of diversity in the genome across evolutionary time scales by comparing collared flycatcher to the hooded crow (Corvus (corone) corone). Third, I study how selection can maintain variation through pervasive evolutionary conflict between sexes. Lastly, I explore how shifts in genome-wide variant frequencies across few generations can be utilised to estimate the effective size of population.

From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability. I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse. Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.

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

A obtenção de genótipos superiores no melhoramento de plantas depende da existência de variabilidade genética. A existência de coleções de germoplasma representativas e a utilização de um tamanho adequado de amostra são fundamentais para a preservação das frequências alélicas e genotípicas, diminuindo a perda de variabilidade genética e postergando o aparecimento dos efeitos da deriva genética. Assim, teve-se como objetivo avaliar os efeitos da deriva genética em caracteres quantitativos em subpopulações de milho. Este estudo foi realizado a partir das populações originais BR-105 e BR-106, das quais 10 subpopulações foram obtidas em cada um dos cinco ciclos sucessivos de amostragem com tamanho efetivo reduzido, totalizando 50 subpopulações para cada população original, as quais foram posteriormente autofecundadas, gerando um nível a mais de endogamia. Os tratamentos foram constituídos de 10 amostras da população original sem autofecundação, 10 amostras com autofecundação, 50 subpopulações obtidas da população original e 50 subpopulações autofecundadas, totalizando 120 tratamentos para cada população, avaliados separadamente. Utilizou-se o delineamento em blocos casualizados no esquema de parcelas subdivididas em faixas hierárquico, em quatro ambientes com duas repetições por ambiente. Os caracteres avaliados foram produção de grãos (PG), prolificidade (PROL), comprimento e diâmetro de espigas (CE e DE), número de fileiras por espiga (NFE), número de grãos por fileira (NGF), altura de planta e espiga (AP e AE), florescimento masculino e feminino (FM e FF) e número de ramificações do pendão (NRP). Foram estimados os efeitos da deriva genética entre as médias das subpopulações nos dois níveis de endogamia e os efeitos da depressão por endogamia nas subpopulações dentro dos ciclos. Posteriormente, realizaram-se análises de regressão linear para as subpopulações nos dois níveis de endogamia, separadamente, e em conjunto. Foi verificada uma grande variação nas médias das subpopulações ao longo dos ciclos, indicando que a deriva genética causou diferenciação entre as mesmas e que estas se diferenciaram das populações originais. Detectaram-se efeitos significativos da deriva genética nas populações não autofecundadas para todos os caracteres avaliados, em maior número para PG, já que este caráter é mais sensível à deriva genética por possuir maior grau de dominância que os demais. Houve diminuição no número de estimativas de deriva significativas para as populações autofecundadas, incluindo mudanças na magnitude e no sinal das mesmas em relação às populações não autofecundadas. Para as estimativas de depressão por endogamia, os caracteres PG, NGF, FM e FF apresentaram maior quantidade de estimativas significativas que os demais. Para a maioria dos caracteres, a regressão linear explicou a maior parte da variação encontrada com o aumento dos coeficientes de endogamia. As populações BR-105 e BR-106, por terem estruturas genéticas distintas, apresentaram performances diferentes quanto aos efeitos da deriva genética. Enfim, como a deriva genética interfere na integridade genética das populações, torna-se importante considerar seus efeitos na coleta e manutenção dos bancos de germoplasma e nas populações utilizadas no melhoramento genético de plantas. / Obtaining superior genotypes in plant breeding depends on the existence of genetic variability. The existence of representative germplasm collections and the use of appropriate sample size are essential for preserving allelic and genotypic frequencies, reducing loss of genetic variability and delaying genetic drift effects. This study aimed to evaluate the effects of genetic drift in quantitative traits in subpopulations of maize. The original populations used were BR-105 and BR-106, of which 10 subpopulations were obtained in each five successive sample cycles with reduced effective size, accounting 50 subpopulations for each original population that were subsequently selfed to generate an additional level of inbreeding. The treatments consisted in 10 samples of the original population, 10 samples of the selfed original population, 50 non selfed subpopulations obtained from the original population and 50 selfed subpopulations, accounting 120 treatments for each population evaluated separately. It was used the randomized block strip-plot design, in four environments with two replications. The traits assessed were grain yield (GY), prolificacy (PROL), ear length and ear diameter (EL and ED), number of rows per ear (NRE), kernel-row number (KRN), plant and ear height (PH and EH), days to anthesis and silking (DA and DS), and number of tassel branches (NTB). It was estimated the effects of genetic drift between subpopulations means at both inbreeding levels, and the effect of the inbreeding depression in subpopulations within cycles. It was also performed linear regression analysis for subpopulations at both levels of inbreeding separately and together. A large variation was observed in the subpopulations means over cycles, indicating that genetic drift caused differentiation between them, and that they differed from the original populations. The effects of genetic drift were significant for all traits in the non selfed subpopulations, especially for GY, which is more sensitive to genetic drift effects by having a greater degree of dominance than the other traits. There was a decrease in the number of significant genetic drift estimates for selfed populations, including changes in magnitude and signs, compared to the non selfed populations. GY, KRN, DA and DS had higher number of significant inbreeding depression estimates than the other traits. Linear regression analysis explained most of the variation found with increasing homozygosity. As BR-105 and BR-106 populations have distinct genetic structures, they showed different performances regarding the effects of genetic drift. Therefore, genetic drift interferes in the genetic integrity of populations and it is important to consider its effect on the collection and maintenance of germplasm banks and populations used in plant breeding.

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

The objectives of this thesis relate to questions needed to be addressed in the context of genetic monitoring for implementing the Convention on Biological Diversity for the gene level. Genetic monitoring is quantifying temporal changes in population genetic metrics. Specific goals of this thesis include i) synthesizing existing information relevant to genetic monitoring of Swedish species, ii) providing a genetic baseline for the Swedish moose, iii) evaluating the relative performance of nuclear versus organelle genetic markers for detecting population divergence, iv) actually monitoring the genetic composition, structure, level of variation, and effective population size (Ne) and assessing the relation between Ne and the actual number of individuals for an unexploited brown trout population. The concept of conservation genetic monitoring is defined and Swedish priority species for such monitoring are identified; they include highly exploited organisms such as moose, salmonid fishes, Norway spruce, Atlantic cod, and Atlantic herring. Results indicate that the Swedish moose might be more genetically divergent than previously anticipated and appears to be divided into at least three different subpopulations, representing a southern, a central, and a northern population. The relative efficiency of nuclear and organelle markers depends on the relationship between the degree of genetic differentiation at the two types of markers. In turn, this relates to how far the divergence process has progressed. For the monitored brown trout population no indication of systematic change of population structure or allele frequencies was observed over 30 years. Significant genetic drift was found, though, translating into an overall Ne-estimate of ~75. The actual number of adult fish (NC) was assessed as ~600, corresponding to an Ne/NC ratio of 0.13. In spite of the relatively small effective population size monitoring did not reveal loss of genetic variation.

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.

Orientador: Alexandre Magno Sebbenn / Banca: Mario Luiz Teixeira de Moraes / Banca: Ananda Virgínia de Aguiar / Resumo: O fluxo e padrões de dispersão de pólen foram investigados em um pequeno fragmento florestal isolado da espécie arbórea neotropical, polinizada por insetos da Copaifera langsdorffii, por meio da análise de paternidade e oito locos microssatélites, também foi investigado a coancestria e o tamanho efetivo populacional dentro de progênies para a conservação e recuperação ambiental. Sementes de polinização aberta (20 a 25 sementes) foram coletadas de 15 árvores matrizes de um fragmento, onde todos os indivíduos adultos foram previamente mapeados, medidos e genotipados para oito locos microssatélites. Vinte sementes foram coletadas da árvore vizinha mais próxima (1,2 km) do fragmento. Os níveis de diversidade genética foram significativamente maiores nos adultos do que nas progênies. Níveis significativos de endogamia foram detectados em progênies (F = 0,226), o que foi atribuído principalmente ao cruzamento entre parentes. A partir da análise de paternidade, baixos níveis de autofecundação (s = 8%) e imigração de pólen (m = 8%) foram observados no fragmento florestal, mas níveis muito altos foram detectados na árvore isolada (s = 20%; m = 75%), indicando que o fragmento e a árvore não estão reprodutivamente isolados e são conectados por dispersão de pólen a longas distancias (máximo detectado 1,420 m). Dentro do fragmento, o padrão de dispersão de pólen foi o vizinho próximo, com cerca de 49% do pólen se dispersando até 50 m. O tamanho efetivo populacional da árvore-matriz foi baixa, indicando a necessidade de se coletar muitas sementes de árvores (mínimo de 76 árvores) para fins de conservação. Em termos gerais, os resultados mostraram que o fragmento e a árvore isolada pela fragmentação florestal não estão reprodutivamente isoladas, embora o isolamento espacial parecesse aumentar a taxa de autofecundação e cruzamentos correlacionados / Abstract: Pollen flow, dispersal and patterns were investigated in a small and isolated forest fragment of the neotropical, insect pollinated tree Copaifera langsdorffii, using paternity analysis and eight microsatellite loci, we also investigated the coancestry and effective population size of progeny array for conservation and environmental restoration purpose. Open-pollinated seeds (20 to 25 seeds) were collected from 15 seed trees of forest fragment, where all adults trees were previously mapped, measured and genotyped by eight microsatellite loci. Twenty seeds were also collected from the neighbour tree (1.2 km) of the forest fragment. Levels of genetic diversity were significantly higher in adults than offspring. Significant levels of inbreeding were detected in offspring (F=0.226), which was attributed mainly to the mating among relatives. From paternity analysis, low levels of selfing (s=8%) and pollen immigration (m=8%) were observed in the forest fragment, but very high levels were detected in the isolated tree (s=20%; m=75%), indicating that the forest fragment and the tree are not reproductive isolated and are connected by long pollen dispersal (maximum detected 1,420 m). Within the forest fragment, the pattern of pollen dispersal was the near neighbor with about 49% of the pollen being dispersed until 50 m. The effective population size of the progeny array was low, indicating the necessity to collect seeds from many seed trees (minimum of 76 trees) for conservation purposes. In general terms, the results showed that the fragment and the tree isolated by forest fragment are not brooked the genetic connectivity, although the spatial isolation seems increase selfing rate and correlated mating / Mestre