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For a sexually reproducing species, the two major decisions facing all individuals are when and with whom to reproduce. When scaled to the population level, the outcome from all individual decisions determines reproductive variance, and age-class contribution to population growth rate. Both of these attributes determine a population‟s effective size (Ne), which is directly correlated with its fitness, persistence probability, and adaptability. The questions of when and with whom to reproduce, and their subsequent effects on Ne and age-at-maturity were assessed for wild brook trout (Salvelinus fontinalis) populations. Mating pairs were significantly size-assortative, with individual length accounting for 37% of the variation. This pattern of size assortative mate choice resulted in a reproductive strategy closer to monogamy than polygamy. Of all reproducing adults (n=157), 80% (n=126) produced only one full-sibling family, and only 6% (n= 9) contributed to more than two full-sibling families. The number of families and offspring contributed increased with length for both males and females. Comparison of the effective population size estimate to the adult census size (Nc) estimate returned an Ne:Nc ratio of 0.49 averaged over both populations. This value is nearly five times greater than the average reported across 165 (0.14) and 102 (0.10) different species. Age-at-maturity ranged from 0 to 2 years, with the proportion of age-0 and age-1 individuals maturing in a given year dependent upon growth opportunities determined primarily by environmental conditions. Mature fish were significantly larger than immature fish within an age-class, however, survival rates of mature and immature fish were similar. Furthermore, parental length did not influence offspring survival. These data suggest that the cost of early maturation is instead manifested through a reduction in egg number for females, and a reduced ability to acquire mates for males, both determined by an individual‟s size. Indeed, fecundity predicted by mean length of immature and mature fish within an age-class would result in mature fish producing an average of 38% (age-0) and 33% (age-1) more eggs than immature fish. These findings are discussed in the context of population persistence given the trend of increasing habitat fragmentation and looming climate change.

The goals of captive breeding programs for endangered species include preserving genetic diversity and avoiding inbreeding. Typically this is accomplished by minimizing population mean kinship; however, this approach becomes less effective when errors in the pedigree exist and may result in inbreeding depression, or reduced survival. Here, both pedigree- and DNA-based methods were used to assess inbreeding depression in the critically endangered Attwater’s prairie-chicken (Tympanuchus cupido attwateri). Less variation in the pedigree-based inbreeding coefficients and parental relatedness values were observed compared to DNA-based measures suggesting that errors exist in the pedigree. Further, chicks identified with high parental DNA-based relatedness exhibited decreased survival at both 14- and 50-days post-hatch. A similar pattern was observed in later life stages (> 50 days post-hatch) with birds released to the wild; however, the pattern varied depending on the time post-release. While DNA-based inbreeding coefficient was positively correlated with mortality to one month post-release, an opposite pattern was observed at nine months suggesting purging of deleterious alleles. I also investigated whether immunocompetence, or the ability to produce a normal immune response, was correlated with survival; however, no significant correlation was observed suggesting that inbreeding was a more important factor influencing survival. Pairing individuals for breeding by minimizing DNA-based parental relatedness values resulted in a significant increase in chick survival. This study highlights the importance of using DNA-based methods to avoid inbreeding depression when errors exist in the pedigree.

A inclusão de grupos genéticos na avaliação de reprodutores tem sido comumente empregada para a representação de possíveis diferenças genéticas entre os animais não contabilizadas pela ausência de informações de parentesco. Entretanto, a definição destes grupos ainda é arbitrária, sendo inexistentes trabalhos que avaliem as estratégias de agrupamento genético quanto aos seus efeitos sobre a eficiência de seleção. Dessa forma, o objetivo desta pesquisa foi comparar estratégias de agrupamento genético na predição de valores genéticos, determinando-se a estrutura adequada à avaliação genética. Para tanto, foram utilizados dados de peso ao nascimento, peso ao desmame, ganho de peso pós-desmame, circunferência escrotal e escore de musculosidade de uma população de bovinos compostos da raça Montana Tropical. Foram avaliadas as estratégias de agrupamento envolvendo safra de nascimento do animal (SAF); sexo do parental desconhecido (SEX); fazenda de nascimento do animal (FAZ); caminho de seleção (SEL); composição racial (RACA) safra de nascimento do animal e sexo do parental desconhecido (SAFSEX); fazenda de nascimento do animal e sexo do parental desconhecido (FAZSEX); safra e fazenda de nascimento do animal (SAFFAZ); e safra, fazenda de nascimento do animal e sexo do parental desconhecido (SAFFAZSEX). Para cada estratégia, foram realizadas cem análises para a predição de valores genéticos simulando-se a perda de informação de parentesco de 10, 30 e 50% dos indivíduos. Posteriormente, estes valores genéticos foram comparados aos obtidos em uma análise envolvendo a matriz de relacionamentos completa, de maneira a se estimar a eficiência de seleção e as correlações entre os valores genéticos e a classificação dos animais. As estratégias de SAF e RACA apresentaram eficiências de seleção e correlações altas independente da característica e amostra de animais com parentesco desconhecido consideradas, mostrando-se adequadas à avaliação e seleção de reprodutores. Perdas de seleção elevadas foram observadas para SAFFAZ e SAFFAZSEX, possivelmente devido à formação de muitos grupos com poucos animais, dificultando-se assim a estimativa dos efeitos dos grupos genéticos. A partir dos resultados é possível concluir que a definição da estratégia de agrupamento deve considerar as decisões vinculadas à seleção de reprodutores e o número de grupos genéticos formados, de forma que os mesmos representem as diferenças genéticas da população e permitam a adequada predição dos valores genéticos. / The inclusion of genetic groups in sire evaluation has been widely used to represent genetic differences among animals not accounted by the absence of parentage information. However, the definition of these groups is still arbitrary, and research assessing the effects of genetic grouping strategies on the selection efficiency is rare. Thus, the aim of this study was to compare genetic grouping strategies in breeding values prediction, determining the appropriate structure for the genetic evaluation. Data on birth weight, weaning weight, post-weaning weight gain, scrotal circumference and muscling score of Montana Tropical composite beef cattle population were used. Grouping strategies involving birth season of the animal (SAF), sex of the unknown parent (SEX), birth farm of the animal (FAZ), path selection (SEL), breed composition (RACA), birth season of the animal and sex of the unknown parent (SAFSEX), birth farm of the animal and sex of the unknown parent (FAZSEX), birth season and farm of the animal (SAFFAZ), and birth season and farm of the animal and sex of the unknown parent (SAFFAZSEX) were evaluated. For each strategy, one hundred analyses were performed to predict breeding values, simulating a loss of genealogy information of 10, 30 and 50% of individuals. Thereafter, these breeding values were compared to those obtained in an analysis involving the complete relationship matrix, in order to estimate the selection efficiency and the correlations between breeding values and animal rankings. The grouping strategies SAF and RACA showed high selection efficiencies and correlations, regardless of the trait and sample of animals with unknown parentage considered, and therefore, they are suitable for sire evaluation and selection. High selection losses were observed for SAFFAZ and SAFFAZSEX, possibly due to the formation of many groups with few animals, since this could lead to some confounding with other fixed effects and hamper the estimation effects of genetic groups. These results allow to conclude that the definition of grouping strategy must consider the decisions regarding the selection and the number of genetic groups formed, so that genetic groups represent the genetic differences in population and allow an adequate prediction of breeding values.

Stroke is a common disorder of later life with a complex etiology, including both environmental and genetic risk factors. The inherited predisposition is challenging to study due to the complexity of the stroke phenotype. Genetic studies in an isolated population have successfully identified a positional candidate gene for stroke, phosphodiesterase 4D (PDE4D). The aim of this thesis was to identify stroke susceptibility loci and positional candidate genes, taking advantage of low genetic variation in the northern Sweden population. All stroke cases were identified in a population-based stroke registry at the northern Sweden MONICA Centre. 56 families containing multiple cases of stroke and a follow up set of an additional 53 families were used for linkage studies. For association studies, 275 cases of first ever stroke together with 550 matched community controls were included. In paper I, we used a candidate region approach to investigate the PDE4D region on chromosome 5q. Linkage was obtained with a maximum allele-sharing LOD score of 2.06; P = 0.001. However, no significant association of ischemic stroke to the previously defined at-risk allele in PDE4D was observed. We next performed a genome wide linkage scan to explore new susceptibility loci for common forms of stroke (paper II). Non-parametric multipoint linkage analysis yielded allele-sharing LOD scores > 1.2 at nine locations; 1p34, 5q13, 7q35, 9q22, 9q34, 13q32, 14q32, 18p11, 20q13. The highest allele-sharing LOD score was obtained on chromosome 18p (LOD = 2.14). Fine mapping resulted in increased allele-sharing LOD scores for chromosome 5q13 and 9q22. In the follow up analysis of the nine regions, including all 109 families, the highest allele-sharing LOD scores were obtained on chromosomes 5q, 13q and 18p although none reached the initial genome wide values. In paper III, we focused on the chromosome 5q region, and further mapping and haplotype analysis in the families was performed. A common 1 cM haplotype was found to be shared among affected members of five families. In this region only the regulatory subunit 1 of phosphatidylinositol 3-kinase (PIK3R1) gene was located. Association of three single nucleotide polymorphisms in the PIK3R1 gene to common stroke was obtained in the case-control material. Finally, in paper IV, an extended pedigree containing seven families connected to common founders eight generations back was identified by genealogical analysis, and submitted to a separate genome wide scan analysis. A significant allele-sharing LOD score of 4.66 (genome wide P < 0.001) at chromosome 9q31-33 was obtained. Haplotype analysis identified a minimal common region of 3.2 cM, which was shared by four of the seven families. These four families contained all of the primary intracerebral hemorrhagic cases present in the extended pedigree. In conclusion we have replicated linkage of stroke susceptibility to the PDE4D region on chromosome 5q, but no significant association of ischemic stroke to PDE4D was observed. Linkage analysis of stroke did not identify any new major stroke loci, indicating that multiple minor susceptibility loci in addition to the previously known locus on chromosome 5q could contribute to the disease. In the chromosome 5q region a novel positional candidate gene for stroke was identified, the PIK3R1 gene. The PIK3R1 protein has several biological actions with potential roles in stroke susceptibility. Also a novel susceptibility locus for common forms of stroke at chromosome 9q was identified in a large pedigree, which may be of special importance for susceptibility to hemorrhagic stroke.

Genealogy reconstruction is widely used in biology when relationships among entities are studied. Phylogenies, or evolutionary trees, show the differences between species. They are of profound importance because they help to obtain better understandings of evolutionary processes. Pedigrees, or family trees, on the other hand visualize the relatedness between individuals in a population. The reconstruction of pedigrees and the inference of parentage in general is now a cornerstone in molecular ecology. Applications include the direct infer- ence of gene flow, estimation of the effective population size and parameters describing the population’s mating behaviour such as rates of inbreeding. In the first part of this thesis, we construct genealogies of various types of cancer. Histopatho- logical classification of human tumors relies in part on the degree of differentiation of the tumor sample. To date, there is no objective systematic method to categorize tumor subtypes by maturation. We introduce a novel algorithm to rank tumor subtypes according to the dis- similarity of their gene expression from that of stem cells and fully differentiated tissue, and thereby construct a phylogenetic tree of cancer. We validate our methodology with expression data of leukemia and liposarcoma subtypes and then apply it to a broader group of sarcomas and of breast cancer subtypes. This ranking of tumor subtypes resulting from the application of our methodology allows the identification of genes correlated with differentiation and may help to identify novel therapeutic targets. Our algorithm represents the first phylogeny-based tool to analyze the differentiation status of human tumors. In contrast to asexually reproducing cancer cell populations, pedigrees of sexually reproduc- ing populations cannot be represented by phylogenetic trees. Pedigrees are directed acyclic graphs (DAGs) and therefore resemble more phylogenetic networks where reticulate events are indicated by vertices with two incoming arcs. We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatel- lites and single nucleotide polymorphism (SNPs) in the second part of the thesis. If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical data set with known pedigree. The parentage inference is robust even in the presence of genotyping errors. We further demonstrate the accuracy of the algorithm on simulated clonal populations. We show that the joint estimation of parameters of inter- est such as the rate of self-fertilization or clonality is possible with high accuracy even with marker panels of moderate power. Classical methods can only assign a very limited number of statistically significant parentages in this case and would therefore fail. The method is implemented in a fast and easy to use open source software that scales to large datasets with many thousand individuals.

Made available in DSpace on 2016-06-02T19:32:14Z (GMT). No. of bitstreams: 1 6527.pdf: 2310287 bytes, checksum: 6b506abf65a5fa7b4ec9bb3b44d34a22 (MD5) Previous issue date: 2014-08-14 / Financiadora de Estudos e Projetos / Species kept in captivity are of great importance for in situ conservation of natural populations. In order to fulfill this role, they need to be properly managed with the aim to avoid the consequences of a captive environment, such as: loss of genetic diversity, inbreeding depression, accumulation of deleterious alleles and genetic adaptation to captivity (the first three due to the small number of breeding stock). Thus, with the aim to test founder effects in captive ―populations‖, we used as study model the spectacled bears from Brazilian zoos. This ―population‖ consists of twenty-one bears found in eight zoos along the country, which are originated from just twelve founding individuals. To test a possible founder effect, we analyzed twelve heterologous microsatellite loci for all the specimens of the species in Brazil. Results for the number of alleles and allelic richness obtained through the rarefaction method showed that spectacled bears in captivity have reduced levels of allelic richness in relation to three natural populations (Colombia, Ecuador and Venezuela) studied by other authors; suggesting that bears from Brazilian zoos suffered the consequences of a founding effect, as they have only a fraction of the gene pool of the ancestral population. From the information present in the studbook was possible to verify that there are two families of spectacled bears, and according to the individuals´s multilocus genotypes, we found alleles that are present in a same family and absent in the other. Regarding the kinship, there was a discrepancy in the results with the molecular estimators through the softwares ML-Relate and Coancestry and the information given by the institutions. The information obtained in this work are fundamental to the ex situ conservation program in Brazil with the objective of maintain as high as possible the genetic diversity for future reintroduction plans of the species in nature. / Espécies mantidas em cativeiro são de grande importância na conservação in situ de populações naturais. A fim de que possam desempenhar este papel é necessário que sejam devidamente manejadas, para que as consequências que o cativeiro traz sejam evitadas, como por exemplo: perda de diversidade genética, depressão endogâmica, acúmulo de alelos deletérios e adaptação genética ao cativeiro (as três primeiras devido ao pequeno número de espécimes dos plantéis). No Brasil, uma espécie de mamífero que vem sendo criada em cativeiro desde 1970 e que passou por um efeito fundador, é o urso de óculos (Tremarctos ornatus). O plantel existente hoje totaliza o número de vinte e um ursos, encontrados em oito zoológicos do país, o qual se originou de apenas doze indivíduos fundadores. Para avaliar as consequências de um conhecido efeito fundador, analisamos doze locos heterólogos de microssatélites para todos os exemplares da espécie nos zoos do país, através de amostragem não-invasiva. Resultados referentes ao número de alelos e à riqueza alélica obtida por meio do método de rarefação mostraram que os ursos de óculos de cativeiro possuem valores reduzidos de riqueza alélica em relação a três populações naturais (Colômbia, Equador e Venezuela) estudadas por outros autores; sugerindo que os ursos dos zoológicos brasileiros sofreram as consequências de um efeito fundador, pois possuem apenas uma fração do pool gênico da população ancestral. A partir das informações presentes no studbook foi possível verificar que existem duas famílias de ursos de óculos, e de acordo com os genótipos multilocos dos indivíduos, encontramos alelos que estão presentes em uma mesma família e ausentes na outra. Em relação ao parentesco, houve uma discrepância nos resultados encontrados com os estimadores moleculares através dos softwares ML-Relate e Coancestry e o histórico cedido pelas instituições. As informações obtidas em nosso trabalho, portanto, são fundamentais para que os ursos encontrados nos zoológicos do Brasil possam participar na formação de casais em futuros programas de reprodução ex situ com o propósito de serem utilizados em planos de reintrodução da espécie na natureza.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Promote the interest of students to the scientific knowledge does not make sense, if there is no correlation between what is taught in school with life and the student's context. In the teaching of Biology, the theme heredity is among the first topics of the program of Genetics for high school. The use of graphics, such as pedigrees, permeates different content of human heritage. However, this teaching resource can not only teach specific concepts and procedures of Genetics, but also promote knowledge of the socio-historical and cultural context of the students. Also, deserves to be optimized to awaken critical and scientific attitudes in the earliest school years and not only in the high school. Thus, this research aimed to investigate how the pedigrees of the families of students can contribute to the teaching and learning of heredity and social-historical and cultural context at different levels and types of education of basic education. A qualitative and qualitative-quantitative approach was used. It is used as a data collection instrument, teaching materials produced by students that were interpreted by content analysis. This research is presented in five chapters. The first four articles, accentuate the didactic potential of the study of the inheritance patterns at different levels and types of basic education: the early years of elementary school, high school and youth and adult education. The didactic proposal is presented as a possibility to qualify the teaching and learning of Natural Sciences for the initial years. The results show that the pedigrees act as catalysts of contextualized and interdisciplinary educational activities in different educational contexts. These resources are capable of causing different knowledge about science and the reality to be studied and may be proposed for different levels and types of education, depending of the focus and conceptual reach. The survey also signals the misuse, in some books and teaching resources, for the pedigree term as synonymous of genealogy, as well as the analogy sometimes controversial to build family trees in the early years, to demonstrate the pedigree of students. This research could contribute to the reflection of teachers in the search for pedagogical proposals accessing knowledge of the school routine, interpreting them scientifically, and to enable greater security in the use of terminology and educational proposals, when working with data and family records. / Despertar o interesse dos estudantes para os conhecimentos científicos não faz sentido, se não houver a correlação do que é ensinado na escola com a vida e o contexto do aluno. No ensino de Biologia, o tema hereditariedade encontra-se entre os primeiros tópicos dos programas escolares em Genética para o ensino médio. O uso de gráficos, como heredogramas, perpassa e problematiza diferentes conteúdos de heranças humanas. No entanto, esse recurso de ensino e aprendizagem pode, além de ensinar conceitos e procedimentos específicos da Genética, desencadear conhecimentos do contexto histórico-social e cultural dos estudantes. Também merece ser otimizado para despertar atitudes críticas e científicas desde os primeiros anos escolares e não só ao final do ensino médio. Assim, nesta pesquisa, teve-se como objetivo investigar como os heredogramas das famílias dos estudantes podem contribuir no processo de ensino e aprendizagem da hereditariedade e do contexto histórico-social e cultural em diferentes níveis e modalidades de ensino da educação básica. Apresenta uma abordagem qualitativa e qualiquantitativa. Utiliza-se, como instrumento de coleta de dados, a análise documental de materiais didáticos, produzidos pelos estudantes que foram interpretados pela análise de conteúdo. Esta pesquisa se desdobra em cinco capítulos.Os quatro primeiros artigos, de modo geral, acentuam as potencialidades didáticas do estudo dos heredogramas nos diferentes níveis e modalidades da educação básica: dos anos iniciais do ensino fundamental, ensino médio e educação de jovens e adultos. A proposta didática se apresenta como uma possibilidade para qualificar o ensino e aprendizagem das Ciências da Natureza para os anos iniciais. Os resultados demonstram que os heredogramas atuaram como catalisadores de ações educativas contextualizadas e interdisciplinares nos diferentes contextos de ensino. São, dessa forma, recursos capazes de provocar diferentes conhecimentos acerca das ciências e da realidade em estudo e podem ser propostos para diferentes níveis e modalidades de ensino, dependendo do seu enfoque e abrangência conceitual. A pesquisa também sinaliza o uso indevido, em alguns livros e recursos didáticos, do termo heredograma, como sinônimo de genealogia, bem como a analogia, por vezes, controversa de se construir árvores genealógicas nos anos iniciais, para demonstrar o pedigree de um estudante. Esta pesquisa para o ensino de Ciências poderá contribuir para a reflexão dos docentes na busca de propostas pedagógicas que acessem conhecimentos do cotidiano escolar, interpretando-os cientificamente, bem como possibilitar uma maior segurança no uso de terminologias e propostas didáticas, quando se trabalha com dados e registros familiares.