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Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/123306
Applications of next-generation sequencing in conservation genomics: kinship analysis and dispersal patterns
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[eng] Knowledge of the genealogical relationships among individuals of a population and their dispersal patterns are essential to many studies of endangered species, especially those with small and fragmented populations. The main objective of this doctoral thesis is to use genomic data obtained with next-generation sequencing techniques to infer contemporary dispersal patterns of species from relatedness networks, to construct pedigrees from kinship categories, and to quantify the effect of anthropogenic and geographic barriers on the dispersal of individuals, using as a model the Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic to the Iberian Peninsula. First, the contact zone between two lineages of the Pyrenean desman in the Iberian Range (La Rioja) was studied using SNPs obtained from ddRAD (double-digest restriction associated DNA) genomic libraries. According to the genomic tree, the principal component analysis, and the population structure analyses, the genetic variability in the area was structured by rivers instead of by mitochondrial lineages. Relatedness and inbreeding coefficients were then calculated with a maximum-likelihood estimator. Mean relatedness was found to be very high in the area. Individuals also showed high inbreeding levels. The reliability of these estimates was assessed with bioinformatics simulations based on artificial pedigrees that included as founders actual genotypes of the studied population. The relatedness networks showed a low level of contemporary inter-river dispersal compared to intra-river dispersal, indicating poor connectivity between rivers. Then, kinship relationships and pedigrees of Pyrenean desmans of two rivers of the northwestern part of the Iberian Peninsula (Zamora) were inferred. The ddRAD protocol was modified to allow processing each sample independently, which enabled the use of minimally invasive hair samples. Mean relatedness and inbreeding coefficients obtained from the SNPs were much lower than those from La Rioja. In addition, relatedness was higher for female dyads than for male dyads, suggesting a higher degree of female philopatry. Kinship categories were determined and their reliability was assessed using bioinformatics simulations based on artificial pedigrees. Using these kinship categories, pedigrees were reconstructed and their congruence was evaluated with the age of the individuals, the mitochondrial haplotypes, and the inbreeding coefficients. Pedigrees allowed the estimation of the average dispersal distance per generation, as well as preliminary data about the reproductive biology of the species. Finally, the assortativity coefficient obtained from the kinships networks was used to quantify the effect of specific barriers on the dispersal of individuals in the two rivers studied of Zamora, the Tera and the Tuela. The most important barrier found with this approach was the watershed divide between both rivers, followed by a dam located in one of them. These results were highly congruent with those obtained from the population structure analysis. The information obtained with the approaches presented in this thesis can be used to unravel fundamental aspects about the biology of endangered species, such as their dispersal patterns and their reproductive biology, as well as to quantify the effect of potential barriers on dispersal. These data may be fundamental to develop conservation plans aimed at improving the connectivity between populations.
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ESCODA ASSENS, Lídia. Applications of next-generation sequencing in conservation genomics: kinship analysis and dispersal patterns. [consulta: 26 de novembre de 2025]. [Disponible a: https://hdl.handle.net/2445/123306]