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Estimation of recombination rates from population genetics data in Daphnia pulex

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Haubold,  Bernhard
Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Urban, L. (2018). Estimation of recombination rates from population genetics data in Daphnia pulex. Master Thesis, University of Lübeck, Lübeck.


Cite as: http://hdl.handle.net/21.11116/0000-0002-9C49-D
Abstract
Meiotic recombination generates novel combinations of genetic variants by shuffling genome regions. As a result, these regions differ in their genealogies. Interestingly, recombination has been found to be not uniform along chromosomes but to occur in some regions with a significantly elevated rate. The discovery of these so-called recombination hotspots has led to great interest in estimating local rates of recombination from sequence data. In this thesis, methods for estimating the rate of recombination from population genotype data were tested and applied to a population of the water flea Daphnia pulex, a widely used model organism in ecological and evolutionary research. The results indicate a rather uniform recombination landscape with a few peaks. In total, 49 hotspot-like regions were identified, of which the hottest exhibits an approximately 17-fold increased recombination rate compared to the background. The identified regions are approximately 0.5 to 8 kb wide and exhibit a significantly higher density of single nucleotide polymorphisms. Average recombination rates imply a slight suppression of recombination close to transcription start sites (TSS). On the other hand, evaluation of recombination for individual genes revealed that high recombination rates are associated with developmental genes, which indicates that recombination in D. pulex occurs selectively in the proximity of genes which are expressed during or shortly after meiosis. However, tests with simulated data show that estimates of recombination rates are not accurate for all orders of magnitudes, and particularly rates in hotspot-like regions tend to be overestimated. Therefore, our observation of elevated recombination rates near the TSS of developmental genes need to be validated by direct measurements of crossover rates.