Estimation of recombination rates from population genetics data in Daphnia pulex

Urban, Lina

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Estimation of recombination rates from population genetics data in Daphnia pulex

Urban, L. (2018). Estimation of recombination rates from population genetics data in Daphnia pulex. Master Thesis, Universität zu Lübeck, Institut für Neuro- und Bioinformatik, Lübeck.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0002-9C49-D Version Permalink: https://hdl.handle.net/21.11116/0000-0005-1A05-9

Genre: Thesis

Other : Agschätzung von Rekominationsraten aus Populationsgenetikdaten in Daphnia pulex

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Creators:
Urban, Lina, Author
Haubold, Bernhard¹, Referee

Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644

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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.

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Language(s): eng - English

Dates: Accepted: 2018-10-10Date issued: 2018-10-10

Publication Status: Issued

Pages: 136

Publishing info: Lübeck : Universität zu Lübeck, Institut für Neuro- und Bioinformatik

Table of Contents: Contents
Abstract III
Zusammenfassung V
Abbreviations IX
1 Introduction 1
1.1 Structure of this thesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2 Population genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2.1 Idealized populations and the Wright-Fisher model . . . . . . . . 3
1.2.2 Coalescent theory . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2.3 Homologous recombination . . . . . . . . . . . . . . . . . . . . . 6
1.3 Daphnia pulex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
2 Software, Methods and Data 13
2.1 Reconstruction of haplotypes with fastPHASE . . . . . . . . . . . . . . . 13
2.2 LDhat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2.1 Estimation of recombination rates with LDhat interval . . . . . 13
2.2.2 Simulation of haplotype data with LDhat fin . . . . . . . . . . . 14
2.3 Daphnia pulex data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3 Results 17
3.1 Estimation of recombination rates . . . . . . . . . . . . . . . . . . . . . 17
3.1.1 Simulated data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.1.2 Daphnia pulex data . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.2 Recombination rates near genes . . . . . . . . . . . . . . . . . . . . . . . 23
3.3 Identification of recombination hotspots . . . . . . . . . . . . . . . . . . 27
3.3.1 Simulated data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
3.3.2 Candidate hotspot regions in Daphnia pulex . . . . . . . . . . . . 32
4 Discussion 37
4.1 Future work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.2 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Acknowledgments 43
References 45
5 Appendix 57

Rev. Type: -

Identifiers: Other: Dipl/13100

Degree: Master

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