Abstract

The Red Queen Hypothesis postulates that reciprocal selection arising from host-parasite interactions should accelerate evolutionary rates through the need for continual adaptation and counter-adaptation. A process driving such rapid reciprocal adaptation is referred to as negative frequency-dependent selection, in which the most common genotypes decrease over time because they have a higher probability of becoming infected by coevolving parasites. This proposed mechanism of host-parasite coevolution was commonly tested in laboratory experiments under controlled conditions. Regarding field investigations of natural populations, temporal changes in relative frequencies of genotypes were mostly tested for host only, because tracking parasite dynamics over time remained difficult. As parasite population dynamics are highly sensitive to environmental changes, studies under natural conditions are essential to understand host-parasite coevolution. The commonly explored model system to address coevolutionary questions are the water fleas of the genus Daphnia and their microparasites. In this PhD thesis, I analysed the population structure of two major microparasites of Daphnia: Caullerya mesnili (Chapters 2 and 3) and microsporidia (Chapter 4). First, in Chapter 2, I developed a new bioinformatic pipeline to analyse molecular data generated by next-generation-sequencing (NGS) platforms. C. mesnili populations from different water reservoirs in the Czech Republic were sequenced at the first internal transcribed spacer (ITS1) of the ribosomal gene cluster, analysed with this new pipeline and compared with published results from the same populations but using cloning and Sanger sequencing method. I detected that relative frequencies of C. mesnili ITS1 sequence types were similar when compared to other sequencing methods, thereby validating the bioinformatic pipeline, and showing the suitability of 454 platform to perform population biology analyses. After this validation, in Chapter 3, I analysed the population dynamics and host-genotype specificity of C. mesnili, in long-term samples collected from a single lake, and based on the sequence variations in the ITS1 region. I found that the most abundant C. mesnili ITS1 sequence type decreased, while rare sequences increased over the course of the study (4 years). The observed pattern is consistent with the negative frequency-dependent selection. However, only a weak signal of host-genotype specificity between C. mesnili and Daphnia genotypes was detected, which supports the lack of host-genotype specificity in this system. Finally, in Chapter 4, I described the patterns of geographical population structure, intraspecific genetic variation, and recombination of two Daphnia-infecting microsporidia: Berwaldia schaefernai and the unknown microsporidium MIC1. These patterns were used to predict the existence of secondary hosts in the life cycle of these microsporidia. I observed little variation among B. schaefernai parasite strains infecting different host populations; in contrast, there was significant genetic variation among populations of MIC1. Additionally, ITS genetic diversity was lower in B. schaefernai than in MIC1. These findings suggest that the presumed secondary host for B. schaefernai is expected to be mobile, while in MIC1 the secondary host (if exists) does not appear to facilitate dispersal to the same degree. Finally, recombination analyses indicated cryptic sex in B. schaefernai and pure asexuality in MIC1. All these findings enable a more comprehensive understanding of the biology of Daphnia-infecting microparasites and the genetic basis of Daphnia-microparasites coevolution in natural populations.