Population structure and host-parasite interactions in the Daphnia longispina hybrid complex

Natural hybridization, the interbreeding of species, can contribute to understanding the processes of maintaining biodiversity. There are different theories to explain the coexistence of hybrids with their parental species. Some models assume that hybrids are temporarily more or equally successful as parental taxa in a specific environment; but even in case of lower fitness of hybrids, a dynamic equilibrium between natural selection against hybrids and dispersal explains the maintenance of hybrid zones. Although the long-term significance of hybridization in animals is poorly understood, it is common among cyclical parthenogens, especially in zooplankton species of the genus Daphnia. In the first part of my thesis (Chapters 2-4), I investigated the population structure of Daphnia longispina assemblages under different selection pressures. First of all, in Chapter 2, I detected a nearly perfect correspondence in the assignment of Daphnia individuals to different parental and hybrid taxa based on microsatellite markers (15 loci) when examining reference clones which had been previously classified by different markers (allozymes, mtDNA). This allowed me to identify species and different hybrid classes from field samples by microsatellite markers alone and their assignment was verified by a set of statistical approaches (Factorial Correspondence Analysis and two Bayesian methods). Secondly, by applying microsatellite markers on Daphnia samples isolated from eight different lakes, I explored the dynamics of the hybridizing system (Chapter 2). Within taxa, replicated genotypes were of clonal origin but clonal lineages rarely persisted in subsequent years suggesting that populations must go through sexual reproduction to be re-established in spring, from sexually produced diapause eggs. In addition, I also observed a complete replacement of taxa between two spring seasons (Chapter 2). Such a year-to-year taxon replacement has not been reported for the D. longispina complex before. I additionally detected that the genotypic diversity is lower in hybrids than in parental species (Chapters 2 and 3), supporting the existence of reproductive incompatibilities between the parental genomes. Thirdly, in order to understand the impact of cyclically parthenogenetic reproduction on populations, I explored the changes in taxon and clonal composition of Daphnia populations, across time (generation-to-generation) and space (between sampling stations), during a period of seasonal environmental change (Chapter 3). I observed that clonal diversity increased with time, as a few dominant clones were replaced by a higher number of less common clones. I assumed that a loss in selective advantage for the dominant clones may have been due to parasite selection acting in a negative frequency-dependent manner. Therefore, in Chapter 4, I investigated the possibility of parasite-mediated selection in D. longispina populations. I found significant differences in clonal composition between random and infected parts of the host population. This suggests that parasite-driven selection might operate in natural Daphnia populations, as parasites influence the clonal structure of host population. In the second part of my thesis (Chapters 5), I investigated how host-parasite interactions could be altered by predation. Specifically, I tested the potential costs of simultaneous prey exposure to enemies from different functional levels (i.e. predators and parasites). I found that the proportion of successful infections and the number of parasite spores were higher among defended (against predators) than undefended Daphnia, demonstrating a previously unknown and environmentally relevant cost to inducible defences. These results enhance our understanding of how epidemiology can be integrated into the concept of phenotypic plasticity

Fine-scale temporal and spatial variation of taxon and clonal structure in the Daphnia longispina hybrid complex in heterogeneous environments

Background: Cyclical parthenogenetic water fleas of the genus Daphnia have become a prominent model organism in ecology and evolution. In the past, analyses of their population structure have been limited by the prevailing use of allozyme markers, which in general do not allow for the distinction of individual clones. In this study, we used 10 microsatellite markers to track changes in the taxonomic and clonal composition of Daphnia populations, and traced the abundance of the most common clones in two European reservoirs. One of the localities was inhabited by a single species of the Daphnia longispina complex (D. galeata), the other by two parental species (D. galeata and D. longispina) and their interspecific hybrids. The study took place during the transition from summer stratification to autumn mixing, representing a period of major environmental change within lake habitats. Results: In both reservoirs, we observed temporal (generation-to-generation) and spatial (along the heterogeneous reservoir environment) changes in Daphnia community structure. In the single-species reservoir, the clonal diversity of D. galeata increased with time, as a few dominant clones were replaced by a higher number of less common clones. A loss in selective advantage for the dominant clones may have been due to gradual changes in the environment, or due to selection acting in a negative frequency-dependent manner. In the multispecies reservoir, there were no apparent temporal trends in clonal diversity but we observed significantly lower clonal diversity in the interspecific hybrids than in the coexisting parental species, supporting the existence of reproductive barriers between the parental genomes. Conclusions: Our study, tracing clonal lineages of Daphnia in time and space by the fine-resolution markers, contributes to the understanding of how clonal reproduction impacts community structure in cyclically parthenogenetic organisms

Hybridizing Daphnia communities from ten neighbouring lakes: spatio-temporal dynamics, local processes, gene flow and invasiveness

Background In natural communities of cyclical parthenogens, rapid response to environmental change is enabled by switching between two reproduction modes. While long periods of asexual reproduction allow some clones to outcompete others, and may result in “clonal erosion”, sexual reproduction restores genetic variation in such systems. Moreover, sexual reproduction may result in the formation of interspecific hybrids. These hybrids can then reach high abundances, through asexual clonal reproduction. In the present study, we explored genetic variation in water fleas of the genus Daphnia. The focus was on the short-term dynamics within several clonal assemblages from the hybridizing Daphnia longispina complex and the impact of gene flow at small spatial scales. Results Daphnia individuals belonged either to the parental species D. galeata and D. longispina, or to different hybrid classes, as identified by 15 microsatellite markers. The distribution and genotypic structure of parental species, but not hybrids, corresponded well with the geographical positions of the lakes. Within parental species, the genetic distance among populations of D. galeata was lower than among populations of D. longispina. Moreover, D. galeata dominance was associated with higher phosphorous load. Finally, there was no evidence for clonal erosion. Conclusions Our results suggest that the contemporary structure of hybridizing Daphnia communities from ten nearby lakes is influenced by colonization events from neighbouring habitats as well as by environmental factors. Unlike the parental species, however, there was little evidence for successful dispersal of hybrids, which seem to be produced locally. Finally, in contrast to temporary Daphnia populations, in which a decrease in clonal diversity was sometimes detectable over a single growing season, the high clonal diversity and lack of clonal erosion observed here might result from repeated hatching of sexually produced offspring. Overall, our study provides insights into spatio-temporal dynamics in a hybridizing Daphnia species complex in a recently established lake system, and relates genetic similarities of populations to a scenario of secondary invasion enhanced by environmental factors

Temporal genetic diversity of Schistosoma japonicum in two endemic sites in China revealed by microsatellite markers

Background: Schistosomiasis is one of the neglected tropical diseases. The causative agent of schistosomiasis in China, Schistosoma japonicum, has long been a major public health problem. An understanding of fundamental evolutionary and genetic processes in this species has major implications for its control and elimination. Intensive control efforts have greatly reduced the incidence of schistosomiasis in China, but little is known about the genetic consequences of these efforts. Methods: To investigate this, we sampled twice (years 2003 and 2011) from two endemic regions where populations of S. japonicum had persisted despite control efforts and genotyped these samples using ten microsatellite markers. Our main hypothesis was that parasite genetic diversity would be greatly reduced across this time period. Conclusions: There was no apparent reduction in allelic diversity, and a non-significant reduction in clonal diversity in these parasite populations between 2003 and 2011. We did, however, detect temporal genetic differentiation among the samples. Such a significant temporal genetic variation of S. japonicum populations has not been reported before

Population structure of a microparasite infecting Daphnia: spatio-temporal dynamics

Background: Detailed knowledge of spatial and temporal variation in the genetic population structure of hosts and parasites is required for understanding of host - parasite coevolution. As hot-spots of contemporary coevolution in natural systems are difficult to detect and long-term studies are restricted to few systems, additional population genetic data from various host - parasite systems may provide important insights into the topic. This is particularly true for parasites, as these players have been under-investigated so far due to the lower availability of suitable molecular markers. Here, we traced genetic variation (based on sequence variants in the internal transcribed spacer region, ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili, a common microparasite of the cladoceran Daphnia (here, the D. longispina hybrid complex). At three sites, we also studied parasite genetic variation over time (three to four sampling points) and tested for associations between parasite genotypes and host species. Results: Parasite (and host) populations were significantly structured across space, indicating limited dispersal. Moreover, the frequency of parasite genotypes varied significantly over time, suggesting rapid evolutionary change in Caullerya. However, the distribution of parasite genotypes was similar across different host species, which might in turn have important consequences for parasite epidemiology. Conclusions: The approach proposed here can be applied to track spatial and temporal changes in the population structure of other microparasite species for which sequence variation in the ITS or other highly variable genome regions has been documented but other types of polymorphic markers are lacking. Screening of parasite sequence variants allows for reliable detection of cross-species infections and, using advanced sequencing techniques in the near future, for detailed studies of parasite evolution in natural host - parasite systems

Extreme Environments Facilitate Hybrid Superiority - The Story of a Successful Daphnia galeata x longispina Hybrid Clone

Hybridization within the animal kingdom has long been underestimated. Hybrids have often been considered less fit than their parental species. In the present study, we observed that the Daphnia community of a small lake was dominated by a single D. galeata x D. longispina hybrid clone, during two consecutive years. Notably, in artificial community set-ups consisting of several clones representing parental species and other hybrids, this hybrid clone took over within about ten generations. Neither the fitness assay conducted under different temperatures, or under crowded and non-crowded environments, nor the carrying capacity test revealed any outstanding life history parameters of this hybrid clone. However, under simulated winter conditions (i.e. low temperature, food and light),the hybrid clone eventually showed a higher survival probability and higher fecundity compared to parental species. Hybrid superiority in cold-adapted traits leading to an advantage of overwintering as parthenogenetic lineages might consequently explain the establishment of successful hybrids in natural communities of the D. longispina complex. In extreme cases, like the one reported here, a superior hybrid genotype might be the only clone alive after cold winters. Overall, superiority traits, such as enhanced overwintering here, might explain hybrid dominance in nature, especially in extreme and rapidly changing environments. Although any favoured gene complex in cyclic parthenogens could be frozen in successful clones independent of hybridization, we did not find similarly successful clones among parental species. We conclude that the emergence of the observed trait is linked to the production of novel recombined hybrid genotypes

Genetic diversity and population differentiation of the freshwater copepod Sinocalanus tenellus (Calanoida, Centropagidae) in China

Copepods, present in a wide range of water bodies, are an important component of freshwater ecosystems and their biodiversity has been much studied in marine and freshwater ecosystems. However, no previous genetic data are available that allow an assessment of population-genetic diversity and differentiation of the copepod Sinocalanus tenellus from Chinese freshwaters. We analyzed DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene from eleven S. tenellus populations (individual lakes) from China, ten of which exhibited a high genetic diversity. Low to high population differentiation was detected among the populations. Interestingly, substantial genetic divergence was detected between WLS (Wuliangsu, in Inner Mongolia) and other locations, indicating the presence of two lineages of S. tenellus in East Asia. Moreover, we found that two distinct clades of S. tenellus were separated by the reference “S. sinensis” clade, suggesting they were parts of a complex of cryptic species of S. tenellus. This study will contribute to an understanding of the diversity and biogeography of copepods in freshwater ecosystem in China

Genetic Structure of Daphnia galeata Populations in Eastern China

This study presents the first examination of the genetic structure of Daphnia longispina complex populations in Eastern China. Only one species, D. galeata, was present across the eight investigated lakes; as identified by taxon assignment using allelic variation at 15 microsatellite loci. Three genetically differentiated D. galeata subgroups emerged independent of the type of statistical analysis applied. Thus, Bayesian clustering, discriminant analysis based on results from factorial correspondence analysis, and UPGMA clustering consistently showed that populations from two neighbouring lakes were genetically separated from a mixture of genotypes found in other lakes, which formed another two subgroups. Clonal diversity was high in all D. galeata populations, and most samples showed no deviation from Hardy-Weinberg equilibrium, indicating that clonal selection had little effect on the genetic diversity. Overall, populations did not cluster by geographical origin. Further studies will show if the observed pattern can be explained by natural colonization processes or by recent anthropogenic impact on predominantly artificial lakes

Cryptic diversity and gene introgression of Moinidae (Crustacea: Cladocera) in Nigeria

The distribution and species/lineage diversity of freshwater invertebrate zooplankton is understudied in Sub-Saharan Africa. In the present study, we explored the lineage diversity and regional distribution of Moinidae (Crustacea: Cladocera) species in Southeast Nigeria. Three species of Moinidae were identified, based on morphology, in 11 of 32 Nigerian lakes examined. Their phylogenetic relationships were investigated based on mitochondrial dna sequences (cytochrome oxidase c subunit I gene; coi) and two nuclear internal transcribed spacer regions (its-1 and its-2). Three coi lineages were detected, corresponding to the morphological species. Two of the coi lineages are newly reported, but one coi lineage (and the haplotype found) is globally distributed, suggesting an ability of moinids to disperse over long distances. Interestingly, two individuals that were morphologically M. cf. macrocopa and had its alleles typical of that species had mtDNA sequences typical of M. cf. micrura. Additionally, one individual that corresponded morphologically to M. cf. macrocopa (and also had a mitochondrial sequence typical of M. cf. micrura) had one its-2 allele typical of that species and one typical of M. cf. micrura. This discordance between mtDNA and nuclear phylogenies suggests gene introgression and/or hybridization between different species within the genus. Our data shows the lineage distribution/diversity and the presence of gene introgression/interspecific hybridization among moinid species from a tropical region

Genetic diversity and selection of three nuclear genes in Schistosoma japonicum populations

Background: The blood fluke, Schistosoma japonicum still causes severe disease in China, the Philippines and Indonesia. Although there have been some studies the molecular epidemiology of this persistent and harmful parasite, few have explored the possibility and implications of selection in S. japonicum populations. Methods: We analyzed diversity and looked for evidence of selection at three nuclear genes (SjIpp2, SjFabp and SjT22.6) in 13 S. japonicum populations. Results: SjT22.6 was found to exhibit high nucleotide diversity and was under positive selection in the mountainous region of mainland China. As a tegumental protein, its secondary and tertiary structure differed between S. japonicum strains from the mountainous and lakes regions. In contrast, SjIpp2 and SjFabp had relatively low levels of nucleotide diversity and did not show significant departure from neutrality. Conclusions: As a tegument-associated antigen-encoding gene of S. japonicum, SjT22.6 has high nucleotide diversity and appears to be under positive selection in the mountainous region of mainland China