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

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

New possibilities arise for studies of hybridization: SNP-based markers for the multi-species Daphnia longispina complex derived from transcriptome data

In order to trace community dynamics and reticulate evolution in hybrid species complexes, long-term comparative studies of natural populations are necessary. Such studies require the development of tools for fine-scale genetic analyses. In the present study, we developed species-diagnostic SNP-based markers for hybridizing freshwater crustaceans: the multispecies Daphnia longispina complex. Specifically, we took advantage of transcriptome data from a key species of this hybrid complex, the annotated genome of a related Daphnia species and well-defined reference genotypes from three parental species. Altogether eleven nuclear loci with several species-specific SNP sites were identified in sequence alignments of these reference genotypes from three parental species and their interspecific hybrids. A PCR-RFLP assay was developed for cost-efficient large population screening by SNP-based genotyping. Taxon assignment by RFLP patterns was nearly perfectly concordant with microsatellite genotyping across several screened populations from Europe. Finally, we were able to amplify two short regions of these loci in formaldehyde-preserved samples dating back to the year 1960. The species-specific SNP-based markers developed here provide valuable tools to study hybridization over time, including the long-term impact of various environmental factors on hybridization and biodiversity changes. SNP-based genotyping will finally allow eco-evolutionary dynamics to be revealed at different time scale

Daphnia parasite dynamics across multiple Caullerya epidemics indicate selection against common parasite genotypes

Studies of parasite population dynamics in natural systems are crucial for our understanding of host–parasite coevolutionary processes. Some field studies have reported that host genotype frequencies in natural populations change over time according to parasite-driven negative frequency-dependent selection. However, the temporal patterns of parasite genotypes have rarely been investigated. Moreover, parasite-driven negative frequency-dependent selection is contingent on the existence of genetic specificity between hosts and parasites. In the present study, the population dynamics and host-genotype specificity of the ichthyosporean Caullerya mesnili, a common endoparasite of Daphnia water fleas, were analysed based on the observed sequence variation in the first internal transcribed spacer (ITS1) of the ribosomal DNA. The Daphnia population of lake Greifensee (Switzerland) was sampled and subjected to parasite screening and host genotyping during C. mesnili epidemics of four consecutive years. The ITS1 of wild-caught C. mesnili-infected Daphnia was sequenced using the 454 pyrosequencing platform. The relative frequencies of C. mesnili ITS1 sequences differed significantly among years: the most abundant C. mesnili ITS1 sequence decreased and rare sequences increased over the course of the study, a pattern consistent with negative frequency-dependent selection. However, only a weak signal of host-genotype specificity between C. mesnili and Daphnia genotypes was detected. Use of cutting edge genomic techniques will allow further investigation of the underlying micro-evolutionary relationships within the Daphnia–C. mesnili system

反応蒸留プロセスの合成と動的最適化

京都大学0048新制・課程博士博士(工学)甲第8343号工博第1908号新制||工||1168(附属図書館)UT51-2000-F247京都大学大学院工学研究科化学工学専攻(主査)教授 橋本 伊織, 教授 谷垣 昌敬, 教授 田門 肇学位規則第4条第1項該当Doctor of EngineeringKyoto UniversityDA

Data from: Capturing the population structure of microparasites: using ITS-sequence data and a pooled DNA approach

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a common marker not only for the molecular identification of different taxa and strains, but also for the analysis of population structure of wild microparasite communities. Importantly, the multicopy nature of this region allows the amplification of low-quantity samples of the target DNA, a common problem in studies on unicellular, unculturable microparasites. We analysed ITS sequences from the protozoan parasite Caullerya mesnili (class Ichthyosporea) infecting waterflea (Daphnia) hosts, across several host population samples. We showed that analysing representative ITS-types [as identified by statistical parsimony network analysis (SPN)] is a suitable method to address relevant polymorphism. The spatial patterns were consistent regardless of whether parasite DNA was extracted from individual hosts or pooled host samples. Remarkably, the efficiency in detecting different sequence types was even higher after sample pooling. As shown by simulations, an easily manageable number of sequences from pooled DNA samples are sufficient to resolve the spatial population structure in this system. In summary, the ITS region analysed from pooled DNA samples can provide valuable insights into the spatial and temporal dynamics of microparasites. Moreover, the application of SPN analysis is a good alternative to the well-established neighbour-joining method (NJ) for the identification of representative ITS-types. SPN can even outperform NJ by joining most of the singleton sequences to representative sequence clusters

caullerya_ITS_alignment

caullerya_ITS_alignmen

Molecular Identification and Hidden Diversity of Novel Daphnia Parasites from European Lakes▿ †

Parasites play important roles in local population dynamics and genetic structure. However, due to insufficient diagnostic tools, detailed host-parasite interactions may remain concealed by hidden parasite diversity in natural systems. Microscopic examination of 19 European lake Daphnia populations revealed the presence of three groups of parasites: fungi, microsporidia, and oomycetes. For most of these parasites no genetic markers have been described so far. Based on sequence similarities of the nuclear small-subunit and internal transcribed spacer (ITS) rRNA gene regions, one fungus, four microsporidian, and nine oomycete taxa were discovered in 147 infected Daphnia (and/or three other zooplankton crustaceans). Additionally, cloning of rRNA gene regions revealed parasite sequence variation within host individuals. This was most pronounced in the ITS region of one microsporidian taxon, where the within-host sequence variation ranged from 1.7% to 5.3% polymorphic sites for parasite isolates from 14 different geographical locations. Interestingly, the parasite isolates from close locations grouped together based on sequence similarities, suggesting that there was parasite dispersal. Taken together, the data obtained in this study revealed hidden diversity of parasite communities in Daphnia lake populations. Moreover, a higher level of resolution for identifying parasite strains makes it possible to test new hypotheses with respect to parasite dispersal, transmission routes, and coinfection