Parasites driving host diversity: Incidence of disease correlated with Daphnia clonal turnover

According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency‐dependant selection by coevolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia–Caullerya host–parasite system. The clonal make‐up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme and later microsatellite markers. Significant differences in the clonal composition between random and infected subsamples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host–parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite‐based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis

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

Clonal structure and depth selection during a Caullerya mesnili epidemic in a hybridizing population of the Daphnia longispina complex

Daphnia perform diel vertical migration (DVM), a predator-avoidance strategy to migrate towards deeper and colder layers in the water column in the morning and movement to the algae-rich surface layers in the evening. However, individuals performing DVM incur several trade-offs since they might suffer from resource limitation and a slower instantaneous birth rate in deeper depths. DVM patterns may be modified by abiotic factors such as temperature, food concentration, or pH and vary among different Daphnia species and genotypes. Furthermore, Daphnia host a variety of microparasites that might pose an additional factor influencing DVM behaviour. For infected individuals, migration into cooler temperature layers might slow down parasite growth. Moreover, parasites can increase opacity of their hosts. Non-migrating individuals might then be selectively purged from the upper layers by visually hunting predators. With these premises we asked, whether epidemics of the ichthyosporean parasite Caullerya mesnili affect or are affected by the DVM behaviour of Daphnia in Lake Greifensee, Switzerland by analysing the vertical distribution of Daphnia during day and night on two dates. Furthermore, we were interested whether a potential interaction depends on host genotype. We therefore studied the genotypic composition of the integrated population in regular sampling intervals over the course of one year and on a fine-grained vertical resolution during the Caullerya epidemic in late summer. Since Caullerya-infected Daphnia migrated equally well as uninfected ones, the findings of this study suggest that Caullerya epidemics neither affected nor were affected by the DVM behaviour of Daphnia. We observed clonal succession in the lake but could not link this succession to the Caullerya epidemic; all except one of the common multilocus genotypes were under-infected. In addition, outbreak and course of this Caullerya epidemic seemed to rely mainly on environmental cues. Because this first study only provides a snapshot of time, we hope that further studies will be done to verify our results.ISSN:0018-8158ISSN:1573-511

Who’s Driving? Switch of Drivers in Immunotherapy-Treated Progressing Sinonasal Melanoma

Mucosal melanoma can be driven by various driver mutations in genes such as NRAS, KIT, or KRAS. However, some cases present with only weak drivers, or lacking known oncogenic drivers, suggesting immunotherapy over targeted therapy. While resistance mechanisms to immunotherapy in cutaneous melanoma have been uncovered, including alterations in JAK1/2, B2M, or STK11, a switch of oncogenic drivers under immunotherapy has not yet been observed. We report three cases of metastatic sinonasal melanoma that switched oncogenic drivers from KRAS, KIT, or no driver to NRAS during or after immunotherapy, thereby showing progressive disease. One of the cases presented with three spatially separate driver mutations in the primary tumor, whereas the NRAS clone persisted under immunotherapy. In comparison, three different control cases receiving radiotherapy only did not show a change of the detectable molecular drivers in their respective recurrences or metastases. In summary, these data provide an important rationale for longitudinal molecular testing, based on evidence for an unforeseen recurrent event of molecular driver switch to NRAS in progressing sinonasal melanoma. These findings provide the basis for further studies on a potential causal relation of emerging NRAS mutant clones and immunotherapy

Life history and microsatellite data

Contains four workbooks, with two types of data for two lakes. Those workbooks called "life_table" contain the results of our Pb exposure life history experiment. Each row represents one individual, which was kept in its own jar. Columns identify each clone, clone age, and Pb treatment. The columns labeled with day numbers give the number of live births counted on that day. Deaths are recorded as NAs: the first NA appears on the day that an animal was found dead. The workbooks called "msats" contain the microsatellite data retrieved from sedimentary eggs. Each row represents one egg. A column gives the year the egg was produced, and for Greifensee, another column gives the species identity. The remainder of the columns give the diploid microsatellite genotype of each egg. The names of the columns correspond to the names of the markers

Data from: Parasites driving host diversity: incidence of disease correlated with Daphnia clonal turnover

According to the Red Queen hypothesis, clonal diversity in asexual populations could be maintained by negative frequency-dependant selection by co-evolving parasites. If common clones are selected against and rare clones gain a concomitant advantage, we expect that clonal turnover should be faster during parasite epidemics than between them. We tested this hypothesis exploring field data of the Daphnia – Caullerya host-parasite system. The clonal make-up and turnover of the Daphnia host population was tracked with high temporal resolution from 1998 until 2013, using first allozyme markers and later microsatellite markers. Significant differences in the clonal composition between random and infected sub-samples of Daphnia populations were detected on six of seven tested occasions, confirming genetic specificity of the host-parasite interaction in this system. We used time series analysis to compare the rates of host clonal turnover to the incidence of parasitism, and found that Caullerya prevalence was significantly associated with microsatellite-based clonal turnover. As alternate hypotheses, we further tested whether turnover was related to a variety of biotic, abiotic, and host demographic parameters. Other significant correlates of turnover were cyanobacterial biomass and (weakly) temperature. Overall, parasitism seems to be a strong driver of host clonal turnover, in support of the Red Queen hypothesis