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468 results for “Daphnia”
Data from: Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna
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Data from: Thermal tolerance in the keystone species Daphnia magna –a candidate gene and an outlier analysis approach
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Thermal plasticity of setae of the second limb of Daphnia
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Data from: Daphnia females adjust sex allocation in response to current sex ratio and density
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Raw data used in: Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets
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Does salinization impact long-term Daphnia assemblage dynamics? Evidence from the sediment egg bank in a small hard-water lake
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Data from: Genetic structure of Daphnia galeata populations in Eastern China
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Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families
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Data from: The QRS (Quantification of Representative Sequences) pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia
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Resurrecting the metabolome: Rapid evolution magnifies the metabolomic plasticity to predation in a natural Daphnia population
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Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes
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Trans-specific polymorphisms between cryptic Daphnia species
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Dataset: A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between Daphnia magna's gut microbiota and bacterioplankton
<p>Dataset and R codes for the publication "A methodological framework to analyse determinants of host-microbiota networks, with an application to the relationships between <em>Daphnia magna</em>’s gut microbiota and bacterioplankton"</p>
Data from: Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold
Maturation is a critical developmental process, and the age and size at which it occurs have important fitness consequences. Although maturation is remarkably variable, certain mechanisms, including a minimum size or state threshold, are proposed to underlie the process across a broad diversity of taxa. Recent evidence suggests that thresholds may themselves be developmentally plastic, and in the crustacean Daphnia pulex it is unclear whether maturation follows a threshold or is a gradual process more akin to a rate. Changes in gene expression across four instars before and during maturation were compared in a cDNA microarray experiment. Developmental stage was treated statistically both as a discontinuous and a continuous variable, to determine whether genes showed gradual or discrete changes in expression. The continuous analysis identified a greater number of genes with significant differential expression (45) than the discontinuous analysis (11). The majority of genes, including those coding for histones, factors relating to transcription and cell cycle processes, and a putative developmental hormone showed continuous increases or decreases in expression from the first to the fourth instar, suggestive of a prolonged and gradual maturation process. Three genes coding for a fused Vitellogenin/super-oxide dismutase showed increases in expression following the second instar and coincided with the posited maturation threshold, but even their expression increased in a continuous fashion.
Data from: The effects of natural and anthropogenic microparticles on individual fitness in Daphnia magna
Concerns are being raised that microplastic pollution can have detrimental effects on the feeding of aquatic invertebrates, including zooplankton. Both small plastic fragments (microplastics, MPs) produced by degradation of larger plastic waste (secondary MPs; SMPs) and microscopic plastic spheres used in cosmetic products and industry (primary MPs; PMPs) are ubiquitously present in the environment. However, despite the fact that most environmental MPs consist of weathered plastic debris with irregular shape and broad size distribution, experimental studies of organism responses to MP exposure have largely used uniformly sized spherical PMPs. Therefore, effects observed for PMPs in such experiments may not be representative for MP-effects in situ. Moreover, invertebrate filter-feeders are generally well adapted to the presence of refractory material in seston, which questions the potential of MPs at environmentally relevant concentrations to measurably affect digestion in these organisms. Here, we compared responses to MPs (PMPs and SMPs) and naturally occurring particles (kaolin clay) using the cladoceran Daphnia magna as a model organism. We manipulated food levels (0.4 and 9 μg C mL-1) and MP or kaolin contribution to the feeding suspension (<1 to 74%) and evaluated effects of MPs and kaolin on food uptake, growth, reproductive capacity of the daphnids, and maternal effects on offspring survival and feeding. Exposure to SMPs caused elevated mortality, increased inter-brood period and decreased reproduction albeit only at high MP levels in the feeding suspension (74% by particle count). No such effects were observed in either PMP or kaolin treatments. In daphnids exposed to any particle type at the low algal concentration, individual growth decreased by ~15%. By contrast, positive growth response to all particle types was observed at the high algal concentration with 17%, 54% and 40% increase for kaolin, PMP and SMP, respectively. When test particles comprised 22% in the feeding suspension, both MP types decreased food intake by 30%, while kaolin had no effect. Moreover, SMPs were found to homoaggregate in a concentration-dependent manner, which resulted in a 77% decrease of the ingested SMPs compared to PMPs. To better understand MP-processing in the gut, gut passage time (GPT) and evacuation rate of MPs were also assayed. SMPs and PMPs differed in their effects on daphnids; moreover, the particle effects were dependent on the MP: algae ratio in the suspension. When the MP contribution to the particle abundance in the medium changed from 1 to 4%, GPT for daphnids exposed to SMPs increased 2-fold. Our results suggest that MPs and, in particular, SMPs, have a greater capacity to negatively affect feeding in D. magna compared to naturally occurring mineral particles of similar size. Moreover, grazer responses observed in experiments with PMPs cannot be extrapolated to the field where SMPs dominate, because of the greater effects caused by the latter.
Data from: Offspring provisioning explains clone specific maternal age effects on life history and lifespan in the water flea, Daphnia pulex
Genetic inheritance underpins evolutionary theories of aging, but the role that nongenetic inheritance plays is unclear. Parental age reduces the life span of offspring in a diverse array of taxa but has not been explained from an evolutionary perspective. We quantified the effect that maternal age had on the growth and maturation decisions, life history, rates of senescence, and life span of offspring from three Daphnia pulex clones collected from different populations. We then used those data to test general hypotheses proposed to explain maternal age effects on offspring life span. Three generations of breeding from young or old mothers produced dramatic differences in the life histories of fourth-generation offspring, including significant reductions in life span. The magnitude of the effect differed between clones, which suggests that genetic and nongenetic factors ultimately underpin trait inheritance and shape patterns of aging. Older parents did not transmit a senescent state to their offspring. Instead, offspring from older ancestors had increased early-life reproductive effort, which resulted in an earlier onset of reproductive senescence, and an increased rate of actuarial senescence, which shortened their life span. Our results provide a clear example of the need to consider multiple inheritance mechanisms when studying trait evolution.
Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits
Background: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories. Results: Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures. Conclusions: The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones.
Data from: Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across-generations in Daphnia
Research has shown that a change in environmental conditions can alter the expression of traits during development (i.e., 'within-generation phenotypic plasticity') as well as induce heritable phenotypic responses that persist for multiple generations (i.e., 'transgenerational plasticity'). It has long been assumed that shifts in gene expression are tightly linked to observed trait responses at the phenotypic level. Yet, the manner in which organisms couple within- and trans-generational plasticity at the molecular level is unclear. Here we tested the influence of fish predator chemical cues on patterns of gene expression within- and across-generations using a clone of Daphnia ambigua that is known to exhibit strong transgenerational plasticity but weak within-generation plasticity. Daphnia were reared in the presence of predator cues in generation 1 and shifts in gene expression were tracked across two additional asexual experimental generations that lacked exposure to predator cues. Initial exposure to predator cues in generation 1 was linked to ~50 responsive genes but such shifts were 3-4x larger in later generations. Differentially expressed genes included those involved in reproduction, exoskeleton structure, and digestion; major shifts in expression of genes encoding ribosomal proteins were also identified. Furthermore, shifts within the first generation and transgenerational shifts in gene expression were largely distinct in terms of the genes that were differentially expressed. Such results argue that the gene expression programs involved in within- versus trans-generation plasticity are fundamentally different. Our study provides new key insights into the plasticity of gene expression and how it relates to phenotypic plasticity in nature.
Data from: Resistance to a bacterial parasite in the Crustacean Daphnia magna shows Mendelian segregation with dominance
The influence of host and parasite genetic background on infection outcome is a topic of great interest because of its pertinence to theoretical issues in evolutionary biology. In the present study we use a classical genetics approach to examine the mode of inheritance of infection outcome in the crustacean Daphnia magna when exposed to the bacterial parasite Pasteuria ramosa. In contrast to previous studies in this system we use a clone of P. ramosa, not field isolates, which allows for a more definitive interpretation of results. We test parental, F1, F2, backcross and selfed parental clones (total 284 genotypes) for susceptibility against a clone of P. ramosa using 2 different methods, infection trials and the recently developed attachment-test. We find that D. magna clones reliably exhibit either complete resistance or complete susceptibility to P. ramosa clone C1 and that resistance is dominant and inherited in a pattern consistent with Mendelian segregation of a single-locus with two alleles. The finding of a single host locus controlling susceptibility to P. ramosa suggests that the previously observed genotype-genotype interactions in this system have a simple genetic basis. This has important implications for the outcome of host-parasite coevolution. Our results add to the growing body of evidence that resistance to parasites in invertebrates is mostly coded by one or few loci with dominance.
Data from: Rapid evolution of antioxidant defense in a natural population of Daphnia magna
Natural populations can cope with rapid changes in stressors by relying on sets of physiological defense mechanisms. Little is known onto what extent these physiological responses reflect plasticity and/or genetic adaptation, evolve in the same direction and result in an increased defense ability. Using resurrection ecology, we studied how a natural Daphnia magna population adjusted its antioxidant defense to ultraviolet radiation (UVR) during a period with increasing incident UVR reaching the water surface. We demonstrate rapid evolution of the induction patterns of key antioxidant enzymes under UVR exposure in the laboratory. Notably, evolutionary changes strongly differed among enzymes and mainly involved the evolution of UV-induced plasticity. While D. magna evolved a strong plastic upregulation of glutathione peroxidase under UVR, it evolved a lower plastic upregulation of glutathione S-transferase and superoxide dismutase, and a plastic downregulation of catalase. The differentially evolved antioxidant strategies were collectively equally effective in dealing with oxidative stress since they resulted in the same high levels of oxidative damage (to lipids, proteins and DNA) and lowered fitness (intrinsic growth rate) under UVR exposure. The lack of better protection against UVR may suggest that the UVR exposure did not increase between both periods. Predator-induced evolution to migrate to lower depths that occurred during the same period may have contributed to the evolved defense strategy. Our results highlight the need for a multiple trait approach when focusing on the evolution of defense mechanisms.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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