A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex.

BACKGROUND: Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. RESULTS: In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. CONCLUSIONS: The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.

Evolution of asexual Daphnia pulex in Japan: variations and covariations of the digestive, morphological and life history traits.

BACKGROUND: Several genetic lineages of obligate parthenogenetic Daphnia pulex, a common zooplankton species, have invaded Japan from North America. Among these, a lineage named JPN1 is thought to have started colonization as a single genotype several hundred to thousand years ago and subsequently produced many genotypes in Japan. To examine the phenotypic variations due to ecological drivers diverging the genotypes in new habitats, we measured heritability and variation in 17 traits, including life history, morphology and digestive traits, and the genetic distance among the D. pulex JPN1 genotypes in Japan. RESULTS: We found that most of the traits measured varied significantly among the genotypes and that heritability was highest in the morphological traits, followed by the digestive and life history traits. In addition, 93% of the variation in these traits was explained by the first three components in the principal component analysis, implying that variation of these heritable traits is not random but rather converged into a few directions. These relations among traits revealed the potential importance of predation pressures and food conditions as factors for diverging and selecting different genotypes. However, the magnitude of the difference in any single trait group did not correlate with the genetic distance. CONCLUSIONS: Our findings show that the divergent traits evolved within D. pulex JPN1 lineage without genetic recombination, since their ancestral clone invaded Japan. Large variations and covariations of the phenotypic traits, irrespective of the genetic distance among the genotypes, support the view that the invasive success of D. pulex JPN1 was promoted by a genetic architecture that allowed for large phenotypic variations with a limited number of functionally important mutations without recombination.

Genetic and environmental effects on the scaling of metabolic rate with body size.

Metabolic rate (MR) often scales with body mass (BM) following a power function of the form MR=aBM b , where log(a) is the allometric intercept and b is the allometric exponent (i.e. slope on a log-log scale). The variational properties of b have been debated, but very few studies have tested for genetic variance in b, and none have tested for a genotype-by-environment (G×E) interaction in b Consequently, the short-term evolutionary potentials of both b and its phenotypic plasticity remain unknown. Using 10 clones of a population of Daphnia magna, we estimated the genetic variance in b and assessed whether a G×E interaction affected b We measured MR on juveniles of different sizes reared and measured at three temperatures (17, 22 and 28°C). Overall, b decreased with increasing temperature. We found no evidence of genetic variance in b at any temperature, and thus no G×E interaction in b However, we found a significant G×E interaction in size-specific MR. Using simulations, we show how this G×E interaction can generate genetic variation in the ontogenetic allometric slope of animals experiencing directional changes in temperature during growth. This suggests that b can evolve despite having limited genetic variation at constant temperatures.

Rediscovery after Almost 120 Years: Morphological and Genetic Evidence Supporting the Validity of Daphnia mitsukuri (Crustacea: Cladocera).

We examined the morphology of Daphnia individuals maintained in our laboratory for several years, originally collected in Lake Inbanuma, Chiba, Japan. We determined partial sequences of the mitochondrial cytochrome c oxidase subunit I and 12S rRNA genes from specimens in the cultured material. These animals are morphologically similar to D. obtusa Kurz, 1874 , but genetically distinct from this species. Our detailed observation shows that the morphological characteristics in the female and male individuals of our material are highly congruent with those of D. mitsukuri Ishikawa, 1896 , which has not been identified positively for more than 120 years since its original description, with its taxonomic identity having been questioned for almost 90 years. Based on our morphological and genetic data, we conclude that D. mitsukuri should be regarded as a taxonomically valid species. A search among public DNA sequence databases suggests D. mitsukuri is also distributed in China, although these Chinese sequences have been labeled as 'Daphnia pulex', representing misidentification.

The heat is on: Genetic adaptation to urbanization mediated by thermal tolerance and body size.

Worldwide, urbanization leads to tremendous anthropogenic environmental alterations, causing strong selection pressures on populations of animals and plants. Although a key feature of urban areas is their higher temperature ("urban heat islands"), adaptive thermal evolution in organisms inhabiting urban areas has rarely been studied. We tested for evolution of a higher heat tolerance (CTMAX ) in urban populations of the water flea Daphnia magna, a keystone grazer in freshwater ecosystems, by carrying out a common garden experiment at two temperatures (20°C and 24°C) with genotypes of 13 natural populations ordered along a well-defined urbanization gradient. We also assessed body size and haemoglobin concentration to identify underlying physiological drivers of responses in CTMAX . We found a higher CTMAX in animals isolated from urban compared to rural habitats and in animals reared at higher temperatures. We also observed substantial genetic variation in thermal tolerance within populations. Overall, smaller animals were more heat tolerant. While urban animals mature at smaller size, the effect of urbanization on thermal tolerance is only in part caused by reductions in body size. Although urban Daphnia contained higher concentrations of haemoglobin, this did not contribute to their higher CTMAX . Our results provide evidence of adaptive thermal evolution to urbanization in the water flea Daphnia. In addition, our results show both evolutionary potential and adaptive plasticity in rural as well as urban Daphnia populations, facilitating responses to warming. Given the important ecological role of Daphnia in ponds and lakes, these adaptive responses likely impact food web dynamics, top-down control of algae, water quality, and the socio-economic value of urban ponds.

Neuroanatomy of the optic ganglia and central brain of the water flea Daphnia magna (Crustacea, Cladocera).

We reveal the neuroanatomy of the optic ganglia and central brain in the water flea Daphnia magna by use of classical neuroanatomical techniques such as semi-thin sectioning and neuronal backfilling, as well as immunohistochemical markers for synapsins, various neuropeptides and the neurotransmitter histamine. We provide structural details of distinct neuropiles, tracts and commissures, many of which were previously undescribed. We analyse morphological details of most neuron types, which allow for unravelling the connectivities between various substructural parts of the optic ganglia and the central brain and of ascending and descending connections with the ventral nerve cord. We identify 5 allatostatin-A-like, 13 FMRFamide-like and 5 tachykinin-like neuropeptidergic neuron types and 6 histamine-immunoreactive neuron types. In addition, novel aspects of several known pigment-dispersing hormone-immunoreactive neurons are re-examined. We analyse primary and putative secondary olfactory pathways and neuronal elements of the water flea central complex, which displays both insect- and decapod crustacean-like features, such as the protocerebral bridge, central body and lateral accessory lobes. Phylogenetic aspects based upon structural comparisons are discussed as well as functional implications envisaging more specific future analyses of ecotoxicological and endocrine disrupting environmental chemicals.

The alignment between phenotypic plasticity, the major axis of genetic variation and the response to selection.

Phenotypic plasticity is the ability of a genotype to produce more than one phenotype in order to match the environment. Recent theory proposes that the major axis of genetic variation in a phenotypically plastic population can align with the direction of selection. Therefore, theory predicts that plasticity directly aids adaptation by increasing genetic variation in the direction favoured by selection and reflected in plasticity. We evaluated this theory in the freshwater crustacean Daphnia pulex, facing predation risk from two contrasting size-selective predators. We estimated plasticity in several life-history traits, the G matrix of these traits, the selection gradients on reproduction and survival, and the predicted responses to selection. Using these data, we tested whether the genetic lines of least resistance and the predicted response to selection aligned with plasticity. We found predator environment-specific G matrices, but shared genetic architecture across environments resulted in more constraint in the G matrix than in the plasticity of the traits, sometimes preventing alignment of the two. However, as the importance of survival selection increased, the difference between environments in their predicted response to selection increased and resulted in closer alignment between the plasticity and the predicted selection response. Therefore, plasticity may indeed aid adaptation to new environments.

Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?

Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced transgenerational effects, determined when transgenerational responses are induced, and quantified the cues that activate transgenerational plasticity. We show that predator exposure during embryonic development causes earlier maturation and increased reproductive output. Such effects are detectable two generations removed from predator exposure and are similar in magnitude in response to exposure to cues emitted by injured conspecifics. Moreover, all experimental contexts and traits yielded a negative correlation between within- versus across-generation responses. That is, responses to predator cues within- and across-generations were opposite in sign and magnitude. Although many models address transgenerational plasticity, none of them explain this apparent negative relationship between within- and across-generation plasticities. Our results highlight the need to refine the theory of transgenerational plasticity.

Interclonal proteomic responses to predator exposure in Daphnia magna may depend on predator composition of habitats.

Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterizing the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the water flea, is a textbook example for predator-induced phenotypic plastic defences; however, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages. We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. To get a more comprehensive idea of this phenomenon, we studied four genotypes with five biological replicates each, originating from habitats characterized by different predator composition, ranging from predator-free habitats to habitats containing T. cancriformis. We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype-dependent manner. Proteins connected to genotype-dependent responses were related to the cuticle, protein synthesis and calcium binding, whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype-dependent responses at the proteome level were most distinct for the only genotype that shares its habitat with Triops. Altogether, our study provides new insights concerning genotype-dependent and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.

Selection on incremental variation of eye size in a wild population of Daphnia.

Several studies of eye morphology have analysed macroevolutionary patterns in the diversity of eyes, and although these studies are often linked to environment or behaviour, they provide only indirect evidence of selection. Specific data to show the microevolutionary potential for adaptation by natural selection in eye morphology have been lacking. We document directional selection on eye size, an important determinant of visual capabilities, in a wild population of the freshwater microcrustacean Daphnia. We show that even slight changes in eye size may have major consequences for fitness. An increase in eye diameter of 19.9 µm - slightly more than one standard deviation - is associated with an increase in clutch size of one egg, or an increase of nearly 20% of the mean clutch size. Furthermore, relative eye size is genetically variable and thus could evolve in response to the observed selective pressure. We conclude that selection on incremental variation in eye size may have led to differences observed on broader taxonomic scales.

Effects of Tris(1,3-dichloro-2-propyl) Phosphate on Growth, Reproduction, and Gene Transcription of Daphnia magna at Environmentally Relevant Concentrations.

The synthetic flame retardant tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) has been frequently detected in natural waters, and its maximum concentration ever reported is 377 ng/L. However, information on the adverse effects of environmentally relevant concentrations of TDCIPP on aquatic organisms are totally unknown. In this study, <12-h old water fleas, D. magna, were exposed to concentrations of 0, 65±7.1, 550±33, or 6500±1400 ng/L TDCIPP, and dose- and time-dependent effects on reproduction and development were evaluated. Sequences of genes of D. magna were obtained from the National Center for Biotechnology Information and were used to develop PCR arrays for D. magna. Arrays were then used to study transcriptional responses of D. magna to TDCIPP. Exposure to environmentally relevant concentrations of TDCIPP significantly decreased fecundity as well as length of F0 and F1 generations. Transcriptional responses showed that, of the 155 genes tested, expressions of 57 genes were significantly changed, and some changes occurred following exposure to environmentally relevant concentrations (i.e., 65±7.1 and 550±23 ng/L). Furthermore, pathways related to protein synthesis and metabolism and endocytosis were considered to be significantly affected in a dose- and time-dependent manner and might be responsible for TDCIPP-induced reproductive and developmental toxicities.

Ecological constraints on sensory systems: compound eye size in Daphnia is reduced by resource limitation.

Eye size is an indicator of visual capability, and macroevolutionary patterns reveal that taxa inhabiting dim environments have larger eyes than taxa from bright environments. This suggests that the light environment is a key driver of variation in eye size. Yet other factors not directly linked with visual tasks (i.e., non-sensory factors) may influence eye size. We sought to jointly investigate the roles of sensory (light) and non-sensory factors (food) in determining eye size and ask whether non-sensory factors could constrain visual capabilities. We tested environmental influences on eye size in four species of the freshwater crustacean Daphnia, crossing bright and dim light levels with high and low resource levels. We measured absolute eye size and eye size relative to body size in early and late adulthood. In general, Daphnia reared on low resources had smaller eyes, both absolutely and relatively. In contrast to the dominant macroevolutionary pattern, phenotypic plasticity in response to light was rarely significant. These patterns of phenotypic plasticity were true for overall diameter of the eye and the diameter of individual facets. We conclude that non-sensory environmental factors can influence sensory systems, and in particular, that resource availability may be an important constraint on visual capability.

Endocrine regulation of predator-induced phenotypic plasticity.

Elucidating the developmental and genetic control of phenotypic plasticity remains a central agenda in evolutionary ecology. Here, we investigate the physiological regulation of phenotypic plasticity induced by another organism, specifically predator-induced phenotypic plasticity in the model ecological and evolutionary organism Daphnia pulex. Our research centres on using molecular tools to test among alternative mechanisms of developmental control tied to hormone titres, receptors and their timing in the life cycle. First, we synthesize detail about predator-induced defenses and the physiological regulation of arthropod somatic growth and morphology, leading to a clear prediction that morphological defences are regulated by juvenile hormone and life-history plasticity by ecdysone and juvenile hormone. We then show how a small network of genes can differentiate phenotype expression between the two primary developmental control pathways in arthropods: juvenoid and ecdysteroid hormone signalling. Then, by applying an experimental gradient of predation risk, we show dose-dependent gene expression linking predator-induced plasticity to the juvenoid hormone pathway. Our data support three conclusions: (1) the juvenoid signalling pathway regulates predator-induced phenotypic plasticity; (2) the hormone titre (ligand), rather than receptor, regulates predator-induced developmental plasticity; (3) evolution has favoured the harnessing of a major, highly conserved endocrine pathway in arthropod development to regulate the response to cues about changing environments (risk) from another organism (predator).

The expression of virulence for a mixed-mode transmitted parasite in a diapausing host.

Many parasites survive harsh periods together with their hosts. Without the possibility of horizontal transmission during host diapause, parasite persistence depends entirely on host survival. We therefore hypothesize that a parasite should be avirulent during its host's diapausing stage. In contrast, the parasite may express higher virulence, i.e. parasite-induced fitness reduction of the host, during host life stages with good opportunities for horizontal transmission. Here we study the effects of a vertically and horizontally transmitted microsporidium parasite, Hamiltosporidium tvaerminnensis, on the quantity and survival of resting eggs of its host Daphnia magna. We find that the parasite did not affect egg volume, hatching success and time to hatching of the Daphnia's resting eggs, although it did strongly reduce the number of resting eggs produced by infected females, revealing high virulence during the non-diapause phase of the host's life cycle. These results also explain another aspect of this system - namely the strong decline in natural population prevalence across diapause. This decline is not caused by mortality in infected resting stages, as was previously hypothesized, but because infected female hosts produce lower rates of resting eggs. Together, these results help explain the epidemiological dynamics of a microsporidian disease and highlight the adaptive nature of life stage-dependent parasite virulence.

Modality matters for the expression of inducible defenses: introducing a concept of predator modality.

BACKGROUND: Inducible defenses are a common and widespread form of phenotypic plasticity. A fundamental factor driving their evolution is an unpredictable and heterogeneous predation pressure. This heterogeneity is often used synonymously to quantitative changes in predation risk, depending on the abundance and impact of predators. However, differences in 'modality', that is, the qualitative aspect of natural selection caused by predators, can also cause heterogeneity. For instance, predators of the small planktonic crustacean Daphnia have been divided into two functional groups of predators: vertebrates and invertebrates. Predators of both groups are known to cause different defenses, yet predators of the same group are considered to cause similar responses. In our study we question that thought and address the issue of how multiple predators affect the expression and evolution of inducible defenses. RESULTS: We exposed D. barbata to chemical cues released by Triops cancriformis and Notonecta glauca, respectively. We found for the first time that two invertebrate predators induce different shapes of the same morphological defensive traits in Daphnia, rather than showing gradual or opposing reaction norms. Additionally, we investigated the adaptive value of those defenses in direct predation trials, pairing each morphotype (non-induced, Triops-induced, Notonecta-induced) against the other two and exposed them to one of the two predators. Interestingly, against Triops, both induced morphotypes offered equal protection. To explain this paradox we introduce a 'concept of modality' in multipredator regimes. Our concept categorizes two-predator-prey systems into three major groups (functionally equivalent, functionally inverse and functionally diverse). Furthermore, the concept includes optimal responses and costs of maladaptions of prey phenotypes in environments where both predators co-occur or where they alternate. CONCLUSION: With D. barbata, we introduce a new multipredator-prey system with a wide array of morphological inducible defenses. Based on a 'concept of modality', we give possible explanations how evolution can favor specialized defenses over a general defense. Additionally, our concept not only helps to classify different multipredator-systems, but also stresses the significance of costs of phenotype-environment mismatching in addition to classic 'costs of plasticity'. With that, we suggest that 'modality' matters as an important factor in understanding and explaining the evolution of inducible defenses.

Hard X-ray nanoprobe investigations of the subtissue metal distributions within Daphnia magna.

The unique potential of nanoscale elemental imaging of major/minor and trace-level elemental distributions within thin biological tissue sections of the ecotoxicological model organism Daphnia magna is demonstrated by synchrotron radiation nano-X-ray fluorescence (nano-XRF). The applied highly specialized sample preparation method, coupled with the high spatial resolution (∼180 nm) and high X-ray photon flux (6 × 10(11) photons/s) available at the European Synchrotron Radiation Facility (ESRF) ID22NI beamline proved to be critical for the high-quality visualization of (trace-)metal distributions on the submicron level within the target structures of interest. These include the branchial sacs on the thoracic appendages (epipodites) of D. magna, which are osmoregulatory regions where ion exchange occurs. For the main element of interest (Zn), detection limits of 0.7 ppm (3 ag) was reached in fast-scanning mode using an acquisition time of 0.3 s/pixel. As demonstrated, synchrotron radiation nano-XRF revealed the elemental distributions of Ca, Fe, and Zn within this osmoregulatory region on the submicron scale, aiding the exploration of possible detoxification mechanisms of Zn within D. magna at the subtissue level.

Sex-specific effects of a parasite evolving in a female-biased host population.

BACKGROUND: Males and females differ in many ways and might present different opportunities and challenges to their parasites. In the same way that parasites adapt to the most common host type, they may adapt to the characteristics of the host sex they encounter most often. To explore this hypothesis, we characterized host sex-specific effects of the parasite Pasteuria ramosa, a bacterium evolving in naturally, strongly, female-biased populations of its host Daphnia magna. RESULTS: We show that the parasite proliferates more successfully in female hosts than in male hosts, even though males and females are genetically identical. In addition, when exposure occurred when hosts expressed a sexual dimorphism, females were more infected. In both host sexes, the parasite causes a similar reduction in longevity and leads to some level of castration. However, only in females does parasite-induced castration result in the gigantism that increases the carrying capacity for the proliferating parasite. CONCLUSIONS: We show that mature male and female Daphnia represent different environments and reveal one parasite-induced symptom (host castration), which leads to increased carrying capacity for parasite proliferation in female but not male hosts. We propose that parasite induced host castration is a property of parasites that evolved as an adaptation to specifically exploit female hosts.

[Morphology and age variation of Daphnia galeata Sars (Cladocera: Daphniidae) in two adjacent water bodies of the Kola Peninsula].

The morphology and age variation of Daphnia galeata Sars (Cladocera: Daphniidae) in two adjacent water bodies of the Kola Peninsula are studied. The reliability of characters usually used for diagnosis of adult individuals of the given species was verified, and their formation in the postembryonic period was traced. If the identification of D. galeata from Lake Bolshoi Vudvyar caused no doubts, the population from Lake Malyi Vudvyar was atypical with respect to several morphological characters. We concluded that plastic characters, such as body shape, as well as the shape of the dorsal keel and helmet on the head are unreliable for distinguishing closely related species of water fleas. At the same time, some small-size characters, for instance, the relative depth of the medial crest on the posterior side of the head, allow us to diagnose this species with confidence.

A "crown of thorns" is an inducible defense that protects Daphnia against an ancient predator.

Genetic data has become an essential part of ecological studies, because the analyses of diversity within and among natural populations may grant access to previously overlooked ecological and evolutionary causalities, especially among cryptic species. Here, we present an example of how phylogenetic analysis of molecular data obtained within a DNA barcoding study, in combination with morphological and ecological data from the field and laboratory experiments, unraveled a striking predator-prey interaction between aquatic organisms. The "crown of thorns," a conspicuous morphological feature among water fleas of the Daphnia atkinsoni species complex (Crustacea: Cladocera), is considered to represent a species-specific trait. However, our study, initiated by the analysis of sequence variation in 2 mitochondrial genes, shows that this feature is phenotypically plastic and is induced by chemical cues released by Triops cancriformis, the tadpole shrimp (Notostraca). The trait acts as an effective antipredator defense, and is found in several Daphnia lineages coexisting with notostracans. These facts suggest that the "crown of thorns" evolved in coexistence with this ancient predator group.

A new redescription of Daphnia pusilla (Serventy, 1929) (Cladocera: Daphniidae) with emphasis on the thoracic limbs of Daphnia (Ctenodaphnia) Dybowski amp; Grochowski, 1895.

The genus Daphnia O.F. Mller, 1776 (Crustacea: Cladocera) still has a confused taxonomy for several objective and subjective reasons. Still there are many taxa with inadequately described morphology, primarily among the subgenus Daphnia (Ctenodaphnia) Dybowski Grochowski, 1895. We provide a redescription of an Australian endemic taxon Daphnia (Ctenodaphnia) pusilla (Serventy, 1929) according to recent standards of morphological study with special attention to the thoracic limbs. We conclude that main differences between thoracic limbs of the subgenera D. (Ctenodaphnia) and Daphnia s. str. concern the limb I only as it is well-known among the cladocerans of other families. But still only a few species of D. (Ctenodaphnia) have been studied adequately, and efforts to redescribe their morphology need to be continued.