Inducible Defenses with a "Twist": Daphnia barbata Abandons Bilateral Symmetry in Response to an Ancient Predator

Differences in alternative splicing events in the adaptive strategies of two Daphnia galeata genotypes induced by fish kairomones

BACKGROUND

Daphnia galeata is a suitable model organism for investigating predator-induced defense. Genes and pathways exhibiting differential expression between fish kairomone-treated and untreated groups in D. galeata have been identified. However, understanding of the significance of alternative splicing, a crucial process of the regulation of gene expression in eukaryotes, to this mechanism remains limited. This study measured life-history traits and conducted short-read RNA sequencing and long-read isoform sequencing of two Korean D. galeata genotypes (KB1 and KE2) to uncover the genetic mechanism underlying their phenotypic plasticity under predation stress.

RESULTS

KB1 exhibited strategies to enhance fertility and decrease body length when exposed to fish kairomones, while KE2 deployed an adaptive strategy to increase body length. Full-length transcriptomes from KB1 and KE2 yielded 65,736 and 57,437 transcripts, respectively, of which 32 differentially expressed transcripts (DETs) were shared under predation stress across both genotypes. Prominent DETs common to both genotypes were related to energy metabolism and the immune system. Additionally, differential alternative splicing (DAS) events were detected in both genotypes in response to fish kairomones. DAS genes shared between both genotypes may indicate their significant role in the post-transcriptional stress response to fish predation. Calpain-3, involved in digestion and nutrient absorption, was identified as a DAS gene in both genotypes when exposed to fish kairomones. In addition, the gene encoding thymosin beta, which is related to growth, was found to be a statistically significant DAS only in KB1, while that encoding ultraspiracle protein, also associated with growth, was only identified in KE2. Moreover, transcripts encoding proteins such as EGF-like domain-containing protein, vitellogenin fused with superoxide dismutase, and others were identified overlapping between DAS events and DETs and potentially elucidating their association with the observed phenotypic variation in each genotype.

CONCLUSIONS

Our findings highlight the crucial role of alternative splicing in modulating transcriptome landscape under predation stress in D. galeata, emphasizing the requirement for integrating gene expression and splicing analyses in evolutionary adaptation studies.

Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea

BACKGROUND

Phenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustacean Daphnia galeata is a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two Korean Daphnia galeata genotypes, KE1, and KB11, collected in the same environment.

RESULTS

When exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1.

CONCLUSIONS

The current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two Korean D. galeata genotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.

Daphnia as a versatile model system in ecology and evolution

Water fleas of the genus Daphnia have been a model system for hundreds of years and is among the best studied ecological model organisms to date. Daphnia are planktonic crustaceans with a cyclic parthenogenetic life-cycle. They have a nearly worldwide distribution, inhabiting standing fresh- and brackish water bodies, from small temporary pools to large lakes. Their predominantly asexual reproduction allows for the study of phenotypes excluding genetic variation, enabling us to separate genetic from non-genetic effects. Daphnia are often used in studies related to ecotoxicology, predator-induced defence, host–parasite interactions, phenotypic plasticity and, increasingly, in evolutionary genomics. The most commonly studied species are Daphnia magna and D. pulex, for which a rapidly increasing number of genetic and genomic tools are available. Here, I review current research topics, where the Daphnia model system plays a critical role.

Coping with antagonistic predation risks: Predator-dependent unique responses are dominant in Ceriodaphnia cornuta

Inducible defences of prey are evolved under diverse and variable predation risks. However, during the co-evolution of prey and multiple predators, the responses of prey to antagonistic predation risks, which may put the prey into a dilemma of responding to predators, remain unclear. Based on antagonistic predation pressure from an invertebrate (Chaoborus larvae) and a vertebrate (Rhodeus ocellatus) predator, we studied the responses of multiple traits and transcriptomes of the freshwater crustacean Ceriodaphnia cornuta under multiple predation risks. Chaoborus predation risk altered the expression of genes encoding cuticle proteins and modulated the biosynthesis of steroid hormones, cutin, suberine, and wax, leading to the development of horns and increase in size at the late developmental stage. Meanwhile, fish predation risk primarily triggered genes encoding ribosomes and those involved in unsaturated fatty acid biosynthesis and cysteine and methionine metabolism, resulting in smaller individual size and earlier reproduction. Inducible responses of both transcriptome and individual traits revealed that predator-dependent unique responses were dominant and the dilemma of antagonistic responses was relatively limited. However, the unique individual traits in response to invertebrate predation could be significantly impaired by vertebrate predation risk, even though the unique responses to different predators were extremely weakly correlated and could be elicited simultaneously. These results indicate that diverse predator-dependent unique responses are favoured by Ceriodaphnia during its co-evolution with multiple predators. Nonetheless, Ceriodaphnia is not a generalist that can fully adopt all predator-dependent unique responses simultaneously under multiple predation risks.

Inter- and Intraspecific Trait Compensation of Behavioural and Morphological Defences in a Damselfly Genus

Predation is a key driver of phenotypic diversification with prey having evolved sets of correlated anti-predator traits. Changes in anti-predator traits can be studied on an evolutionary as well as on a developmental timescale. Using a common garden setup, we studied inter- and intraspecific correlations of behavioural and morphological defences in four damselfly species that either occur in habitats dominated by predatory fish (fish habitats) or fishless habitats by raising larvae either with predatory fish or in a control treatment. We found inter- as well as intraspecific trait compensation (negative correlations) between behavioural and morphological defences. Compared to fishless habitat species, fish habitat species invested more in behavioural defences and less in morphological defences. This was mirrored by fish habitat species investing more in behavioural defences and less in morphological defences when reared with predatory fish whereas fishless habitat species invested less in morphological defences only. Our results emphasise the role of context-specific combinations of defensive traits to avoid predation. We suggest, considering changes in multiple correlated traits on different timescales when studying the evolution of anti-predator traits.

Artificial Light Pollution with Different Wavelengths at Night Interferes with Development, Reproduction, and Antipredator Defenses of Daphnia magna

Artificial light at night (ALAN) dramatically alters the natural daily cycle of light and may cause a suite of physiological and behavioral responses of freshwater crustacean Daphnia. Here, we conducted a life table experiment to investigate the effect of different wavelengths [white (L-L, 400-800 nm), red (R, 614 nm), green (G, 527 nm), and blue (B, 447 nm)] and flashing modes [three colors flash alternately (3-Flash), seven colors strobe alternately (7-Strobe)] of ALAN on the development, reproduction, and predator-induced defenses of Daphnia magna. The results showed that G inhibited the development of the body and tail spine of Daphnia at sexual maturity and decreased their reproduction. The 7-Strobe promoted Daphnia to develop a larger eye. There was an interaction between fish kairomones and ALAN, which intensified over time. ALAN enhanced the response of the relative tail spine length to fish kairomone at sexual maturity. In addition, L-L and R inhibited the body length of 10th instar D. magna in response to fish kairomone. Through the hierarchical cluster method, the 3-Flash and B are recommended as friendly artificial lighting to Daphnia. Our results highlight the interference effects of ALAN on Daphnia, which are helpful to assess the potential impact of light pollution on zooplankton.

Pricklier with the proper predator? Predator-induced small-scale changes of spinescence in Daphnia

Phenotypic plasticity in defensive traits is a common response of prey organisms to variable and unpredictable predation regimes and risks. Cladocerans of the genus Daphnia are keystone species in the food web of lentic freshwater bodies and are well known for their ability to express a large variety of inducible morphological defenses in response to invertebrate and vertebrate predator kairomones. The developed defenses render the daphnids less susceptible to predation. So far, primarily large-scale morphological defenses, like helmets, crests, and tail-spines, have been documented. However, less is known on whether the tiny spinules, rather inconspicuous traits which cover many Daphnia's dorsal and ventral carapace margins, respond to predator kairomones, as well. For this reason, we investigated two Daphnia species (D. magna and D. longicephala) concerning their predator kairomone-induced changes in dorsal and ventral spinules. Since these small, inconspicuous traits may only act as a defense against predatory invertebrates, with fine-structured catching apparatuses, and not against vertebrate predators, we exposed them to both, an invertebrate (Triops cancriformis or Notontecta maculata) and a vertebrate predator (Leucaspius delineatus). Our results show that the length of these spinules as well as spinules-covered areas vary, likely depending on the predator the prey is exposed to. We further present first indications of a Daphnia species-specific elongation of the spinules and an increase of the spinules-bearing areas. Although we cannot exclude that spinescence is altered because it is developmentally connected to changes in body shape in general, our results suggest that the inducible alterations to the spinule length and spinules-covered areas disclose another level of predator-induced changes in two common Daphnia species. The predator-induced changes on this level together with the large-scale and ultrastructural defensive traits may act as the overall morphological defense, adjusted to specific predator regimes in nature.

Thwarting predators? A three-dimensional perspective of morphological alterations in the freshwater crustacean Daphnia

Predation is a major selective agent, so that many taxa evolved phenotypically plastic defensive mechanisms. Among them are many species of the microcrustacean genus Daphnia, which respond to an increased predation risk by developing inducible morphological alterations. Some of these features are obvious and easily recognized, e.g., crests in D. longicephala, while others are rather hidden, such as the bulkier shape of D. magna induced by the presence of the tadpole shrimp Triops. In this study we investigated the extraordinary diversity of morphological adaptations in the presence of predators with different foraging strategies in six predator-prey systems. For the first time we were able to analyze the unexposed and predator-exposed morphs comprehensively using three-dimensional scanning and reconstruction. We show that morphological changes are manifold in appearance between species and predators, and go beyond what has been known from previous 2D analyses. This further demonstrates the enormous trait flexibility of Daphnia. Interestingly, we found that among this variety some species share morphological strategies to counter a predator, while others use a different strategy against the same predator. Based on these intra- and interspecific comparisons, we discuss the mechanisms by which the respective defense might operate. These data therefore contribute to a deeper understanding of the inducible defenses' morphology as well as their diversified modes of operation in Daphnia, being a cornerstone for subsequent investigations, including the determination of costs associated with morphological change.

Insights into the genetic basis of predator-induced response in Daphnia galeata

Phenotypic plastic responses allow organisms to rapidly adjust when facing environmental challenges-these responses comprise morphological, behavioral but also life-history changes. Alteration of life-history traits when exposed to predation risk have been reported often in the ecological and genomic model organism Daphnia. However, the molecular basis of this response is not well understood, especially in the context of fish predation. Here, we characterized the transcriptional profiles of two Daphnia galeata clonal lines with opposed life histories when exposed to fish kairomones. First, we conducted a differential gene expression, identifying a total of 125 candidate transcripts involved in the predator-induced response, uncovering substantial intraspecific variation. Second, we applied a gene coexpression network analysis to find clusters of tightly linked transcripts revealing the functional relations of transcripts underlying the predator-induced response. Our results showed that transcripts involved in remodeling of the cuticle, growth, and digestion correlated with the response to environmental change in D. galeata. Furthermore, we used an orthology-based approach to gain functional information for transcripts lacking gene ontology (GO) information, as well as insights into the evolutionary conservation of transcripts. We could show that our candidate transcripts have orthologs in other Daphnia species but almost none in other arthropods. The unique combination of methods allowed us to identify candidate transcripts, their putative functions, and evolutionary history associated with predator-induced responses in Daphnia. Our study opens up to the question as to whether the same molecular signature is associated with fish kairomones-mediated life-history changes in other Daphnia species.

Predator-specific inducible morphological defenses of a water flea against two freshwater predators

The expression of inducible morphological defenses in Daphnia in response to a single predator is a well-known phenomenon. However, predator-specific modifications of the same defensive traits as an adaption to different predator regimes is so far only described for Daphnia barbata. It is unknown if this accounts only for this species or if it is a more widespread, general adaptive response in the genus Daphnia. In the present study, we therefore investigated whether a clone of the pond-dwelling species Daphnia similis responds to different predatory invertebrates (Triops cancriformis; Notonecta maculata) with the expression of predator-specific modifications of the same defensive traits. We showed that Triops-exposed individuals express a significantly longer tail-spine, while body width decreased in comparison to control individuals. Additionally, they also expressed inconspicuous defenses, that is, significantly longer spinules on the dorsal ridge. The Notonecta-exposed D. similis showed a significantly longer tail-spine, longer spinules and a larger spinules bearing area on the dorsal ridge than control individuals as well. However, a geometric morphometric analysis of the head shape revealed significant, predator-specific changes. Triops-exposed individuals expressed a flattened head shape with a pronounced dorsal edge, while Notonecta-exposed individuals developed a high and strongly rounded head. Our study describes so far unrecognized inducible defenses of D. similis against two predators in temporary waters. Furthermore, the predator-dependent change in head shape is in concordance with the 'concept of modality', which highlights the qualitative aspect of natural selection caused by predators.

Knowing the Enemy: Inducible Defences in Freshwater Zooplankton

Phenotypic plasticity in defensive traits is an appropriate mechanism to cope with the variable hazard of a frequently changing predator spectrum. In the animal kingdom these so-called inducible defences cover the entire taxonomic range from protozoans to vertebrates. The inducible defensive traits range from behaviour, morphology, and life-history adaptations to the activation of specific immune systems in vertebrates. Inducible defences in prey species play important roles in the dynamics and functioning of food webs. Freshwater zooplankton show the most prominent examples of inducible defences triggered by chemical cues, so-called kairomones, released by predatory invertebrates and fish. The objective of this review is to highlight recent progress in research on inducible defences in freshwater zooplankton concerning behaviour, morphology, and life-history, as well as difficulties of studies conducted in a multipredator set up. Furthermore, we outline costs associated with the defences and discuss difficulties as well as the progress made in characterizing defence-inducing cues. Finally, we aim to indicate further possible routes in this field of research and provide a comprehensive table of inducible defences with respect to both prey and predator species.

Chemically induced plasticity in early life history of Palaemon argentinus: are chemical alarm cues conserved within palaemonid shrimps?

Most aquatic animals use infochemicals from both conspecifics and heterospecifics to assess local predation risks and enhance predator detection. Released substances from injured conspecifics and other species (chemical alarm cues) are reliable cues to indicate an imminent danger in a specific habitat and often mediate the development of inducible defenses. Amphibian and fish embryos have been shown to acquire this information while at the embryonic stage of development, in relation to the developing nervous system and sensory development. With the exception of Daphnia, there is no information on chemically mediated responses to alarm cues in embryos of any crustacean groups. Therefore, we tested whether embryo exposure to chemical cues simulating predation on conspecifics or heterospecifics (closely related, non-coexisting species), or a mixture of both, alters embryonic developmental time, size and morphology of the first larval instar in Palaemon argentinus (Crustacea: Decapoda). Embryonic exposure to chemical alarm cues from conspecifics shortened the embryonic developmental time and elicited larger larvae with a longer rostrum. Rostrum length of the first larval instar changed independently of their size, thus elongated rostra can be considered a defensive feature. Embryonic developmental time was not altered by chemical alarm cues from either heterospecifics or the mixed cues treatment; however, exposure to these cues resulted in larger larvae compared with the control group. Chemically induced morphological plasticity in larvae in response to alarm cues from con- and heterospecifics suggests that such cues are conserved in palaemonids shrimps, providing embryos with an innate recognition of heterospecific alarm cues as predicted by the phylogenetic relatedness hypothesis.

Intraspecific phenotypic variation in life history traits of Daphnia galeata populations in response to fish kairomones

Phenotypic plasticity is the ability of a genotype to produce different phenotypes depending on the environment. It has an influence on the adaptive potential to environmental change and the capability to adapt locally. Adaptation to environmental change happens at the population level, thereby contributing to genotypic and phenotypic variation within a species. Predation is an important ecological factor structuring communities and maintaining species diversity. Prey developed different strategies to reduce their vulnerability to predators by changing their behaviour, their morphology or their life history. Predator-induced life history responses in Daphnia have been investigated for decades, but intra-and inter-population variability was rarely addressed explicitly. We addressed this issue by conducting a common garden experiment with 24 clonal lines of European Daphnia galeata originating from four populations, each represented by six clonal lines. We recorded life history traits in the absence and presence of fish kairomones. Additionally, we looked at the shape of experimental individuals by conducting a geometric morphometric analysis, thus assessing predator-induced morphometric changes. Our data revealed high intraspecific phenotypic variation within and between four D. galeata populations, the potential to locally adapt to a vertebrate predator regime as well as an effect of the fish kairomones on morphology of D. galeata.

Nociceptive Biology of Molluscs and Arthropods: Evolutionary Clues About Functions and Mechanisms Potentially Related to Pain

Important insights into the selection pressures and core molecular modules contributing to the evolution of pain-related processes have come from studies of nociceptive systems in several molluscan and arthropod species. These phyla, and the chordates that include humans, last shared a common ancestor approximately 550 million years ago. Since then, animals in these phyla have continued to be subject to traumatic injury, often from predators, which has led to similar adaptive behaviors (e.g., withdrawal, escape, recuperative behavior) and physiological responses to injury in each group. Comparisons across these taxa provide clues about the contributions of convergent evolution and of conservation of ancient adaptive mechanisms to general nociceptive and pain-related functions. Primary nociceptors have been investigated extensively in a few molluscan and arthropod species, with studies of long-lasting nociceptive sensitization in the gastropod, Aplysia, and the insect, Drosophila, being especially fruitful. In Aplysia, nociceptive sensitization has been investigated as a model for aversive memory and for hyperalgesia. Neuromodulator-induced, activity-dependent, and axotomy-induced plasticity mechanisms have been defined in synapses, cell bodies, and axons of Aplysia primary nociceptors. Studies of nociceptive sensitization in Drosophila larvae have revealed numerous molecular contributors in primary nociceptors and interacting cells. Interestingly, molecular contributors examined thus far in Aplysia and Drosophila are largely different, but both sets overlap extensively with those in mammalian pain-related pathways. In contrast to results from Aplysia and Drosophila, nociceptive sensitization examined in moth larvae (Manduca) disclosed central hyperactivity but no obvious peripheral sensitization of nociceptive responses. Squid (Doryteuthis) show injury-induced sensitization manifested as behavioral hypersensitivity to tactile and especially visual stimuli, and as hypersensitivity and spontaneous activity in nociceptor terminals. Temporary blockade of nociceptor activity during injury subsequently increased mortality when injured squid were exposed to fish predators, providing the first demonstration in any animal of the adaptiveness of nociceptive sensitization. Immediate responses to noxious stimulation and nociceptive sensitization have also been examined behaviorally and physiologically in a snail (Helix), octopus (Adopus), crayfish (Astacus), hermit crab (Pagurus), and shore crab (Hemigrapsus). Molluscs and arthropods have systems that suppress nociceptive responses, but whether opioid systems play antinociceptive roles in these phyla is uncertain.

Biomechanical properties of predator-induced body armour in the freshwater crustacean Daphnia

The freshwater crustacean Daphnia is known for its ability to develop inducible morphological defences that thwart predators. These defences are developed only in the presence of predators and are realized as morphological shape alterations e.g. 'neckteeth' in D. pulex and 'crests' in D. longicephala. Both are discussed to hamper capture, handling or consumption by interfering with the predator's prey capture devices. Additionally, D. pulex and some other daphniids were found to armour-up and develop structural alterations resulting in increased carapace stiffness. We used scanning transmission electron microscopy (STEM) and confocal laser scanning microscopy (CLSM) to identify predator-induced structural and shape alterations. We found species specific structural changes accompanying the known shape alterations. The cuticle becomes highly laminated (i.e. an increased number of layers) in both species during predator exposure. Using nano- and micro-indentation as well as finite element analysis (FEA) we determined both: the structure's and shape's contribution to the carapace's mechanical resistance. From our results we conclude that only structural alterations are responsible for increased carapace stiffness, whereas shape alterations appear to pose handling difficulties during prey capture. Therefore, these defences act independently at different stages during predation.