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

Molecular mechanisms that regulate scopolamine effects on inducible fish antipredation responses in Daphnia magna

Daphnia's antipredator responses are regulated largely by the nervous system, making these responses particularly susceptible to compounds that impact neurodevelopmental or neurofunctional processes. This study aimed to determine the molecular pathways involved in modulating the effects of scopolamine on inducible antipredation responses triggered by fish kairomones. We used two clones showing two contrasting responses. The positive phototactic clone 85 responds strongly to fish kairomones showing a marked negative phototactism and higher developmental rates. Consistently, the negative phototactic clone F shows the opposite behavior to the same stimuli. Adults of both clones were exposed to fish kairomones, scopolamine alone and a mixture of both. Scopolamine is a muscarine antagonist able to mimic fish kairomones inducible behavioral responses in both clones, while affecting differently morphological and life-history traits. Whole transcriptomic Illumina analyses indicated a greater number of de-regulated genes of the fish kairomone sensitive clone 85 (1650) compared to the F one (1138), which were grouped in four clusters (two per clone). The mixture of scopolamine and fish kairomone treatments on gene transcription was additive in both clones, indicating similar modes of action. Most enriched metabolic routes were related with neurological pathways and regulation of cell proliferation/differentiation. Our results indicate that fish kairomones and scopolamine deregulate not only neurological signaling pathways but also cell differentiation and proliferation pathways, which are linked to the observed behavioral responses as well as the developmental, morphological, and reproductive effects.

An integrative taxonomic assessment leads to the synonymy of the Waccamaw Crayfish Procambarus braswelli Cooper 1998 with the Cedar Creek Crayfish Procambarus chacei Hobbs 1958 (Decapoda: Cambaridae)

The southeastern United States (U.S.) is a global hotspot for crayfish diversity, with the majority of the >350 species known in the U.S. occurring here. Crayfishes in the genus Procambarus are common in lower gradient lotic and lentic systems of the southeast, but from both a taxonomic and systematic perspective, this genus is largely neglected in comparison to other crayfish genera. The aim of this study is to clarify the taxonomic status of two conservation priority crayfishes from the southeastern U.S. by testing the hypothesis that Procambarus braswelli Cooper, 1998 and Procambarus chacei Hobbs, 1958 are distinct species. We conducted a geometric morphometric analysis of these species, including 16 morphological metrics across 51 specimens throughout the ranges of these species in North Carolina and South Carolina. We then isolated, extracted, and sequenced a fragment of the COI gene and used maximum likelihood phylogenetic analysis to determine genetic distinctness. Results of multivariate analyses show overlapping morphologies between species and genetic structure that does not co-vary with original species determinations. Together, the available morphological and genetic information indicates that P. chacei and P. braswelli be synonymized. Additional taxonomic, life history, and ecological work is sorely needed for Procambarus crayfishes of the species-rich southeastern U.S.

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.

Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution

Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata.

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.

Proteomic changes associated with predator-induced morphological defenses in oysters

Inducible prey defenses occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defenses. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defenses. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with up-regulation of calcium transport proteins that could influence biomineralization. Inducible defenses evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were down-regulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defense response evolved in oysters that co-occur with drills through modification of an existing mechanism.

Metabolic Phenotype of Daphnia Under Hypoxia: Macroevolution, Microevolution, and Phenotypic Plasticity

Daphnia is a freshwater crustacean that is able to upregulate hemoglobin (Hb) in response to hypoxia, imparting a red color. We combine multiple field surveys across season with a lab experiment to evaluate changes in the metabolic phenotype of Daphnia in relation to environmental hypoxia. Looking at the zooplankton community, we found that D. pulicaria was restricted to lakes with a hypoxic hypolimnion. Comparing D. pulicaria with different amounts of Hb, red animals showed higher mRNA levels for several Hb genes, whereas most glycolytic genes showed red/pale differences of less than 50%. We also observed seasonal changes in the metabolic phenotype that differed between red and pale animals. Hb was upregulated early in the season in hypoxic lakes, and a relationship between Hb and lactate dehydrogenase only emerged later in the season in a temporal pattern that was lake specific. To evaluate whether these differences were due to specific lake environments or microevolutionary differences, we tested the induction of genes under controlled hypoxia in isofemale lines from each of four lakes. We found a strong response to 18 h hypoxia exposure in both Hb and lactate dehydrogenase mRNA, although the magnitude of the acute response was greater than the steady state differences in mRNA levels between pale and red Daphnia. The baseline expression of Hb and lactate dehydrogenase also varied between isofemale lines with different lake origins. These results, in combination with comparison of glycogen measurements, suggests that Hb functions primarily to facilitate oxygen delivery, mitigating systemic hypoxia, rather than an oxygen store. The combination of lab and field studies suggest that the metabolic phenotype of the animal is influenced by both microevolutionary differences (within and between lakes) as well as the spatial and temporal environmental heterogeneity of the lakes. The differences between Daphnia species, and the unexpected lack of hypoxia sensitivity of select glycolytic genes provide evidence of macroevolutionary differences in metabolic strategies to cope with hypoxia.

Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families

Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of Daphnia mitsukuri, a primary forage for many fish species. Transcriptional profiling of D. mitsukuri exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow Daphnia to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow Daphnia to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.