Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins

Effects of food quantity on the ingestion and egestion of MPs with different colors by Daphnia magna

Aquatic organism uptake and accumulate microplastics (MPs) through various pathways, with ingestion alongside food being one of the primary routes. However, the impact of food concentration on the accumulation of different types of MPs, particularly across various colors, remains largely unexplored. To address this gap, we selected Daphnia magna as a model organism to study the ingestion/egestion kinetics and the preference for different MP colors under varying concentrations of Chlorella vulgaris. Our findings revealed that as the concentration of Chlorella increased, the ingestion of MPs by D. magna initially increased and then showed a decline. During the egestion phase within clean medium without further food supply, an increase in food concentration during the ingestion phase led to a slower rate of MP discharge; while when food was present during the egestion phase, the discharge rate accelerated for all treatments, indicating the importance of food ingestion/digestion process on the MPs bioaccumulation. Furthermore, in the presence of phytoplankton, D. magna demonstrated a preference for ingesting green-colored MPs, especially at low and medium level Chlorella supply, possibly due to the enhanced food searching activities. Beyond gut passage, we also examined the attachment of MPs to the organism's body surface, finding that the number of adhered MPs increased with increasing food concentration, likely due to the intensified filtering current during food ingestion. In summary, this study demonstrated that under aquatic environment with increasing phytoplankton concentrations, the ingestion and egestion rates, color preferences, as well as surface adherence of MPs to filter feeding zooplanktons will be significantly influenced, which may further pose ecological risks. Our results offer novel insights into the unintentional accumulation of MPs by zooplankton, highlighting the complex interactions between food availability and MPs accumulation dynamics.

Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.

Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum

In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.

The diversity of invertebrate visual opsins spanning Protostomia, Deuterostomia, and Cnidaria

Across eumetazoans, the ability to perceive and respond to visual stimuli is largely mediated by opsins, a family of proteins belonging to the G protein-coupled receptor (GPCR) superclass. Lineage-specific gains and losses led to a striking diversity in the numbers, types, and spectral sensitivities conferred by visual opsin gene expression. Here, we review the diversity of visual opsins and differences in opsin gene expression from well-studied protostome, invertebrate deuterostome, and cnidarian groups. We discuss the functional significance of opsin expression differences and spectral tuning among lineages. In some cases, opsin evolution has been linked to the detection of relevant visual signals, including sexually selected color traits and host plant features. In other instances, variation in opsins has not been directly linked to functional or ecological differences. Overall, the array of opsin expression patterns and sensitivities across invertebrate lineages highlight the diversity of opsins in the eumetazoan ancestor and the labile nature of opsins over evolutionary time.

Crustacean conundrums: a review of opsin diversity and evolution

Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

G protein-coupled receptors (GPCRs) in rotifers and cladocerans: Potential applications in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology

The G protein-coupled receptor (GPCR) superfamily plays a fundamental role in both sensory functions and the regulation of homeostasis, and is highly conserved across the eukaryote taxa. Its functional diversity is related to a conserved seven-transmembrane core and invariant set of intracellular signaling mechanisms. The interplay between these properties is key to the evolutionary success of GPCR. As this superfamily originated from a common ancestor, GPCR genes have evolved via lineage-specific duplications through the process of adaptation. Here we summarized information on GPCR gene families in rotifers and cladocerans based on their evolutionary position in aquatic invertebrates and their potential application in ecotoxicology, ecophysiology, comparative endocrinology, and pharmacology. Phylogenetic analyses were conducted to examine the evolutionary significance of GPCR gene families and to provide structural insight on their role in aquatic invertebrates. In particular, most GPCR gene families have undergone sporadic evolutionary processes, but some GPCRs are highly conserved across species despite the dynamics of GPCR evolution. Overall, this review provides a better understanding of GPCR evolution in aquatic invertebrates and expand our knowledge of the potential application of these receptors in various fields.

Genome-wide identification of 194 G protein-coupled receptor (GPCR) genes from the water flea Daphnia magna

In crustaceans, G protein-coupled receptors (GPCRs) are the largest transmembrane receptor family and function by mediating various environmental stimuli in cells. Understanding GPCR signaling is crucial to better understanding of crustacean endocrinology. GPCRs evolved from early eukaryotes, and genome-wide identification of GPCRs in a particular taxon can provide insight into evolutionary tendencies and adaptive strategies of GPCR response to environmental stimuli. Here, we identified 194 full-length GPCR genes in the water flea Daphnia magna that can be divided into five distinct classes (A, B, C, F, and other). A strong orthologous relationship for amine, neuropeptide, and opsin receptors was found in the phylogenetic comparison of D. magna GPCRs to those of humans and two well-known insects (Drosophila melanogaster and Solenopsis invicta). Our results based on phylogenetic relationships suggest that most GPCRs subfamilies have undergone sporadic evolutionary processes for adaptation to environmental pressures. Despite the dynamics of GPCR evolution, some GPCRs are highly conserved between species. This study provides a better understanding of the evolution of GPCRs and expands our knowledge of the potential physiological mechanisms in D. magna in response to various environmental stimuli.

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.

Recent Duplications Dominate VQ and WRKY Gene Expansions in Six Prunus Species

Genes encoding VQ motif-containing (VQ) transcriptional regulators and WRKY transcription factors can participate separately or jointly in plant growth, development, and abiotic and biotic stress responses. In this study, 222 VQ and 645 WRKY genes were identified in six Prunus species. Based on phylogenetic tree topologies, the VQ and WRKY genes were classified into 13 and 32 clades, respectively. Therefore, at least 13 VQ gene copies and 32 WRKY gene copies were present in the genome of the common ancestor of the six Prunus species. Similar small Ks value peaks for the VQ and WRKY genes suggest that the two gene families underwent recent duplications in the six studied species. The majority of the Ka/Ks ratios were less than 1, implying that most of the VQ and WRKY genes had undergone purifying selection. Pi values were significantly higher in the VQ genes than in the WRKY genes, and the VQ genes therefore exhibited greater nucleotide diversity in the six species. Forty-one of the Prunus VQ genes were predicted to interact with 44 of the WRKY genes, and the expression levels of some predicted VQ-WRKY interacting pairs were significantly correlated. Differential expression patterns of the VQ and WRKY genes suggested that some might be involved in regulating aphid resistance in P. persica and fruit development in P. avium.

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

BACKGROUND

Vision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species.

RESULTS

We evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning.

CONCLUSIONS

This repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.

A comprehensive system for detection of behavioral change of D. magna exposed to various chemicals

The purpose of the present study was to develop a sensitive and comprehensive method, based on D. magna swimming behavior, for toxicity assessment of environmental chemicals. Firstly, D. magna swimming in several chambers with different diameters were compared to determine the most suitable container, and then baseline behaviors during light/dark periods as well as reactions to light/dark switching and vibration stimulation were determined. Secondly, after exposure to sub-lethal concentrations of the selected 42 typical chemicals, which were classified into heavy metals, pesticides, fungicides and flame retardants, the alterations in the swimming parameters were evaluated. Our results indicated the 48-well plate was the most suitable chamber for behavioral monitoring of D. magna, and specific responsive patterns of D. magna neonates to light/dark switching and vibration stimulation were observed. The results of the behavioral assays of chemicals suggested that D. magna was the most sensitive to methylmercury-chloride and then to abamectin and chlorpyrifos. The three chemicals at several to dozens of ng/L significantly changed swimming behaviors of D. magna. Furthermore, the alteration in the behavioral parameters (average swimming speed, etc.) induced by the selected chemicals could be ascribed to various modes of actions, confirming the reliability and practicability of the monitoring method.

A ciliary opsin in the brain of a marine annelid zooplankton is ultraviolet-sensitive, and the sensitivity is tuned by a single amino acid residue

Ciliary opsins were classically thought to function only in vertebrates for vision, but they have also been identified recently in invertebrates for non-visual photoreception. Larvae of the annelid Platynereis dumerilii are used as a zooplankton model, and this zooplankton species possesses a "vertebrate-type" ciliary opsin (named c-opsin) in the brain. Platynereis c-opsin is suggested to relay light signals for melatonin production and circadian behaviors. Thus, the spectral and biochemical characteristics of this c-opsin would be directly related to non-visual photoreception in this zooplankton model. Here we demonstrate that the c-opsin can sense UV to activate intracellular signaling cascades and that it can directly bind exogenous all-trans-retinal. These results suggest that this c-opsin regulates circadian signaling in a UV-dependent manner and that it does not require a supply of 11-cis-retinal for photoreception. Avoidance of damaging UV irradiation is a major cause of large-scale daily zooplankton movement, and the observed capability of the c-opsin to transmit UV signals and bind all-trans-retinal is ideally suited for sensing UV radiation in the brain, which presumably lacks enzymes producing 11-cis-retinal. Mutagenesis analyses indicated that a unique amino acid residue (Lys-94) is responsible for c-opsin-mediated UV sensing in the Platynereis brain. We therefore propose that acquisition of the lysine residue in the c-opsin would be a critical event in the evolution of Platynereis to enable detection of ambient UV light. In summary, our findings indicate that the c-opsin possesses spectral and biochemical properties suitable for UV sensing by the zooplankton model.