The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Michael Lynch - One of the best experts on this subject based on the ideXlab platform.
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the recombinational landscape in Daphnia pulex
bioRxiv, 2020Co-Authors: Michael Lynch, Takahiro MarukiAbstract:Abstract Through the analysis of linkage disequilibrium from genome-wide sequencing data for multiple individuals from eight populations, the general features of the recombinational landscape are revealed in the microcrustacean Daphnia pulex. The data suggest an exceptionally uniform pattern of recombination across the genome, while also confirming general patterns that are inconsistent with existing population-genetic models for the relationship between linkage dis-equilibrium and physical distances between genomic sites. Patterns of linkage disequilibrium are highly consistent among populations, and average rates of recombination are quite similar for all chromosomes. There is no evidence of recombination hotspots, and although there does appear to be suppressed recombination in the vicinity of gene bodies, this effect is quite small. Although this species reproduces asexually in ∼ 80% of generations, the mean per-generation recombination rate per nucleotide site is ∼ 37× the per-nucleotide mutation rate. Contrary to expectations for models in which crossing-over is the primary mechanism of recombination, and consistent with data for other species, the gradient of linkage disequilibrium with increasing physical distance between sites is far too high at short distances and far too low at long distances, suggesting an important role for factors such as the nonindependent appearance of pairs of mutations on haplotypes and long-range gene-conversion-like processes. Combined with other observations on patterns of nucleotide variation, these results provide a strong case for the utility of D. pulex as a model system for the study of mechanisms of evolution in natural populations.
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genomic analyses of population structure reveal metabolism as a primary driver of local adaptation in Daphnia pulex
bioRxiv, 2019Co-Authors: Takahiro Maruki, Michael LynchAbstract:ABSTRACT Elucidating population structure is important for understanding evolutionary features of an organism. In the freshwater microcrustacean Daphnia pulex, an emerging model system in evolutionary genomics, previous studies using a small number of molecular markers indicated that genetic differentiation among populations is high. However, the dispersal ability of D. pulex is potentially high, and evolutionary forces shaping genetic differentiation among populations are not understood well. In this study, we carried out genomic analyses using high-throughput sequencing to investigate the population structure of D. pulex. We analyzed 10 temporary-pond populations widely distributed across the midwestern United States, with each sample consisting of 71 to 93 sexually reproducing individuals. The populations are generally in Hardy-Weinberg equilibrium and have relatively large effective sizes. The genetic differentiation among the populations is moderate and positively correlated with geographic distance. To find outlier regions showing significantly high or low genetic differentiation, we carried out a sliding-window analysis of the differentiation estimates using the bootstrap. Genes with significantly high genetic differentiation show striking enrichment of gene ontology terms involved in food digestion, suggesting that differences in food quality and/or quantity among populations play a primary role in driving local adaptation of D. pulex.
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genetic control of male production in Daphnia pulex
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Cecile Molinier, Chaoxian Zhao, Christoph R Haag, Michael LynchAbstract:Daphnia normally reproduce by cyclical parthenogenesis, with offspring sex being determined by environmental cues. However, some females have lost the ability to produce males. Our results demonstrate that this loss of male-producing ability is controlled by a dominant allele at a single locus. We identified the locus by comparing whole-genome sequences of 67 nonmale-producing (NMP) and 100 male-producing (MP) clones from 5 Daphnia pulex populations, revealing 132 NMP-linked SNPs and 59 NMP-linked indels within a single 1.1-Mb nonrecombining region on chromosome I. These markers include 7 nonsynonymous mutations, all of which are located within one unannotated protein-coding gene (gene 8960). Within this single gene, all of the marker-linked NMP haplotypes from different populations form a monophyletic clade, suggesting a single origin of the NMP phenotype, with the NMP haplotype originating by introgression from a sister species, Daphnia pulicaria Methyl farnesoate (MF) is the innate juvenile hormone in daphnids, which induces the production of males and whose inhibition results in female-only production. Gene 8960 is sensitive to treatment by MF in MP clones, but such responsiveness is greatly reduced in NMP clones. Thus, we hypothesize that gene 8960 is located downstream of the MF-signaling pathway in D. pulex, with the NMP phenotype being caused by expression change of gene 8960.
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insertion polymorphisms of mobile genetic elements in sexual and asexual populations of Daphnia pulex
Genome Biology and Evolution, 2017Co-Authors: Xiaoqian Jiang, Haixu Tang, Michael LynchAbstract:Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual reproduction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals.
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Population Genomics of Daphnia pulex.
Genetics, 2016Co-Authors: Michael Lynch, Ken Spitze, Ryan N. Gutenkunst, Matthew S. Ackerman, Takahiro Maruki, Zhiyuan JiaAbstract:Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short ([Formula: see text] bp) distances in D. melanogaster and at long distances in D. pulex The study population adheres closely to the expectations under Hardy-Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies [Formula: see text] appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an [Formula: see text] higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations.
Taisen Iguchi - One of the best experts on this subject based on the ideXlab platform.
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targeted gene disruption by use of crispr cas9 ribonucleoprotein complexes in the water flea Daphnia pulex
Genes to Cells, 2018Co-Authors: Chizue Hiruta, Taisen Iguchi, Keiichi Kakui, Knut E TollefsenAbstract:The microcrustacean Daphnia pulex is an important model for environmental, ecological, evolutionary and developmental genomics because its adaptive life history displays plasticity in response to environmental changes. Even though the whole-genome sequence is available and omics data have actively accumulated for this species, the available tools for analyzing gene function have thus far been limited to RNAi (RNA interference) and TALEN (the transcription activator-like effector nuclease) systems. The development of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9) system is thus expected to further increase the genetic tractability of D. pulex and to advance the understanding of this species. In this study, we developed a genome editing system for D. pulex using CRISPR/Cas9 ribonucleoprotein complexes (Cas9 RNPs). We first assembled a CRISPR single-guide RNA (sgRNA) specific to the Distal-less gene (Dll), which encodes a homeodomain transcription factor essential for distal limb development in invertebrates and vertebrates. Then, we injected Cas9 RNPs into eggs and evaluated its activity in vivo by a T7 endonuclease I assay. Injected embryos showed defective formation of the second antenna and disordered development of appendages, and indel mutations were detected in Dll loci, indicating that this technique successfully knocked out the target gene.
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juvenile hormone independent function of kruppel homolog 1 in early development of water flea Daphnia pulex
Insect Biochemistry and Molecular Biology, 2018Co-Authors: Hitoshi Miyakawa, Shinichi Miyagawa, Yukiko Ogino, Minae Watanabe, Marina Araki, Taisen IguchiAbstract:Elaborate regulation of insect metamorphosis is the consequence of physiological cooperation among multiple endocrine factors such as juvenile hormones (JHs) and ecdysteroids. Hormone-induced transcription factors play important roles in substantive interactions between hormonal signaling pathways. In insects, zinc finger transcription factor Kruppel homolog 1 (Kr-h1) is a key gene of the endocrine signaling pathway in which it is directly upregulated by JH receptor Methoprene-tolerant (Met) in the presence of JH and then regulates multiple downstream factors, including components of the ecdysteroid signaling pathway. Although JH also plays a role in various biological phenomena in other arthropod species, little is known about the molecular basis of the JH signaling pathway. Here we cloned Kr-h1 from a branchiopod crustacean, Daphnia pulex, (DappuKr-h1) and analyzed its expression profile and developmental function together with consideration of its relationship to the JH signaling pathway. We suggest that DappuKr-h1 lacks JH responsiveness and regulatory relationship with the JH receptor. Moreover our loss-of-function analysis revealed that maternal mRNA of DappuKr-h1 plays a critical role in early development independent from the JH signaling pathway. These findings provide insights about whether and how the JH signaling pathway influenced evolution, leading to greater diversity in phylum Arthropoda.
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Intra-specific variations in reaction norms of predator-induced polyphenism in the water flea Daphnia pulex
Ecological Research, 2015Co-Authors: Hitoshi Miyakawa, Naoki Sugimoto, Taisen Iguchi, Tetsuo I. Kohyama, Toru MiuraAbstract:Phenotypic plasticity is considered an important factor leading to phenotypic evolution through adaptations to changing environments. Interactions between environmental inputs and expressed phenotypes can be evaluated as “reaction norms”. Comparisons of these reaction norms among geographically distinct populations may provide evidence for genetic diversity and, moreover, important clues into understanding how the interactions affect evolutionary processes. The water flea Daphnia pulex exhibits predator-induced polyphenism in response to a kairomone released by predatory phantom midge larvae ( Chaoborus spp.). The polyphenism, a defensive structure formed on the head that enables juvenile larvae to avoid predation, is referred to as neckteeth. Differences in shape and/or plasticity of defensive structures have also been reported among related Daphnia species, suggesting that the species-specific variation in defensive morphology is derived from intra-specific differences in reaction norms. By determining reaction norms based on the incidence and number of neckteeth, we clarified differences in patterns of neckteeth formation in response to varying concentrations of Chaoborus kairomone. We then compared these differences among populations (strains) collected from six locations in Japan. Our findings showed that the reaction norms of both traits differed among strains. Furthermore, a molecular phylogeny using mitochondrial ND5 and COI sequences suggested that differences in the reaction norms of Japanese strains corresponded to their genetically different lineages, which likely originated from North American populations that were probably introduced to Japan independently.
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ionotropic glutamate receptors mediate inducible defense in the water flea Daphnia pulex
PLOS ONE, 2015Co-Authors: Hitoshi Miyakawa, John K Colbourne, Masanao Sato, Taisen IguchiAbstract:Phenotypic plasticity is the ability held in many organisms to produce different phenotypes with a given genome in response to environmental stimuli, such as temperature, nutrition and various biological interactions. It seems likely that environmental signals induce a variety of mechanistic responses that influence ontogenetic processes. Inducible defenses, in which prey animals alter their morphology, behavior and/or other traits to help protect against direct or latent predation threats, are among the most striking examples of phenotypic plasticity. The freshwater microcrustacean Daphnia pulex forms tooth-like defensive structures, “neckteeth,” in response to chemical cues or signals, referred to as “kairomones,” in this case released from phantom midge larvae, a predator of D. pulex. To identify factors involved in the reception and/or transmission of a kairomone, we used microarray analysis to identify genes up-regulated following a short period of exposure to the midge kairomone. In addition to identifying differentially expressed genes of unknown function, we also found significant up-regulation of genes encoding ionotropic glutamate receptors, which are known to be involved in neurotransmission in many animal species. Specific antagonists of these receptors strongly inhibit the formation of neckteeth in D. pulex, although agonists did not induce neckteeth by themselves, indicating that ionotropic glutamate receptors are necessary but not sufficient for early steps of neckteeth formation in D. pulex. Moreover, using co-exposure of D. pulex to antagonists and juvenile hormone (JH), which physiologically mediates neckteeth formation, we found evidence suggesting that the inhibitory effect of antagonists is not due to direct inhibition of JH synthesis/secretion. Our findings not only provide a candidate molecule required for the inducible defense response in D. pulex, but also will contribute to the understanding of complex mechanisms underlying the recognition of environmental changes, which form the basis of phenotypic plasticity.
Hitoshi Miyakawa - One of the best experts on this subject based on the ideXlab platform.
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juvenile hormone independent function of kruppel homolog 1 in early development of water flea Daphnia pulex
Insect Biochemistry and Molecular Biology, 2018Co-Authors: Hitoshi Miyakawa, Shinichi Miyagawa, Yukiko Ogino, Minae Watanabe, Marina Araki, Taisen IguchiAbstract:Elaborate regulation of insect metamorphosis is the consequence of physiological cooperation among multiple endocrine factors such as juvenile hormones (JHs) and ecdysteroids. Hormone-induced transcription factors play important roles in substantive interactions between hormonal signaling pathways. In insects, zinc finger transcription factor Kruppel homolog 1 (Kr-h1) is a key gene of the endocrine signaling pathway in which it is directly upregulated by JH receptor Methoprene-tolerant (Met) in the presence of JH and then regulates multiple downstream factors, including components of the ecdysteroid signaling pathway. Although JH also plays a role in various biological phenomena in other arthropod species, little is known about the molecular basis of the JH signaling pathway. Here we cloned Kr-h1 from a branchiopod crustacean, Daphnia pulex, (DappuKr-h1) and analyzed its expression profile and developmental function together with consideration of its relationship to the JH signaling pathway. We suggest that DappuKr-h1 lacks JH responsiveness and regulatory relationship with the JH receptor. Moreover our loss-of-function analysis revealed that maternal mRNA of DappuKr-h1 plays a critical role in early development independent from the JH signaling pathway. These findings provide insights about whether and how the JH signaling pathway influenced evolution, leading to greater diversity in phylum Arthropoda.
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Intra-specific variations in reaction norms of predator-induced polyphenism in the water flea Daphnia pulex
Ecological Research, 2015Co-Authors: Hitoshi Miyakawa, Naoki Sugimoto, Taisen Iguchi, Tetsuo I. Kohyama, Toru MiuraAbstract:Phenotypic plasticity is considered an important factor leading to phenotypic evolution through adaptations to changing environments. Interactions between environmental inputs and expressed phenotypes can be evaluated as “reaction norms”. Comparisons of these reaction norms among geographically distinct populations may provide evidence for genetic diversity and, moreover, important clues into understanding how the interactions affect evolutionary processes. The water flea Daphnia pulex exhibits predator-induced polyphenism in response to a kairomone released by predatory phantom midge larvae ( Chaoborus spp.). The polyphenism, a defensive structure formed on the head that enables juvenile larvae to avoid predation, is referred to as neckteeth. Differences in shape and/or plasticity of defensive structures have also been reported among related Daphnia species, suggesting that the species-specific variation in defensive morphology is derived from intra-specific differences in reaction norms. By determining reaction norms based on the incidence and number of neckteeth, we clarified differences in patterns of neckteeth formation in response to varying concentrations of Chaoborus kairomone. We then compared these differences among populations (strains) collected from six locations in Japan. Our findings showed that the reaction norms of both traits differed among strains. Furthermore, a molecular phylogeny using mitochondrial ND5 and COI sequences suggested that differences in the reaction norms of Japanese strains corresponded to their genetically different lineages, which likely originated from North American populations that were probably introduced to Japan independently.
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ionotropic glutamate receptors mediate inducible defense in the water flea Daphnia pulex
PLOS ONE, 2015Co-Authors: Hitoshi Miyakawa, John K Colbourne, Masanao Sato, Taisen IguchiAbstract:Phenotypic plasticity is the ability held in many organisms to produce different phenotypes with a given genome in response to environmental stimuli, such as temperature, nutrition and various biological interactions. It seems likely that environmental signals induce a variety of mechanistic responses that influence ontogenetic processes. Inducible defenses, in which prey animals alter their morphology, behavior and/or other traits to help protect against direct or latent predation threats, are among the most striking examples of phenotypic plasticity. The freshwater microcrustacean Daphnia pulex forms tooth-like defensive structures, “neckteeth,” in response to chemical cues or signals, referred to as “kairomones,” in this case released from phantom midge larvae, a predator of D. pulex. To identify factors involved in the reception and/or transmission of a kairomone, we used microarray analysis to identify genes up-regulated following a short period of exposure to the midge kairomone. In addition to identifying differentially expressed genes of unknown function, we also found significant up-regulation of genes encoding ionotropic glutamate receptors, which are known to be involved in neurotransmission in many animal species. Specific antagonists of these receptors strongly inhibit the formation of neckteeth in D. pulex, although agonists did not induce neckteeth by themselves, indicating that ionotropic glutamate receptors are necessary but not sufficient for early steps of neckteeth formation in D. pulex. Moreover, using co-exposure of D. pulex to antagonists and juvenile hormone (JH), which physiologically mediates neckteeth formation, we found evidence suggesting that the inhibitory effect of antagonists is not due to direct inhibition of JH synthesis/secretion. Our findings not only provide a candidate molecule required for the inducible defense response in D. pulex, but also will contribute to the understanding of complex mechanisms underlying the recognition of environmental changes, which form the basis of phenotypic plasticity.
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nmda receptor activation upstream of methyl farnesoate signaling for short day induced male offspring production in the water flea Daphnia pulex
BMC Genomics, 2015Co-Authors: Kenji Toyota, Norihisa Tatarazako, Hitoshi Miyakawa, Yukiko Ogino, Katsushi Yamaguchi, Shuji Shigenobu, Shinichi MiyagawaAbstract:Background The cladoceran crustacean Daphnia pulex produces female offspring by parthenogenesis under favorable conditions, but in response to various unfavorable external stimuli, it produces male offspring (environmental sex determination: ESD). We recently established an innovative system for ESD studies using D. pulex WTN6 strain, in which the sex of the offspring can be controlled simply by changes in the photoperiod: the long-day and short-day conditions can induce female and male offspring, respectively. Taking advantage of this system, we demonstrated that de novo methyl farnesoate (MF) synthesis is necessary for male offspring production. These results indicate the key role of innate MF signaling as a conductor between external environmental stimuli and the endogenous male developmental pathway. Despite these findings, the molecular mechanisms underlying up- and downstream signaling of MF have not yet been well elucidated in D. pulex.
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development of a microinjection system for rna interference in the water flea Daphnia pulex
BMC Biotechnology, 2013Co-Authors: Chizue Hiruta, Kenji Toyota, Norihisa Tatarazako, Hitoshi Miyakawa, Shinichi Miyagawa, Yukiko Ogino, Joseph R ShawAbstract:Background The ubiquitous, freshwater microcrustacean Daphnia pulex provides a model system for both human health research and monitoring ecosystem integrity. It is the first crustacean to have a well annotated, reference genome assembly that revealed an unusually high gene count highlighted by a large gene orphanage,-i.e., previously uncharacterized genes. Daphnia are capable of either clonal or sexual reproduction, making them ideally suited for genetic manipulation, but the establishment of gene manipulation techniques is needed to accurately define gene functions. Although previous investigations developed an RNA interference (RNAi) system for one congener D. magna, these methods are not appropriate for D. pulex because of the smaller size of their early embryos. In these studies, we develop RNAi techniques for D. pulex by first determining the optimum culture conditions of their isolated embryos and then applying these conditions to the development of microinjection techniques and proof-of-principle RNAi experiments.
John K Colbourne - One of the best experts on this subject based on the ideXlab platform.
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a comprehensive epigenomic analysis of phenotypically distinguishable genetically identical female and male Daphnia pulex
BMC Genomics, 2020Co-Authors: Jouni Kvist, John K Colbourne, Michael E Pfrender, Camila Goncalves Athanasio, James B Brown, Leda MirbahaiAbstract: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. 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. 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.
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novel cadmium responsive micrornas in Daphnia pulex
Environmental Science & Technology, 2015Co-Authors: Shuai Chen, John K Colbourne, Garrett J Mckinney, Krista M Nichols, Maria S SepulvedaAbstract:Daphnia pulex is a widely used toxicological model and is known for its sensitivity to cadmium (Cd). Recent research suggests that microRNAs (miRNAs) play a critical role in animal responses to heavy metals. To investigate the functions of D. pulex miRNAs under Cd exposure, we analyzed the miRNA profiles of D. pulex after 48 h using miRNA microarrays and validated our findings by q-PCR. miRNA dpu-let-7 was identified as a stably expressed gene and used as a reference. We identified 22 and 21 differentially expressed miRNAs under low (20 μg/L CdCl2) and high-exposure (40 μg/L CdCl2) concentrations compared to controls, respectively. Cellular functions of predicted miRNA target Cd-responsive genes included oxidative stress, ion transport, mitochondrial damage, and DNA repair. An insulin-related network was also identified in relation to several Cd-responsive miRNAs. The expression of three predicted target genes for miR-71 and miR-210 were evaluated, and expression of two of them (SCN2A and SLC31A1) was negatively correlated with the expression of their regulator miRNAs. We show miR-210 is hypoxia-responsive in D. pulex and propose Cd and hypoxia induce miR-210 via a same HIF1α modulated pathway. Collectively, this research advances our understanding on the role of miRNAs in response to heavy-metal exposure.
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ionotropic glutamate receptors mediate inducible defense in the water flea Daphnia pulex
PLOS ONE, 2015Co-Authors: Hitoshi Miyakawa, John K Colbourne, Masanao Sato, Taisen IguchiAbstract:Phenotypic plasticity is the ability held in many organisms to produce different phenotypes with a given genome in response to environmental stimuli, such as temperature, nutrition and various biological interactions. It seems likely that environmental signals induce a variety of mechanistic responses that influence ontogenetic processes. Inducible defenses, in which prey animals alter their morphology, behavior and/or other traits to help protect against direct or latent predation threats, are among the most striking examples of phenotypic plasticity. The freshwater microcrustacean Daphnia pulex forms tooth-like defensive structures, “neckteeth,” in response to chemical cues or signals, referred to as “kairomones,” in this case released from phantom midge larvae, a predator of D. pulex. To identify factors involved in the reception and/or transmission of a kairomone, we used microarray analysis to identify genes up-regulated following a short period of exposure to the midge kairomone. In addition to identifying differentially expressed genes of unknown function, we also found significant up-regulation of genes encoding ionotropic glutamate receptors, which are known to be involved in neurotransmission in many animal species. Specific antagonists of these receptors strongly inhibit the formation of neckteeth in D. pulex, although agonists did not induce neckteeth by themselves, indicating that ionotropic glutamate receptors are necessary but not sufficient for early steps of neckteeth formation in D. pulex. Moreover, using co-exposure of D. pulex to antagonists and juvenile hormone (JH), which physiologically mediates neckteeth formation, we found evidence suggesting that the inhibitory effect of antagonists is not due to direct inhibition of JH synthesis/secretion. Our findings not only provide a candidate molecule required for the inducible defense response in D. pulex, but also will contribute to the understanding of complex mechanisms underlying the recognition of environmental changes, which form the basis of phenotypic plasticity.
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functional characterization of four metallothionein genes in Daphnia pulex exposed to environmental stressors
Aquatic Toxicology, 2012Co-Authors: Jana Asselman, John K Colbourne, Joseph R Shaw, Stephen P Glaholt, Zachary Smith, Guy Smagghe, Colin R Janssen, K A C De SchamphelaereAbstract:We characterized the metallothionein genes (Mt1, Mt2, Mt3, and Mt4) in Daphnia pulex on both molecular and ecotoxicological level. We therefore conducted a bioinformatical analysis of the gene location and predicted protein sequence, and screened the upstream flanking region for regulatory elements. The number of these elements and their positions relative to the start codon varied strongly among the four genes and even among two gene duplicates (Mt1A and Mt1B), suggesting different roles of the four proteins in the organisms’ response to stress. We subsequently conducted a chronic 16-day exposure of D. pulex to different environmental stressors (at sublethal levels causing approximately 50% reduction in reproduction). Based on prior knowledge, we exposed them to the metals Cd, Cu, and Ni, the moulting hormone hydroxyecdysone (20E), and the oxidative stressors cyanobacteria (Microcystis aeruginosa), and paraquat (Pq). We then compared mRNA expression levels of the four Mt genes under these stress conditions with control conditions in “The Chosen One” clone (TCO), for which the full genome was sequenced and annotated. All together, the mRNA expression results under the different stress regimes indicate that different Mt genes may play different and various roles in the response of D. pulex to stress and that some (but not all) of the differences among the four genes could be related to the pattern of regulatory elements in their upstream flanking region.
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the ecoresponsive genome of Daphnia pulex
Science, 2011Co-Authors: John K Colbourne, Abraham E Tucker, Kelley W Thomas, Michael E Pfrender, Donald L Gilbert, Todd H Oakley, Shinichi Tokishita, Andrea AertsAbstract:We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
Stanley I Dodson - One of the best experts on this subject based on the ideXlab platform.
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methoprene and 20 oh ecdysone affect male production in Daphnia pulex
Environmental Toxicology and Chemistry, 2001Co-Authors: Jane K Peterson, Donna R Kashian, Stanley I DodsonAbstract:Exposure of Daphnia pulex to the insecticide and juvenile hormone-mimic methoprene resulted in a decrease in the incidence of all-male broods and an increase in the incidence of all-female broods compared with controls. These effects were observed at nominal concentrations of 10 and 100 mg/L, within the upper range of concentrations at which methoprene is applied in the environment. Because methoprene has been found to bind to the mammalian retinoid X receptor, we also tested the effects of retinoic acid on Daphnia reproduction. Neither 9-cis-retinoic acid nor all-trans-retinoic acid had any observable effect. Because juvenile hormone and ecdysteroids interact in many insect systems, we also exposed Daphnia to 20-OH-ecdysone. Exposure to the crustacean hormone 20-OH-ecdysone at levels of 1 and 10 mg/L resulted in an increase in all-male broods and a decrease in all-female broods, but 100 mg/L 20-OH-ecdysone resulted in a decrease in all-male broods and an increase in all-female broods. Our results suggest that juvenile hormone and ecdysteroids might play a role in the Daphnia sex determination system.
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free swimming Daphnia pulex can avoid following stokes law
Limnology and Oceanography, 1996Co-Authors: Patrick R Gorski, Stanley I DodsonAbstract:The swimming behavior of Daphnia pulex was compared between two temperatures (5 and 25°C), with two acclimation protocols, using three-dimensional video techniques. Our hypotheses, based on Stokes' law and metabolic considerations, predicted large changes in swimming behavior. However, free-swimming individuals did not follow Stokes' law. They sank slower than predicted, having increased their sinking rate by ∼23% from 5 to 25°C. Anesthetized Daphnia followed Stokes' law, showing an increase in sinking rate of 70% over the temperature range. The Q 10 values of all swimming behaviors were between 0.91 and 1.11 (which are significantly less than Q 10 values for metabolic rates) and were nearly uniform over a 20°C range. Our results also indicate that acclimation to different temperatures for 1 h is sufficient to minimize acclimation effects.
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behavioral responses of Daphnia pulex exposed to carbaryl and chaoborus kairomone
Environmental Toxicology and Chemistry, 1995Co-Authors: Stanley I Dodson, Takayuki Hanazato, Patrick R GorskiAbstract:An analysis of digitized three-dimensional video records of free-swimming Daphnia pulex identified six measurements of swimming behavior that can be used to quantify individual behavioral responses to pesticides or natural chemical signals. Protocols are given for measuring the parameters that showed statistically significant changes in pesticide treatments. The most efficient experimental design would involve observing as many animals as possible, with one observation per animal. Parameters most likely to be useful in future studies are velocity, turning angle, upward and downward angles during hops, variance in vertical position, and hopping frequency. The parameters varied in usefulness, defined as the ratio of within-treatment to among-treatment variance (F ratios). Velocity was the most useful (i.e., had the highest F ratio); hopping frequency was the least useful. Daphnia exhibited three kinds of swimming behavior, as defined by eight parameters: (a) “spinning” (extreme and continuous escape response) to acutely toxic levels of Carbaryl (40 ppb); (b) “irritation” (an increase in escape-like behavior) to low levels of Carbaryl (1 ppb); and (c) “null” behavioral responses to Chaoborus-conditioned water, in which there was no detectable change in any measurement of swimming behavior. In predation trials, bluegill sunfish preferentially selected individuals showing “spinning” behavior. Results from this and other studies of Daphnia swimming behavior suggest a conservative-swimming hypothesis for understanding constraints on Daphnia swimming behavior.
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THE EVOLUTIONARY ECOLOGY OF AN ANTIPREDATOR REACTION NORM: Daphnia pulex AND CHAOBORUS AMERICANUS.
Evolution; international journal of organic evolution, 1991Co-Authors: Ken Parejko, Stanley I DodsonAbstract:Ponds containing the parthenogenetic zooplankter Daphnia pulex with and without chaoborid predators were sampled over the course of a season. A significant (P < 0.05) Spearman rank correlation was found between predator density and the expression of an antipredator defense (neckteeth) by the Daphnia. The reaction norms (percent induction of a single genotype versus predator density) of clones isolated from predator-free and predator-rich habitats were determined in a laboratory setting. There was a statistically significant different response among the six clones tested (P < 0.05). Clones isolated from chaoborid ponds showed significantly greater sensitivity to the presence of predator than clones from predator-free ponds (P < 0.05). In the laboratory, food levels under which prey were cultured affected induction of the antipredator response. Highest induction was found at the lowest food level used.
