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468 results for “Daphnia”
Centennial clonal stability of asexual Daphnia in Greenland lakes despite climate variability
<p><strong>Daphnia_microsatellite_data_Dane_etal.2020.csv: </strong></p> <p><strong>Microsatellite genotypes from three study lakes (SS4, SS1381, and SS1590) in the Kangerlussuaq area, West Greenland. </strong>Microsatellite loci were amplified in single, 12.5 µl multiplex reactions (Type-it PCR kit, Qiagen Inc, Valencia, CA, USA), using an Eppendorf Nexus Thermal Cycler with thermal cycle conditions recommended in the Type-it PCR kit manual. Ten microsatellite primers representing genome-wide loci were used for genotyping; details in (Colbourne et al. 2004; Frisch et al., 2014). Two primers (Dp90, Dp377) failed to amplify in a consistent manner and were therefore excluded from further analysis. Amplified microsatellites were genotyped on an Applied Biosystems 3730 genetic analyser. We used the microsatellite plugin for Geneious 7.0.6 (https://www.geneious.com) for peak calling and binning. Called peaks were visually inspected and manually adjusted when necessary. </p> <p><strong>SS4_sediment.core_data_Fig2_Dane_et_al2020.xlsx</strong>: </p> <p><strong>Information on various parameters of sediment cores collected in Lake SS4, Kangerlussuq area, West Greenland. </strong>Data used in Dane et al. 2020, Figure 2 (panels B and C) are derived from two sediment cores: one for fluorescence (section at 0.5 cm intervals, <em>Depth</em>) and one for <em>Daphnia </em>ephippia analyses (1-cm intervals). Percentage organic matter content (loss-on-ignition at 550 °C,<em>OM%</em>) was used to correlate the two cores to each other and to a previously-dated sediment core (see Dane et al. 2020, Methods). The fluorescence derived parameter Parafac component C2 was used as an indicator of the abundance of purple sulphur bacteria. The organic carbon burial rate (<em>OC AR</em>, g C m–2 yr–1) was also calculated for this core (see Anderson et al. 2019). The <em>Daphnia</em> core was used for the microsatellite analyses and the accumulation rate of ephippia (<em>ephippia AR</em>) at the core site was estimated.</p> <p>For further details please see associated publication in Ecology and Evolution.</p> <p> </p>
Daphnia behavioural data and MFC field data
<p>The uploaded files contain several datasets.</p><p>The <i>Daphnia</i> calibration dataset contains the data obtained from <i>Daphnia</i> behavioural experiments with the use of salt. Videos were taken every hour for 30 seconds of 5 individuals.</p><p>dumpMfcVeniceCertosaS3_2019-10.csv contains field data obtained from 5 MFCs. The file contains the timestamps, energy accumulated per MFC and their total energy accumulated—data collected in Venice Lagoon.</p><p>Millstatt_Mussel_Data contains the mussel behavioural data from Lake Millstatt in Austria (2022). It contains the x y coordinates of the top valve of a Zebra Mussel. The data was taken as a calibration of the valve movement in reaction to a sudden disturbance (in this case, a heavy rock).</p>
Data for: Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its Daphnia host
<p>This dataset supports the findings of the study 'Prior exposure of a fungal parasite to cyanobacterial extracts does not impair infection of its <em>Daphnia</em> host', published in Hydrobiologia (https://doi.org/10.1007/s10750-022-04889-7)</p>
Data for: Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host Daphnia magna
<p>This dataset supports the findings of the study 'Polystyrene nanoplastics differentially influence the outcome of infection by two microparasites of the host <em>Daphnia magna</em>', published in Philosophical Transactions of the Royal Society B (https://doi.org/10.1098/rstb.2022.0013).</p>
Data for: Sequential infection of Daphnia magna by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites
<p>This dataset supports the findings presented in:<br> <br> Manzi, F., Halle, S., Seemann, L., Ben-Ami, F., & Wolinska, J. (2021). Sequential infection of <em>Daphnia magna</em> by a gut microsporidium followed by a haemolymph yeast decreases transmission of both parasites. <em>Parasitology,</em> 1-42. doi:10.1017/S0031182021001384</p>
Consensus QSAR models estimating acute aquatic toxicity for three trophic levels organisms: Algae, Daphnia and Fish
<p>We report new consensus models estimating acute toxicity for algae, daphnia and fish endpoints. We assembled a large collection of 3680 public unique compounds annotated by, at least, one experimental value for the given endpoint. Support Vector Machine models were internally and externally validated following the OECD principles. Reasonable predictive performances were achieved (RMSE<sub>ext</sub> = 0.56 – 0.78) which are in line with those of state-of-the-art models. The known structural alerts are compared with analysis of the atomic contributions to these models obtained using the ISIDA/<em>ColorAtom</em> utility. A benchmarking against existing tools has been carried out on a set of compounds considered more representative and relevant for the chemical space of the current chemical industry. Our model scored one of the best accuracies and data coverage.</p> <p>Nevertheless, industrial data performances were noticeably lower than those on public data, indicating that existing models fail to meet the industrial needs. Thus, final models were updated with the inclusion of new industrial compounds, extending applicability domain and relevance for application in an industrial context. Generate models and collected public data are made freely available.</p> <p><strong>Available fields in the SDF file:</strong></p> <ul> <li>SMILES_Canonical: canonical SMILES code</li> <li>DB: source of the data, "Litterature set" means that the data is originated from an article (see the companion article of the dataset for details).</li> <li>endpoint: organism for which endpoint is available</li> <li>CASRN: CAS registration number</li> <li>98-81-7</li> <li>pEC50 - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the log median effective concentration (pEC50)</li> <li>mg/L - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the median effective concentration (EC50)</li> <li>pLC50 - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (pLC50)</li> <li>mg/L - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (LC50)</li> <li>pEC50 - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the log median effective concentration (pEC50) measured at 72 hours</li> <li>mg/L - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the median effective concentration (EC50) measured at 72 hours</li> </ul>
Metagenome assemblies and metagenome-assembled genomes from the Daphnia magna microbiota
<p>Metagenome assemblies generated from raw reads not mapping to the Daphnia magna genome for six samples assembled individually (G4, G14, S1-S4) and a coassembly of all six samples (a_assembly) using metaSPAdes in SPAdes v3.14. Assemblies can be found in metagenome_assemblies.zip.</p> <p>Metagenome-assembled genomes generated using VAMB v3.0.2 (vamb_bins.zip) and ProxiMeta (proximeta_bins.zip). These MAGs were taxonomically identified using GTDB-Tk v1.3 and quality checked using CheckM v1.1. Outputs from GTDB-Tk and CheckM can be found in the .tsv and .tab files, respectively.</p>
Figure 8 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 8. Daphnia tanakai sp. nov., male from Lake Midori-ga-ike, Japan. A, lateral view. B, caudal spine. C, head. D, E, armature of antero-ventral and posterior portion of valve. F, G, postabdomen and postabdominal claw. H, male antenna I. I, tip of male seta ('flagellum') on antenna I. J, K, limb I and its distal portion. L–O, distal-most endite of limb II.
Figure 7 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 7. Daphnia tanakai sp. nov., thoracic limbs of parthenogenetic female from Lake Midori-ga-ike, Japan. A, B, limb I. C, D, anterior seta on its endite 3 and 2. E, limb II. F, G, stiff seta on its inner-distal end. H, gnathobase II. I, J, limb III and its inner-distal portion. K, L, limb IV and its inner-distal portion. M, N, limb V and distal portion of its exopodite.
Figure 6 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 6. Daphnia tanakai sp. nov. from Lake Midori-ga-ike, collected on August 30, 2004 by S. Tanaka (A–F, K–O) and Lake Kagami-ike, collected on September 01, 2004 by S. Tanaka (G–J, P–R); both lakes are in Hida Mountain Range, Honshu Island, Japan. A, parthenogenetic female, lateral view. B, head of parthenogenetic female. C, D, armature of postero-ventral and posterior region of valve. E, postabdomen. F–I, postabdominal claws of adults. J, postabdominal claw of juvenile. K, L, antenna I in lateral and distal view. M, N, distal portion of basal segment in posterior and anterior view. O, swimming seta. P, Q, ephippial female and postero-dorsal portion of its carapace. R, ephippium.
Figure 3 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 3. Daphnia curvirostris, large parthenogenetic female from Lake Glubokoe, Moscow area, European Russia, collected on August 9, 2004 by AAK. A, lateral view. B, caudal spine. C–E, head. F, G, armature of postero-ventral and posterior region of valve. H, postabdomen. I, J, postabdominal claw. K, L, antenna I in lateral and posterior view.
Figure 5 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 5. Daphnia curvirostris from Lake Glubokoe, Moscow area, European Russia, collected on September 9, 2004 by N. N. Smirnov. A, B, ephippial female and its postero-dorsal region. C, fresh ephippium. D, adult male. E, male head. F, G, armature of ventral margin of valve. H, armature of posterior portion of valve. I, J, postabdomen and abdomen. K, antenna I. L, antenna II. M, N, limb I and its distal portion. O, armature of distal portion of largest seta of outer distal lobe. P, innerdistal portion of limb II.
Figure 2 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 2. Mapping the characters of chromosome number and postabdominal claw morphology onto the Daphnia ND2 consensus tree (Fig. 1). A, the left cladogram shows the evolution of chromosome number. Black line denotes 2n = 22, white line denotes 2n = 20 and dot line denotes 2n = 24. B, the right cladogram shows the evolution of postabdominal claw morphology. Black line denotes variable phenotype between the longispina-claw and pulex-claw types, white line denotes the longispina- claw type, dot line denotes the pulex-claw type and grey line denotes equivocal.
Figure 4 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 4. Daphnia curvirostris, appendages of parthenogenetic female from Lake Glubokoe, European Russia. A, coxal part of antenna II. B, distal portion of basal segment and basal portion of branches. C, distal portion of endopod. D, swimming seta. E, maxilla I. F, limb I: ODL indicates outer distal lobe; IDL indicates inner distal lobe. G–I, limb II, second seta on its inner-distal end, and gnathobase II. J–L, limb III, its inner-distal portion and filtering seta of gnathobase. M, N, limb IV and its inner-distal portion. O, limb V.
Figure 1 in A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887
Figure 1. ME bootstrap consensus tree of Daphnia ND2 sequences. The numbers on each branch show support values of the branch. Upper numbers indicate ME, and ML bootstrap support values for nucleotide sequences. Middle numbers indicate MP bootstrap support values and Bayesian clade credibility values for nucleotide sequences. Lower numbers indicate MP bootstrap support values and Bayesian clade credibility values for amino acid sequences. Asterisks indicate no support values.
Fig. 2 in Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera) Distribution And Location In Composition Of Zooplankton Cenosis In Lake Dridzis
Fig. 2. Redundancy analysis (RDA) ordination plot for zooplankton abundance from Lake Dridzis during the sampling period of May to September 2011. Abbreviations: ORP- Oxidation-reduction potential; NTU- Turbidity.
Fig. 1 in Daphnia Cucullata Sars, 1862 (Crustacea: Cladocera) Distribution And Location In Composition Of Zooplankton Cenosis In Lake Dridzis
Fig. 1. Redundancy analysis (RDA) ordination plot for zooplankton abundance from Lake Dridzis during the sampling period of May to September 2010. Abbreviations: ORP- Oxidation-reduction potential; NTU- Turbidity.
Fig. 2 in Allozyme-Based Genetic Variability Of The Daphnia Atkinsoni-Bolivari Species Complex (Cladocera: Daphniidae) In The Hungarian Great Plain
Fig. 2. UPGMAclusteringofNei'soriginalgeneticdistancesbetweenpopulationsof Daphniaatkinsoni and D. bolivari. Themorphological D. bolivari populationsaremarkedwith
Spatially mapping the baseline and bisphenol-A exposed Daphnia magna lipidome using desorption electrospray ionisa-tion - mass spectrometry
<p>Data from desorption electrospray ionisation - mass spectrometry of <em>Daphnia magna</em> tissue section from control and daphnids exposed to 5 ppm of bisphenol A over their 7<sup>th</sup> adult instar, specifically four sampling points; 8, 24, 48 and 72 h after the 6<sup>th</sup> brood, as well as data acquired from a blank DESI slide.</p> <p>Data is provided in the form of *imzML files with the associated *.ibd of the same name.</p>
Data and code from: Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia
<p>Data and code accompanying: </p> <p>Hegg, Radersma & Uller. 2022. Seasonal variation in the response to a toxin-producing cyanobacteria in Daphnia. Freshwater Biology, accepted.</p> <p><strong>Abstract</strong></p> <ol> <li>Many populations of water fleas (<em>Daphnia</em>) are exposed to algal blooms dominated by microcystin-producing cyanobacteria. However, the severity of these effects on <em>Daphnia</em> fitness remain poorly understood in natural populations. </li> <li>We investigated seasonal changes in body size, reproduction and survival of <em>Daphnia</em> <em>longispina</em> individuals from five eutrophic lakes in southern Sweden. We tested whether individuals collected before, during or following algal blooms differed in their reproduction and survival when experimentally exposed to microcystin-producing cyanobacteria. </li> <li>The concentration of microcystin in the lakes was significantly higher during summer and autumn compared to spring, but there were substantial differences between lakes. The reproductive output of individuals declined consistently over the season, and this decline was stronger for <em>Daphnia</em> collected during periods of, or lakes from, high microcystin concentration. There was little evidence that individuals adapted to the toxin over the season. </li> <li>The strong seasonal changes in body size, reproduction and survival in these <em>Daphnia</em> <em>longispina</em> appears to be partly caused by variation in the abundance of toxin-producing cyanobacteria. Populations were unable to adapt sufficiently quickly during summer and autumn to recover from the negative effects of microcystin. We therefore suggest that seasonal increases in tolerance to microcystin-producing cyanobacteria have limited effects on the eco-evolutionary dynamics between <em>Daphnia</em> and phytoplankton.</li> </ol>
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