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31 results for “Calanus”
Raw Data: Timing of Calanus finmarchicus diapause in stochastic environments
<p><strong>This dataset contains the raw (unprocessed) model outputs of the Individual-Based Model used to generate the research article: </strong></p> <p>Bandara, K., Varpe, Ø., Maps, F., Ji, R., Eiane, K., & Tverberg, V. (2021). Timing of Calanus finmarchicus diapause in stochastic environments. <em>Ecological Modelling</em>, <em>460</em>, 109739.</p> <p><strong>Description</strong></p> <p>ITEM DESCRIPTION<br> ----------------<br> CONTENTS : RAW DATA FILES<br> UNCOMPRESSED SIZE : 19.6 GB <br> COMPRESSION : YES<br> COMPRESSED SIZE : 3.74 GB<br> COMPRESSION FORMAT : .ZIO<br> ENCRYPTION : NO<br> ENCRYPT METHOD : N/A<br> INTERNAL FILE TYPE(S) : .CSV<br> SOURCE : PASCAL <br> ID : v3.x (2020-2022)<br> DECRYPTION PASSWD : N/A<br> DOWNLOADABLE FROM : 10.5281/zenodo.7646734</p> <p>DATA DESCRIPTION<br> ----------------<br> THIS ARCHIVE CONTAINS FIVE (05) DIRECTORIES. EACH FROM A SINGLE SIMULATION EXPERIMENT, INDICATED BY THE FILE NAMES. <br> + DeterministicSetting : SIMULATION RAN IN DETERMINISTIC MODEL ENVIRONMENT (FIG. 2A-C)<br> + STStochasticSetting : SIMULATION RAN IN SHORTER-TERM (6-H) STOCHASTIC ENVIRONMENT (FIG. 2D-F)<br> + LTStochasticSetting-TFI : SIMULATION RAN IN LONGER-TERM (INTERANNUAL) STOCHASTIC ENVIRONMENT WITH GROWTH POTENTIAL VARIABILITY ONLY (FIG. 2G)<br> + LTStochasticSetting-VPR : SIMULATION RAN IN LONGER-TERM (INTERANNUAL) STOCHASTIC ENVIRONMENT WITH GROWTH POTENTIAL + VISUAL PREDATION RISK VARIABILITY (FIG. 2G)<br> + LTStochasticSetting-NVPR : SIMULATION RAN IN LONGER-TERM (INTERANNUAL) STOCHASTIC ENVIRONMENT WITH GROWTH POTENTIAL VARIABILITY + NON-VISUAL PREDATION RISK VARIABILITY (FIG. 2G)</p> <p>KEY<br> ---<br> + AnnualLog : DOUBLE VALUES OF LOW-RESOLUTION TRACKERS <br> + DailyLog_I : INTEGER VALUES OF HIGH-RESOLUTION TRACKERS<br> + DailyLog_R : DOUBLE VALUES OF HIGH-RESOLUTION TRACKERS<br> + VerticalPosition_N : INTEGER VALUES OF POPULATION VERTICAL DISTRIBUTION (NUMBER OF INDIVIDUALS IN EACH 1M x 6H BIN)<br> + VerticalPosition_CW : DOUBLE VALUES OF AVERAGE BODYMASS VERTICAL DISTRIBUTION (AVERAGE INDIVIDUAL BODYMASS IN EACH 1M x 6H BIN) :: UNUSED IN ANALYSES<br> + VerticalPosition_SW : DOUBLE VALUES OF AVERAGE ENERGY RESERVE VERTICAL DISTRIBUTION (AVERAGE INDIVIDUAL ENERGY RESERVES [LIPIDSCAPE] IN EACH 1M x 6H BIN) :: UNUSED IN ANALYSES<br> + FoodConcentration : DOUBLE VALUES OF 1D FOOD ENVIRONMENT<br> + Irradiance : DOUBLE VALUES OF 1D SUB-SURFACE IRRADIANCE ENVIRONMENT<br> + Temperature : DOUBLE VALUES OF 1D TEMPERATURE ENVIRONMENT<br> + VisualPredationRisk : DOUBLE VALUES OF 1D UNSCALED VISUAL PREDATION ENVIRONMENT</p> <p>NOTES<br> -----<br> The above attributes (excl. AnnualLog) are recorded for 100 calendar year in the LTStochasticSetting-TFI, LTStochasticSetting-VPR & LTStochasticSetting-NVPR simulations.<br> These are named after the year number (e.g. DailyLog_I_1, DailyLog_I_2....)</p> <p>ADDITIONAL FILES<br> ----------------<br> SOME DIRECTORIES MAY CONTAIN ADDITIONAL FILES, SUCH AS THOSE USED AS PCA INPUTS. THESE ARE PROCESSED FILES.<br> AVERAGE ANNUAL ENVIRONMENTAL VARIABLES TRACED IN THE "ENV" DIRECTORY (ONLY FOR LONGER-TERM STOCHASTIC SIMULATIONS).</p> <p>FURTHER QUESTIONS?<br> ------------------<br> Direct further question, either to: info@kanchanabandara.com (personal) or kba@akvaplan.niva.no (official)</p>
Copepod diapause duration estimation code for manuscript: Lipid load triggers migration to diapause in Arctic Calanus copepods - insights from underwater imaging
<p>This is a script and data upload by Frederic Maps (Université Laval) which creates figure 10 as well as other exploratory plots for publication Schmid, Maps, Fortier 2018: Lipid load triggers migration to diapause in Arctic Calanus copepods - insights from underwater imaging, to be published in the journal of plankton research (JPR).</p>
Figure 2 in Oxygen consumption rates and respiratory carbon losses in three species of copepods (Acartia clausi, Calanus helgolandicus and Limnocalanus macrurus) during starvation
Figure 2. Changes in Total (Ɣ, black lines), Basal (ż,blue lines) and Active (Ÿ, red lines) respiration in the Marmara Sea copepods Acartia clausi (A) and Calanus helgolandicus (B), and the Baltic Sea Limnocalanus macrurus (C) during starvation. Low-case letters (a, b and c) are the significant variable differences from Duncan's multiple range test (DMRT), p <0.05.
Figure 1 in Oxygen consumption rates and respiratory carbon losses in three species of copepods (Acartia clausi, Calanus helgolandicus and Limnocalanus macrurus) during starvation
Figure 1. Acartia clausi (a), Limnocalanus macrurus (b) and Calanus helgolandicus (c). Arrows indicate anterior (1) and posterior (2) oil sacs of L. macrurus and oil sac of C. helgolandicus (3).
Data from: Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean
<p><span>Species identification is pivotal in biodiversity assessments, and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1-C6 females) of three co-occurring <em>Calanus</em> species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic <em>Calanus</em> species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.</span></p>
Filtration rate of Calanus finmarhicus at medio (day five) tefluenzuron exposure period.
<p>Data registrations of filtration rate from Calanus finmarchicus were measured as particles/ml water sample from exposure study with teflubenzuron sampled on day five. </p>
Data repository for the paper titled: "The intriguing co-distribution of the copepods Calanus hyperboreus and Calanus glacialis in the subsurface chlorophyll maximum of Arctic seas"
<p>Data and R-code for publication: “The intriguing co-distribution of the copepods <em>Calanus hyperboreus </em>and <em>Calanus glacialis </em>in the subsurface chlorophyll maximum of Arctic seas”.</p> <p> </p> <p>By Moritz S Schmid and Louis Fortier</p> <p> </p> <p>Attached are R data files of copepod lipids, copepod vertical distributions, and chl <em>a </em>profiles, as well as R-code.</p> <p>The following sea ice data was used: Nimbus-7 SMMR and DMSP SSM/I-SSMIS passive microwave data, available at : https://nsidc.org/data/nsidc-0051.</p> <p>The following ocean color data was used: MODerate resolution Imaging Spectroradiometer (MODIS), Aqua satellite, available here: https://oceandata.sci.gsfc.nasa.gov/MODIS-Aqua</p> <p> </p> <p>Regards</p>
Environmental niche overlap in sibling planktonic species calanus finmarchicus and c. glacialis in Arctic fjords
<p><span>Knowledge of the environmental preferences of the key planktonic species, such as Calanus copepods in the Arctic, is crucial to understand ecosystem function and its future under climate change. Here we assessed the environmental conditions influencing the development stages of Atlantic C. finmarchicus and Arctic C. glacialis, and quantified the extent to which their niches overlap by incorporating multiple environmental data. We based our analysis on a three-year seasonal collection of zooplankton by sediment traps, located on moorings in two contrasting Svalbard fjords: the Arctic Rijpfjorden, and the Atlantic-influenced Kongsfjorden. Despite large differences in water temperature between the fjords, local realized niches of the sibling Calanus species overlapped almost perfectly. The exception was the earliest copepodites of C. glacialis in Rijpfjorden, which probably utilized the local ice algal bloom in spring. However, during periods with no sea ice, like in Kongsfjorden, the siblings of both Calanus species showed high synchronization in the population structure. Interestingly, differences in temperature preferences of C. finmarchicus and C. glacialis were much higher between the studied fjords than between the species. Our analysis confirmed the high plasticity of Calanus copepods and their </span><span>abilities to adapt to highly variable environmental settings, not only on an interannual basis, but also </span><span>in a climate warming context</span><span>, indicating some resilience in the Calanus community.</span></p>
Diapause vs. reproductive programs: transcriptional phenotypes in Calanus finmarchicus
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Environmental niche overlap in sibling planktonic species calanus finmarchicus and c. glacialis in Arctic fjords
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Data from: Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean
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Calanus InDel genotypes from: No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry
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Genotypes of 6 InDel markers for species identification from the Calanus culture at the EMBRC-ERIC laboratory for low-level trophic interactions, NTNU SeaLab
<p><span><span><span><span><span><span><span><span><span><span><span>Late developmental stages of marine copepods in the genus <i>Calanus</i> can spend extended periods in a dormant stage (diapause). During the growth season, copepods must accumulate sufficient lipid stores to survive diapause. Predation risk is often overlooked as a potential diapause-inducing cue. We tested experimentally if predation risk in combination with high or low food availability leads to differences in lipid metabolism, and potentially diapause initiation. Expression of lipid metabolism genes showed that food availability influences the copepods' ability to cope with predator stress. Predation caused upregulation of lipid catabolism with high food, and downregulation with low food. Stage development and molecular markers demonstrated that copepods did not enter diapause, instead, development occurred faster in copepods with predator stress. This study demonstrates that lipid metabolism may be a sensitive endpoint for changes in the environment. Our findings can contribute towards understanding the mechanisms behind diapause timing. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Assessing stable isotope dynamics of diapausing Calanus finmarchicus and C. hyperboreus during the overwintering period: a laboratory experiment
This study aimed at describing changes in the stable isotopic composition of late copepodite stage V (CV) subarctic marine copepods (Calanus finmarchicus and C. hyperboreus) during overwintering non-feeding periods. Diapausing stage CVs sampled in deep waters of the Lower St. Lawrence Estuary (Québec, Canada) in late-September 2009 were monitored for 4 months under controlled laboratory conditions. CVs and newly moulted adults were analyzed for δ13C and δ15N signatures as well as lipid, carbon and nitrogen content. Lipids were extracted in half of the samples to compare δ13C of individuals with and without lipids and to evaluate the accuracy of mass balance correction models for δ13C under lipid influence. Lipid content generally decreased with time for both species, which was reflected in an increase of δ13C values of CVs but a constant δ13C in newly moulted adults. Accordingly, lipid extraction resulted in an increase of δ13C in CVs and adults. The mean δ13C signature of lipid-extracted individuals remained constant through the time for CVs of both species and for C. finmarchicus adults. δ15N signatures of individuals increased after lipid extraction, but this did not result in a constant value over time, suggesting that several endogenous metabolic processes affected nitrogen isotopic content. The accuracy of the mass balance model differed between species and stages, suggesting that lipid extraction should always be performed prior to applying mathematical corrections.
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae.
Data from: Tracing the origins of Calanus sp. in the Saguenay‑St. Lawrence Marine Park (Québec, Canada) using δ13C as a marker
The Saguenay-St. Lawrence Marine Park (SSLMP) is a region that sustains a high abundance of zooplankton. The connectivity between zooplankton populations within the SSLMP and the surrounding areas was investigated for Calanus finmarchicus and C. hyperboreus. Deep-dwelling stage V copepodites (CVs) were collected in the Marine Park as well as in putative source regions in the St. Lawrence system in July 2009 (a time when they were entering into diapause). In May 2010, at the end of the overwintering period, diapausing CVs were sampled again in the Marine Park. To discriminate the origins and to predict the probable regions of origin of these deep-dwelling diapausing CVs in the SSLMP, a quadratic discriminant function analysis (QDFA) was performed. The classification algorithm was based on the carbon isotopic composition (δ13C) and percent carbon (%C) of individual copepods, as these variables are conservative when lipids are extracted prior to analysis. Our results suggest that about 23% of the Calanus spp. population sampled in SSLMP in late spring 2010 originated from the Saguenay Fjord (inside the SSLMP). The remainder of this population originated from regions outside the SSLMP, including the Lower St. Lawrence Estuary, and likely further east in the Gulf of St. Lawrence. Our results revealed high connectivity across the Saguenay and the St. Lawrence systems, as well as the potential for significant local production and recruitment of Calanus spp. within the Saguenay Fjord. This study also revealed the effectiveness of using δ13C as a marker in delineating the origin of Calanus spp., which has a relatively long non-feeding overwintering and diapausing period making it amenable to the conservation of isotopic signatures.
Master-thesis supplement Del 2 CSV-files of dataset for calanus and others
<p>CSV-files of dataset for calanus and others</p>
Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method
<p>Gene expression data from qPCR analysis of molting relevant genes in Calanus finmarchicus utilizing double delta-Ct method for calculations of fold change and mean fold change. </p>
Data from: Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense
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Genotypes of 6 InDel markers for species identification from the Calanus culture at the EMBRC-ERIC laboratory for low-level trophic interactions, NTNU SeaLab
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