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Replication Data for: Interactive population effects of sublethal copper exposure and predation risk in a naturally stressful environment
No full textThe dataset contains data used in the study “Interactive population effects of sublethal copper exposure and predation risk in a naturally stressful environment
”. It contains experimental data from a mesocsom with the copepod Tigriopus brevicornis. The project was part of the MULTICOP project financed by the Norwegian Research Council (project number 301153). (2024-01-21)
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Methods
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We investigated the cumulative effects of copper and predation risk exposure on T. brevicornis over three generations. T. brevicornis is commonly found along European Atlantic shorelines and in high densities in tidal and splash water pools. The experiment was conducted at the University of Oslo Biological Research Station “Biologen” in Drøbak, Norway,. We established 36 populations by transferring 11 ovigerous T. brevicornis females from nearby splash pools into glass trays placed on the quay of the station’s harbor at th shoreline.
Two days before adding copepods, we filled each tray with 2.5 liters of seawater and their respective treatments: predation risk, copper (10 µg Cu L-1), combined, and control. Predation risk was simulated using fish kairomones. We incubated three-spined stickleback in seawater, similar to Lode et al. (2020). The 12-week experiment involved water and treatment renewals every 2 weeks. Before each renewal, we screened each microcosm for copepods (fewer than 10 or many) and other visible animals and debris. We sampled populations every 4th week by taking down 1/3 of the replicates, resulting in three independent replicates per timepoint and treatment. If possible, we randomly picked 100 individual late-stage copepodites and adults for pigment and stable isotope analysis. They were depurated in filtered seawater for two hours at ambient salinity. We then sampled adults for pigment analysis and stable isotope analysis. The remaining microcosm was filtered and preserved in 96% ethanol to determine T. brevicornis population density, structure, and abundances of other organisms. To analyze copepods’ Astaxanthin pigment content of individidual copepods, we used Thrane et al.’s (2015) spectrophotometric analysis. To calculate the specific Astaxanthin content, we used the ashfree dryweight derived from the length-weight regression for harpactcoids (Hopcroft et al., 1998). The δ15N and δ13C ratios of individual copepod samples were measured on a Thermo Fisher DeltaV Stable Isotope Mass Spectrometer configured with a Flash Elemental Analyzer Isolink system at the CLIPTlab of the Univeristy of Oslo.
References
Hopcroft, R.R., Lombard, D., Roff, J.C., 1998. Production of tropical copepods in Kingston Harbour, Jamaica: the importance of small species. Marine Biology 130, 593–604. https://doi.org/10.1007/s002270050281
Thrane, J.-E., Kyle, M., Striebel, M., Haande, S., Grung, M., Rohrlack, T., Andersen, T., 2015. Spectrophotometric Analysis of Pigments: A Critical Assessment of a High-Throughput Method for Analysis of Algal Pigment Mixtures by Spectral Deconvolution. PLOS ONE 10, e0137645. https://doi.org/10.1371/journal.pone.0137645
Lode, Torben, Jan Heuschele, Tom Andersen, Josefin Titelman, Ketil Hylland, and Katrine Borgå. 2020. Contrasting effects of predation risk and copper on copepod respiration rates. Environmental Toxicology and Chemistry, 39(9), pp.1765-1773. https://doi.org/10.1002/etc.4804.https://doi.org/10.1002/etc.4804.
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Datafiles
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MesocosmDataHeuscheleetal.csv
ID: unique mesocosm id
Counting.order: The order in which the samples were counted.
Copper: “Copper” indicates that the treatment had added copper at a concentration of 10 ug L-1, while “No copper” was not treated with copper.
Kairomone: “Kairomone” indicates that the smell of fish was added to the treatment, while “No kairomone” indicates the lack thereof.
Date: Sampling date as d/m/y
Month: Month
Day: Day in the year
MeanT: Average daily temperature of sampling day
maxT: maximum daily temperature of sampling day
minT: minimum daily temperature of sampling day
rangeT: daily temperature range of sampling day
ESDD needed to calculate accumulated extreme stress degree days.
ESDDaccum accumulated extreme stress degree days, i.e. days mesocosm inhabitants mesocosm likely experienced above 32 degrees.
filamentous_green_algae: amount of filamentous algae present in the mesocosms. None,Few,Many,Lots, “NA” indicates that it was not assessed
water_colour: Assessment of the color of the water in the mesocosm, “NA” indicates that it was not assessed.
salinity_psu: Salinity of the mesososm measured with a refractometer.
Nauplii: Number of Tigriopus brevicornis Nauplii
Copepodites: Number of Tigriopus brevicornis copepodites
Copepod.with.eggsac: Number of Tigriopus brevicornis females with eggsacs
Chironomide Number of Chironomides
Other Number of other animals (dead or alive), such as drowned bumblebees, etc.
Shorefly: Number of Ephydridae
Adults: Number of Tigriopus brevicornis adults
AllCopepodites: Sum of copepodites and adult copepods
Allcopepods: Sum of all copepod individuals
STRESS: Stress factor
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Concentration.animals.csv
Sample: MesocosmID
Date: Date of takedown
Month: Takedown month in the year
X: identifier
Sample.ID.new: name of the image the measurements were taken from
Imagenames: name of the image the measurements were taken from
AvgProsomeLength: prosome length in um
DWug:ash free dryweight calculated (ug)
uniqueID: unique ID of the individual
ng.well: nanogram astaxanthin in the well
Dataset: Indicating whether it is from actual animal measurements or not
Treatment: Treatment the animal was exposed to in the experiment
Plate: microwell plate id
ng.animal: ng astaxanthin per animal
Kairomone: “Kairomone” indicates that the smell of fish was added to the treatment, while “No kairomone” indicates the lack thereof.
Copper: “Copper” indicates that the treatment had added copper at a concentration of 10 ug L-1, while “No copper” was not treated with copper.
Censored: indicating whether the Astaxanthin value was below the assumed limit fo detection
AstaxanthinPerDW: Astaxanthin per animal dryweight / specific Astaxanthin mass (ng Astaxanthin per ug dry weight)
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StableIsotopeData.csv
ID: Mesocosm ID
Treatment: treatment coded as a four-level factor
Copper: “Copper” indicates that the treatment had added copper at a concentration of 10 ug L-1, while “No copper” was not treated with copper.
Kairomone: “Kairomone” indicates that the smell of fish was added to the treatment, while “No kairomone” indicates the lack thereof.
Date: Sampling date as d/m/y
Month: Sampling month
ID2: id specific to the stable isotope analysis
c13: delta 13C isotope value
%C: percent carbon
C Notes: annotation for the carbon values (all NA)
N15: delta 15N isotope value
%N: percent nitrogen
N Notes: annotation for the nitrogen values (all NA
Replication Data for: Acute effects of copper exposure and predation risk in five coastal copepods
No full textThe two tables contains the necessary data to replicate the study "Acute effects of copper exposure and predation risk in five coastal copepods".
In short, we tested for copper effects on survival in the presence and absence of kairomones (to mimic predation) in five species from three orders of coastal copepods. We exposed adult copepods to four copper concentrations (0-1350 µg/L, 48h) on an automated imaging platform and analyzed survival over time. The methods are described in detail in the publication
The following describes the contents of each column in each file.
Survivaldata Brochmann.csv
Treatment: indicates the presence (Kairomone) and absence (Control) of kairomones in the experiment
Time_d Time in days when a change in survival was registered
Cu_0: Number of alive copepods at Time_d at a 0 ug L-1 Cu concentration.
Cu_150: Number of alive copepods at Time_d at a 150 ug L-1 Cu concentration.
Cu_450: Number of alive copepods at Time_d at a 450 ug L-1 Cu concentration.
Cu_1350: Number of alive copepods at Time_d at a 450 ug L-1 Cu concentration.
Species: The species that was exposed in the experiment.
Copepod_Length.csv
Species: The species that was measured
Well: the well number the animal was in
Mean_length: prosome length of the animal in px
Well_diameter: the diameter of the well in px
mm_per_pixel: the relationship between mm and px measurements
length_mm: the copepod prosome length in m
Replication Data for: Parasite infection shapes the pathobiome and behavior of marine zooplankton
No full textData and scripts for replicating the results in the article `Garvang et al., 2025. Parasite infection shapes the pathobiome and behavior of marine zooplankton. Limnology and Oceanography Letters`.
We collected Calanus helgolandicus from the Oslofjord, both healthy individuals and infected with a conspicuous "yellow-hyphal" parasite that changes the host behavior. We incubated them for 7 days and measured behavior and survival. At the start and end of the incubation we sampled animals for 16S rRNA microbial community analysis. Infected Calanus had higher mortality, more risky behavior and altered microbiomes compared to the uninfected.
The repository contains a workflow description of how to process and analyze the raw 16S, survival, and behavior data, and all necessary scripts. The raw 16S sequence data is not available in this repository, but has been deposited to the European Nucleotide Archive with project accession PRJEB84185.Abstract from related publication:
When assessing the total impact of disease in a host, it is important to consider not only the disease-carrying agent but also all symbionts, as they affect and are affected by the course of disease. This concept of a pathobiome is increasingly recognized in disease ecology, but is not well-investigated in natural systems. Copepods are key organisms in marine ecosystems and host a variety of symbionts, including bacteria and eukaryotic parasites. We investigated the impact of a taxonomically uncertain yellow-hyphal parasite (YHP) on its copepod host Calanus helgolandicus with an incubation experiment, comparing survival, behavior, and microbiomes of uninfected and infected hosts. Infected hosts had higher mortality, and altered behavior which can increase predation risk. The microbiomes differed between infected and uninfected hosts, and we identified several potential contributing taxa to the Calanus-YHP pathobiome using model-based ordination.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
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koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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