cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25903/chbr-5x77
title: Data from: Meta-analysis reveals weak associations between fishes and corals

description: <p>This study aims to evaluate the degree of association between fishes and coral by conducting a meta-analysis on peer-reviewed published literature extracted from two databases. We extracted 7863 articles from the two databases (Web of science and scopus), which after removing for duplicates, yielded 4653 unique articles. Articles were first screened for their title and abstract, and subsequently for their full text, both of which utilised a deliberate decision tree (provided in methods/supplemental). Within this decision tree, the inclusion criteria was formulated such that the final set of studies only contained original research articles that were 1) conducted on tropical, shallow (&lt;30 metres) coral reefs where corals and fishes (unbaited) were synchronously surveyed in-situ, 2) contained appropriate metrics (percent coral cover, fish abundance, biomass, and species richness) from which fish-coral associations can be quantified, and 3) provided clear documentation of the statistical analyses (e.g. sample size, statistical test used etc.) used to obtain the result. First, a scoping/preliminary search for key literature (including existing reviews on fish-coral associations) was performed to familiarise on typically used nomenclature, and to subsequently formulate specific keywords to be used in the systematic search string. Keywords were chosen (see decision tree included in methods/supplemental) to allow for a broad, yet relevant collection of studies to be gathered. These keywords were typical terms used in empirical coral reef studies in which corals and fishes were quantified synchronously for the metrics of interest (i.e. coral cover, fish abundance, biomass, and species richness). As we only wanted studies that had documented species richness along with surveys of abundance/denisty and/or biomass, richness was not included as an initial search term. Through this process, we found that certain studies (particularly those pre-dating 1990s) did not have their abstract recorded in the database. Thus, another search string was formulated to account for this (see decision tree). This search string basically was to account for studies that had no abstract and hence we used used AND NOT with terms that would commonly be in an abstract (e.g. the OR a OR and). Our final dataset includes 723 effect sizes extracted from 66 papers (from 2 databases: web of science and Scopus) that document a statistical relationship between percent coral cover and fish metrics (abundance, biomass and richness), with articles published between 1984 and 2022.</p>
<p>Software/equipment used to create/collect the data: Microsoft excel</p>
<p>Software/equipment used to manipulate/analyse the data: Rstudio</p>
DOI: 10.15468/dl.5kuxv8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((142.932422 -36.840619, 142.932422 -36.842865, 142.936914 -36.842865, 142.936914 -36.840619, 142.932422 -36.840619))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075347-240626123714530/datasets/export for details.
DOI: 10.25903/5eb0f568fad20
title: Convergent validity and reliability of a novel repeated agility protocol in junior rugby league players

description: <p>Raw data set for the study, entitled "Convergent validity and reliability of a novel repeated agility protocol in junior rugby league players".</p><p>Data consists of a spreadsheet containing 7 worksheets:</p><ul><li>Time to completion</li><li>RPE (Rated Perceived Exertion)</li><li>Muscle soreness</li><li>HR (Heart Rate)</li><li>Speed & Agility </li><li>Repeated speed</li><li>Aerobic capacity</li></ul><p>The full methodology is available in the publication shown in the Related Publications link below.</p><p> </p>
DOI: 10.4225/28/583781146dd7e
title: A comparative study on sexual reproduction of scleractinian and alcyonacean corals
DOI: 10.25903/tvcv-c322
title: Data: Cognitive Vulnerabilities Animal Attributions Survey

description: <p><strong>Background:</strong></p>
<p>This study employed a correlational and predictive research design. The predictor variables in the study were cognitive vulnerability (CV) and anthropomorphic attributions (AA) towards animals, while the outcome variable was willingness to own (WTO). Fear was investigated as the third variable acting as the mediator between cognitive vulnerability and the WTO and as the moderator for the effects of anthropomorphic attributions on the WTO. The type of animal was considered an independent variable in the study with two levels: high fear (snake and spider) and low fear (cat and rabbit). </p>
<p><strong>Methods: </strong>A total of 341 respondents were recruited for an online survey through convenience and snowball sampling; 121 datasets (35%) were excluded from the analyses because they were mostly incomplete. The final sample consisted of 220 participants (68.6% female and 83.6% pet owners). Nine participants identified as non-binary/third gender and one preferred not to disclose. Their ages ranged between 18 and 64 years (M age = 34.14 years, SD = 10.96). The sample included students from James Cook University (JCU) and other universities who were recruited through email via a specified person of contact, as well as community participants. Ethical approval for the study was obtained from the JCU Human Research Ethics Committee (H9129). </p>
<p><strong>This data record contains:</strong></p>
<ul>
<li>De-identified survey data and variable names in .csv, .sav and .ods format</li>
</ul>
<p>Software/equipment used to create/collect the data: Qualtrics Experience Management platform used to create and disseminate the survey, and to export data<br />SPSS Version 29.0.1.1 used to export Survey data</p>
<p>Software/equipment used to manipulate/analyse the data: SPSS Version 29.0.1.1</p>
DOI: 10.25903/rsp3-r033
title: Data from: Testing the reliability of adaptive capacity as a proxy for adaptive and transformative responses to climate change

description: <p>Data used for thesis chapter and journal article on relationship between adaptive capacity and adaptive responses implemented in response to climate change impacts by Asian-Pacific reef tourism operators.</p>
<p>Please refer to the thesis and article (Related publications) for further details and the full methods.</p>
<p>This dataset consists of:</p>
<p>Raw dataset including anonymized information on operators, their adaptive responses, and adaptive capacity; seven anonymised lists (zip file) with reef tourism operators (population) by location and raw data for Figure 4 of the manuscript. Data is in MS Excel (.xlsx) format and has also been saved into OpenDocument format (zip) to ensure ongoing access. The R markdown file and corresponding HTML file showing the code used to get the results are also included.</p>
<p>These files are open access and can be downloaded from the links provided.</p>
<p>Software/equipment used to create/collect the data: <a href="https://www.kobotoolbox.org/">https://www.kobotoolbox.org/</a></p>
<p>Software/equipment used to manipulate/analyse the data: Excel and R programming language</p>
DOI: 10.4225/28/58732594db504
title: Population allele data (microsatellites) for Holothuria scabra sea cucumbers
DOI: 10.25903/5cad5e22a7f35
title: Data for: Warren DT, McCormick MI. Intrageneric differences in the effects of acute temperature exposure on competitive behaviour of damselfishes

description: <p>Abstract [Related Publication]: Projected increases in global temperatures brought on by climate change threaten to disrupt many biological and ecological processes. Tropical ectotherms, like many fishes, can be particularly susceptible to temperature change as they occupy environments with narrow thermal fluctuations. While climate change models predict temperatures to increase over decades, thermal fluctuations are already experienced on a seasonal scale, which may affect the ability to capture and defend resources across a thermal gradient. For coral reef fish, losers of competitive interactions are often more vulnerable to predation, and this pressure is strongest just after settlement. Competitive interactions may determine future success for coral reef fishes, and understanding how temperature experienced during settlement can influence such interactions will give insight to community dynamics in a future warmer world. We tested the effect of increased temperatures on intraspecific competitive interactions of two sympatric species of reef damselfish, the blue damselfish <em>Pomacentrus nagasakiensis</em>, and the whitetail damselfish <em>Pomacentrus chrysurus</em>. Juvenile fishes were exposed to one of four temperature treatments, ranging from 26-32° C, for seven days then placed into competitive arenas where aggressive interactions were recorded between sized matched individuals within each species. While there was no apparent effect of temperature treatment on aggressive behaviour for <em>P. chrysurus</em>, we observed up to a four-fold increase in aggression scores for <em>P. nagasakiensis</em> with increasing temperature. Results suggest that temperature experienced as juveniles can impact aggressive behaviour, however species-specific thermal tolerances led to behavioural affects that differ among closely related species. Differential thermal tolerance among species may cause restructuring of the interaction network that underlies the structure of reef assemblages.</p><p>The full methodology is available in the Open Access publication from the Related Publications link below.</p><p> </p>
DOI: 10.4225/28/546a9d8961ba2
title: Inshore GBR Reefs, derelict fishing line and benthic data, 2007-2009
DOI: 10.25903/nb3m-0634
title: Effect of elevated carbon dioxide on shoal familiarity and metabolism in a coral reef fish: corrected version

description: <p>This study examined the influence of elevated carbon dioxide on shoal familiarity and the metabolic benefits of group living in gregarious damselfish species of the blue-green puller (<em>Chromis viridis</em>). Shoals were acclimated to one of three CO<sub>2</sub> treaments (ambient control, mid and high levels based on the range of of levels projected for 2100) and 2 experiments conducted to determine the effect of elevated CO<sub>2</sub> on familiarity and the calming effect respectively. The dataset includes physiological, behavioural and water chemistry data.</p>
<p>The full methodology is available in the Open Access publication from the Related Publications link below.</p>
DOI: 10.25903/5f4301f43296d
title: Tidal-diel patterns of movement, activity and habitat use by juvenile mangrove whiprays using towed-float GPS telemetry

description: <p>Stingrays are a relatively diverse and widespread group of elasmobranchs. Despite their ecological and economical importance, many aspects of stingray ecology remain poorly understood. Few studies have examined juvenile stingrays fine-scale movements within nursery areas. This study aimed to examine diel movement patterns in juvenile mangrove whiprays (<em>Urogymnus granulatus</em>) using towed-float GPS telemetry within a reef flat habitat of the Great Barrier Reef.</p>
<p>The dataset consists of an Excel spreadsheet including GPS tracks of 10 young-of-the-year and juvenile (3 males and 7 females) mangrove whiprays. Tracking occured between 2016 and 2017. Two individuals were tracked twice, thus a total of 12 tracks were analyzed, five during the day and seven at night, ranging from 1.35 to 9 hours.</p>
<p>Tracking data were analysed using the adehabitatLT, adehabitatHR and glmmTMB packages in R.</p>
<p>Disc width and Tide height values are in cm; Tank time and duration of track in h; Total displacement in m; Activity space in km<sup>2</sup> ; Rate of Movement in m min<sup>-1</sup></p>
DOI: 10.25903/gjj8-c722
title: Data from: Are fish communities on coral reefs becoming less colourful?

description: This project uses a community-level approach to study the links between coral reef fish colouration and the environment. Then, it merges these findings with long term data on fish community composition to assess how the appearance of fish communities on coral reefs have changed in response to global environments impacts.

Software/equipment used to create/collect the data: Camera - Nikon D200 - ISO: 400, f-number: 9, shutter speed: 1/40 - 1/80
Microsoft Windows 10 Home, version 20H2
Microsoft Excel, version 2110

Software/equipment used to manipulate/analyse the data: Microsoft Windows 10 Home, version 20H2
Microsoft Excel, version 2110
R, version 4.0.2
DOI: 10.25903/jw1s-h864
title: StressSet

description: <p>A data set in CSV format containing wearable device sensor biomarkers that can be used for predicting acute stress response using machine learning models.</p>
<p>Software/equipment used to create/collect the data: Data sets were accessed and downloaded using Google Chrome 96.0.4664.45 using Ubuntu Linux 20.10 as the operating system. <br />R version 4.0.4 on RStudio 2021.09.0 build 351 was used to merge and transform the original data into this final form used in the research project.</p>
<p>Software/equipment used to manipulate/analyse the data: Ubuntu Linux 20.10, R version 4.0.4 on RStudio 2021.09.0 build 351.</p>
DOI: 10.25903/5c493e2ac3154
title: Data from: Testing the adaptive potential of yellowtail kingfish to ocean warming and acidification

description: <p>Abstract [Related Publication]: Estimating the heritability and genotype by environment (GxE) interactions of performance-related traits (e.g. growth, survival, reproduction) under future ocean conditions is necessary for inferring the adaptive potential of marine species to climate change. To date, no studies have used quantitative genetics techniques to test the adaptive potential of large pelagic fishes to the combined effects of elevated water temperature and ocean acidification. We used an experimental approach to test for heritability and GxE interactions in morphological traits of juvenile yellowtail kingfish, <em>Seriola lalandi</em>, under current-day and predicted future ocean conditions. We also tracked the fate of genetic diversity among treatments over the experimental period to test for selection favoring some genotypes over others under elevated temperature and CO<sub>2</sub>. Specifically, we reared kingfish to 21 days post hatching (dph) in a fully crossed 2 x 2 experimental design comprising current-day average summer temperature (21°C) and seawater pCO<sub>2</sub> (500 µatm CO<sub>2</sub>) and elevated temperature (25°C) and seawater pCO<sub>2</sub> (1,000 µatm CO<sub>2</sub>). We sampled larvae and juveniles at 1, 11 and 21 dph and identified family of origin of each fish (1,942 in total) by DNA parentage analysis. The animal model was used to estimate heritability of morphological traits and test for GxE interactions among the experimental treatments at 21 dph. Elevated temperature, but not elevated CO<sub>2</sub> affected all morphological traits. Weight, length and other morphological traits in juvenile yellowtail kingfish exhibited low but significant heritability under current day and elevated temperature. However, there were no measurable GxE interactions in morphological traits between the two temperature treatments at 21 dph. Similarly, there was no detectable change in any of the measures of genetic diversity over the duration of the experiment. Nonetheless, one family exhibited differential survivorship between temperatures, declining in relative abundance between 1 and 21 dph at 21°C, but increasing in relative abundance between 1 and 21 dph at 25°C. This suggests that this family line could perform better under future warming than in current-day conditions. Our results provide the first preliminary evidence of the adaptive potential of a large pelagic fisheries species to future ocean conditions.</p><p>The full methodology is available in the Open Access publication from the Related Publications link below.</p><p> </p>
DOI: 10.4225/28/598a913c88c41
title: Predation on settling crown-of-thorns starfish larvae by benthic predators
DOI: 10.25903/gxg0-p558
title: Habitat degradation drives increased gnathiid isopod ectoparasite infection rate on juvenile but not adult fish: dataset

description: Widespread coral mortality is leading to coral reef degradation worldwide. Many juvenile reef fishes settle on live coral and their predator-avoidance behaviour is disrupted in seawater exposed to dead corals, ultimately increasing predation risk. Gnathiid isopods are micropredatory fish ectoparasites that occur in higher abundances in dead coral. However, the effect of seawater associated with dead coral on the susceptibility of fish to micropredators has never been investigated. We tested whether the infection rate of cultured gnathiid ectoparasites on individual damselfish, Pomacentrus amboinensis Bleeker 1868, from two different ontogenetic stages (juveniles and adults) was influenced by seawater exposed to three different treatments: dead coral, live coral, or no coral. Seawater treatments were presumed to contain different chemical properties, and are meant to represent environmental changes associated with habitat degradation on coral reefs. Gnathiid infection of juvenile fish in seawater exposed to dead coral was twice as high as that of fish in live coral or no coral. Infection rates did not significantly differ between live coral and no coral treatments. In contrast to juveniles, the susceptibility of adults to gnathiids was not affected by seawater treatment. During experiments, juvenile fish mortality was relatively low, but was higher for infected fish (9.7 %), compared to fish held without exposure to gnathiids (1.7%). No mortality occurred in adult fish that became infected with gnathiids. Our results suggest that chemical cues released from dead corals and/or dead coral colonisers affect the ability of juvenile, but not adult fish to avoid parasite infection. Considering increased habitat degradation on coral reefs and that gnathiids are more abundant in dead coral substrate, it is possible that wild juvenile fish may experience increased susceptibility to parasitic infection and reduced survival rate. This highlights the importance of including parasitism in ecological studies of global environmental change.

Software/equipment used to create/collect the data: Excel

Software/equipment used to manipulate/analyse the data: R studio
DOI: 10.25903/5dd21c638f492
title: Evaluation of bacteriophage in a rat model of PJI

description: <p>Investigation of the <em>in vivo</em> efficacy of single or combination therapy using a bacteriophage cocktail and vancomycin for reducing <em>S. aureus</em> burden within the implanted knee of the rat model of <em>S. aureus</em> biofilm-associated PJI (periprosthetic joint infection). </p><p>This dataset consists of 6 PRISM (.pzfz) projects containing data tables, results of statistical analyses and graphs. The data tables for each project are also saved in comma-separated values (.csv) format, for preservation purposes.</p><p>The projects can be opened using the GraphPad Prism software if owned, otherwise they can be opened using the Prism view utility. More details on the free viewer are available from the GraphPad <a href="https://www.graphpad.com/support/faq/where-can-i-find-the-free-prism-viewer/">website</a>.</p><p>The files consists of:</p><p>PRISM projects:</p><ul><li>Bacterial Loads.pzfx - Bacterial load in implanted knees from treated and untreated rats</li><li>In vitro vancomycin sensitivity.pzfx - In vitro vancomycin sensitivity for S. aureus isolates recovered from implants from knees of treated and untreated rats</li><li>In vitro phage sensitivity.pzfx - In vitro phage sensitivity for S. aureus isolates recovered from implants from knees of treated and untreated rats</li><li>Joint pathology.pzfx - Macroscopic changes in implanted knees from treated and untreated rats</li><li>Joint cytokines.pzfx - Inflammatory cytokines in implanted knees from treated and untreated rats</li><li>Plasma cytokines.pzfx - Inflammatory cytokines in treated and untreated rats</li></ul><p>Data Tables (exported from Prism in .csv format):</p><ul><li>Bacterial loads_DataTables.zip</li><li>In vitro vancomycin sensitivity_DataTables.zip</li><li>In vitro phage sensitivity_DataTables.zip</li><li>Joint pathology_DataTables.zip</li><li>Plasma cytokines_DataTables.zip</li></ul><p> The full methodology is available in the Open Access publication from the Related Publications link below.</p><p> </p>
DOI: 10.25903/5b8c97c1254c3
title: Disturbance, recovery and the depletion of functional diversity on coral reefs

description: <p>Data used in a thesis chapter entitled "Disturbance, recovery and the depletion of functional diversity on coral reefs," by Mike McWilliam, co-authored by Morgan Pratchett and Terry Hughes. The study uses time series data of coral assemblages from three biogeographical locations in addition to trait data from the coral traits database.  </p><p>Time series data: </p><p>gbr.csv. Abundances of 28 coral taxonomic groups at Lizard Island, Great Barrier Reef. Abundance columns are marked with "flat," "crest," "slope," or "base," followed by year to distinguish the habitat and time where data was collected. </p><p>polynesia.csv. Abundances of 20 coral taxonomic groups at Tiahura Reef, French Polynesia. Abundance columns are marked with "flat" (Outer flat), "crest," "shall" (shallow slope), or "deep" (deep slope), followed by year to distinguish the habitat and time where data was collected. </p><p>jamaica.csv. Abundances of 16 coral taxonomic groups at Rio Bueno, Jamaica. Abundance columns are marked with depth ("7m", "10m", "15m", or "30m") followed by year to distinguish the habitat and time where data was collected. </p><p>Trait data: </p><p>traits.csv. Trait data for 44 taxonomic groups of corals. Trait data was downloaded from the coral traits database and mean values for four traits (max diameter, corallite width, growth rate, and skeletal density) was found. These values are presented alongside the typical growth form (column H) and reproductive mode (column G) of each taxonomic group. Columns J to O indicate seven numerical trait categories used for the analysis, including three additional traits (sa_vol = surface area to volume ratio, spaces = interstitial space size, height = colony height) derived from colony growth form. </p><p> </p><p> </p>
DOI: 10.4225/28/579ab6341d6f2
title: Incidental achievement of fine-resolution objectives by coarse-resolution priorities
DOI: 10.4225/28/5743ed872a28c
title: Nutrient contents and associated parameters for cocoa tree leaves, ripe cocoa pods and soil from 63 cocoa farms in Papua New Guinea in 2007
DOI: 10.25903/5dc0d73461bd6
title: Habitat complexity results in high preference of lower, but not higher temperature by a common coral reef fish, Chromis atripectoralis