cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.878vn25
title: Data from: Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water-and air-breathers

description: Global warming appears to favour smaller-bodied organisms, but whether
 larger species are also more vulnerable to thermal extremes, as suggested
 for past mass-extinction events, is still an open question. Here, we
 tested whether interspecific differences in thermal tolerance (heat and
 cold) of ectotherm organisms are linked to differences in their body mass
 and genome size (as a proxy for cell size). Since the vulnerability of
 larger, aquatic taxa to warming has been attributed to the oxygen
 limitation hypothesis, we also assessed how body mass and genome size
 modulate thermal tolerance in species with contrasting breathing modes,
 habitats and life stages. A database with the upper (CTmax) and lower
 (CTmin) critical thermal limits and their methodological aspects was
 assembled comprising more than 500 species of ectotherms. Our results
 demonstrate that thermal tolerance in ectotherms is dependent on body mass
 and genome size and these relationships became especially evident in
 prolonged experimental trials where energy efficiency gains importance.
 During long-term trials, CTmax was impaired in larger-bodied
 water-breathers, consistent with a role for oxygen limitation. Variation
 in CTmin was mostly explained by the combined effects of body mass and
 genome size and it was enhanced in larger-celled, air-breathing species
 during long-term trials, consistent with a role for depolarization of cell
 membranes. Our results also highlight the importance of accounting for
 phylogeny and exposure duration. Especially when considering long-term
 trials, the observed effects on thermal limits are more in line with the
 warming-induced reduction in body mass observed during long-term rearing
 experiments.
description: 1. Leiva_et_al_DataBase_PhilTransB
 This file contains the taxonomic information, the geographical
 coordinates of collection, life-stage, habitat, breathing mode and CTmax
 and CTmin data for the species used in this study. 
 2. README_Leiva_et_al_Metadata_PhilTransB_update
 This file contains the metadata information.
 3.
 Leiva_et_al_References_PhilTransB_update List of
 primary references in which the thermal limits (CTmax and CTmin) were
 extracted.
DOI: 10.5061/dryad.n6d4mm5
title: Data from: RAD‐sequencing for estimating genomic relatedness matrix‐based heritability in the wild: a case study in roe deer

description: Estimating the evolutionary potential of quantitative traits and reliably
 predicting responses to selection in wild populations are important
 challenges in evolutionary biology. The genomic revolution has opened up
 opportunities for measuring relatedness among individuals with precision,
 enabling pedigree-free estimation of trait heritabilities in wild
 populations. However, until now, most quantitative genetic studies based
 on a genomic relatedness matrix (GRM) have focused on long-term monitored
 populations for which traditional pedigrees were also available, and have
 often had access to knowledge of genome sequence and variability. Here, we
 investigated the potential of RAD-sequencing for estimating heritability
 in a free-ranging roe deer population for which no prior genomic resources
 were available. We propose a step-by-step analytical framework to optimize
 the quality and quantity of the genomic data and explore the impact of the
 SNP calling and filtering processes on the GRM structure and GRM-based
 heritability estimates. As expected, our results show that sequence
 coverage strongly affects the number of recovered loci, the genotyping
 error rate and the amount of missing data. Ultimately, this had little
 effect on heritability estimates and their standard errors, provided that
 the GRM was built from a minimum number of loci (above 7000). GRM-based
 heritability estimates thus appear robust to a moderate level of
 genotyping errors in the SNP dataset. We also showed that quality filters,
 such as the removal of low-frequency variants, affect the relatedness
 structure of the GRM, generating lower h² estimates. Our work illustrates
 the huge potential of RAD-sequencing for estimating GRM-based heritability
 in virtually any natural population.
description: NCBI BioProject
 PRJNA533008Provide all FASTQ data
 already demultiplexed and preprocessed.sensitivity_analysisSTACKS_and_QCfilter
DOI: 10.5061/dryad.95t9g4r
title: Data from: Facile immobilisation of glucose oxidase onto gold nanostars with enhanced binding affinity and optimal function

description: Gold nanoparticles provide a user-friendly and efficient surface for
 immobilisation of enzymes and proteins. In this paper, we present a novel
 approach for enzyme bioconjugation to gold nanostars (AuNSs). AuNSs were
 modified with L-cysteine (Cys) and covalently bound to
 N-hydroxysulfosuccinimide (NHS)-terminated glucose oxidase (GOx) to
 fabricate a stable and sensitive AuNSs-Cys-GOx bioconjugate complex.
 Observed, were: 1) Increased attachment affinity without protein
 absorption onto the AuNSs surface. 2) Good dispersity in buffer
 suspension, as well as stability in high ionic environments. 3) Greater
 sensitivity in the measuring of low concentrations of glucose based on
 plasmonic and colorimentric detection. Such a novel approach for enzyme
 immobilisation can lead to AuNSs-Cys-GOx bioconjugate complexes that can
 be used as catalytic nanodevices in nanobiosensors based on oxidases in
 biomedical applications.
description: Data for
 Dryad
DOI: 10.5061/dryad.bd3v5gk
title: Data from: What factors explain the geographic range of mammalian parasites?

description: Free-living species vary substantially in the extent of their spatial
 distributions. However, distributions of parasitic species have not been
 comprehensively compared in this context. We investigated which factors
 most influence the geographic extent of mammal parasites. Using the Global
 Mammal Parasite Database we analyzed 17,818 individual geospatial records
 on 1,806 parasite species (encompassing viruses, bacteria, protozoa,
 arthropods, and helminths) that infect 396 carnivore, ungulate, and
 primate host species. As a measure of the geographic extent of each
 parasite species we quantified the number and area of world ecoregions
 occupied by each. To evaluate the importance of variables influencing the
 summed area of ecoregions occupied by a parasite species, we used Bayesian
 network analysis of a subset (n=866) of the parasites in our database that
 had at least two host species and complete information on parasite traits.
 We found that parasites that covered more geographic area had a greater
 number of host species, higher average phylogenetic relatedness between
 host species, and more sampling effort. Host and parasite taxonomic groups
 had weak and indirect effects on parasite ecoregion area; parasite
 transmission mode had virtually no effect. Mechanistically, a greater
 number of host species likely increases both the collective abundance and
 habitat breadth of hosts, providing more opportunities for a parasite to
 have an expansive range. Furthermore, even though mammals are one of the
 best studied animal classes, the ecoregion area occupied by their
 parasites is strongly sensitive to sampling effort, implying mammal
 parasites are undersampled. Overall, our results support that parasite
 geographic extent is largely controlled by host characteristics, many of
 which are subsumed within host taxonomic identity.
description: Data and R code for
 Bayesian Network AnalysisZip folder containing 2
 files. Byers_et_al_2019.Rmd: an R markdown file containing code use for
 Bayesian network analyses and Byers_et_al_2019.RData: an R workspace file
 containing data for use with
 "Byers_et_al_2019.Rmd."Byers_model_code-and-data-zipped.zip
DOI: 10.25918/data.316
title: From dawn ‘til dusk: daytime progression regulates primary and secondary metabolism in Cannabis glandular trichomes

description: <em>Cannabis sativa </em>L. glandular trichomes (GTs) synthesise large amounts of specialised secondary metabolites, predominantly cannabinoids and terpenoids. The associated demand for carbon and energy makes GTs strong sink tissues and there is indication that their secondary metabolism is coupled to the availability of photoassimilates. Many metabolites, including secondary metabolites, show diurnal patterns of flux but it is unknown whether cannabinoids and terpenoids are regulated by time of day. We quantified cannabinoids, terpenoids and the GT proteome over a 12-hour light period in flowers of Hindu Kush, a high-tetrahydrocannabinol (THC) cultivar. Major cannabinoids showed significant changes over the course of day, resulting in an increase in total measured cannabinoids. Major terpenoids also showed changes, with sesquiterpenes generally decreasing with day progression. While monoterpenes generally did not decrease, the second most abundant, a-pinene, increased. The GT proteome changed the most within the first six hours of the day and analysis of differentially abundant proteins indicated upregulation of primary metabolism. Surprisingly, key cannabinoid biosynthetic enzymes decreased with daytime progression despite increases in cannabinoid content, which might indicate that daytime increases of photoassimilates are the main driver of cannabinoid regulation. This first reporting of variability of cannabinoid and terpenoid biosynthesis over the course of the day has implications for Cannabis research and production.
DOI: 10.25918/data.413
title: Culturing coral larvae with food supplements enhances larval size and settlement

description: The cultivation of coral larvae in controlled aquaculture systems has the potential to improve survivorship during early life stages and support coral reef restoration efforts. Maximising the health and energy of coral larvae is important for scaling up larval production for recruitment and restoration initiatives. Increasingly, research is focusing on optimising larval rearing practices but larval feeding during ex situ culture remains under explored. Although feeding larvae can enhance settlement in &lt;em&gt;Acropora&lt;/em&gt; species, an optimal feeding regime has not yet been determined. Therefore, this research aimed to quantify the effects of supplying different amounts of food on larval survival and settlement of &lt;em&gt;Acropora &lt;/em&gt;cf.&lt;em&gt; kenti&lt;/em&gt; larvae. Larvae were reared in 14L culture tanks and exposed daily to one of three doses of homogenised &lt;em&gt;Artemia &lt;/em&gt;(5mL, 50mL, or 100mL) and an unfed control of no &lt;em&gt;Artemia&lt;/em&gt;. Larval survival, larval size, settlement, and size of settlers were measured. There was a significant positive effect of feeding on settlement for medium (50mL) and high doses (100mL) of homogenised &lt;em&gt;Artemia&lt;/em&gt;, resulting in a 2.5-fold increase in settlement compared with unfed larvae. Further, feeding medium and high doses of food significantly increased the size of larvae and settlers. However, feeding did not significantly affect survival. Understanding the biological parameters influencing larval nutrition and settlement can refine aquaculture methodologies for scaling up restoration initiatives.
DOI: 10.5061/dryad.rq2dg6m
title: Data from: Quality and quantity of genetic relatedness data affect the analysis of social structure

description: Kinship plays a fundamental role in the evolution of social systems and is
 considered a key driver of group living. To understand the role of kinship
 in the formation and maintenance of social bonds, accurate measures of
 genetic relatedness are critical. Genotype-by-sequencing technologies are
 rapidly advancing the accuracy and precision of genetic relatedness
 estimates for wild populations. The ability to assign kinship from genetic
 data varies depending on a species’ or population’s mating system and
 pattern of dispersal, and empirical data from longitudinal studies are
 crucial to validate these methods. We use data from a long-term behavioral
 study of a polygynandrous, bisexually philopatric marine mammal to measure
 accuracy and precision of parentage and genetic relatedness estimation
 against a known partial pedigree. We show that with moderate but
 obtainable sample sizes of approximately 4235 SNPs and 272 individuals,
 highly accurate parentage assignments and genetic relatedness coefficients
 can be obtained. Additionally, we subsample our data to quantify how data
 availability affects relatedness estimation and kinship assignment.
 Lastly, we conduct a social network analysis to investigate the extent to
 which accuracy and precision of relatedness estimation improve statistical
 power to detect an effect of relatedness on social structure. Our results
 provide practical guidance for minimum sample sizes and sequencing depth
 for future studies, as well as thresholds for post hoc interpretation of
 previous analyses.
description: DolphinGenotypeDataGenotypes for 272 individual Tursiops aduncus at 4235 lociSimulatedGenotypeDataGenotypes simulated using the program Conancestry (Wang 2011) for 100 pairs at each of 6 levels of relatedness. Allele frequencies and genotyping error are set to match those found in the real dolphin genotype data in the study.social_model_variabes_dryadAll pairwise variables included in the social network model: the association strength (simple ratio index), the total number of sightings of both individuals, home range overlap (volume of intersection), age difference in years, and the sexes of the pair
DOI: 10.25918/data.431
title: Raw spectral data - SWATH-MS of Cannabis sativa glandular trichomes in response to abscisic acid and drought stress

description: Cannabis (<em>Cannabis sativa</em> L.) is a medicinally important drought resistant plant. The glandular trichomes (GT) on female flowers of cannabis are the main site of production and storage of cannabinoids and terpenoids. While water deficit stress (WD) modulates cannabinoid content in cannabis, it is unknown how GT regulation is affected to achieve this. We quantified the GT proteome and floral cannabinoid and terpenoid content in late flowering ‘Hindu Kush’ cannabis treated with either short-term WD or with an abscisic acid (ABA) foliar spray. We found that WD and ABA changed the abundance of many of the same proteins in the GT, with changes reflecting a decrease in primary metabolic processes and an increase in stress response mechanisms. Results suggested ABA likely mediates changes in the GT indirectly by affecting salicylic acid and ethylene signalling. Interestingly, WD caused cannabinoid content to increase, while ABA caused monoterpene content to increase, and proteins involved in cannabinoid or terpenoid biosynthesis were either downregulated or did not change in either treatment. Since photosynthesis and the total photoassimilate pool typically decline in response to WD in plants, we postulate that the remaining photoassimilate pool is reallocated to support secondary metabolism in the <em>Cannabis</em> GT when responding to WD.
description: This dataset release contains the associated SWATH-MS raw spectral data for protein abundance in glandular trichomes. Also included are the floral cannabinoid, terpenoid and biomass values.
DOI: 10.5061/dryad.6062s6t
title: Data from: Cost of transport is a repeatable trait but is not determined by mitochondrial efficiency in zebrafish (Danio rerio)

description: The energy used to move a given distance (cost of transport; CoT) varies
 significantly between individuals of the same species. A lower CoT allows
 animals to allocate more of their energy budget to growth and
 reproduction. A higher CoT may cause animals to adjust their movement
 across different environmental gradients to reduce energy allocated to
 movement. The aim of this project was to determine whether CoT is a
 repeatable trait within individuals, and to determine its physiological
 causes and ecological consequences. We found that the CoT is a repeatable
 trait in zebrafish (Danio rerio). We rejected the hypothesis that
 mitochondrial efficiency (P/O ratios) predicted CoT. We also rejected the
 hypothesis that CoT is modulated by temperature acclimation, exercise
 training, or their interaction, although CoT increased with increasing
 acute test temperature. There was a weak but significant negative
 correlation between CoT and dispersal, measured as the number of
 exploration decisions made by fish, and the distance travelled against the
 current in an artificial stream. However, CoT did not correlate with the
 voluntary speed of fish moving against the current. The implications of
 these results are that CoT reflects a fixed physiological phenotype of an
 individual, which is not plastic in response to persistent environmental
 changes. Consequently, individuals may have fundamentally different energy
 budgets as they move across environments, and may adjust movement patterns
 as a result of allocation trade-offs. It was surprising that mitochondrial
 efficiency did not explain differences in CoT, and our working hypothesis
 is that the energetics of muscle contraction and relaxation may determine
 CoT. The increased in CoT with increasing acute environmental temperature
 means that warming environments will increase the proportion of the energy
 budget allocated to locomotion unless individuals adjust their movement
 patterns.
description: JEXBIO_2019_201400_dataAll data used in this publication. Each sheet in the Excel file refers to one experiment, and the first sheet provides explanatory information.
DOI: 10.5061/dryad.3t5602f
title: Data from: Contingency rules for pathogen competition and antagonism in a genetically based, plant defense hierarchy

description: 1. Plant defense against pathogens includes a range of mechanisms,
 including, but not limited to, genetic resistance, pathogen-antagonizing
 endophytes, and pathogen competitors. The relative importance of each
 mechanism can be expressed in a hierarchical view of defense. Several
 recent studies have shown that pathogen antagonism is inconsistently
 expressed within the plant defense hierarchy. Our hypothesis is that the
 hierarchy is governed by contingency rules that determine when and where
 antagonists reduce plant disease severity. 2. Here, we investigated
 whether pathogen competition influences pathogen antagonism using Populus
 as a model system. In three independent field experiments, we asked
 whether competition for leaf mesophyll cells between a Melampsora rust
 pathogen and a microscopic, eriophyid mite affects rust pathogen
 antagonism by fungal leaf endophytes. The rust pathogen has an annual,
 phenological disadvantage in competition with the mite because the rust
 pathogen must infect its secondary host in spring before infecting
 Populus. We varied mite-rust competition by utilizing Populus genotypes
 characterized by differential genetic resistance to the two organisms. We
 inoculated plants with endophtyes and allowed mites and rust to infect
 plants naturally. 3. Two contingency rules emerged from the three field
 experiments: 1) pathogen antagonism by endophytes can be preempted by host
 genes for resistance that suppress pathogen development, and 2) pathogen
 antagonism by endophtyes can secondarily be preempted by competitive
 exclusion of the rust by the mite. 4. Synthesis: Our results point to a
 Populus defense hierarchy with resistance genes on top, followed by
 pathogen competition, and finally pathogen antagonism by endophytes. We
 expect these rules will help to explain the variation in pathogen
 antagonism that is currently attributed to context dependency.
description: Experiment1_dataExperiment2_data_PtriExperiment2_data_hybridsExperiment3_data
DOI: 10.25918/data.382
title: An in vitro phytohormone survey reveals concerted regulation of the Cannabis glandular trichome proteome

description: Glandular trichomes (GTs) are major sites of cannabinoid and terpenoid metabolism in &lt;em&gt;Cannabis sativa&lt;/em&gt; L flowers. Several phytohormones, such as jasmonic acid (JAS) and salicylic acid (SAL) cause increased cannabinoid content in &lt;em&gt;Cannabis&lt;/em&gt; flowers, but how they regulate GTs to cause this change is unknown. This study aimed to understand the mechanisms of action of phytohormones on mature GTs using a novel &lt;em&gt;in vitro&lt;/em&gt; assay. Live GTs were isolated from ‘Hindu Kush’ <em>Cannabis&lt;/em&gt;, a high-tetrahydrocannabinol cultivar, and incubated on basal media plates with either kinetin (KIN), JAS, SAL, abscisic acid, ethephon, gibberellic acid, brassinolide, or sodium diethyldithiocarbamate (DIE), an inhibitor of jasmonic acid synthesis. Quantitative proteomic analysis (SWATH-MS) revealed that KIN, JAS and SAL caused the greatest number of changes in the GT proteome while the other treatments exerted much smaller changes. Surprisingly, metabolite analysis showed none of the treatments caused cannabinoids to increase in the GT, while DIE caused cannabigerolic acid content to decrease. Nor was there any concerted increased abundance of cannabinoid biosynthetic pathway proteins by any treatments. This indicates that cannabinoid increases in previous &lt;em&gt;in planta&lt;/em&gt; phytohormone studies are likely due to other processes, such as through increased GT density. As well, KIN, JAS and SAL treated GT’s had a large proportion of differentially abundant proteins in common. Several were key proteins for leucoplast differentiation and function, cuticular wax and fatty acid metabolism and primary metabolism regulation. This points towards cytokinin, jasmonic acid and salicylic acid signalling likely being important for coordinating &lt;em&gt;Cannabis&lt;/em&gt; GT differentiation and development. </em>