cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p1bd1
title: Data from: Efficacy of a probiotic bacterium to treat bats affected by the disease white-nose syndrome

description: The management of infectious diseases is an important conservation concern
 for a growing number of wildlife species. However, effective disease
 control in wildlife is challenging because feasible management options are
 often lacking. White-nose syndrome (WNS) is an infectious disease of
 hibernating bats that currently threatens several North American species
 with extinction. Currently, no effective treatments exist for WNS. We
 conducted a laboratory experiment to test the efficacy of treatment with
 Pseudomonas fluorescens, a bacterium that naturally occurs on bats, to
 reduce disease severity and improve survival of little brown bats (Myotis
 lucifugus) exposed to Pseudogymnoacus destructans, the fungal pathogen
 that causes WNS. Application of the bacteria at the time of P. destructans
 infection reduced several measures of disease severity and increased
 survival, whereas bacterial treatment prior to pathogen exposure had no
 effect on survival and worsened disease severity. Our results suggest that
 probiotic treatment with Ps. fluorescens has potential for WNS disease
 management but the timing of application is critical and should coincide
 with natural exposure of bats to P. destructans. More broadly, these
 results add to the growing knowledge of how the natural host microbiota
 can influence disease outcomes.
description: Captive Bat
 DataThis file contains
 natural history and disease data for live bats used in our captive
 treatment trial.ChengJAEdata.csviButton DataThis file contains skin temperature (celsius) data downloaded from iButtons attached to captive bats in our experiment.JAEcheng_EnergeticsData.csv
DOI: 10.5061/dryad.3703v
title: Data from: Assortative mating but no evidence of genetic divergence in a species characterized by a trophic polymorphism

description: Disruptive selection is a process that can result in multiple subgroups
 within a population, which is referred to as diversification.
 Foraging-related diversification has been described in many taxa, but many
 questions remain about the contribution of such diversification to
 reproductive isolation and potentially sympatric speciation. Here, we use
 stable isotope analysis of diet and morphological analysis of body shape
 to examine phenotypic divergence between littoral and pelagic foraging
 ecomorphs in a population of pumpkinseed sunfish (Lepomis gibbosus). We
 then examine reproductive isolation between ecomorphs by comparing the
 isotopic compositions of nesting males to eggs from their nests (a proxy
 for maternal diet) and use nine microsatellite loci to examine genetic
 divergence between ecomorphs. Our data support the presence of distinct
 foraging ecomorphs in this population and indicate that there is
 significant positive assortative mating based on diet. We did not find
 evidence of genetic divergence between ecomorphs, however, indicating that
 isolation is either relatively recent or is not strong enough to result in
 genetic divergence at the microsatellite loci. Based on our findings,
 pumpkinseed sunfish represent a system in which to further explore the
 mechanisms by which natural and sexual selection contribute to
 diversification, prior to the occurrence of sympatric speciation.
description: 2011 Pumpkinseed
 SummaryStable isotope
 measurements of male and female pumpkinseed sunfish (Lepomis gibbosus)
 collected from littoral and pelagic habitats during 2011. Fish were
 collected over two time periods: May – June 2011 (Spring 2011) or August
 2011 (Summer 2011). Isotopic compositions (δ13C and δ15N) of liver tissues
 are shown, as well as % Littoral resource estimates (see methods for
 details).Colborne_DRYAD_2011data.xlsx2012 Male Pumpkinseed and Eggs SummaryStable isotope measurements of nesting male pumpkinseed sunfish (Lepomis gibbosus) and eggs collected from the males’ nests in the littoral and pelagic habitats. Nesting males were collected during Spring 2012 (11 – 22 June). Isotopic compositions (δ13C and δ15N) of nesting male liver tissue and egg samples from the male’s nests are shown. Diet estimates of nesting males are shown based on % Littoral resource contributions to diet for each individual (see methods for details).Colborne_DRYAD_2012data.xlsx
DOI: 10.5061/dryad.1g3gp03
title: Data from: It’s all about connections: hubs and invasion in habitat networks

description: During the early stages of invasion, the interaction between the features
 of the invaded landscape, notably its spatial structure, and the internal
 dynamics of an introduced population, has a crucial impact on
 establishment and spread. By approximating introduction areas as networks
 of patches linked by dispersal, we characterized their spatial structure
 with specific metrics and tested their impact on two essential steps of
 the invasion process: establishment and spread. By combining simulations
 with experimental introductions of Trichogramma chilonis (Hymenoptera:
 Trichogrammatidae) in artificial laboratory microcosms, we demonstrated
 that spread was hindered by clusters and accelerated by hubs but was also
 affected by small-population mechanisms prevalent for invasions, such as
 Allee effects. Establishment was also affected by demographic mechanisms,
 in interaction with network metrics. These results highlight the
 importance of considering the demography of invaders as well as the
 structure of the invaded area to predict the outcome of invasions.
description: exp_datasetExperimental data obtained from the artificial invasions of T. chilonis, with the following treatments: L = introduction in lowC landscapes, HH = introduction in highC landscapes in the hub, HF = introduction in highC landscapes outside of the hub.Simulation scriptThe R script used to perform the simulations presented in the main text of the articleScript.r
DOI: 10.15468/dl.pfsmca
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Shortia rotundifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 151 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001157-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v3462
title: Data from: The price of insurance: costs and benefits of worker production in a facultatively social bee

description: Kin selection theory is foundational in helping to explain the evolution
 of sociality; however, the degree to which indirect fitness benefits may
 underlie helping behavior in species of early stage sociality has received
 relatively little empirical attention. Facultatively social bees, which
 demonstrate multiple forms of social organization, provide prime systems
 in which to empirically test hypotheses regarding the evolutionary origins
 of sociality. The subsocial small carpenter bee, Ceratina calcarata, may
 establish a social nest by manipulating brood provisions to rear a worker
 daughter, which then assists in critical late-season alloparental care.
 Here, we combine nest demographic and behavioral data with genetic
 relatedness estimates to calculate the relative inclusive fitness of both
 subsocial and social reproductive strategies in C. calcarata. Social
 mothers benefit from improved likelihood of brood survivorship and have
 higher fitness than subsocial mothers. Worker daughters have low indirect
 fitness on average, and will not produce their own offspring.
 Among-sibling relatedness is significantly higher in social nests than
 subsocial nests, though mothers of either reproductive strategy may mate
 multiply. Though this study corroborates the ultimate role of indirect
 fitness and assured fitness returns in the evolution of social traits, it
 also offers additional support for maternal manipulation as the proximate
 mechanism underlying evolutionary transitions in early stage insect
 societies.
description: ShellRehan2017_AllelicProfilesAllelic profile data for Ceratina calcarata nestmates. Data was generated from microsatellite loci and was called manually using Peak Scanner. Data can be used for relatedness analyses.ShellRehan2017_DemographicDataNest demographic data for Ceratina calcarata, collected during nest dissections during the 2014-2016 field seasons. Data file includes information regarding nest type, maternal body size, brood composition (e.g. clutch size; male and female counts; female:male ratio), and brood survivorship (e.g. counts of parasitism; die-off; total live brood).
DOI: 10.5061/dryad.hb62394
title: Data from: High serum MMP-14 predicts worse survival in gastric cancer

description: Matrix metalloproteinases (MMPs), endopeptidases with diverse biochemical
 functions, can promote cancer cell invasion and metastasis by degrading
 the extracellular matrix. A high matrix metalloproteinase-14 (MMP-14)
 expression in gastric cancer tissue has been associated with metastasis
 and poor prognosis. To further understand this association, we
 investigated serum MMP-14 as a biomarker in gastric cancer patients. The
 patient cohort consisted of 240 gastric adenocarcinoma patients who
 underwent surgery at Helsinki University Hospital, Finland, between 2000
 and 2009. We determined the soluble MMP-14 serum levels using an
 enzyme-linked immunosorbent assay. We then calculated the associations
 between serum levels and clinicopathologic variables using the
 Mann-Whitney U-test or the Kruskal-Wallis test. We constructed survival
 curves using the Kaplan-Meier method and calculating the hazard ratios
 using the Cox proportional hazard model. We revealed a positive
 association between a high serum MMP-14 level and stages III–IV (p =
 0.029), and between a high serum MMP-14 and distant metastasis (p =
 0.022). Patients with a low serum MMP-14 had a 5-year disease-specific
 survival of 49.2% (95% confidence interval [CI] 45.5–52.9), whereas
 patients with a high serum MMP-14 had a 5-year survival of 22.1% (95% CI
 15.2–29.0; p = 0.001). High serum MMP-14 was a statistically significant
 prognostic factor among patients with an intestinal type of cancer (hazard
 ratio [HR] 3.54; 95% CI 1.51–8.33; p = 0.004), but not among patients with
 a diffuse type. The serum MMP-14 level remained an independent prognostic
 factor in our multivariate survival analysis (HR 1.55; 95% CI 1.02–2.35; p
 = 0.040). This study indicates for the first time that high serum soluble
 MMP-14 levels in gastric cancer serves as a marker for a poor prognosis,
 possibly indicating the presence of distant metastases.
description: High serum MMP-14
 predicts worse survival in gastric cancer dataHigh serum MMP-14
 predicts worse survival in gastric cancer data
DOI: 10.5061/dryad.f32n1
title: Data from: Density-dependent intraspecific aggression regulates survival in northern Yellowstone wolves (Canis lupus)

description: 1. Understanding the population dynamics of top predators is essential to
 assess their impact on ecosystems and to guide their management. Key to
 this understanding is identifying the mechanisms regulating vital rates.
 2. Determining the influence of density on survival is necessary to
 understand the extent to which human-caused mortality is compensatory or
 additive. In wolves (Canis lupus), empirical evidence for
 density-dependent survival is lacking. Dispersal is considered the
 principal way in which wolves adjust their numbers to prey supply or
 compensate for human exploitation. However, studies to date have primarily
 focused on exploited wolf populations, in which density-dependent
 mechanisms are likely weak due to artificially low wolf densities. 3.
 Using 13 years of data on 280 collared wolves in Yellowstone National
 Park, we assessed the effect of wolf density, prey abundance and
 population structure, as well as winter severity, on age-specific survival
 in two areas (prey-rich vs. prey-poor) of the national park. We further
 analysed cause-specific mortality and explored the factors driving
 intraspecific aggression in the prey-rich northern area of the park. 4.
 Overall, survival rates decreased during the study. In northern
 Yellowstone, density-dependence regulated adult survival through an
 increase in intraspecific aggression, independent of prey availability. In
 the interior of the park, adult survival was less variable and
 density-independent, despite reduced prey availability. There was no
 effect of prey population structure in northern Yellowstone, nor of winter
 severity in either area. Survival was similar among yearlings and adults,
 but lower for adults older than 6 years. 5. Our results indicate that
 density-dependent intraspecific aggression is a major driver of adult wolf
 survival in northern Yellowstone, suggesting intrinsic density-dependent
 mechanisms have the potential to regulate wolf populations at high
 ungulate densities. When low prey availability or high removal rates
 maintain wolves at lower densities, limited inter-pack interactions may
 prevent density-dependent survival, consistent with our findings in the
 interior of the park.
description: data_CubaynesJAEThis file gathers all data used in the manuscript. Explanation about the data are given in the first sheet. Individual capture histories (including location, age and sex) of the 280 radio-collared wolves in the Northern Range and the Interior area of Yellowstone National Park, between 1998-2010, are presented in Sheet1. Environmental covariates used in the survival analysis (about wolves, elk and weather data) are presented in Sheet2. Variables used in the path analysis are presented in Sheet3.data_CubaynesetalJAE.xlsx
DOI: 10.5061/dryad.115g6
title: Data from: Microtopographic specialization and flexibility in tropical peat swamp forest tree species

description: Tropical tree species distributions are determined by a wide range of
 biotic and abiotic factors, including topography and hydrology. Tropical
 peat swamp forests (TPSFs) are characterized in part by small-scale
 variations in topography (‘hummocks’ and ‘hollows’) that create distinct
 microhabitats and thus may contribute to niche diversification among TPSF
 tree species. Using tree elevations calibrated to daily peat water levels
 collected using a data logger and a permutation test, we evaluated
 topographical microhabitat preferences for 21 tree species in a relatively
 undisturbed TPSF in Central Kalimantan, Indonesia, to determine whether
 these species show preferential association with hummocks or hollows and
 to quantify the prevalence of microhabitat specialization among them. Only
 one species, Tetractomia tetrandrum, emerged as a hollow specialist, with
 no hummock specialists among the species tested. The remaining 20 species,
 including Psydrax dicoccos, which had the lowest mean observed elevation,
 and Maasia hypoleuca, which had the highest mean observed elevation,
 showed no clear microtopographic preference. This suggests that many TPSF
 species may be resilient to the natural hydrologic variations that occur
 in relatively intact peat swamp forests. Such studies of microtopographic
 preferences of tree species in TPSF and other wetland forest ecosystems
 can inform selection of tree species for reforestation projects, and
 potentially also provide information on how future climate change may
 impact these habitats and their resident tree species.
description: Microtopographic_TPSFSee README file.
DOI: 10.5061/dryad.7d2m4pp
title: Data from: Age and quality-dependent DNA methylation correlate with melanin-based colouration in a wild bird

description: Secondary sexual trait expression can be influenced by fixed individual
 factors (such as genetic quality) but also by dynamic factors (such as age
 and environmentally induced gene expression) that may be associated with
 variation in condition or quality. In particular, melanin-based traits are
 known to relate to condition and there is a well-characterized genetic
 pathway underpinning their expression. However, the mechanisms linking
 variable trait expression to genetic quality remain unclear. One plausible
 mechanism is that genetic quality could influence trait expression via
 differential methylation and differential gene expression. We therefore
 conducted a pilot study examining DNA methylation at a candidate gene
 (agouti-related neuropeptide: AgRP) in the black grouse Lyrurus tetrix. We
 specifically tested whether CpG methylation covaries with age and
 multilocus heterozygosity (a proxy of genetic quality) and from there
 whether the expression of a melanin-based ornament (UV blue chroma)
 correlates with DNA methylation. Consistent with expectations, we found
 clear evidence for age- and heterozygosity-specific patterns of DNA
 methylation, with two CpG sites showing the greatest DNA methylation in
 highly heterozygous males at their peak age of reproduction. Furthermore,
 DNA methylation at three CpG sites was significantly positively correlated
 with UV blue chroma. Ours is the first study to our knowledge to document
 age- and quality-dependent variation in DNA methylation and to show that
 dynamic sexual trait expression across the lifespan of an organism is
 associated with patterns of DNA methylation. Alhough we cannot demonstrate
 causality, our work provides empirical support for a mechanism that could
 potentially link key individual factors to variation in sexual trait
 expression in a wild vertebrate.
description: Black grouse DNA
 methylation and blue chromaDataset containing
 age-specific DNA methylation and blue chroma for male black
 grouse.DataDryad_grouse
 epigenetics.xlsx
DOI: 10.15468/dl.33bhze
title: Occurrence Download

description: A dataset containing 1164 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (China, Hong Kong, Chinese Taipei)",
 "OccurrenceStatus is Present",
 "TaxonKey is Rattus losea",
 "Year 1970-2024"
 ]
}

 The dataset includes 1164 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001156-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.c3575
title: Data from: Growth and nitrogen uptake characteristics reveal outbreak mechanism of the opportunistic macroalga Gracilaria tenuistipitata

description: Macroalgae has bloomed in the brackish lake of Shenzhen Bay, China
 continuously from 2010 to 2014. Gracilaria tenuistipitata was identified
 as the causative macroalgal species. The aim of this study was to explore
 the outbreak mechanism of G. tenuistipitata, by studying the effects of
 salinity and nitrogen sources on growth, and the different nitrogen
 sources uptake characteristic. Our experimental design was based on
 environmental conditions observed in the bloom areas, and these main
 factors were simulated in the laboratory. Results showed that salinity 12
 to 20 ‰ was suitable for G. tenuistipitata growth. When the nitrogen
 sources' (NH4+, NO3−) concentrations reached 40 µM or above, the
 growth rate of G. tenuistipitata was significantly higher. Algal biomass
 was higher (approximately 1.4 times) when cultured with NH4+ than that
 with NO3− addition. Coincidentally, macroalgal bloom formed during times
 of moderate salinity (~12 ‰) and high nitrogen conditions. The NH4+ and
 NO3− uptake characteristic was studied to understand the potential
 mechanism of G. tenuistipitata bloom. NH4+ uptake was best described by a
 linear, rate-unsaturated response, with the slope decreasing with time
 intervals. In contrast, NO3− uptake followed a rate-saturating mechanism
 best described by the Michaelis-Menten model, with kinetic parameters Vmax
 = 37.2 µM g−1 DM h−1 and Ks = 61.5 µM. Further, based on the isotope 15N
 tracer method, we found that 15N from NH4+ accumulated faster and reached
 an atom% twice than that of 15N from NO3−, suggesting when both NH4+ and
 NO3− were available, NH4+ was assimilated more rapidly. The results of the
 present study indicate that in the estuarine environment, the combination
 of moderate salinity with high ammonium may stimulate bloom formation.
description: PLOS ONE Growth and
 nitrogen uptake characteristics reveal outbreak mechanims of the
 opportunistic macroalga Gracilaria tenuistipitataSalinity effects on RGR
 of Gracilaria tenuistipitata; Nitrogen source effects on RGR of Gracilaria
 ; Nitrogen source uptake characteristic; Nitrogen
 preferencesdata.xls
DOI: 10.7910/dvn/rp7mkp
title: Replication Data for: What Kind of Energy Transition? Public Opinion Trade-Offs between Economic Growth, Ecological Sustainability and Equity

description: This replication material accompanies the article “What Kind of Energy Transition? Public Opinion Trade-Offs among Economic Growth, Ecological Sustainability and Equity” by Natili, Pellegata, and Visconti, published in the European Journal of Political Research. The replication materials allow readers to fully reproduce all empirical results presented in the main text (Figures 2–12) and in the Online Appendix (Figures A1–A8).
DOI: 10.5061/dryad.7117c
title: Data from: Socially cued developmental plasticity in web-building spiders

description: Background: Socially cued anticipatory plasticity (SCAP) has been proposed
 as a widespread mechanism of adaptive life-history shifts in semelparous
 species with extreme male mating investment. Such mating systems evolved
 several times independently in spiders and male reproductive success
 should critically depend on timely maturation and rapid location of a
 receptive and, ideally, virgin female. We experimentally investigated
 socially cued anticipatory plasticity in two sympatric, closely related
 Nephila species that share many components of their mating systems, but
 differ in the degree to which male reproductive success depends on mating
 with virgin females. Juveniles of both species were reared either in the
 presence or absence of virgin female silk cues. We predicted strong
 selection on socially cued plasticity in N. fenestrata in which males
 follow a highly specialized terminal investment strategy, but expected a
 weaker plastic response in N. senegalensis in which males lost the ability
 to monopolize females. Results: Contrary to our predictions, N. fenestrata
 males presented with virgin female silk cues did not mature earlier than
 siblings reared isolated from such cues. Males in N. senegalensis,
 however, showed a significant response to female cues and matured several
 days earlier than control males. Plastic adjustment of maturation had no
 effect on male size. Conclusions: Our results indicate that a strong
 benefit of mating with virgins due to first male sperm priority does not
 necessarily promote socially cued anticipatory plasticity. We emphasize
 the bidirectional mode of developmental responses and suggest that this
 form of plasticity may not only yield benefits through accelerated
 maturation, but also by avoiding costs of precipitate maturation in the
 absence of female cues.
description: Nephila fenestrata
 DURATION dataThis is an original
 dataset providing data on male developmental durations in the study
 species Nephila fenestrata.NF
 DURATION.TXTNephila fenestrata SIZE
 dataThis is an original
 dataset providing data on adult size in the study species Nephila
 fenestrata.NF
 SIZE.TXTNephila fenestrata
 WEIGHT dataThis is an original
 dataset providing data on adult weight in the study species Nephila
 fenestrata.NF
 WEIGHT.TXTNephila senegalensis
 DURATION dataThis is an original
 dataset providing data on male developmental durations in the study
 species Nephila senegalensis.NS
 DURATION.TXTNephila senegalensis
 SIZE dataThis is an original
 dataset providing data on adult size in the study species Nephila
 senegalensis.NS
 SIZE.TXTNephila senegalensis
 WEIGHT dataThis is an original
 dataset providing data on adult weight in the study species Nephila
 senegalensis.NS
 WEIGHT.TXT