cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7md1755
title: Data from: No evidence that warmer temperatures are associated with selection for smaller body sizes

description: Reductions in animal body size over recent decades are often interpreted
 as an adaptive evolutionary response to climate warming. However, for
 reductions in size to reflect adaptive evolution, directional selection on
 body size within populations must have become negative, or, where already
 negative, more so, as temperatures increased. To test this hypothesis, we
 performed a meta-analysis of the association between annual estimates of
 directional selection on body size from wild populations and annual mean
 temperatures in 39 studies. We found no evidence that warmer environments
 were associated with selection for smaller size. Instead, selection
 consistently favoured larger individuals, and was invariant to
 temperature. These patterns were similar in ectotherms and endotherms. An
 analysis using year rather than temperature revealed similar patterns,
 suggesting no evidence that selection has changed over time, and also
 indicating that the lack of association with annual temperature was not an
 artefact of choosing an erroneous time window for aggregating the
 temperature data. Although phenotypic trends in size will be driven by a
 combination of genetic and environmental factors, our results suggest
 little evidence for a necessary ingredient - negative directional
 selection - for declines in body size to be considered an adaptive
 evolutionary response to changing selection pressures.
description: Supplemental code and
 dataThe files contained here
 are as follows: seln_diffs_SEs_size_animals.csv – this is the key data
 file including the study id, species, name, year, population, dataset (see
 main text for description), latitude and longitude, selection
 differentials (estSelCoef), standard errors (seSelCoef), taxon
 (invertebrate or vertebrate), a finer naming of taxa, trait class, and
 temperature data (raw temperatures, and standardized temperatures), and
 therm (denoting ectotherm or endotherm), for the analyses.
 seln_grads_SEs_size_animals.csv – this is the key data file including the
 study id, species, name, year, population, dataset (see main text for
 description), latitude and longitude, selection gradients (estSelCoef),
 standard errors(seSelCoef), taxon (invertebrate or vertebrate), a finer
 naming of taxa, trait class, and temperature data (raw temperatures, and
 standardized temperatures), and therm (denoting ectotherm or endotherm),
 for the analyses. animal taxa.nex – a nexus file of the phylogeny used in
 the phylogenetic random regression. Siepielski temperature selection R
 commands.Rmd – this is the main analysis file. To run this code all of the
 above files should be in the same directory. Analysis_selection_dbase.csv
 – the complete database of selection coefficients.
DOI: 10.5061/dryad.84bq56t
title: Data from: A Grinnellian niche perspective on species-area relationships

description: In this work, Grinnellian niche theory (a body of theory about geographic
 distributions of species in terms of non-interacting niche variables) is
 used to demonstrate that species-area relationships emerge with both size
 of environmental space and size of geographic area. As environmental space
 increases, more species' fundamental niches are included, thus
 increasing the number of species capable of living in the corresponding
 region. This idea is made operational by proposing a size measure for
 multidimensional environmental space and approximating fundamental niches
 with minimum-volume ellipsoids. This framework allows estimating a
 presence-absence matrix based on the distribution of fundamental niches in
 environmental space, from which many biodiversity measures can be
 calculated, such as beta diversity. I establish that Whittaker’s equation
 for beta diversity is equivalent to MacArthur’s formula relating species
 numbers and niche breadth; this latter equation provides a mechanism for
 the species niche-space relationship. I illustrate the theoretical results
 via exploration of niches of the terrestrial mammals of North America
 (north of Panama). Each world region has a unique structure of its
 environmental space, and the position of fundamental niches in niche space
 is different for different clades; therefore, species-area relationships
 depend on the clades involved and the region of focus, mostly as a
 function of MacArthur’s niche beta diversity. Analyzing species-area
 relationships from the perspective of niche position in environmental
 space is novel, shifting emphasis from demographic processes to
 historical, geographic, and climatic factors; moreover, the Grinnellian
 approach is based on available data and is computationally feasible.
description: GBIF_Thinned_2A flat file of 70299 records of terrestrial mammals of Panama to Canada, containing the Global Biodiversity Information Facility and IUCN taxonomies, the decimal latitude and longitudes of each observation, and the values of four bioclimatic variables for each pair of unique coordinates. Please see README file for further details.
DOI: 10.5061/dryad.n98q8s3
title: Data from: Nest site selection and nest survival of Black-backed Woodpeckers after wildfire

description: Recently burned coniferous forests host wildlife communities that respond
 to variation in burn severity, post-fire habitat structure, and patch
 configuration. Habitat selection theory predicts that birds inhabiting
 these variable post-fire landscapes will select nesting locations that
 confer an adaptive advantage through increased fitness and reproductive
 success. Understanding the effect of post-fire habitat on avian nesting
 ecology can provide valuable information to guide restoration and
 management after wildfire. The Black-backed Woodpecker (Picoides arcticus)
 is strongly associated with recently burned forests in the western U.S.,
 where it is used as an indicator species for the effects of post-fire
 forest management. Between 2011 and 2018, we located and monitored 118
 Black-backed Woodpecker nests in burned forests of northern California. We
 evaluated the influence of habitat and nest characteristics on nest site
 selection and daily nest survival. Our results demonstrate a pattern of
 neutral congruence between habitat selection and fitness. Black-backed
 Woodpeckers showed strong selection for each of the nest habitat variables
 that we measured: woodpeckers selected moderately-sized trees in areas of
 high snag density burned at high severity, but also in areas relatively
 close to low severity or unburned edges. However, only nest initiation
 date affected nest survival, with decreased survival in late-season nests.
 Our results suggest that management actions aimed at maintaining breeding
 habitat for Black-backed Woodpeckers should prioritize retention and
 creation of pyrodiverse landscapes that include dense stands of snags
 (&gt;5 snags/100 m2) within ~500 m of forest that burned at low
 severity or remained unburned.
description: READMEDescription of data and
 variables for each .csv fileNest_Habitat_DataRaw data collected at each nest site.Nest_Survival_DataInput data for the nest survival analysis.Nest_Stand_SelectionInput data for the nest stand selection analysis.Nest_Tree_SelectionInput data for the nest tree selection analysis.
DOI: 10.5061/dryad.bs78391
title: Data from: Adrenalectomy completely cured hypertension in familial hyperaldosteronism type I patients with somatic KCNJ5 mutation

description: Context: Familial hyperaldosteronism type I or glucocorticoid-remediable
 aldosteronism (FH-I; GRA) is caused by unequal crossing-over of the
 steroid 11β-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2)
 genes. Somatic KCNJ5 mutations have not been reported in patients with
 GRA; therefore, the appropriate treatment and prognosis of such concurrent
 cases remain unknown. Case description: Two siblings of a Taiwanese family
 with GRA were found to have adrenal adenomas and somatic KCNJ5 mutations.
 Complete clinical cure was achieved after unilateral adrenalectomy.
 Furthermore, the conversion site of the chimeric gene was identified by
 direct sequencing. Conclusions: We report for the first time the
 coexistence of a somatic KCNJ5 mutation and GRA. GRA patients whose blood
 pressure management develops resistance to glucocorticoid treatment could
 therefore benefit from a lateralization test. The promising outcomes after
 unilateral adrenalectomy presented in this report offer new perspectives
 for further research into various PA subtypes.
description: Supplementary_MaterialSupplementary Table 1. Adrenal vein sampling results of the proband. Supplementary Figure 1: Changes in plasma aldosterone concentration (PAC), plasma renin activity (PRA), aldosterone renin ratio (ARR), and blood pressure in the proband and younger brother . Supplementary Figure 2. The pedigree of the family.Supplementary Table 2. Baseline characteristics of the two patients
DOI: 10.5061/dryad.7h95044
title: Data from: Early emergence increases survival of tree seedlings in Central European temperate forests despite severe late frost

description: Global warming is expected to result in earlier emergence of tree
 seedlings that may experi-ence higher damages and mortality due to late
 frost in spring. We monitored emergence, characteristics and survival of
 seedlings across ten tree species in temperate mixed deciduous forests of
 Central Europe over one and a half year. We tested whether the timing of
 emergence represents a trade-off for seedling survival between mini-mising
 frost risk and maximising the length of the growing period. Almost
 two-thirds of the seedlings died during the first growing period. The
 timing of emer-gence was decisive for seedling survival. Although
 seedlings that emerged early faced a se-vere late frost event, they
 benefited from a longer growing period resulting in increased overall
 survival. Larger seedling height and higher number of leaves positively
 influenced survival. Seedlings growing on moss had higher survival
 compared to mineral soil, litter or herbaceous vegetation. Synthesis. Our
 findings demonstrate the importance of emergence time for survival of tree
 seedlings, with early emerging seedlings more likely surviving the first
 growing period.
description: Data
DOI: 10.5061/dryad.bj3t434
title: Data from: Genetic structure at three spatial scales is consistent with limited philopatry in Ricord’s Rock Iguanas (Cyclura ricordii)

description: Cyclura ricordii is an endemic iguana from Hispaniola Island and is
 threatened on the IUCN Red List. The main threats are predation by
 introduced mammals, habitat destruction, and hunting pressure. The present
 study focused on two nesting sites from Pedernales Province in the
 Dominican Republic. The hypothesis that natal philopatry influences
 dispersal and nest site selection was tested. Monitoring and sampling took
 place in 2012 and 2013. Polymorphic markers were used to evaluate whether
 natal philopatry limits dispersal at multiple spatial scales. Ripley’s K
 revealed that nests were significantly clustered at multiple scales, when
 both nesting sites were considered and within each nesting site. This
 suggests a patchy, non-random distribution of nests within nest sites.
 Hierarchical AMOVA revealed that nest site aggregations did not explain a
 significant portion of genetic variation within nesting sites. However, a
 small but positive correlation between geographic and genetic distance was
 detected using a Mantel’s test. Hence, the relationship between geographic
 distance and genetic distance among hatchlings within nest sites, while
 detectable, was not strong enough to have a marked effect on fine scale
 genetic structure. Spatial and genetic data combined determined that the
 nesting sites included nesting females from multiple locations, and the
 hypothesis of ‘natal philopatry’, was not supported because females
 nesting in the same cluster were no more closely related to each other
 than to other females from the same nesting site. These findings imply
 that nesting aggregations are more likely associated with cryptic habitat
 variables contributing to optimal nesting conditions.
description: Genotypes_Dominican
 Republic_ReptilThe data file contains
 genotypes of Cyclura ricordii using 13 nuclear microsatellite loci.
 Individual sample origin is from the wild. Two Excel sheets are included,
 one for Adult individuals genotypes from two separate locations (CAB,
 Cabritos Island; PED, Pedernales Province) in the Dominican Republic. The
 second sheet contains the genotypes of hatchlings for the same species and
 markers from two nesting sites in Pedernales Province (TIE, Tierra; and
 MAL, Malagueta). Individual labels include one decimal place to refer to
 the origin of hatchlings from the same nest. The data is in Genalex format
 in Excel which I later use to convert to other formats such as Arlequin
 and Genepop input files.
DOI: 10.5061/dryad.77447g3
title: Data from: Plant traits and species interactions along gradients of N, P and K availabilities

description: 1. Plant performance is driven by nutrient availability. So far, studies
 on plant nutrient relationships mostly focused on nitrogen (N) and
 phosphorus (P), whereas potassium (K) received less attention. We
 evaluated whether plant responses to variation in nutrient availability is
 similar or different for the nutrients N, P and K and whether the same
 plant traits are decisive for the competitive ability of species along
 gradients of N, P and K availabilities. 2. We studied plant trait
 responses of three temperate perennial grass species (Alopecurus
 pratensis, Agrostis capillaris and Anthoxanthum odoratum, each dominant
 under N limitation, P limitation and K limitation, respectively). Each
 gradient consisted of eight treatments (N1-N8, P1-P8, K1-K8), with N:P:K
 supply rates being 1:0.8:6 (N1), 128:0.8:6 (N8), 12:0.075:6 (P1), 12:9.6:6
 (P8), 12:0.8:0.56 (K1) and 12:0.8:72 (K8) (total supply per plant
 individual in mg). Plant individuals were kept either in single-species
 pots (intraspecific competition) or in mixed species pots (interspecific
 competition). After two months, plant biomass, leaf and root traits and
 root enzyme activity were measured. 3. Most belowground traits (e.g. total
 root length, root diameter) responded most strongly to competition as
 predictor variable and only secondly to the type of nutrient or their
 supply rates (unlike RGRTotal and SLA). Leaf chlorophyll content and root
 enzyme activity responded most strongly to supply rate of nutrients and
 the interaction of nutrient type and supply rate, respectively. In line
 with our prediction A. pratensis was the superior competitor under N
 limitation and A. odoratum was the superior competitor under K limitation
 (assessed by relative dominance (RD) and relative competitive strength
 (RCS)). Both species showed high investment in total root length. Opposite
 to our expectation, A. capillaris was a bad competitor under P limitation,
 with low root length but higher root phosphatase activity. 4. Our results
 indicate that belowground plant traits are decisive in nutrient-related
 competition between plant species. Further, competitive strength is
 determined by a total high root length per soil volume both under N and K
 limitation. Under P limitation the model species A. capillaris showed a
 weak competitive performance either because it was lacking colonization
 with mycorrhiza and/or the high investment in phosphatase activity posed a
 trade-off with higher N investment in phosphatase production.
description: Dryad - NPK
 ExperimentMetadata (species names,
 functional groups) and information on experimental design (type of varied
 nutrient). Dates of start and end of the experiment for each pot. Measured
 traits with units.
DOI: 10.5061/dryad.3282cq2
title: Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales

description: Social animals that live in domiciles constructed from biomaterials may
 facilitate microbial growth. Spider webs are one of the most conspicuous
 biomaterials in nature, yet almost nothing is known about the potential
 for webs to harbor microbes, even in social spiders that live in dense,
 long-term aggregations. Here, we tested whether the dominant bacteria
 present in social spider webs vary across sampling localities and whether
 the more permanent retreat web harbors compositionally distinct microbes
 from the more ephemeral capture webs in the desert social spider
 Stegodyphus dumicola. We also sampled spider cuticles and prey items in a
 subset of colonies. We found that spider colonies across large spatial
 scales harbored similar web-associated bacterial communities. We also
 found substantial overlap in bacterial community composition between
 spider cuticle, prey, and web samples. These data suggest that social
 spider webs can harbor characteristic microbial communities and
 potentially facilitate microbial transmission among individuals, and this
 study serves as the first step towards understanding the microbial ecology
 of these peculiar animal societies.
description: Keiser et al -
 Stegodyphus colony microbiome metadata - TEXT FILEKeiser et al - Stegodyphus
 colony microbiomes -
 rep_set_zotus_filt_relabeled.faKeiser et al -
 Stegodyphus colony microbiome metadata - zotutab_wTaxKeiser et al -
 Stegodyphus colony microbiome metadata - TEXT FILE
DOI: 10.5061/dryad.57c0420
title: Data from: Migration distance does not predict blood parasitism in a migratory songbird

description: Migration can influence host-parasite dynamics in animals by increasing
 exposure to parasites, by reducing the energy available for immune
 defence, or by culling of infected individuals. These mechanisms have been
 demonstrated in several comparative analyses; however, few studies have
 investigated whether conspecific variation in migration distance may also
 be related to disease susceptibility. Here, we ask whether autumn
 migration distance, inferred from stable hydrogen isotope analysis of
 summer-grown feathers (δ2Hf) in Europe, correlates with blood parasite
 prevalence and intensity of infection for willow warblers (Phylloscopus
 trochilus) wintering in Zambia. We also investigated whether infection was
 correlated with individual condition (assessed via corticosterone, scaled
 mass index, and feather quality). We found that 43% of birds were infected
 with Haemoproteus palloris (lineage WW1). Using generalized linear models,
 we found no relationship between migration distance and either
 Haemoproteus infection prevalence or intensity. There was spatial
 variation in breeding ground origins of infected vs. non-infected birds,
 with infected birds originating from more northern sites than non-infected
 birds, but this difference translated into only slightly longer estimated
 migration distances (~214 km) for infected birds. We found no relationship
 between body condition indices and Haemoproteus infection prevalence or
 intensity. Our results do not support any of the proposed mechanisms for
 migration effects on host-parasite dynamics, and cautiously suggest that
 other factors may be more important for determining individual
 susceptibility to disease in migratory bird species.
description: Wintering ground data
 from migratory willow warblersThis file contains data
 collected from migratory willow warblers (Phylloscopus trochilus) on their
 wintering grounds in Zambia. Data includes malaria prevalence and
 intensity, feather quality variables, corticosterone, stable hydrogen
 isotope analysis of feathers (H), and body size
 measurements.Sorensenetal_EcolEvol_data.csv
DOI: 10.5061/dryad.j6n470c
title: Data from: Inferring new relations between medical entities using literature curated term co-occurrences

description: ABSTRACT Objectives Identifying new relations between medical entities,
 such as drugs, diseases, and side-effects, is typically a
 resource-intensive task, involving experimentation and clinical trials.
 The increased availability of related data and curated knowledge enables a
 computational approach to this task, notably by training models to predict
 likely relations. Such models rely on meaningful representations of the
 medical entities being studied. We propose a generic features vector
 representation that leverages co-occurrences of medical terms, linked with
 PubMed citations. Materials and Methods We demonstrate the usefulness of
 the proposed representation by inferring two types of relations: a drug
 causes a side effect, and a drug treats an indication. To predict these
 relations and assess their effectiveness, we applied two modeling
 approaches: multi-task modeling using neural networks, and single-task
 modeling based on gradient-boosting machines and logistic regression.
 Results These trained models, which predict either side effects or
 indications, obtained significantly better results than baseline models
 that use a single direct co-occurrence feature. The results demonstrate
 the advantage of a comprehensive representation. Discussion Selecting the
 appropriate representation has an immense impact on the predictive
 performance of machine learning models. Our proposed representation is
 powerful, as it spans multiple medical domains and can be used to predict
 a wide range of relation types. Conclusion The discovery of new relations
 between various medical entities can be translated into meaningful
 insights, for example, related to drug development or disease
 understanding. Our representation of medical entities can be used to train
 models that predict such relations, thus accelerating healthcare-related
 discoveries.
description: CID_to_MeSH_mappingA mapping between PubChem Compound ID (CID) to one or more MeSH terms.
DOI: 10.5061/dryad.364j18m
title: Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus

description: Anthozoans are a class of Cnidarians that includes scleractinian corals,
 anemones and their relatives. Despite a global rise in disease epizootics
 impacting scleractinian corals, little is known about the immune response
 of this key group of invertebrates. To better characterize the anthozoan
 immune response, we used the model anemone Exaiptasia pallida to explore
 the genetic links between the anthozoan-algal symbioses and immunity in a
 two-factor RNA-Seq experiment using both symbiotic and
 aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial
 pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of
 Exaiptasia gene expression demonstrated that exposure to live Vibrio
 coralliilyticus had strong and significant impacts on transcriptome-wide
 gene expression for both symbiotic and aposymbiotic anemones, but we did
 not observe strong interactions between symbiotic state and Vibrio
 exposure. There were 4,164 significantly differentially expressed (DE)
 genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE
 genes for the additive combinations of Vibrio and aposymbiosis. KEGG
 enrichment analyses identified 11 pathways - involved in immunity (5),
 transport and catabolism (4) and cell growth and death (2) - that were
 enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing
 strongest differential expression included complement, coagulation,
 nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio
 exposure and coagulation and apoptosis for aposymbiosis.
description: S1 - DESeq2
 OutputThe DESeq2 output of a
 two-factor RNA-Seq experiment comparing the immune response of symbiotic
 and aposymbiotic Exaiptasia pallida to immune challenge with Vibrio
 Coralliilyticus.S1.xlsx