cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7296h
title: Data from: Nest decoration as social signals by males and females: greenery and feathers in starling colonies

description: The expression of elaborated displays provides reliable information to
 conspecifics about the quality of the signaler. Competition for breeding
 resources or mates is predicted to affect the expression of signals in
 both males and females; however, the literature has been typically focused
 on male behaviors. The spotless starling is an interesting example where
 both sexes decorate the nest to signal their condition and social status:
 males add green plants at the beginning of the breeding period, and
 females place foreign feathers during the incubation period. In this
 study, we investigate nest decoration by males and females in relation to
 the intensity of conspecific competition during the breeding period. We
 distributed nest boxes at either a high (HD) or a low density (LD) and
 recorded the amount of green plant material added before laying, the
 number of feathers at hatching, and the breeding productivity under these
 different density treatments. The amount of green plant material and the
 number of feathers at hatching were higher in HD than in LD nests.
 Furthermore, nest boxes at higher density had lower breeding productivity.
 Our results suggest that manipulating the density of nest boxes increased
 competition for breeding resources. The aggregation of males competing for
 territories and mates may stimulate them to add greater amounts of plants,
 and competition over those males or other resources for reproduction may
 induce females to add feathers. This study shows that social environment
 has the potential to influence the expression of signaling behaviors in
 both males and females.
description: Rubalcaba_etal
DOI: 10.5061/dryad.b5s87dt
title: Data from: Comparison of the validity of the checklist assessment in the cardiac arrest simulations with the app in an academic hospital in Taiwan: a retrospective observational study

description: Background: Robust assessment is a crucial component in Advanced Cardiac
 Life Support (ACLS) training to determine whether participants have
 achieved learning objectives with little or no variation in their overall
 outcomes. This study aimed to evaluate resuscitation performance by
 real-time logs. We hypothesized that instructors may not be able to
 evaluate time-sensitive parameters, namely, chest compression fraction,
 time to initiating chest compression, and time to initiating
 defibrillation efficiently in a subjective manner. Methods: Video records
 and formal checklist-based test results of Megacode scenarios for the ACLS
 certification examination at several hospitals in Taipei were examined.
 For the study interest, three time-sensitive parameters were measured via
 video review assisted by a mobile phone application, and were used for
 evaluation. We evaluated if the pass/fail results made by instructors via
 checklists were correlated with these parameters. Results: A total of 185
 Megacode scenarios were eligible for the final analysis. Among the three
 parameters, good chest compression fraction was statistically significant
 with higher odds ratio (OR) of passing (OR = 3.65; 95% confidence interval
 [CI]: 1.36-9.91; P = 0.01). In 112 participants with one parameter that
 did not meet the criteria, 25 were graded as fail, making the specificity
 22.3% (95% CI: 15.0-31.2%). Conclusions: Visual observation of
 cardiopulmonary resuscitation performance is not accurate when evaluating
 time-sensitive parameters. Objective results should be offered for
 training outcome evaluation, and also for feedback to participants.
description: ACLS
 results
DOI: 10.15468/dl.vf4rc2
title: Occurrence Download

description: A dataset containing 100266 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amphibalanus"
 ]
}

 The dataset includes 100266 records from 334 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001125-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.62p1q
title: Data from: Environmental correlates of the Late Quaternary regional extinctions of large and small Palaearctic mammals

description: Most studies of mammal extinctions during the Pleistocene–Holocene
 transition explore the relative effects of climate change vs. human
 impacts on these extinctions, but the relative importance of the different
 environmental factors involved remains poorly understood. Moreover, these
 studies are strongly biased towards megafauna, which may have been more
 influenced by human hunting than species of small body size. We examined
 the potential environmental causes of Pleistocene–Holocene mammal
 extinctions by linking regional environmental characteristics with the
 regional extinction rates of large and small mammals in 14 Palaearctic
 regions. We found that regional extinction rates were larger for
 megafauna, but extinction patterns across regions were similar for both
 size groups, emphasizing the importance of environmental change as an
 extinction factor as opposed to hunting. Still, the bias towards megafauna
 extinctions was larger in Southern Europe and smaller in central Eurasia.
 The loss of suitable habitats, low macroclimatic heterogeneity within
 regions and an increase in precipitation were identified as the strongest
 predictors of regional extinction rates. Suitable habitats for many
 species of the Last Glacial fauna were grassland and desert, but not
 tundra or forest. The low-extinction regions identified in central Eurasia
 are characterized by the continuous presence of grasslands and deserts
 until the present. In contrast, forest expansion associated with an
 increase in precipitation and temperature was likely the main factor
 causing habitat loss in the high-extinction regions. The shift of
 grassland into tundra also contributed to the loss of suitable habitats in
 northern Eurasia. Habitat loss was more strongly related to the
 extinctions of megafauna than of small mammals. Ungulate species with low
 tolerance to deep snow were more likely to go regionally extinct. Thus,
 the increase in precipitation at the Pleistocene–Holocene transition may
 have also directly contributed to the extinctions by creating deep snow
 cover which decreases forage availability in winter.
description: Data_Pavelkova_Ricankova_et_al_2017_EcographyA matrix of occurrences of 346 mammal species in 14 Palaearctic regions in the Last Glacial and the Recent period.
DOI: 10.5061/dryad.g743c
title: Data from: Natural selection on immune defense: a field experiment

description: Predicting the evolution of phenotypic traits requires an understanding of
 natural selection on them. Despite its indispensability in the fight
 against parasites, selection on host immune defense has remained
 understudied. Theory predicts immune traits to be under stabilizing
 selection due to associated trade-offs with other fitness-related traits.
 Empirical studies, however, report mainly positive directional selection.
 This discrepancy could be caused by low phenotypic variation in the
 examined individuals and/or variation in host resource level that
 confounds trade-offs in empirical studies. In a field experiment where we
 maintained Lymnaea stagnalis snails individually in cages in a lake, we
 investigated phenotypic selection on two immune defense traits,
 phenoloxidase (PO)-like activity and antibacterial activity, in hemolymph.
 We used a diverse laboratory population and manipulated snail resource
 level by limiting their food supply. For six weeks, we followed immune
 activity, growth, and two fitness components, survival and fecundity of
 snails. We found that PO-like activity and growth were under stabilizing
 selection, while antibacterial activity was under positive directional
 selection. Selection on immune traits was mainly driven by variation in
 survival. The form of selection on immune defense apparently depends on
 the particular trait, possibly due to its importance for countering the
 present parasite community.
description: data
DOI: 10.5061/dryad.j2654
title: Data from: Development and characterization of 15 polymorphic di-nucleotide microsatellite markers for tule elk using HiSeq3000

description: The tule elk (Cervus elaphus nannodes) experienced a severe bottleneck in
 the 1800s, resulting in low genetic diversity. There is a need for
 high-resolution genetic assays that can be used to differentiate
 individual elk, including close relatives, with high confidence. An
 efficient assay requires multiple markers both polymorphic and that can be
 amplified in concert with other markers in multiplex reactions. To develop
 such markers, we employed 150-bp paired-end whole genome shotgun
 sequencing on an Illumina HiSeq3000 platform to discover dinucleotide
 microsatellite markers. After preliminary screening of these markers, we
 selected and screened 15 candidate loci and 5 existing tetra nucleotide
 markers in 56 tule elk. We combined these markers in 2 multiplex reactions
 and report primer concentrations and PCR conditions enabling their
 efficient amplification.
description: Metadata and genotypes
 for tule elk and contigs containing microsatellitesMetadata and genotypes
 for tule elk and contigs containing microsatellites4Dryad_25Aug2016.xlsx
DOI: 10.5061/dryad.8dc26
title: Data from: Color patterns of closely-related bird species are more divergent at intermediate levels of breeding range sympatry

description: Closely related species of birds often differ markedly in their color
 patterns. Here we examine the influence of breeding-range overlap
 (breeding sympatry) on the evolution of color pattern differences in a
 sample of closely related bird species. We used a sister-lineage method to
 analyze 73 phylogenetically independent comparisons among 246 species and
 39 families of birds worldwide. We found that divergence of color patterns
 among closely related species was greater between sympatric than between
 allopatric lineages, but only at intermediate levels of sympatry (50%–80%
 breeding-range overlap). This pattern suggests that closely related
 species incur costs at intermediate levels of sympatry if they exhibit
 similar color patterns—costs that could include hybridization,
 interspecific aggression, competition for signaling space, or ecological
 interactions that secondarily influence color patterns. The decline in
 color pattern divergence with further increase in sympatry suggests either
 the relaxation of divergent selection, increased impediment of gene flow,
 or an increased role for counteracting selection at higher levels of
 sympatry. We also found that the differences in color pattern between
 sympatric and allopatric sister species were greatest at lower latitudes.
 The global scale and broad taxonomic coverage in our study suggest that
 the divergence of color patterns between sympatrically breeding closely
 related species is widespread in birds.
description: color.pattern.dataData set for color pattern divergence analyses of birds.color.pattern.R.codeR code for color pattern divergence analyses of birds.color.pattern.R
DOI: 10.15468/dl.9ubys4
title: Occurrence Download

description: A dataset containing 7931 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Andromeda polifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 7931 records from 253 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001196-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2440v
title: Data from: Microbial diversity in the floral nectar of Linaria vulgaris along an urbanization gradient

description: Background: Microbes are common inhabitants of floral nectar and are
 capable of influencing plant-pollinator interactions. All studies so far
 investigated microbial communities in floral nectar in plant populations
 that were located in natural environments, but nothing is known about
 these communities in nectar of plants inhabiting urban environments.
 However, at least some microbes are vectored into floral nectar by
 pollinators, and because urbanization can have a profound impact on
 pollinator communities and plant-pollinator interactions, it can be
 expected that it affects nectar microbes as well. To test this hypothesis,
 we related microbial diversity in floral nectar to the degree of
 urbanization in the late-flowering plant Linaria vulgaris. Floral nectar
 was collected from twenty populations along an urbanization gradient and
 culturable bacteria and yeasts were isolated and identified by partially
 sequencing the genes coding for small and large ribosome subunits,
 respectively. Results: A total of seven yeast and 13 bacterial operational
 taxonomic units (OTUs) were found at 3 and 1 % sequence dissimilarity
 cut-offs, respectively. In agreement with previous studies, Metschnikowia
 reukaufii and M. gruessi were the main yeast constituents of nectar yeast
 communities, whereas Acinetobacter nectaris and Rosenbergiella epipactidis
 were the most frequently found bacterial species. Microbial incidence was
 high and did not change along the investigated urbanization gradient.
 However, microbial communities showed a nested subset structure,
 indicating that species-poor communities were a subset of species-rich
 communities. Conclusions: The level of urbanization was putatively
 identified as an important driver of nestedness, suggesting that
 environmental changes related to urbanization may impact microbial
 communities in floral nectar of plants growing in urban environments.
description: Microbial OTUs in L.
 vulgaris nectarThis dataset details the
 operational taxonimic units (OTUs) found in individual plants or
 populations of Linaria vulgaris across an urbanization gradient. Moreover,
 it also contains NMDS coordinates for every population.Bartlewicz_dataset_Microbes_in_Linaria_nectar.xlsx
DOI: 10.5061/dryad.3k15h
title: Data from: Convergent adaptation to dangerous prey proceeds through the same first-step mutation in the garter snake Thamnophis sirtalis

description: Convergent phenotypes often result from similar underlying genetics, but
 recent work suggests convergence may also occur in the historical order of
 substitutions en route to an adaptive outcome. We characterized
 convergence in the mutational steps to two independent outcomes of
 tetrodotoxin (TTX) resistance in separate geographic lineages of the
 common garter snake (Thamnophis sirtalis) that coevolved with toxic newts.
 Resistance is largely conferred by amino acid changes in the skeletal
 muscle sodium channel (NaV1.4) that interfere with TTX-binding. We sampled
 variation in NaV1.4 throughout western North America and found clear
 evidence that TTX-resistant changes in both lineages began with the same
 isoleucine-valine mutation (I1561V) within the outer pore of NaV1.4. Other
 point mutations in the pore, shown to confer much greater resistance,
 accumulate later in the evolutionary progression and always occur together
 with the initial I1561V change. A gene tree of NaV1.4 suggests the I1561V
 mutations in each lineage are not identical-by-decent, but rather they
 arose independently. Convergence in the evolution of channel resistance is
 likely the result of shared biases in the two lineages of Th. sirtalis –
 only a few mutational routes can confer TTX resistance while maintaining
 the conserved function of voltage-gated sodium channels.
description: Bayesian consensus
 tree.tre file from the
 partitioned Bayesian analysis in MrBayes.MrBayes_BI.treMaximum likelihood consensus tree.tre file from the partitioned maximum likelihood analysis in RAxML.RAxML_ML.trePhenotypic TTX resistance dataPhysiological TTX resistance data of populations assayed for the first time in this study.50MAMU.csv
DOI: 10.5061/dryad.8175
title: Data from: Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus)

description: Pathogen-driven balancing selection maintains high genetic diversity in
 many vertebrates, particularly in the major histocompatibility complex
 (MHC) immune system gene family, which is often associated with disease
 susceptibility. In large natural populations where subpopulations face
 different pathogen pressures, the MHC should show greater genetic
 differentiation within a species than neutral markers. We examined genetic
 diversity at the MHC-DQB locus and nine putatively neutral microsatellite
 markers in grey seals (Halichoerus grypus) from eight United Kingdom
 colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles
 were identified in grey seals, which varied in prevalence across the grey
 seal range. Among the seal colonies, significant differences in DQB allele
 and haplotype frequencies and in average DQB heterozygosity were observed.
 Additionally, the DQB gene exhibited greater differentiation among
 colonies compared with neutral markers, yet a weaker pattern of
 isolation-by-distance. After correcting for the underlying
 isolation-by-distance pattern, subpopulations breeding in similar habitats
 were more similar to one another in DQB allele frequencies than
 populations breeding in different habitats, but the same did not hold true
 for microsatellites, suggesting that habitat-specific pathogen pressure
 influences MHC evolution. Overall, the data are consistent with selection
 at MHC-DQB loci in grey seals with both varying selective pressures and
 geographic population structure appearing to influence the DQB genetic
 composition of breeding colonies.
description: DQBdataGrey seal haplotype data for exon 2 of the DQB MHC locus, generated using single strand conformation polymorphism (SSCP). Includes: breeding colony where sample was collected, sample ID, and presence(1)/absence(0) of SSCP alleles A, B, C, and D.
DOI: 10.5061/dryad.j33k3
title: Data from: Genetic evidence for landscape effects on dispersal in the army ant Eciton burchellii

description: Inhibited dispersal, leading to reduced gene flow, threatens populations
 with inbreeding depression and local extinction. Fragmentation may be
 especially detrimental to social insects because inhibited gene flow has
 important consequences for cooperation and competition within and among
 colonies. Army ants have winged males and permanently wingless queens;
 these traits imply male-biased dispersal. However, army ant colonies are
 obligately nomadic and have the potential to traverse landscapes. Eciton
 burchellii, the most regularly nomadic army ant, is a forest interior
 species: colony raiding activities are limited in the absence of forest
 cover. To examine whether nomadism and landscape (forest clearing and
 elevation) affect population genetic structure in a montane E. burchellii
 population we reconstructed queen and male genotypes from 25 colonies at
 seven polymorphic microsatellite loci. Pairwise genetic distances among
 individuals were compared to pairwise geographic and resistance distances
 using regressions with permutations, partial Mantel tests, and random
 forests analyses. Though there was no significant spatial genetic
 structure in queens or males in montane forest, dispersal may be
 male-biased. We found significant isolation by landscape resistance for
 queens based on land cover (forest clearing), but not on elevation. Summed
 colony emigrations over the lifetime of the queen may contribute to gene
 flow in this species and forest clearing impedes these movements and
 subsequent gene dispersal. Further forest cover removal may increasingly
 inhibit Eciton burchellii colony dispersal. We recommend maintaining
 habitat connectivity in tropical forests to promote population persistence
 for this keystone species.
description: MEC-13-0399_DRYAD_worker
 genotypesGenotypes at 7
 microsatellite loci for army ant colony workers collected in and around
 Monteverde, Costa Rica.
DOI: 10.5061/dryad.bt816
title: Data from: High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds

description: Yellow, orange, and red coloration is a fundamental aspect of avian
 diversity and serves as an important signal in mate choice and aggressive
 interactions. This coloration is often produced through the deposition of
 diet-derived carotenoid pigments, yet the mechanisms of carotenoid uptake
 and transport are not well-understood. The white recessive breed of the
 common canary (Serinus canaria), which carries an autosomal recessive
 mutation that renders its plumage pure white, provides a unique
 opportunity to investigate mechanisms of carotenoid coloration. We carried
 out detailed genomic and biochemical analyses comparing the white
 recessive with yellow and red breeds of canaries. Biochemical analysis
 revealed that carotenoids are absent or at very low concentrations in
 feathers and several tissues of white recessive canaries, consistent with
 a genetic defect in carotenoid uptake. Using a combination of genetic
 mapping approaches, we show that the white recessive allele is due to a
 splice donor site mutation in the scavenger receptor B1 (SCARB1; also
 known as SR-B1) gene. This mutation results in abnormal splicing, with the
 most abundant transcript lacking exon 4. Through functional assays, we
 further demonstrate that wild-type SCARB1 promotes cellular uptake of
 carotenoids but that this function is lost in the predominant mutant
 isoform in white recessive canaries. Our results indicate that SCARB1 is
 an essential mediator of the expression of carotenoid-based coloration in
 birds, and suggest a potential link between visual displays and lipid
 metabolism.
description: Individual SNP
 genotypesIndividual genotypes
 from 24 individuals from the White recessive breed, 39 individuals from
 three breeds of red canary (Lipochrome red, n = 25; Portuguese Harlequin,
 n = 9; Black red, n = 5) and 22 individuals from four breeds of yellow
 canary (Lipochrome yellow, n = 5; Waterslager, n = 3; Gibber italicus, n =
 10; Black yellow, n = 4). We used 39 SNPs located within and flanking our
 candidate region – 38 randomly chosen from the whole genome resequencing
 data plus the splice-donor site mutation detected in
 SCARB1.SNP
 White Canary Genotypes.xlsx
DOI: 10.6084/m9.figshare.31156774
title: Data and code for: Evidence for chronotypes and associations with fitness related traits in a wild insect

description: Data and R code supporting the analyses of chronotype variation (beginning and end of activity, activity window) and their associations with predation risk, mating success, and lifespan in a wild insect.
DOI: 10.6084/m9.figshare.31156774.v1
title: Data and code for: Evidence for chronotypes and associations with fitness related traits in a wild insect

description: Data and R code supporting the analyses of chronotype variation (beginning and end of activity, activity window) and their associations with predation risk, mating success, and lifespan in a wild insect.