cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q35vj22
title: Data from: Species-specific plant–soil feedbacks alter herbivore-induced gene expression and defense chemistry in Plantago lanceolata

description: Plants actively interact with antagonists and beneficial organisms
 occurring in the above- and belowground domains of terrestrial ecosystems.
 In the past decade, studies have focused on the role of plant–soil
 feedbacks (PSF) in a broad range of ecological processes. However, PSF and
 its legacy effects on plant defense traits, such as induction of
 defense-related genes and production of defensive secondary metabolites,
 have not received much attention. Here, we study soil legacy effects
 created by twelve common grassland plant species on the induction of four
 defense-related genes, involved in jasmonic acid signaling, related to
 chewing herbivore defense (LOX2, PPO7), and in salicylic acid signaling,
 related to pathogen defense (PR1 and PR2) in Plantago lanceolata in
 response to aboveground herbivory by Mamestra brassicae. We also assessed
 soil legacy and herbivory effects on the production of terpenoid defense
 compounds (the iridoid glycosides aucubin and catalpol) in P. lanceolata.
 Our results show that both soil legacy and herbivory influence phenotypes
 of P. lanceolata in terms of induction of Pl PPO7 and Pl LOX2, whereas the
 expression of Pl PR1 and Pl PR2-1 is not affected by soil legacies, nor by
 herbivory. We also find species-specific soil legacy effects on the
 production of aucubin. Moreover, P. lanceolata accumulates more catalpol
 when they are grown in soils conditioned by grass species. Our study
 highlights that PSF can influence aboveground plant–insect interactions
 through the impacts on plant defense traits and suggests that aboveground
 plant defense responses can be determined, at least partly, by
 plant-specific legacy effects induced by belowground organisms.
description: Zhu et al 2018
 OecologiaGene expression data
 (sheet1), plant and herbivore performance data and chemistry data
 (sheet2)
DOI: 10.5061/dryad.mv352kc
title: Data from: Experimental evidence that density mediates negative frequency-dependent selection on aggression

description: 1. Aggression can be beneficial in competitive environments if aggressive
 individuals are more likely to access resources than non-aggressive
 individuals. However, variation in aggressive behaviour persists within
 populations, suggesting that high levels of aggression might not always be
 favoured. 2. The goal of this study was to experimentally assess the
 effects of population density and phenotypic frequency on selection on
 aggression in a competitive environment. 3. We compared survival of two
 strains of Drosophila melanogaster that differ in aggression across three
 density treatments and five frequency treatments (single strain groups,
 equal numbers of each strain, and strains mixed at 3:1 and 1:3 ratios)
 during a period of limited resources. 4. While there was no difference in
 survival across single-strain treatments, survival was strongly
 density-dependent, with declining survival as density increased.
 Furthermore, at medium and high densities, there was evidence of negative
 frequency-dependent selection, where rare strains experienced greater
 survival than common strains. However, there was no evidence of negative
 frequency-dependent selection at low density. 5. Our results indicate that
 the benefits of aggression during periods of limited resources can depend
 on the interaction between the phenotypic composition of populations and
 population density, both of which are mechanisms that could maintain
 variation in aggressive behaviours within natural populations.
description: Survival data across
 density and frequencyThese data were
 collected in the laboratory. They are the data used in Experiment 1.
 Details for this dataset and all datasets can be found in the README
 file.Kilgour_et_al_2018_Survival_Data.csvDifferences in aggression between two strains of Drosophila melanogasterThese data were collected in the laboratory and were used in Experiment 2 of the manuscript.Kilgour_et_al_2018_Strain_Differences_Aggro.csvSurvival data from Experiment 2These data were collected in the laboratory. They were used to assess negative frequency-dependent selection in the Experiment 2.Kilgour_et_al_2018_Strain_Survival_Aggro_Assay.csvFruit fly mass by StrainThese data were collected in the laboratory. Results to the associated analysis are found in the Supporting Information. They were used to assess any differences in mass between the strains across sex and time.Kilgour_et_al_2018_Strain_Differences_Mass.csvReproductive differences between strains of fruit fliesThese data were collected in the laboratory. They were used to assess any differences in reproductive output between the strains used in our experiment.Kilgour_et_al_2018_Strain_Differences_Repro.csvR Code for analyses in Kilgour et al. 2018This document represents all code used for the statistical analyses in our study.Kilgour_et_al_2018_Code_Experiment_evidence_of_NFDS.txt
DOI: 10.5061/dryad.dm383
title: Data from: Tales from the crypt: a parasitoid manipulates the behaviour of its parasite host

description: There are many examples of apparent manipulation of host phenotype by
 parasites, yet few examples of hypermanipulation—where a
 phenotype-manipulating parasite is itself manipulated by a parasite.
 Moreover, few studies confirm manipulation is occurring by quantifying
 whether the host's changed phenotype increases parasite fitness. Here
 we describe a novel case of hypermanipulation, in which the crypt gall
 wasp Bassettia pallida (a phenotypic manipulator of its tree host) is
 manipulated by the parasitoid crypt-keeper wasp Euderus set, and show that
 the host's changed behaviour increases parasitoid fitness. Bassettia
 pallida parasitizes sand live oaks and induces the formation of a ‘crypt’
 within developing stems. When parasitized by E. set, B. pallida adults
 excavate an emergence hole in the crypt wall, plug the hole with their
 head and die. We show experimentally that this phenomenon benefits E. set,
 as E. set that need to excavate an emergence hole themselves are about
 three times more likely to die trapped in the crypt. In addition, we
 discuss museum and field data to explore the distribution of the
 crypt-keeping phenomena.
description: Tales From The Crypt
 Analyses Updated 3.19.17R Code for all
 analysesTales from the Crypt
 Manipulation analysisData from the experiment
 on whether the crypt-keeping phenomenon benefits Euderus
 set.Tales From The Crypt
 Hole Diameter AnalysisData from the analysis
 examining difference in excavation hole diameter between holes created by
 infected and uninfected Bassettia pallida. Description of analysis found
 in the Supplementary Files.
DOI: 10.5061/dryad.60mk699
title: Data from: Linking a mutation to survival in wild mice

description: Adaptive evolution in new or changing environments can be difficult to
 predict because the functional connections between genotype, phenotype,
 and fitness are complex. Here, we make these explicit connections by
 combining field and laboratory experiments in wild mice. We first directly
 estimate natural selection on pigmentation traits and an underlying
 pigment locus, Agouti, by using experimental enclosures of mice on
 different soil colors. Next, we show how a mutation in Agouti associated
 with survival causes lighter coat color through changes in its protein
 binding properties. Together, our findings demonstrate how a sequence
 variant alters phenotype and then reveal the ensuing ecological
 consequences that drive changes in population allele frequency, thereby
 illuminating the process of evolution by natural selection.
description: Field data from mouse
 enclosure experimentSampling, phenotype, and
 survival data from mouse enclosure experiment conducted in Nebraska, USA.
 Column IDs as follows: id: Individual mouse identification number date:
 Date that mouse was introduced to enclosures type: Habitat type that mouse
 was sampled from. Light = light substrate, Dark = dark substrate.
 location: Sampling location for mouse. site: Experimental treatment of
 enclosure that mouse was introduced to. D = dark substrate, L = light
 substrate. enc: Enclosure that mouse was introduced to. sex: Sex of mouse
 age: Age of mouse. A = adult, S = subadult, J = juvenile. DF_BriCon:
 Principal component score corresponding to the brightness and contrast of
 dorsal/flank pigmentation. DF_ChrHue: Principal component score
 corresponding to the chroma and hue of dorsal/flank pigmentation.
 V_BriCon: Principal component score corresponding to the brightness and
 contrast of ventral pigmentation. DF_Hue: Principal component score
 corresponding to the hue of dorsal/flank pigmentation. V_ChrHue: Principal
 component score corresponding to the chroma and hue of ventral
 pigmentation. DV: Dorsal ventral pigmentation boundary. TP: Tail
 pigmentation pattern. surv1: Survival of mouse from time point 0 to time
 point 1. 0 = dead. 1 = alive. surv2: Survival of mouse from time point 1
 to time point 2. 0 = dead. 1 = alive. surv3: Survival of mouse from time
 point 2 to time point 3. 0 = dead. 1 = alive.Mouse.csv
DOI: 10.15468/dl.62s8qy
title: Occurrence Download

description: A dataset containing 1081 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Deutzia parviflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1081 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001049-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pc54g
title: Data from: We'll meet again: revealing distributional and temporal patterns of social contact

description: What are the dynamics and regularities underlying social contact, and how
 can contact with the people in one's social network be predicted? In
 order to characterize distributional and temporal patterns underlying
 contact probability, we asked 40 participants to keep a diary of their
 social contacts for 100 consecutive days. Using a memory framework
 previously used to study environmental regularities, we predicted that the
 probability of future contact would follow in systematic ways from the
 frequency, recency, and spacing of previous contact. The distribution of
 contact probability across the members of a person's social network
 was highly skewed, following an exponential function. As predicted, it
 emerged that future contact scaled linearly with frequency of past
 contact, proportionally to a power function with recency of past contact,
 and differentially according to the spacing of past contact. These
 relations emerged across different contact media and irrespective of
 whether the participant initiated or received contact. We discuss how the
 identification of these regularities might inspire more realistic analyses
 of behavior in social networks (e.g., attitude formation, cooperation).
description: Social contact data in
 humanspachur_etal_plosone.zip
DOI: 10.5061/dryad.q6v0g
title: Data from: Development of resurgent and persistent sodium currents in mesencephalic trigeminal neurons

description: Sodium channels play multiple roles in the formation of neural membrane
 properties in mesencephalic trigeminal (Mes V) neurons and in other neural
 systems. Mes V neurons exhibit conditional robust high-frequency spike
 discharges. As previously reported, resurgent and persistent sodium
 currents (INaR and INaP, respectively) may carry small currents at
 subthreshold voltages that contribute to generation of spike firing. These
 currents play an important role in maintaining and allowing high-frequency
 spike discharge during a burst. In the present study, we investigated the
 developmental changes in tetrodotoxin-sensitive INaR and INaP underlying
 high-frequency spike discharges in Mes V neurons. Whole-cell patch-clamp
 recordings showed that both current densities increased one and a half
 times from postnatal day 0-6 neurons to postnatal day 7-14 neurons.
 Although these neurons do not exhibit subthreshold oscillations or burst
 discharges with high-frequency firing, INaR and INaP do exist in Mes V
 neurons at postnatal day 0-6. When the spike frequency at rheobase was
 examined in firing Mes V neurons, the developmental change in firing
 frequency among P7 to P14 neurons was significant. INaR and INaP density
 at −40 mV also increased significantly among P7 to P14 neurons. The change
 to an increase in excitability in the P7-14 group could result from this
 quantitative change in INaP. In neurons older than P7 that exhibit
 repetitive firing, quantitative increases in INaR and INaP density may be
 major factors that facilitate and promote high-frequency firing as a
 function of age in Mes V neurons.
description: dryad data
 enomotoprimary data (R and P
 enomoto)
DOI: 10.5061/dryad.c2k5t
title: Data from: A novel protocol for studying bee cognition in the wild

description: 1.Understanding how animals perceive, learn and remember stimuli is
 critical for understanding both how cognition is shaped by natural
 selection, and how ecological factors impact behaviour. However, the
 majority of studies on cognition involve captive animals in laboratory
 settings. While controlled settings are required to accurately measure
 aspects of cognition, they may not yield realistic estimates of learning
 performance in natural environments. Wild bees offer a useful system in
 which to study cognitive ecology as well as comparative cognition more
 broadly: they encompass around 20,000 species globally, varying in
 characteristics such as life history strategy, degree of sociality, and
 dietary specialization. Yet the limited number of protocols currently
 available for studying insect cognition has restricted research to a few
 commercially available bee species, in almost exclusively lab settings.
 2.We present a protocol (Free-Moving Proboscis Extension Response [FMPER])
 to measure wild bees’ colour preferences, learning performance, and
 memory. 3.We first used lab-reared bumblebees Bombus impatiens to
 establish that FMPER yielded results consistent with learning theory. We
 then successfully tested wild honeybees Apis mellifera in the lab, and
 Bombus vosnesenskii at field sites. 4. FMPER is straightforward to
 implement, low-cost, and may be readily adapted to other flower-visiting
 insects. We believe it will be useful to a broad range of evolutionary
 biologists, behavioural ecologists, and pollination ecologists interested
 in measuring cognitive performance in the wild and across a broader range
 of species.
description: behaviour and spectral
 data for Muth et al 2017behaviour and spectral
 data for Muth et al 2017: A novel protocol for studying bee cognition in
 the wildMuth et al_Dryad
 data.xlsx
DOI: 10.5061/dryad.46n26
title: Data from: Tree phylogenetic diversity promotes host–parasitoid interactions

description: Evidence from grassland experiments suggests that a plant community's
 phylogenetic diversity (PD) is a strong predictor of ecosystem processes,
 even stronger than species richness per se. This has, however, never been
 extended to species-rich forests and host–parasitoid interactions. We used
 cavity-nesting Hymenoptera and their parasitoids collected in a
 subtropical forest as a model system to test whether hosts, parasitoids,
 and their interactions are influenced by tree PD and a comprehensive set
 of environmental variables, including tree species richness. Parasitism
 rate and parasitoid abundance were positively correlated with tree PD. All
 variables describing parasitoids decreased with elevation, and were,
 except parasitism rate, dependent on host abundance. Quantitative
 descriptors of host–parasitoid networks were independent of the
 environment. Our study indicates that host–parasitoid interactions in
 species-rich forests are related to the PD of the tree community, which
 influences parasitism rates through parasitoid abundance. We show that
 effects of tree community PD are much stronger than effects of tree
 species richness, can cascade to high trophic levels, and promote trophic
 interactions. As during habitat modification phylogenetic information is
 usually lost non-randomly, even species-rich habitats may not be able to
 continuously provide the ecosystem process parasitism if the
 evolutionarily most distinct plant lineages vanish.
description: Dataset for Staab et
 al., Tree phylogenetic diversity...A description of the
 data is provided in the attached ReadMe document.
DOI: 10.5061/dryad.2s4g5
title: Data from: Ignoring spatial effects results in inadequate models for variation in littoral macroinvertebrate diversity

description: Studies focusing on the effects of spatial processes versus environmental
 filtering on aquatic metacommunities have so far been focused almost
 entirely on relatively isolated systems, such as sets of different lakes
 or streams. In contrast, metacommunity patterns and underlying processes
 within a single aquatic system have received less attention. In this
 study, we aimed to examine how strongly variations in different diversity
 indices are affected by spatial processes (dispersal) versus local
 environmental conditions (species sorting) within a large lake system.
 Modern biodiversity research focuses on multiple diversity facets because
 different indices may be uncorrelated within and between facets, and they
 may thus describe different phenomena. We investigated the relationship of
 littoral macroinvertebrate diversity with environmental and spatial
 factors using 10 indices of species, functional and taxonomic diversity.
 Using spatial factors as proxies of dispersal, we decomposed variation in
 diversity indices into fractions attributable to environmental and spatial
 factors. Our results highlighted generally equal or higher importance of
 spatial processes in controlling the variation in diversity indices when
 compared to local environmental variables. Local environmental conditions
 accounted for higher proportion of variation only in a single index (i.e.
 taxonomic diversity). These findings suggest that the effects of high
 dispersal rates (mass effects) may override the influences of local
 environmental conditions (species sorting) on the diversity in
 highly-connected aquatic system, such as large lakes and marine coastal
 systems. Our results further suggest that biodiversity assessment and
 environmental monitoring in highly-connected systems cannot rely solely on
 the idea of environmental control. We hence recommend that the roles of
 both environmental and spatial processes should be integrated in basic and
 applied ecological research of aquatic systems.
description: Tolonen et al. 2016
 OIK-03587 coordinates, environmental variables and diversity
 indicesData used in the paper
 published in Oikos "Tolonen et al. Ignoring spatial effects results
 in inadequate models for variation in littoral macroinvertebrate
 diversity. DOI: 10.1111/oik.03587." including geographic coordinates
 of the sampling sites, environmental variable measurements and diversity
 indices at each sampling site.Tolonen et al. 2016 OIK-03587
 env_macroinv_diversity.xlsx
DOI: 10.5061/dryad.h24r6
title: Data from: Attitude and subjective well being of non-compliant mothers to childhood oral polio vaccine supplemental immunization in Northern Nigeria

description: Introduction: Attitude and subjective well-being are important factors in
 mothers accepting or rejecting Oral Polio Vaccine (OPV) supplemental
 immunization. The purpose of the study was to determine the role of
 mothers’ attitude and subjective wellbeing on non-compliance to OPV
 supplemental immunization in Northern Nigeria. Methods: The study utilized
 a cross-sectional design to assess attitude and subjective well-being of
 mothers using previously validated VACSATC (Vaccine Safety, Attitudes,
 Training and Communication-10 items) & SUBI (Subjective Well-being
 Inventory-40 items) measures. A total of 396 participants (equal number of
 non-compliant and compliant mothers) from 94 non-compliant settlements
 were interviewed, after informed consent. T-test was run to assess
 difference in mean scores between the non-compliant and compliant mothers
 on VACSATC and SUBI measures. Results: The research showed a significant
 difference in mean scores between the non-compliant and compliant groups
 on VACSATC measure of mothers’ attitude (M=18.9 non-compliant, compared to
 26.5 compliant; p &lt; 0.05). On subjective well-being, the study
 showed there was no significant difference in the mean scores of the SUBI
 measure (M=77.4 non-compliant, compared to 78.0 compliant; p &gt;
 0.05). Conclusion: The research has shown that negative attitude is more
 commonly present in non-compliant mothers and may be a factor in vaccine
 refusal in Northern Nigeria.
description: Polio
 Research_1Primary data of the
 research stored in SPSS version 20Polio_Research_Updated.sav
DOI: 10.5061/dryad.h39n1
title: Data from: DNA recovery from wild chimpanzee tools

description: Most of our knowledge of wild chimpanzee behaviour stems from fewer than
 10 long-term field sites. This bias limits studies to a potentially
 unrepresentative set of communities known to show great behavioural
 diversity on small geographic scales. Here, we introduce a new genetic
 approach to bridge the gap between behavioural material evidence in
 unhabituated chimpanzees and genetic advances in the field of primatology.
 The use of DNA analyses has revolutionised archaeological and
 primatological fields, whereby extraction of DNA from non-invasively
 collected samples allows researchers to reconstruct behaviour without ever
 directly observing individuals. We used commercially available forensic
 DNA kits to show that termite-fishing by wild chimpanzees (Pan troglodytes
 schweinfurthii) leaves behind detectable chimpanzee DNA evidence on tools.
 We then quantified the recovered DNA, compared the yield to that from
 faecal samples, and performed an initial assessment of mitochondrial and
 microsatellite markers to identify individuals. From 49 termite-fishing
 tools from the Issa Valley research site in western Tanzania, we recovered
 an average of 52 pg/µl chimpanzee DNA, compared to 376.2 pg/µl in faecal
 DNA extracts. Mitochondrial DNA haplotypes could be assigned to 41 of 49
 tools (84%). Twenty-six tool DNA extracts yielded &gt;25 pg/µl DNA and
 were selected for microsatellite analyses; genotypes were determined with
 confidence for 18 tools. These tools were used by a minimum of 11
 individuals across the study period and termite mounds. These results
 demonstrate the utility of bio-molecular techniques and a primate
 archaeology approach in non-invasive monitoring and behavioural
 reconstruction of unhabituated primate populations.
description: DNA recovery from
 chimpanzee toolsFile contains chimpanzee
 tool sample, genotyping, and DNA quantification dataDyradData.xlsx