cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbch5
title: Data from: Tree diversity effects through a temporal lens: implications for the abundance, diversity, and stability of foraging birds

description: 1. Tree diversity can exert a strong influence on consumers, but most
 studies have involved short-term assessments. Consequently, we have a
 limited understanding of temporal variation in the effects of tree
 diversity on multi-trophic communities and thus how tree diversity impacts
 ecological function. 2. We conducted a year-long study in an experimental
 system in southern Mexico assessing the effects of tree diversity on the
 abundance and diversity of visiting birds. To this end, we recorded bird
 visitation patterns for 32 plots (21 × 21 m; 12 monocultures, 20
 four-species polycultures) every 45 days (n = 8 surveys) and for each plot
 estimated bird abundance, richness, functional diversity (FD), and
 phylogenetic diversity (PD). In each case, we reported temporal
 (intra-annual) variation in the magnitude of such diversity effects, and
 calculated the temporal stability of these bird responses. 3. Across
 surveys, tree diversity noticeably affected bird responses, demonstrated
 by significantly higher abundance (43%), richness (32%), PD (25%), and FD
 (25%) of birds visiting polyculture plots compared to monoculture plots,
 as well as a distinct species composition between plot types. We also
 found some degree of intra-annual variation in diversity effects on these
 response variables, ranging from surveys for which the tree diversity
 effect was not significant to surveys where a significant 80% increase
 (e.g. bird FD and PD) was observed in polyculture relative to monoculture
 plots. Notably, tree diversity increased the stability of all bird
 responses, with polycultures having a greater stability abundance (18%),
 richness (38%), PD (34%), and FD (32%) of birds visiting polycultures
 compared to monocultures. 4. These findings show that tree diversity not
 only increases bird visitation to plots, but also stabilizes bird habitat
 usage over time in ways that could lead to insurance-related mechanisms.
 These results are highly relevant for understanding the long-term effects
 of plant diversity on vertebrates and the persistence of bird-related
 ecosystem functions. Accordingly, more work is needed to unveil the
 ecological mechanisms underlying temporal variation in vertebrate
 responses to tree diversity and their consequences for community structure
 and function.
description: Visual bird surveys were conducted for monoculture and
 polyculture tree plots ca. every 45 days during a one-year period from
 February 2017 to January 2018. Each survey lasted one week, during which
 each plot was observed for 20 minutes on three different occasions during
 that survey. A total of eight surveys were conducted throughout the study
 year.
DOI: 10.5061/dryad.djh9w0vx1
title: Microfluidic droplet application for bacterial surveillance in fresh-cut produce wash waters

description: Foodborne contamination and associated illness in the United States is
 responsible for an estimated 48 million cases per year. Increased food
 demand, global commerce of perishable foods, and the growing threat of
 antibiotic resistance are driving factors elevating concern for food
 safety. Foodborne illness is often associated with fresh-cut, ready-to-eat
 produce commodities due to the perishable nature of the product and
 relatively minimal processing from farm to the consumer. The research
 presented here optimizes and evaluates the utility of microfluidic
 droplets, also termed ultraminiaturized bioreactors, for rapid detection
 of viable Salmonella enterica ser. Typhimurium in a shredded lettuce wash
 water acquired from a major Mid-Atlantic produce processing facility
 (denoted as Producer) in the U.S. Using a fluorescentlylabeled anti- S.
 Typhimurium antibody and relative fluorescence intensities, paired with
 in-droplet incubation, S. Typhimurium was detected and identified with
 100% specificity in less than 5 h. In initial optimization experiments
 using S. Typhimuriumspiked sterile water, the relative fluorescence
 intensity of S. Typhimurium was approximately two times that of the
 observed relative intensities of five non- S. Typhimurium negative
 controls at 4-h incubation in droplets containing Rappaport-Vasiliadis
 (RV) broth at 37 ° C: relative fluorescence intensity for S. Typhimurium =
 2.36 (95% CI: 2.15-2.58), Enterobacter aerogens 1.12 (95% CI: 1.09-1.16),
 Escherichia coli 700609 = 1.13 (95% CI: 1.09-1.17), E. coli 13706 1.13
 (95% CI: 1.07-1.19), E. coli 700891 1.05 (95% CI: 1.03-1.07) and
 Citrobacter freundii 1.04 (95% CI: 1.03-1.05). S. Typhimurium - and E.
 aerogens -spiked shredded lettuce wash waters acquired from the Producer
 were then incubated 4 h in-droplet at 37 ° C with RV broth. The observed
 relative fluorescence of S. Typhimurium was significantly higher than that
 of E. aerogens , 1.56 (95% CI: 1.42-1.71) and 1.10 (95% CI: 1.08-1.12),
 respectively. While further optimization focusing on compatible
 concentration methodologies for highly-dilute produce water samples is
 needed, this application of droplet microfluidics shows great promise in
 dramatically shortening the time necessary – from days to hours – to
 confirm viable bacterial contamination in ready-to-eat produce wash waters
 used throughout the domestic and international food industry.
DOI: 10.5061/dryad.4tmpg4f6j
title: Data from: Estimating dispersal and evolutionary dynamics in diploporan blastozoans (Echinodermata) across the Great Ordovician Biodiversification Event

description: Echinoderms make up a substantial component of Ordovician marine
 invertebrates, yet their speciation and dispersal history as inferred
 within a rigorous phylogenetic and statistical framework is lacking. We
 use Biogeographic Stochastic Mapping (BSM; implemented in the R package
 BioGeoBEARS) to infer ancestral area relationships and the number and type
 of dispersal events through the Ordovician for diploporan blastozoans and
 related species. The BSM analysis was divided into three time slices to
 analyze how dispersal paths changed before and during the Great Ordovician
 Biodiversification Event (GOBE) and within the Late Ordovician mass
 extinction intervals. The best-fit biogeographical model incorporated jump
 dispersal, indicating this was an important speciation strategy.
 Reconstructed areas within the phylogeny indicate the first diploporan
 blastozoans likely originated within Baltica or Gondwana. Dispersal, jump
 dispersal, and sympatry dominated the BSM inference through the
 Ordovician, while dispersal paths varied in time. Long-distance dispersal
 events in the Early Ordovician indicate distance was not a significant
 predictor of dispersal, whereas increased dispersal events between Baltica
 and Laurentia are apparent during the GOBE, indicating these areas were
 important to blastozoan speciation. During the Late Ordovician, there is
 an increase in dispersal events among all paleocontinents. The drivers of
 dispersal are attributed to oceanic and epicontinental currents.
 Speciation events plotted against geochemical data indicate that
 blastozoans may not have responded to climate cooling events and other
 geochemical perturbations, but additional data will continue to shed light
 into the drivers of early Paleozoic blastozoan speciation and dispersal
 patterns.
description: Supplementary 1 contains species and occurrences in an Excel and
 PDF format. Supplementary 2 is a zipfile that contains input files,
 analysis scripts, and output files for the Beast2 and BioGeoBEARS analyses
 performed in Lam et al. It is provided for data archiving purposes, but
 does not constitute a tutorial. Researchers will probably first need
 substantial training/experience in Beast2, R, and BioGeoBEARS to modify
 and re-use these scripts.
DOI: 10.5061/dryad.m905qftxx
title: Data from: Genotype-by-genotype epistasis for exploratory behavior in D. simulans

description: Social interactions can influence the expression and underlying genetic
 basis of many traits. Yet, empirical investigations of indirect genetic
 effects (IGEs) and genotype-by-genotype epistasis—quantitative genetics
 parameters representing the role of genetic variation in a focal
 individual and its interacting partners in producing the observed trait
 values—are still scarce. Studying this social plasticity is notoriously
 challenging when individuals interact in groups, rather than (simpler)
 dyads. Here, we investigate the genetic architecture of social plasticity
 for exploratory behavior, one of the most intensively-studied behaviors in
 recent decades. Using isofemale lines of D. simulans, we measured
 genotypes both alone, and in social groups representing a mix of two
 genotypes. We found that females adjusted their exploratory behavior based
 on the behavior of others in the group, representing social plasticity.
 However, the direction of this plasticity depended on the identity of
 group members: focal individuals adjusted their exploratory behavior to
 match that of group members who were the same genotype as the focal, but,
 changed their exploratory behavior to differentiate from partner-genotype
 group members. Exploratory behavior also depended on the identities of
 both genotypes that composed the group. Together, these findings
 demonstrate genotype-by-genotype epistasis for exploratory behavior both
 within and among groups.
description: Please see manuscript for details on data collection.
description: None
DOI: 10.5061/dryad.tht76hdwn
title: Data from: Anonymous faecal sampling and NIRS studies of diet quality: problem or opportunity?

description: Investigating the drivers of diet quality is a key issue in wildlife
 ecology and conservation. Faecal near infrared reflectance spectroscopy
 (f-NIRS) is widely used to study dietary quality since it allows for
 noninvasive, rapid and low-cost analysis of nutrients. Samples for f-NIRS
 can be collected and analyzed with or without knowledge of animal
 identities. While anonymous sampling allows to reduce the costs of
 individual identification, as it neither requires physical captures nor
 DNA genotyping, it neglects the potential effects of individual variation
 in dietary quality and may suffer severe issues of pseudoreplication. I
 investigated the relationship between crude protein and ecological
 predictors at different time periods to assess the level of individual
 heterogeneity in dietary quality of 22 marked chamois Rupicapra rupicapra
 monitored over two years. Models with and without individual grouping
 effect were fitted to simulate identifiable and anonymous faecal sampling,
 and model estimates were compared to evaluate the consequences of
 anonymizing data collection and analysis. The variance explained by the
 individual random effect and the value of diet repeatability varied with
 seasons and peaked in winter. Despite the occurrence of individual
 variation in dietary quality, ecological parameter estimates under
 identifiable or anonymous sampling were consistently similar. This study
 suggests that anonymous faecal sampling may provide robust estimates of
 the relationship between dietary quality and ecological correlates.
 However, since the level of individual heterogeneity in dietary quality
 may vary with species- or study-specific features, inconsequential
 pseudoreplication should not be assumed in other taxa. When individual
 differences are known to be inconsequential, anonymous sampling allows to
 optimize the trade-off between sampling intensity and representativeness.
 When pseudoreplication is consequential, however, no conclusive remedy
 exists to effectively resolve non-independence.
DOI: 10.5061/dryad.t76hdr7xw
title: Data from: Increased sugar concentration in response to a wide range of pollinator sounds can be adaptive for the plant: Answer to Raguso et al.

description: In Veits et al. we showed that flowers respond to a range of pollinator
 sounds by increased nectar sugar concentration. Here we clarify that (i)
 our argument is relevant to most pollinators, and not limited to bees (ii)
 specifically, bees do access O. Drumondii nectar in this area.
DOI: 10.5281/zenodo.18395244
title: THE HISTORICAL AND PHILOSOPHICAL DEVELOPMENT OF THE RELATIONSHIP BETWEEN KNOWLEDGE AND BELIEF

description: The relationship between knowledge and belief has been a central theme in the history of philosophy, shaping debates in epistemology, religion, science, and ethics. Throughout different historical periods, philosophers have offered diverse interpretations of how knowledge and belief interact, conflict, or complement each other. This article examines the historical and philosophical development of the relationship between knowledge and belief, tracing its evolution from ancient philosophy to modern and contemporary thought. The study highlights key philosophical positions and emphasizes the enduring relevance of this relationship in contemporary intellectual discourse.
DOI: 10.5061/dryad.3xsj3txcm
title: Data from: Plant-soil feedback contributes to predicting plant invasiveness of 68 alien plant species differing in invasive status

description: Understanding what species characteristics allow some alien plants to
 become invasive while others fail is critical to our understanding of
 community assembly processes. While many characteristics have been shown
 to predict plant invasiveness, the importance of plant-soil feedback (PSF)
 in invasions has been difficult to assess since individual studies include
 only a few species and use disparate methodology. We studied PSF of 68
 invasive and non-invasive alien species in a single two-phase common
 garden experiment, and compared the relative importance of PSF, residence
 time, phylogenetic novelty and plant traits for plant invasiveness.
 Additionally, we explored relationships between PSF, residence time and
 phylogenetic novelty. PSF for seedling establishment, but not for biomass,
 was a significant predictor of invasive status, with invasive species
 having more positive PSF than non-invasive species. Its explanatory power
 was, however, much lower than that of specific leaf area, height, and
 residence time. Phylogenetically novel species experienced less negative
 PSF than species with native congeners, suggesting they benefit more from
 enemy release. PSF of non-invasive species, contrary to that of invasive
 species, was becoming more negative with increasing residence time. We
 demonstrated that PSF for seedling establishment plays a role in
 predicting plant invasiveness and is a better predictor than more commonly
 studied PSF for plant biomass. Other species traits, such as specific leaf
 area, however, predict plant invasiveness much better than the PSF.
description: Intraspecific plant-soil feedback of 68 alien species differing
 in their invasive status in the Czech Republic was assessed using a two
 phase garden experiment. We compared plant performance (seedling
 establishment, biomass) of the plants in the second experimental phase
 when grown in self-conditioned soil and in control (unconditioned)
 soil. Plant-soil feedback index was calculated as ln(x/s) where x is performance
 of each individual plant when grown in the conditioned soil and s is
 performance of a plant grown in a paired control pot. For each species, we
 also measured specific leaf area and we gathered data on other plant
 traits used for explaining plant invasiveness as well as on species
 comonness in the Czech Republic, their phylogenetic relatedness to native
 Czech flora and residence time in the Czech Republic from published
 literature and databases. We used the data for assessing the importance of
 plant-soil feedback for plant invasiveness and for determining the
 relationships between plant-soil feedback, phylogenetic relatedness and
 residence time.  
description: For more details
 on the experimental design and data collection please refer to Aldorfová
 et al. (2020),10.1111/oik.07186.
DOI: 10.5281/zenodo.18395243
title: THE HISTORICAL AND PHILOSOPHICAL DEVELOPMENT OF THE RELATIONSHIP BETWEEN KNOWLEDGE AND BELIEF

description: The relationship between knowledge and belief has been a central theme in the history of philosophy, shaping debates in epistemology, religion, science, and ethics. Throughout different historical periods, philosophers have offered diverse interpretations of how knowledge and belief interact, conflict, or complement each other. This article examines the historical and philosophical development of the relationship between knowledge and belief, tracing its evolution from ancient philosophy to modern and contemporary thought. The study highlights key philosophical positions and emphasizes the enduring relevance of this relationship in contemporary intellectual discourse.
DOI: 10.5061/dryad.612jm6411
title: Data from: Salty, mild, and low plant biomass grasslands increase top-heaviness of invertebrate trophic pyramids

description: Aim Multiple hypotheses predict how gradients of nutrient availability,
 plant biomass, and temperature shape trophic pyramids. We aim to
 disentangle the simultaneous influence of those different factors and
 their indirect effects on trophic structure and individual trophic levels.
 Location United States Time period 2017 Major taxa studied Invertebrates
 Methods To examine differences in trophic pyramid shape and abundance
 within trophic levels across ecological gradients, we used a structural
 equation modeling approach to analyze 54 standardized surveys of
 invertebrate communities in North American grasslands. We tested for the
 direct and indirect effects of plant biomass, temperature, sodium (Na),
 other essential elements (e.g. N, P and K), and toxic heavy metals, (e.g.
 Ar and Pb) in plant tissue on individual trophic levels as well as on the
 global trophic pyramid shape estimated as the Community Trophic Mean
 (CTM). Results Plant sodium increased CTM, indicating that high plant
 sodium concentrations are associated with top-heavy invertebrate trophic
 pyramids. Increased plant biomass resulted in higher proportions of
 herbivores compared to higher trophic levels. Finally, increasing
 temperature resulted in more top-heavy trophic pyramids, although effects
 were weaker than those of plant-related factors. Overall, plant biomass,
 temperature and plant chemistry directly and indirectly affected the
 abundances within different trophic levels, highlighting the complexity of
 factors regulating trophic structure. Main conclusions Trophic structure
 of grassland invertebrate communities is strongly influenced by plant
 sodium, plant biomass, and to a lesser extent, temperature. Grasslands
 occupy 30% of the Earth’s terrestrial surface and are an imperiled
 ecosystem due to conversion to row crop agriculture. As biogeochemistry
 and temperature in the Anthropocene are increasingly modified, our results
 have considerable implications for the trophic structure of future
 grassland communities.
description: See metadata sheet in data file.
DOI: 10.5061/dryad.v9s4mw6s1
title: Individual and population fitness consequences associated with large carnivore use of residential development

description: Large carnivores are negotiating increasingly developed landscapes, but
 little is known about how such behavioral plasticity influences their
 demographic rates and population trends. Some investigators have suggested
 that the ability of carnivores to behaviorally adapt to human development
 will enable their persistence, and yet, others have suggested that such
 landscapes are likely to serve as population sinks or ecological traps. To
 understand how plasticity in black bear (Ursus americanus) use of
 residential development influences their population dynamics, we conducted
 a 6 year study near Durango, Colorado, USA. Using space-use data on
 individual bears, we examined the influence of use of residential
 development on annual measures of bear body fat, cub productivity, cub
 survival and adult female survival, after accounting for variation in
 natural food availability and individual attributes (e.g., age). We then
 used our field-based vital rate estimates to parameterize a matrix model
 that simulated asymptotic population growth for bears using residential
 development to different degrees. We found that bear use of residential
 development was highly variable within and across years, with bears
 increasing their foraging within development when natural foods were
 scarce. Increased bear use of development was associated with increased
 body fat and cub productivity, but reduced cub and adult survival. When
 these effects were simultaneously incorporated into a matrix model we
 found that the population was projected to decline as bear use of
 development increased, given that the costs of reduced survival outweighed
 the benefits of enhanced productivity. Our results provide a mechanistic
 understanding of how black bear use of residential development
 exerts opposing effects on different bear fitness traits and a negative
 effect on population growth, with the magnitude of those effects mediated
 by variation in environmental conditions. They also highlight the
 importance of monitoring bear population dynamics, particularly as shifts
 in bear behavior are likely to drive increases in human-bear conflicts and
 the perception of growing bear populations. Finally, our work emphasizes
 the need to consider the demographic viability of large carnivore
 populations when promoting the coexistence of people and carnivores on
 shared landscapes.
description: Excel file with different worksheets for data used to model black
 bear fitness traits (body fat, cub productivity, cub survival, and adult
 female survival). The first worksheet ("DataDescriptions")
 contains data definitions.
DOI: 10.5061/dryad.sqv9s4n1d
title: Population decline of a long-distance migratory passerine at the edge of its range: nest predation, nest replacement, and immigration

description: The relative importance of predators and resources (i.e., food) for the
 dynamics of migratory bird populations is poorly known. Resource
 availability may be more likely in resource poor environments, but given
 that nest failure in most systems is due mainly to predation, predator
 effects may predominate. We document a rapid decline of an isolated
 Eastern Kingbird (Tyrannus tyrannus) population breeding in the Great
 Basin Desert of eastern Oregon, USA, and evaluate whether it was driven by
 limited food resources (water availability ~ food), nest predation, or
 first-year or adult return rate (RRJ and RRA, respectively) that reflect
 nonbreeding season events. Most nests failed (~68% of nests) due mainly to
 nest predation (&gt;90% of failures); nestling starvation was rare.
 Bioyear precipitation (October-April), breeding season precipitation, and
 river flow all varied widely but none could account for annual variation
 in either nest success (NS) or fledging success of successful nest (FSSN).
 Neither RRJ nor RRA varied with year, any measure of water resources, or
 reproductive success. Annual population growth rate (ln[Nt+1/Nt]) was
 independent of year, all measures of water availability, RRJ and RRA, and
 NS of replacement nests, but was high following years of high NS of
 initial nests; FSSN was also higher in years of high NS. High rates of
 nest predation, due likely to the expansion of the local American Crow
 (Corvus brachyrhynchos) population, appeared to drive the population
 decline. Empirical data and population simulations indicated that
 replacement nests contributed little to λ, while simulations revealed
 that, given site-specific vital rates, the decline would have been even
 greater without immigration (λ = 0.812) than the observed (λ = 0.914).
 Long distance dispersal may thus be critical for persistence of kingbirds
 in the naturally highly fragmented habitat that it occupies in the Great
 Basin Desert.