cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n76td
title: Data from: The hawk-dove game in a sexually reproducing species explains a colorful polymorphism of an endangered bird

description: The hawk–dove game famously introduced strategic game theory thinking into
 biology and forms the basis of arguments for limited aggression in animal
 populations. However, aggressive ‘hawks’ and peaceful ‘doves’, with
 strategies inherited in a discrete manner, have never been documented in a
 real animal population. Thus, the applicability of game-theoretic
 arguments to real populations might be contested. Here, we show that the
 head-colour polymorphism of red and black Gouldian finches (Erythrura
 gouldiae) provides a real-life example. The aggressive red morph is
 behaviourally dominant and successfully invades black populations, but
 when red ‘hawks’ become too common, their fitness is severely compromised
 (via decreased parental ability). We also investigate the effects of
 real-life deviations, particularly sexual reproduction, from the simple
 original game, which assumed asexual reproduction. A protected
 polymorphism requires mate choice to be sufficiently assortative.
 Assortative mating is adaptive for individuals because of genetic
 incompatibilities affecting hybrid offspring fitness, but by allowing red
 ‘hawks’ to persist, it also leads to significantly reduced population
 sizes. Because reductions in male contributions to parental care are
 generally known to lead to lower population productivity in birds, we
 expect zero-sum competition to often have wide ranging population
 consequences.
description: Table
 S4A-BSurvival data of
 offspring
DOI: 10.5061/dryad.rt280
title: Data from: Rare events of massive plant reproductive investment lead to long-term density-dependent reproductive success

description: 1. The level of reproductive investment and density and distance dependent
 (DDD) processes are major determinants of plant reproductive output. The
 reproductive investment of a plant population varies temporally, but
 whether and how density- and distance-dependent processes are affected by
 population-level reproductive investment is a puzzle. 2. We used a
 spatially explicit approach in order to examine DDD effects on Sorbus
 acuparia crop sizes for a continuous period of 16 years. Our special
 interest was to investigate whether and how DDD processes affect long-term
 individual plant reproductive success (PRS) and whether such processes
 vary between years of relatively high and low population-level
 reproductive investment, measured as fruit crop size. 3. Our study
 revealed that DDD processes of fruit crop relate to population level
 reproductive investment. In most years, including all years with low and
 most years with moderate reproductive investment, no positive or negative
 DDD was found for PRS. However, significant negative density-dependent
 effects were found during most years of high and some years of moderate
 reproductive investment. During these years, the individual reproductive
 success decreased with increasing density of conspecifics. 4. The overall
 accumulated long-term negative density-dependent pattern of PRS was
 determined by few sporadic years of high reproductive investment, rather
 than by the most frequent years of low or moderate reproductive
 investment, when the DDD effects were usually weak. 5. Synthesis. Our
 study highlights the ecological relevance of relatively infrequent
 processes which affect PRS, stressing thus the importance of long-term
 ecological research.
description: Fruit
 productionThe study was done in a
 subalpine old-growth spruce forest in Babia Góra National Park in the
 Western Carpathians (southern Poland). We established a 27-hectare plot
 representing subalpine spruce forest on the north slope of the Babia Góra
 massif. From 2000 to 2015, all reproductive trees (n = 242-367) were
 searched for fruits at the beginning of September.
DOI: 10.5061/dryad.0qk1h
title: Data from: Interpreting ELISA analyses from wild animal samples: some recurrent issues and solutions

description: 1. Many studies in disease and immunological ecology rely on the use of
 assays that quantify the amount of specific antibodies (immunoglobulin) in
 samples. Enzyme-Linked Immuno Sorbent Assays (ELISAs) are increasingly
 used in ecology due to their availability for a broad array of antigens
 and the limited amount of sampling material they require. Two recurrent
 methodological issues are nevertheless faced by researchers: (i) the
 limited availability of immunological assays and reagents developed for
 non-model species, and (ii) the statistical determination of the cut-off
 threshold used to distinguish individual samples that are likely to have
 or not to have antibodies against a specific antigen. 2. Here, we outline
 two solutions to deal with these issues. First, we show that implementing
 two assays with differing detection methods can help validate the use of
 reagents, such as antibodies, in species different from their intended
 target. We illustrate this by comparing the quantification of specific
 vaccinal antibodies against Newcastle Disease Virus (NDV) using two ELISA
 approaches in four seabird species (Cory’s shearwater, European shag,
 European storm petrel, and Southern rockhopper penguin). 3. Second, we
 provide a simple way to determine from the distribution of ELISA values
 whether the assayed samples are likely to be made of a single group of
 individuals (likely negative) or of two groups of individuals (negative
 and positive). We illustrate the use of this approach with two independent
 datasets: NDV antibody levels following vaccination and anti-Borrelia
 antibody levels following natural exposure. 4. The practical
 implementation of these methodological approaches could provide a way to
 efficiently apply ELISAs and other immune-based assays to address
 questions in the growing fields of ecological immunology and disease
 ecology.
description: Data used to compare
 ELISA techniquesThis file includes all
 the data used to produce Figure 1. Species are included both as full names
 and a shorthand used in the provided code. ELISA results are reported as
 PI (competition ELISA) and as SP (indirect ELISA).Data_comparison_ELISA.csvData used to statistically estimate a cut-off in vaccinated birdsThis file includes the data used to produce figure 2A. The vaccination status is provided as an indication (but not used for the statistical approach), and the ELISA result is provided in the PI column.Data_Cutoff_NDV.csvData use to statistically estimate a cut-off in serological analyses of wild birds exposed to BorreliaThis file includes the data used to produce figure 2B. The species name is included in both scientific and regular formats. All birds are adult, as shown in the age column. The ELISA result is provided as an optical density in the OD column.Data_Cutoff_Borrelia.csv
DOI: 10.5061/dryad.1fv8372
title: Data from: An experimental study on coflow diffusion combustion in a pellet-packed bed with different bed lengths

description: In experimental investigations on axial symmetry, over-ventilated CH4/air
 diffusion combustion in a packed bed is executed to study the height,
 shape, and stability of the flame. The combustor is a quartz tube packed
 with alumina pellets in which a cylindrical fuel stream is surrounded by a
 coflow air nozzle. The results show that the bed length and pellet
 diameter have a significant influence on the flame properties. In general,
 the flame above the pellet surface has axial symmetry, and its shape and
 color are similar to those of a conventional diffusion flame when the bed
 length is smaller. The color of the flame front varies with the bed
 length. The changed color indicates an increased flame-front temperature
 and that the combustion regime above the bed surface may change from
 non-premixed combustion to partially premixed combustion or even premixed
 combustion due to the mix and dispersion effect in the packed bed. In
 addition, multiple flame behaviors, such as an inclined flame front,
 isolated reaction zone, and oscillatory motion followed by a pulsating
 sound with a few Hz in a packed bed, are observed experimentally. The
 possible reasons for these phenomena are discussed.
description: Data
 Accessibility
DOI: 10.5061/dryad.s5935
title: Data from: Too important to tamper with: predation risk affects body mass and escape behaviour but not escape ability

description: 1. Escaping from a predator is a matter of life or death, and prey are
 expected to adaptively alter their physiology under chronic predation risk
 in ways that may affect escape. Theoretical models assume that escape
 performance is mass-dependent whereby scared prey strategically maintain
 an optimal body mass to enhance escape. Experiments testing the
 mass-dependent predation risk (MDPR) hypothesis have demonstrated that
 prior experience of predation risk can affect body mass, and the
 behavioural decisions about evasive actions to take. Other studies on
 natural changes in body mass indicate that mass can affect escape. No
 single experiment has tested if all of these components are indeed linked,
 which is a critical necessary condition underpinning the MDPR. 2. We
 tested all components of the MDPR in a repeated-measures experiment by
 presenting predator and non-predator cues to brown-headed cowbirds housed
 in semi-natural conditions. Exposure to predator cues affected body mass,
 fat, pectoral muscle thickness, and evasive actions (take-off angle and
 speed), but not the physiological capacity to escape, as measured by
 flying ability. Examining individual variation revealed that flying
 ability was unrelated to mass loss in either sex, unrelated to mass gain
 in males, and only females that gained a very large amount of mass flew
 poorly. 3. We next conducted a body mass manipulation in the lab to
 rigorously test whether small to large perturbations in mass can ever
 affect flying ability. We induced either no change in mass (control), a
 moderate reduction of &lt;10%, and a more extreme reduction of
 &gt;10% which the literature suggests should enhance flight. Flying
 ability was maintained regardless of treatment. Examining individual
 variation revealed the same precise patterns as in the first experiment.
 4. We conclude that prey may alter their mass and evasive actions in
 response to predation risk, but their escape ability remains robust and
 inelastic, presumably because dis-abling oneself is likely to lead to
 disastrous consequences. We suggest that animals may only face a
 mass-dependant predation risk trade-off in a narrow set of circumstances
 linked to life history stages that require large amounts of mass gain,
 e.g. parturition and migration.
description: Data from Walters et al
 Functional Ecology 2017
DOI: 10.5061/dryad.pp75d
title: Data from: Hitting the moving target: modelling ontogenetic shifts with stable isotopes reveals the importance of isotopic turnover

description: Ontogenetic niche shifts are widely prevalent in nature and are important
 in shaping the structure and dynamics of ecosystems. Stable isotope
 analysis is a powerful tool to assess these shifts, with δ15N providing a
 measure of trophic level and δ13C a measure of energy source. Previous
 applications of stable isotopes to study ontogenetic niche shifts have not
 considered the appreciable time-lag between diet and consumer tissue
 associated with isotopic turnover. These time-lags introduce significant
 complexity into field studies of ontogenetic niche shifts. Juvenile
 Chinook Salmon (Oncorhynchus tshawytscha) migrate from freshwater to
 marine ecosystems, and shift their diet from feeding primarily on
 invertebrates to feeding primarily on fish. This dual ontogenetic habitat
 and diet shift, in addition to the long time-lag associated with isotopic
 turnover, suggests that there is potential for a disconnect between the
 prey sources that juvenile salmon are consuming, and the inferred prey
 sources from stable isotope analysis. We developed a model that considered
 ontogenetic niche shifts and time-lags associated with isotopic turnover,
 and compared this ‘ontogeny’ model to one that considered only isotopic
 turnover. We used a Bayesian framework to explicitly account for parameter
 uncertainty. Data showed overwhelming support for the ontogeny model
 relative to the isotopic turnover model. Estimated variables from best
 model fits indicate that the ontogeny model predicts a much greater
 reliance on fish prey than does the stomach content data. Overall, we
 found that this method of quantifying ontogenetic niche shifts effectively
 accounted for both isotopic turnover and ontogenetic diet shifts; a
 finding that could be widely applicable to a variety of systems.
description: Hertzetal16ChinookIsotopesd13C, d15N of dorsal muscle tissue and weights (g) of juvenile Chinook Salmon caught off the west coast of Vancouver Island from 2000-2009. d13C values were corrected for differences in sample preparation following Fig S3, and were lipid-corrected following Post et al. 2007.Hertzetal16Iso.csv
DOI: 10.5061/dryad.r10t937
title: Data from: Ontogeny and consistent individual differences mediate trophic interactions

description: Ecologists use species traits to predict individual responses to
 environmental change, and ultimately to understand the composition of
 biological communities. However, this ignores known and substantial
 intraspecific variation that can have important consequences for species
 interactions and community composition. This within-species variation
 results from two distinct sources: ontogeny and consistent individual
 differences. Ontogeny and consistent differences interact to produce
 phenotypes, but the community-level consequences of this interaction have
 not been studied. Using larval dragonfly communities I investigate
 patterns of intraguild predation by manipulating (1) consistent individual
 differences in activity rate, and (2) the ontogeny of the focal and
 interacting species. I show that activity rate is a consistent individual
 trait, but that the effect of activity rate on intraguild predation
 depends on the functional role of an organism in the community (predator
 or prey). An organism's functional role itself varies across ontogeny
 of both the focal and interacting individuals. I suggest that ontogeny and
 consistent individual differences interact to produce intraspecific
 variation, with consequences for species interactions, communities, and
 eco-evolutionary dynamics.
description: behavior_DRYADData for a mescosom experiment examining reciprocal predation across ontogeny.
DOI: 10.5061/dryad.h82r4
title: Data from: Regulatory CD4+CD25+ T cells dampen inflammatory disease in murine mycoplasma pneumonia and promote IL-17 AND IFN-? responses

description: Mycoplasmas cause respiratory diseases characterized by persistent
 infection and chronic airway inflammation. Mycoplasma lung disease is
 immunopathologic, with CD4+ Th cells determining both disease severity and
 resistance to infection. Th2 cell responses promote immunopathology, while
 Th1 cells confer resistance to infection. However, regulatory CD4+ T cells
 may also have a role in the pathogenesis of mycoplasma respiratory
 diseases. We hypothesized Treg cells control the severity of the
 inflammatory lesions and may also promote persistence of infection. To
 examine this, BALB/c mice were depleted of CD25+ cells, and had increased
 disease severity due to Mycoplasma pulmonis infection. Increases in
 mycoplasma antibody responses and lymphocyte infiltration into lungs also
 occurred after CD25+ cell depletion. CD4+CD25+ regulatory T cells promoted
 IFN-? and IL-17 mycoplasma-specific CD4+ T cell responses in vitro and in
 vivo, while dampening IL-13+ Th responses. Neither IL-10 and TGF-?
 expression was detected in CD4+CD25+ T cells from lymph nodes. Thus, a
 regulatory T cell population plays an important role in controlling
 damaging immune responses in mycoplasma respiratory disease but does not
 contribute to persistence of infection. It appears that a regulatory T
 cell population preferentially dampens Th2 cell-mediated inflammatory
 responses to mycoplasma through a mechanism independent of IL-10 or TGF-?
 characteristic of "classic" Treg cells.
description: Archive
 2Contains data used to
 generate figures in manuscript
DOI: 10.5061/dryad.8j60c45
title: Data from: Initial hydraulic failure followed by late-stage carbon starvation leads to drought-induced death in tree, Trema orientalis

description: Drought-induced tree death has become a serious problem in global forest
 ecosystems. Two nonexclusive hypotheses, hydraulic failure and carbon
 starvation, have been proposed to explain tree die-offs. To clarify the
 mechanisms, we investigated the physiological processes of drought-induced
 tree death in saplings with contrasting Huber values (sapwood area/total
 leaf area). First, hydraulic failure and reduced respiration were found in
 the initial process of tree decline, and in the last stage carbon
 starvation leaded to tree death. The carbohydrate reserves at the stem
 bases, low in healthy trees, were accumulated at the beginning of the
 declining process because of phloem transport failure, and then decreased
 just before dying. The concentrations of non-structural carbohydrates at
 the stem bases are a good indicator of tree damage. The physiological
 processes and carbon sink-source dynamics that occur during lethal drought
 provide important insight into the adaptive measures underlying forest
 die-offs under global warming conditions.
description: RawDataSetRaw data set in from Figures 2, 3 and 4.
DOI: 10.5061/dryad.11385
title: Data from: Scale-dependent responses of pollination and seed dispersal mutualisms in a habitat transformation scenario

description: Transformed habitats are the result of deliberate replacement of native
 species by an exotic monoculture, involving changes in biotic and abiotic
 conditions. Despite this, transformed habitats are becoming more common
 and constitute a major biodiversity change driver, little is known about
 the scale-dependent responses of plant-animal mutualisms. Aiming to test
 the multi-scale responses of pollination and seed dispersal in a habitat
 transformation scenario, we examined a gradient of native and transformed
 habitats at three spatial scales (0-50, 50-100, and 100-250 m), focused on
 a highly-specialized mutualistic system composed of a hemiparasitic
 mistletoe (Tristerix corymbosus) that is almost exclusively pollinated by
 a hummingbird (Sephanoides sephaniodes) and dispersed by an arboreal
 marsupial (Dromiciops gliroides). Even though mistletoes were found along
 the gradient, they were more abundant and more densely aggregated when the
 transformed habitat was dominant. Disperser and pollinator activity also
 increased as the transformed habitat become dominant, at the scale of 0-50
 m and 50-100 m, respectively. Furthermore, crop size and disperser
 activity co-varied at broad and intermediate scales, whereas recruitment
 co-varied at intermediate and fine scales. Moreover, disperser activity
 and the number of seedlings were spatially associated, stressing D.
 gliroides’ role in the recruitment of the mistletoe. Synthesis: This
 highly specialized mutualistic system seems to be responding positively to
 the habitat structure modifications associated with Eucalyptus
 plantations. However, the actual costs (e.g., reduced gene flow, increased
 herbivory) in these transformed habitats are yet to be assessed.
description: Pollination and seed
 dispersal dataThis CSV file contains
 all the original field data collected. Please refer to the ReadMe file for
 an explanation of the column headers.Fonturbel_data.csv
DOI: 10.5061/dryad.kk744
title: Data from: Shifts and linkages of functional diversity between above- and below-ground compartments along a flooding gradient

description: Trait-based approaches have the potential to reveal general and predictive
 relationships between organisms and ecosystem functioning. However, the
 mechanisms underlying the functional structure of communities are still
 unclear. Within terrestrial ecosystems, several studies have shown that
 many ecological processes are controlled by the interacting above- and
 below-ground compartments. However, few studies have used traits to reveal
 the functional relationships between plants and soil fauna. Mostly,
 research combining plants and soil fauna solely used the traits of one
 assemblage in predictive studies. Above-ground (plants) and below-ground
 (Collembola) compartments were sampled over a flooding gradient in
 northern France along the Seine River. First, we measured the effect of
 flooding on functional and taxonomic assembly within both communities. We
 then considered the linkages between plant and Collembolan species
 richness, community traits and assessed whether traits of both
 compartments converged at high flooding intensity (abiotic filtering) and
 diverged when this constraint is released (biotic filtering). Species
 richness of both taxa followed the same bell-shaped pattern along the
 gradient, while a similar significant pattern of functional richness was
 only observed for plants. Further analyses revealed a progressive shift
 from trait convergence to divergence for plants, but not for Collembola,
 as constraints intensity decreased. Instead, our results highlighted that
 Collembola traits were mainly linked to the variations in plant traits.
 This leads, within Collembola assemblages, to convergence of a subset of
 perception and habitat-related traits for which the relationship with
 plant traits was assessed. Synthesis. Using a trait-based approach, our
 study highlighted that functional relationships occur between above- and
 below-ground compartments. We underlined that functional composition of
 plant communities plays a key role in structuring Collembola assemblages
 in addition to the role of abiotic variables. Our study clearly shows that
 functional diversity provides a new approach to link the above- and
 below-ground compartments and might, therefore, be further considered when
 studying ecological processes at the interface between both compartments.
description: Matrix Wc: Collembola
 abundanceAbundance data for
 collembolan species (rows) sampled within the various sampling units
 (columns) used in the study.Coll-Ptv-Dryad.csvMatrix Wv: Relative frequency of plant speciesRelative frequency of each plant species (rows) within the various sampling units (columns) used in the study.Veg-Ptv-Dryad.csvMatrix E: Abiotic dataSampling units (rows) caracterized by soil physico-chemical and environmental variables (columns) as used in the study.Envir-Ptv-Dryad.csv