cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m4fs7
title: Data from: Partitioning the sources of demographic variation reveals density-dependent nest predation in an island bird population

description: Ecological factors often shape demography through multiple mechanisms,
 making it difficult to identify the sources of demographic variation. In
 particular, conspecific density can influence both the strength of
 competition and the predation rate, but density-dependent competition has
 received more attention, particularly among terrestrial vertebrates and in
 island populations. A better understanding of how both competition and
 predation contribute to density-dependent variation in fecundity can be
 gained by partitioning the effects of density on offspring number from its
 effects on reproductive failure, while also evaluating how biotic and
 abiotic factors jointly shape demography. We examined the effects of
 population density and precipitation on fecundity, nest survival, and
 adult survival in an insular population of orange-crowned warblers
 (Oreothlypis celata) that breeds at high densities and exhibits a suite of
 traits suggesting strong intraspecific competition. Breeding density had a
 negative influence on fecundity, but it acted by increasing the
 probability of reproductive failure through nest predation, rather than
 through competition, which was predicted to reduce the number of offspring
 produced by successful individuals. Our results demonstrate that
 density-dependent nest predation can underlie the relationship between
 population density and fecundity even in a high-density, insular
 population where intraspecific competition should be strong.
description: Sofaer_etal_OCWAFecundityDataOrange-crowned warbler fecundity data.Sofaer_etal_OCWANestSurvivalOrange-crowned warbler nest survival data.Sofaer_etal_OCWA_AdultSurvivalFiles with input and results from analysis of orange-crowned warbler adult survival in Program MARK.
DOI: 10.5061/dryad.rk6hd
title: Data from: Watch out for your neighbor: climbing onto shrubs is related to risk of cannibalism in the scorpion Buthus cf. occitanus

description: The distribution and behavior of foraging animals usually imply a balance
 between resource availability and predation risk. In some predators such
 as scorpions, cannibalism constitutes an important mortality factor
 determining their ecology and behavior. Climbing on vegetation by
 scorpions has been related both to prey availability and to predation
 (cannibalism) risk. We tested different hypotheses proposed to explain
 climbing on vegetation by scorpions. We analyzed shrub climbing in Buthus
 cf. occitanus with regard to the following: a) better suitability of prey
 size for scorpions foraging on shrubs than on the ground, b) selection of
 shrub species with higher prey load, c) seasonal variations in prey
 availability on shrubs, and d) whether or not cannibalism risk on the
 ground increases the frequency of shrub climbing. Prey availability on
 shrubs was compared by estimating prey abundance in sticky traps placed in
 shrubs. A prey sample from shrubs was measured to compare prey size.
 Scorpions were sampled in six plots (50 m x 10 m) to estimate the
 proportion of individuals climbing on shrubs. Size difference and distance
 between individuals and their closest scorpion neighbor were measured to
 assess cannibalism risk. The results showed that mean prey size was
 two-fold larger on the ground. Selection of particular shrub species was
 not related to prey availability. Seasonal variations in the number of
 scorpions on shrubs were related to the number of active scorpions, but
 not with fluctuations in prey availability. Size differences between a
 scorpion and its nearest neighbor were positively related with a higher
 probability for a scorpion to climb onto a shrub when at a disadvantage,
 but distance was not significantly related. These results do not support
 hypotheses explaining shrub climbing based on resource availability. By
 contrast, our results provide evidence that shrub climbing is related to
 cannibalism risk.
description: Shrub climbing by Buthus
 occitanus scorpionsField collected data in
 Excel files
DOI: 10.5061/dryad.td271t1d
title: Data from: Positive feedback between ecological and reproductive character displacement in a young avian hybrid zone

description: Character displacement can reduce costly interspecific interactions
 between young species. We investigated the mechanisms behind divergence in
 three key traits - breeding habitat choice, timing of breeding and plumage
 coloration - in Ficedula flycatchers. We found that male pied flycatchers
 became expelled from the preferred deciduous habitat into mixed forest as
 the superior competitor, collared flycatchers, increased in numbers. The
 peak in food abundance differs between habitats, and the spatial
 segregation was paralleled by an increased divergence in timing of
 breeding between the two species. Male pied flycatchers vary from brown to
 black with brown coloration being more frequent in sympatry with collared
 flycatchers, a pattern often proposed to result from selection against
 hybridization, i.e. reinforcement. In contrast to this view, we show that
 brown male pied flycatchers more often hybridize than black males. Male
 pied flycatcher plumage coloration influenced the territory obtained in
 areas of co-occurrence with collared flycatchers, and brown male pied
 flycatchers experienced higher relative fitness than black males when
 faced with heterospecific competition. We suggest that allopatric
 divergence in resource defense ability causes a feedback loop at secondary
 contact where male pied flycatchers with the most divergent strategy
 compared to collared flycatchers are favored by selection.
description: DryadDataVallin
DOI: 10.5061/dryad.61hd3122
title: Data from: Correlated evolution of phenotypic plasticity in metamorphic timing

description: Phenotypic plasticity has long been a focus of research, but the
 mechanisms of its evolution remain controversial. Many amphibian species
 exhibit a similar plastic response in metamorphic timing in response to
 multiple environmental factors; therefore, more than one environmental
 factor has likely influenced the evolution of plasticity. However, it is
 unclear whether the plastic responses to different factors have evolved
 independently. In this study, we examined the relationship between the
 plastic responses to two experimental factors (water level and food type)
 in larvae of the salamander Hynobius retardatus, using a cause-specific
 Cox proportional hazards model on the time to completion of metamorphosis.
 Larvae from ephemeral ponds metamorphosed earlier than those from
 permanent ponds when kept at a low water level or fed conspecific larvae
 instead of larval Chironomidae. This acceleration of metamorphosis
 depended only on the permanency of the larvae’s pond of origin, but not on
 the conspecific larval density (an indicator of the frequency of
 cannibalism) in the ponds. The two plastic responses were significantly
 correlated, indicating that they may evolve correlatively. Once plasticity
 evolved as an adaptation to habitat desiccation, it might have relatively
 easily become a response to other ecological factors, such as food type
 via the pre-existing developmental pathway.
description: data
DOI: 10.5061/dryad.7187d
title: Data from: Comparative analysis of animal growth: a primate continuum revealed by a new dimensionless growth rate coefficient

description: The comparative analysis of animal growth still awaits full integration
 into life history studies, partially due to the difficulty of defining a
 comparable measure of growth rate across species. Using growth data from
 50 primate species, we introduce a modified ‘general growth model’ and a
 dimensionless growth rate coefficient β that controls for size scaling and
 phylogenetic effects in the distribution of growth rates. Our results
 contradict the prevailing idea that slow growth characterizes primates as
 a group: the observed range of β values shows that not all primates grow
 slowly, with galago species exhibiting growth rates similar or above the
 mammalian average, while other strepsirrhines and most New World monkeys
 show limited reduction in growth rates. Low growth rate characterizes apes
 and some papionines. Phylogenetic regressions reveal associations between
 β and life history variables, providing tests for theories of primate
 growth evolution. We also show that primate slow growth is an exclusively
 postnatal phenomenon. Our study exemplifies how the dimensionless approach
 promotes the integration of growth rate data into comparative life history
 analysis, and demonstrates its potential applicability to other cases of
 adaptive diversification of animal growth patterns.
description: Appendix A. Data.
 Vinicius and MumbyGrowth curves, life
 history data and growth data from conception.
DOI: 10.5061/dryad.n2s14
title: Data from: Pyoverdin cheats fail to invade bacterial populations in stationary phase

description: Microbes engage in cooperative behaviours by producing and secreting
 public goods, the benefits of which are shared among cells, and are
 therefore susceptible to exploitation by nonproducing cheats. In nature,
 bacteria are not typically colonizing sterile, rich environments in
 contrast to laboratory experiments, which involve inoculating sterile
 culture with few bacterial cells that then race to fill the available
 niche. Here, we study the potential implications of this difference, using
 the production of pyoverdin, an iron-scavenging siderophore that acts as a
 public good in the bacteria Pseudomonas aeruginosa. We show that (1)
 nonproducers are able to invade cultures of producers when added at the
 start of growth or during early exponential growth phase, but not during
 late exponential or stationary phase; (2) the producer strain does not
 produce pyoverdin in the late exponential and stationary phases and so is
 not paying the cost of cooperating during those phases. These results
 suggest that whether a nonproducing mutant can invade will depend upon
 when the mutation arises, as well as the population structure, and raise a
 potential difficulty with the use of antimicrobial treatment strategies
 that propose to exploit the invasive abilities of cheats.
description: Data of competition
 assays and fitness and monoculture assaysM-Ghoul-Dryad
 data.xlsx
DOI: 10.5061/dryad.pm4n81q
title: Data from: Disturbance reverses classic biodiversity predictions in river-like landscapes

description: Global analyses of biodiversity consistently reveal recurrent patterns of
 species distributions worldwide. However, unveiling the specific
 mechanisms behind those patterns remains logistically challenging, yet
 necessary for reliable biodiversity forecasts. Here, we combine theory and
 experiments to investigate the processes underlying spatial biodiversity
 patterns in dendritic, river-like landscapes, iconic examples of highly
 threatened ecosystems. We used geometric scaling properties, common to all
 rivers, to show that the distribution of biodiversity in these landscapes
 fundamentally depends on how ecological selection is modulated across
 space: while uniform ecological selection across the network leads to
 higher diversity in downstream confluences, this pattern can be inverted
 by disturbances when population turnover (i.e., local mortality) is higher
 upstream than downstream. Higher turnover in small headwater patches can
 slow down ecological selection, increasing local diversity in comparison
 to large downstream confluences. Our results show that
 disturbance-mediated slowing down of competitive exclusion can generate a
 specific transient signature in terms of biodiversity distribution when
 applied over a spatial gradient of disturbance, which is a common feature
 of many river landscapes.
description: Turnover_dendritic_network_(20170320)Data in text format to reproduce experimental results from the article. Please note that the associated R code is available at: https://github.com/harveye/Turnover_dendritic_network
DOI: 10.5061/dryad.5535h
title: Data from: Contrasting patterns of leaf trait variation among and within species during tropical dry forest succession in Costa Rica

description: A coordinated response to environmental drivers amongst individual
 functional traits is central to the plant strategy concept. However,
 whether the trait co-ordination observed at the global scale occurs at
 other ecological scales (especially within species) remains an open
 question. Here, for sapling communities of two tropical dry forest types
 in Costa Rica, we show large differences amongst traits in the relative
 contribution of species turnover and intraspecific variation to their
 directional changes in response to environmental changes along a
 successional gradient. We studied the response of functional traits
 associated with the leaf economics spectrum and drought tolerance using
 intensive sampling to analyse inter- and intra-specific responses to
 environmental changes and ontogeny. Although the overall functional
 composition of the sapling communities changed during succession more
 through species turnover than through intraspecific trait variation, their
 relative contributions differed greatly amongst traits. For instance,
 community mean specific leaf area changed mostly due to intraspecific
 variation. Traits of the leaf economics spectrum showed decoupled
 responses to environmental drivers and ontogeny. These findings emphasise
 how divergent ecological mechanisms combine to cause great differences in
 changes of individual functional traits over environmental gradients and
 ecological scales.
description: Functional trait values,
 height and crown illumination index for each treeThis dataset gives the
 value of leaf functional traits (mean value for the three, or fewer,
 measured leaves), height and crown illumination index for 852 sapling
 trees belonging to 69 species of Costa Rican tropical dry
 forests.data_Derroire_etal_2017_ScientificReport_sapling.csvEnvironmental factors in successional tropical dry forests of Costa RicaThis dataset gives the values of environmental factors (micro-climate, soil physical and chemical properties, forest structure) of 12 plots in successional tropical dry forests of Costa Rica.data_Derroire_etal_2017_ScientificReport_enviro.csvSpecies codesThis file gives the list of species measured in a study of sapling in successional tropical dry forests of Costa Rica, their families, and the species code used in the dataset of functional traits.data_Derroire_etal_2017_ScientificReport_species.csv
DOI: 10.15468/dl.ag6zh2
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cercidiphyllum japonicum"
 ]
}

 The dataset includes 183 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000722-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p7h807v
title: Data from: Defaunation and fragmentation erode small mammal diversity dimensions in tropical forests

description: Forest fragmentation and defaunation are considered the main drivers of
 biodiversity loss, yet the synergistic effects of landscape changes and
 biotic interactions on assemblage structure have been poorly investigated.
 Here, we use an extensive dataset of 283 assemblages and 105 species of
 small mammals to understand how defaunation of medium and large mammals
 and forest fragmentation change the community composition and diversity of
 rodents and marsupials in tropical forests of South America. We used
 structured equation models to investigate the relationship between small
 mammal species, functional and phylogenetic diversity with forest size,
 forest cover and the occurrence of medium and large mammals. The best-fit
 model showed that defaunation reduced functional diversity, and that
 species diversity of small mammals increased with forest patch size.
 Forest cover did not affect functional and phylogenetic diversity. Our
 results indicate that occurrence of medium and large sized mammals
 (probably acting as predators, or competitors of small mammals) and forest
 patch size help to retain species and functional diversity in small mammal
 communities. Further, the number of species in a small mammal community
 was critical to the maintenance of phylogenetic diversity, and may have a
 pronounced influence on the ecological functions played by small mammals.
 Identifying how phylogenetic and functional diversity change in function
 of human pressures allows us to better understand the contribution of
 extant lineages to ecosystem functioning in tropical forests.
description: site.abundance.cleanall.traits.clean.ok
DOI: 10.5061/dryad.3r44n
title: Data from: Freshwater eutrophication drives sharp reductions in temporal beta diversity

description: Eutrophication has become one of the most widespread anthropogenic forces
 impacting freshwater biological diversity. One potentially important
 mechanism driving biodiversity changes in response to eutrophication is
 the alteration of seasonal patterns of succession, particularly among
 species with short, synchronous life cycles. We tested the hypothesis that
 eutrophication reduces seasonally driven variation in species assemblages
 by focusing on an understudied aspect of biodiversity: temporal beta
 diversity . We estimated the effect of eutrophication on by sampling
 benthic macroinvertebrate assemblages bimonthly for 2 years across 35
 streams spanning a steep gradient of total phosphorus (P) and benthic
 algal biomass (as chlorophyll). Two widely used metrics of β diversity
 both declined sharply in response to increasing P and chl, regardless of
 covariates. The most parsimonious explanatory model for included an
 interaction between P and macroinvertebrate biomass, which revealed that
 was lower when macroinvertebrate biomass was relatively high.
 Macroinvertebrate biomass explained a greater amount of deviance in at
 lower to moderate concentrations of P, providing additional explanatory
 power where P concentration alone was unable to fully explain declines in.
 Chl-explained similar amounts of deviance in comparison to the best P
 model, but only when temperature variability, which was positively related
 to, also was included in the model. Declines in suggest that nutrient
 enrichment decreases the competitive advantage that specialists gain by
 occupying particular temporal niches, which leads to assemblages dominated
 by generalists that exhibit little seasonal turnover. The collapse of
 seasonal variation in assemblage composition we observed in our study
 suggests that treating dynamic communities as static assemblages is a
 simplification that may fail to detect the full impact of anthropogenic
 stressors. Our results show that eutrophication leads to more temporally
 homogenous communities and therefore degrades a fundamental facet of
 biodiversity.
description: SRJS_invert_wideContains a copy of the benthic macroinvertebrate data accompanying Cook et al. (in press) organized by sampling site and event. Columns denote taxon-specific codes, and the data matrix is filled with observed macroinvertebrate densities (counts/m2). Sampling occurred every other month, and spanned June 2014 to April 2016.
DOI: 10.5061/dryad.6km3j
title: Data from: Immune activation generates corticosterone-mediated terminal reproductive investment in a wild bird

description: Despite classical expectations of a trade-off between immune activity and
 reproduction, an emergent view suggests that individuals experiencing
 activation of their immune system actually increase reproductive effort
 and allocation to offspring as a form of terminal investment in response
 to reduced survival probability. However, the components and mechanisms of
 increased parental investment following immunostimulation are currently
 unknown. We hypothesize that increased glucocorticoid production following
 immunostimulation modulates the increase in reproductive effort that
 constitutes terminal investment. We activated the immune system of
 breeding female house wrens (Troglodytes aedon) with an immunogen and
 cross-fostered the eggs that they subsequently produced to separate
 prenatal and postnatal components of maternal investment. Cross-fostering
 revealed an increase in both pre- and postnatal allocation from
 immunostimulated females, which was confirmed by quantification of egg
 constituents and maternal provisioning behavior. The increase in maternal
 provisioning was mediated, at least in part, by increased corticosterone
 in these females. Offspring immune responsiveness was also enhanced
 through transgenerational immune priming via the egg. Thus, our results
 indicate that maternal immunostimulation induces transgenerational effects
 on offspring through both pre- and postnatal parental effects and support
 an important role for corticosterone in mediating parental investment.
description: EGGSFEMALESNESTLINGS
DOI: 10.5061/dryad.5ms8t
title: Data from: Cohort feasibility study of an intermittent pneumatic compression device within a below-knee cast for the prevention of venous thromboembolism

description: Objectives: To determine the likely enrolment rate of eligible
 participants into a randomised controlled trial (RCT) in which a
 within-cast intermittent pneumatic compression device using Jet Impulse
 Technology (IPC/JIT) is 1 of 3 possible interventions in a RCT for the
 prevention of venous thromboembolism (VTE) in the clinical setting of
 isolated lower limb cast immobilisation. Design: A prospective, open-label
 feasibility study of the IPC/JIT device placed within a lower limb cast.
 Setting: Wellington Regional Hospital Fracture Clinic. Participants:
 Individuals aged 18–70 who presented with a lower limb injury requiring a
 minimum of 4 weeks below-knee cast immobilisation. Intervention: Placement
 of an IPC/JIT device within lower limb cast. Outcome measures: The main
 outcome measure was the proportion of eligible participants who
 participated in the feasibility study. Secondary outcome measures included
 adherence to device usage throughout the study, ease of application of the
 device and adverse events potentially associated with its use. Results:
 The proportion of potentially eligible participants for the IPC/JIT device
 was only 7/142 (5%), 95% CI 2 to 9.9. Devices were used for a mean (range)
 of 4.1 (1.9 to 10.2) hours per day and none of 7 participants had adequate
 adherence to the device. 3 of the 7 participants suffered an adverse
 event, including 1 deep vein thrombosis, 2 dorsal foot ulcer and 1 skin
 maceration. Conclusions: A within-cast IPC/JIT device is unlikely to be a
 feasible randomisation arm for a RCT assessing possible interventions for
 the reduction of VTE risk in the clinical setting of lower limb injury
 requiring below knee cast immobilisation for a minimum of 4 weeks.
description: Data relating to all LLI
 presentationsAll lower limb
 immobilization patients during the period of the study, and appropriate
 pivot tables resulting from the first sheet
 'data'.1.1
 presentations-1.xlsData relating to the
 users of the IPC device1.0
 Participants.xls