cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r47tm
title: Data from: Resilience of tropical dry forests – a meta-analysis of changes in species diversity and composition during secondary succession

description: Assessing the recovery of species diversity and composition after major
 disturbance is key to understanding the resilience of tropical forests
 through successional processes, and its importance for biodiversity
 conservation. Despite the specific abiotic environment and ecological
 processes of tropical dry forests, secondary succession has received less
 attention in this biome than others and changes in species diversity and
 composition have never been synthesised in a systematic and quantitative
 review. This study aims to assess in tropical dry forests 1) the
 directionality of change in species richness and evenness during secondary
 succession, 2) the convergence of species composition towards that of
 old-growth forest and 3) the importance of the previous land use,
 precipitation regime and water availability in influencing the direction
 and rate of change. We conducted meta-analyses of the rate of change in
 species richness, evenness and composition indices with succession in 13
 tropical dry forest chronosequences. Species richness increased with
 succession, showing a gradual accumulation of species, as did Shannon
 evenness index. The similarity in species composition of successional
 forests with old-growth forests increased with succession, yet at a low
 rate. Tropical dry forests therefore do show resilience of species
 composition but it may never reach that of old-growth forests. We found no
 significant differences in rates of change between different previous land
 uses, precipitation regimes or water availability. Our results show high
 resilience of tropical dry forests in term of species richness but a slow
 recovery of species composition. They highlight the need for further
 research on secondary succession in this biome and better understanding of
 impacts of previous land-use and landscape-scale patterns.
description: data_Derroire_et_al_2016_OikosThe provided data give the values of diversity and similarity indices for trees and shrubs, the successional age of the plot and values for environmental factors for 829 plots of 13 chronosequences in successional tropical dry forests used in the meta-analyses presented in the paper.
DOI: 10.5061/dryad.q7j256r
title: Data from: The influence of distance to perennial surface water on ant communities in Mopane woodlands, northern Botswana

description: Studies of biodiversity along environmental gradients provide information
 on how ecological communities change in response to biotic and abiotic
 factors. For instance, distance to water is associated with several
 factors that shape the structure and the functioning of ecosystems at a
 range of spatial scales. We investigated the influence of distance to a
 perennial water source on ant communities in a semi-arid savanna in
 northern Botswana. Ant abundance, taxonomic richness and both alpha and
 beta diversity were generally higher during the wet than the dry season.
 However, there were strong seasonal influences on the effects of distance
 to water, with more pronounced effects during the wet season. While both
 abundance and beta diversity declined with increasing distances to water
 during the wet season, there was a contrasting increase in alpha
 diversity. There was no major effect of distance to water on taxonomic
 richness during either season. Beta diversity was as high across as along
 gradients, and we found support for modular rather than nested community
 structures along gradients. Our study demonstrated that small-scale
 gradients in distance to water can influence several aspects of ant
 communities in semi-arid savannas. However, our results also point to
 strong effects of small-scale environmental variation, for instance
 associated with vegetation characteristics, soil properties and plant
 community structure that are not directly linked to water access.
description: Dalerum-et-alRaw trap data of each morpho-species, as well as the spatial coordinates for each cluster of traps.
DOI: 10.5061/dryad.fd15ff0
title: Data from: Insect herbivory on seedlings of rainforest trees: effects of density and distance of conspecific and heterospecific neighbours

description: 1. Natural enemies of plants such as insect herbivores can contribute to
 structuring and maintaining plant diversity in tropical forests. Most
 research in this area has focused on the role of specialised enemies and
 the extent to which herbivory on individual plant species is
 density-dependent. 2. Relatively few insect herbivores specialise on a
 single host plant species. Insect herbivores that feed on more than one
 plant species may link the regeneration dynamics of their host species
 through ‘apparent competition’ or ‘apparent mutualism’. 3. We investigated
 herbivory and survival of seedlings of two tropical tree species (Cordia
 alliodora and Cordia bicolor) in the forests of Barro Colorado Island
 (Panama). We used experiments and observations to assess seedling fate in
 relation to the presence of conspecifics and heterospecifics across a
 range of spatial scales. 4. Herbivory significantly increased seedling
 mortality and was highest at high local densities of C. alliodora
 seedlings. There was also evidence that high local densities of C.
 alliodora increased herbivory on co-occurring C. bicolor seedlings. 5.
 Synthesis. The elevated rates of seedling herbivory at high densities of
 conspecifics documented in our study are consistent with the predictions
 of the Janzen-Connell hypothesis, which explains how so many plant species
 can coexist in tropical forests. Our data also highlight the possibility
 that herbivore-mediated density-dependence, facilitated by herbivores that
 feed on multiple plant species, can also occur across plant species.
 Enemy-mediated indirect effects of this sort have the potential to
 structure plant communities.
description: Study1RscriptGLMRscript for GLM for study 1 of manuscript25hamodel.Rcsv for study 1 analysiscsv file for study 1 analyses. to be used with study 1 r script.25basalarea.csvrscriptstudy2r script for study 2observations20x20alliobicseparate_SG.Rcsvfilestudy2csv file for study 2 to go with r script study 2cordiabasal.csvstudy3rscriptr script for study 3updatedtransects2017_SG.Rcsv file study 3csv file for study 3 analyses, linked to study 3 r scriptnewtrans.csvrscript study 4r script for study 4 analysesupdatedcatascript.Rstudy4csvcsv file for study 4 analyses , linked to study 4 r scriptcata.csvrscriptstudy5r script for study 5 analysessurvivalreg_SG.Rstudy5csvcsv for study 5 analyses, linked to study 5 r scriptfinalsurvival.csv
DOI: 10.3535/mtg-ag0-k7e
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/nzp-pm8-rsa
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/1pb-n1f-reh
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/v1z-wr4-j5p
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.819236j
title: Data from: Do spatial scale and life history affect fish-habitat relationships?

description: 1. Understanding how animals interact with their environment is a
 fundamental ecological question with important implications for
 conservation and management. The relationships between animals and their
 habitat, however, can be scale dependent. If ecologists work at suboptimal
 spatial scales, they will gain an incomplete picture of how animals
 respond to the landscape. Identifying the scale at which animal-landscape
 relationships are strongest (the ‘scale of effect’) will improve our
 ability to better plan management and conservation activities. 2. Several
 recent studies have greatly enhanced our knowledge about the scale of
 effect, and the potential drivers of inter-specific variability, in
 particular life-history traits. However, while many marine systems are
 inherently multi-scalar, research into the scale of effect has been mainly
 focussed on terrestrial taxa. As the scales of observation in fish-habitat
 association studies are often selected based on convention rather than
 biological reasoning, they may provide an incomplete picture of the scales
 where these associations are strongest. 3. We examined fish-habitat
 associations across four nested spatial scales in a temperate reef system
 to ask: (1.) at what scale are fish-habitat associations the strongest,
 (2.) are habitat elements consistently important across scales, and (3.)
 do scale-dependent fish-habitat associations vary in relation to either
 body size, geographic range size or trophic level? 4. We found that: (1.)
 the strongest fish-habitat associations were observed when these
 relationships were examined at considerably larger spatial scales than
 usually investigated; (2.) the importance of environmental predictors
 varied across spatial scales, indicating that conclusions about the
 importance of habitat elements will depend on the scales at which studies
 are undertaken; and (3.) scale-dependent fish-habitat associations were
 consistent across all life-history traits. 5. Our results highlight the
 importance of considering how animals relate to their environment and
 suggest the small scales often chosen to examine fish-habitat associations
 are likely to be suboptimal. Developing a more mechanistic understanding
 of animal-habitat associations will greatly aid in predicting and managing
 responses to future anthropogenic disturbances.
description: UVC
 dataThis file contains raw
 data collected using underwater visual census (UVC). The data is fish
 abundances and measures of habitat characteristics from three sites
 (Barwon Heads, Apollo Bay and Wilson's Promontory) in south-eastern
 Australia.BRUV
 dataThis file contains raw
 data collected using baited remote underwater video (BRUV). The data is
 fish abundances and measures of habitat characteristics from three sites
 (Barwon Heads, Apollo Bay and Wilson's Promontory) in south-eastern
 Australia.
DOI: 10.3535/676-f1v-dez
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/hhd-kbl-b0s
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/gle-7l0-zje
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.3535/yzc-5fd-6mr
title: Thelodus carinatus

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.7b253
title: Data from: Female discrimination thresholds frequently exceed local male display variation: implications for mate choice dynamics and sexual selection

description: Among the factors that can influence female mate choice decisions is the
 degree to which females differentiate among similar displays: as
 differences decrease, females are expected to eventually stop
 discriminating. This discrimination threshold, in conjunction with the
 magnitude of male trait variation females regularly encounter while making
 mate choice decisions, may have important consequences for sexual
 selection. If local display variation is above the discrimination
 threshold, female preferences should translate into higher mating success
 for the more attractive male. But if display variation is frequently below
 the threshold, the resulting increased pattern of random mating may
 obscure the existence of female mate choice. I investigated the interplay
 between female discrimination and male display variation in green
 treefrogs (Hyla cinerea), and found that call trait differences between
 nearest neighbour males were frequently smaller than what females are
 expected to discriminate. This finding has two important consequences for
 our understanding of sexual selection in the wild: First, low display
 variation should weaken the strength of selection on male display traits,
 but the direction of selection should mirror the one predicted from
 females choice trials. Second, caution is needed when interpreting data on
 realized mating success in the wild: a pattern of random mating with
 respect to male display traits does not always mean that female
 preferences are weak or that conditions are too challenging for females to
 express their preferences. Rather, insufficient display variation can
 generate the same pattern.
description: Male call differences
 and female discrimination thresholdsexcel file containing
 male call recordings, the analysis steps to compare call differences
 between nearest neighbour males, as well as female choice data that were
 the basis for determining female discrimination thresholds. Data file
 contains several sheets. Description of analysis and abbreviations given
 on the respective sheets.JEB-
 data.xlsx
DOI: 10.3535/6qz-p1z-fqp
title: Thelodus laevis

description: Digital Specimen for the physical specimen hosted at Tallinn University of Technology.
DOI: 10.5061/dryad.nm38g
title: Data from: Sexual selection and population divergence II. divergence in different sexual traits and signal modalities in field crickets (Teleogryllus oceanicus)

description: Sexual selection can target many different types of traits. However, the
 relative influence of different sexually-selected traits during
 evolutionary divergence is poorly understood. We used the field cricket
 Teleogryllus oceanicus to quantify and compare how five traits from each
 of three sexual signal modalities and components diverge among allopatric
 populations: male advertisement song, cuticular hydrocarbon (CHC) profiles
 and forewing morphology. Population divergence was unexpectedly
 consistent: we estimated the among-population (genetic)
 variance-covariance matrix, D, for all 15 traits, and Dmax explained
 nearly two-thirds of its variation. CHC and wing traits were most tightly
 integrated, whereas song varied more independently. We modelled the
 dependence of among-population trait divergence on genetic distance
 estimated from neutral markers to test for signatures of selection vs.
 neutral divergence. For all three sexual trait types, phenotypic variation
 among populations was largely explained by a neutral model of divergence.
 Our findings illustrate how phenotypic integration across different types
 of sexual traits might impose constraints on the evolution of mating
 isolation and divergence via sexual selection.
description: Pascoal et al. 2017
 (morphometric data)Wing morphometric data
 includes relative warps 1-3 plus mirror and harp surface areas. Data from
 validations run on a subset of samples are also included. "Unique
 identifier" cross-references each sample to the CHC analysis in
 [Pascoal et al. (2016) Sexual selection and population divergence I. The
 influence of socially flexible cuticular hydrocarbon expression in male
 field crickets (Teleogryllus oceanicus). Evolution 10:82-97.]
 "N/A" indicates the n = 13 samples excluded from morphometric
 analysis as described in the present manuscript.
DOI: 10.5061/dryad.st860bt
title: Data from: Microglia responses to pro-inflammatory stimuli (LPS, IFNγ+TNFα) and reprogramming by resolving cytokines (IL-4, IL-10)

description: Microglia respond to CNS injuries and diseases with complex reactions,
 often called “activation.” A pro-inflammatory phenotype (also called
 classical or M1 activation) lies at one extreme of the reactivity
 spectrum. There were several motivations for this study. First, bacterial
 endotoxin (lipopolysaccharide, LPS) is the most commonly used
 pro-inflammatory stimulus for microglia, both in vitro and in vivo;
 however, pro-inflammatory cytokines (e.g., IFNγ, TNFα) rather than LPS
 will be encountered with sterile CNS damage and disease. We lack direct
 comparisons of responses between LPS and such cytokines. Second, while
 transcriptional profiling is providing substantial data on microglial
 responses to LPS, these studies mainly use mouse cells and models, and
 there is increasing evidence that responses of rat microglia can differ.
 Third, the cytokine milieu is dynamic after acute CNS damage, and an
 important question in microglial biology is: How malleable are their
 responses? There are very few studies of effects of resolving cytokines,
 particularly for rat microglia, and much of the work has focused on
 pro-inflammatory outcomes. Here, we first exposed primary rat microglia to
 LPS or to IFNγ+TNFα (I+T) and compared hallmark functional (nitric oxide
 production, migration) and molecular responses (almost 100 genes),
 including surface receptors that can be considered part of the sensome.
 Protein changes for exemplary molecules were also quantified: ARG1,
 CD206/MRC1, COX-2, iNOS, and PYK2. Despite some similarities, there were
 notable differences in responses to LPS and I+T. For instance, LPS often
 evoked higher pro-inflammatory gene expression and also increased several
 anti-inflammatory genes. Second, we compared the ability of two
 anti-inflammatory, resolving cytokines (IL-4, IL-10), to counteract
 responses to LPS and I+T. IL-4 was more effective after I+T than after
 LPS, and IL-10 was surprisingly ineffective after either stimulus. These
 results should prove useful in modeling microglial reactivity in vitro;
 and comparing transcriptional responses to sterile CNS inflammation in
 vivo.
description: Lively &
 Schlichter_6h_24h NanoString count dataNormalized mRNA
 counts
DOI: 10.5061/dryad.26kb0
title: Data from: Plant-soil feedbacks from 30-year family-specific soil cultures: phylogeny, soil chemistry and plant life stage

description: Intraspecific negative feedback effects, where performance is reduced on
 soils conditioned by conspecifics, are widely documented in plant
 communities. However, interspecific feedbacks are less well studied, and
 their direction, strength, causes, and consequences are poorly understood.
 If more closely related species share pathogens, or have similar soil
 resource requirements, plants may perform better on soils conditioned by
 more distant phylogenetic relatives. There have been few empirical tests
 of this prediction across plant life stages, and none of which attempt to
 account for soil chemistry. Here, we test the utility of phylogeny for
 predicting soil feedback effects on plant survival and performance
 (germination, seedling survival, growth rate, biomass). We implement a
 full factorial experiment growing species representing five families on
 five plant family-specific soil sources. Our experiments exploit soils
 that have been cultured for over 30 years in plant family-specific beds at
 Oxford University Botanic Gardens. Plant responses to soil source were
 idiosyncratic, and species did not perform better on soils cultured by
 phylogenetically more distant relatives. The magnitude and sign of
 feedback effects could, however, be explained by differences in the
 chemical properties of “home” and “away” soils. Furthermore, the direction
 of soil chemistry-related plant-soil feedbacks was dependent on plant life
 stage, with the effects of soil chemistry on germination success and
 accumulation of biomass inversely related. Our results (1) suggest that
 the phylogenetic distance between plant families cannot predict plant–soil
 feedbacks across multiple life stages, and (2) highlight the need to
 consider changes in soil chemistry as an important driver of population
 responses. The contrasting responses at plant life stages suggest that
 studies focusing on brief phases in plant demography (e.g., germination
 success) may not give a full picture of plant–soil feedback effects.
description: Plant-soil feedbacks on
 30-year soil culturesData set for the
 publication associated with this Dryad data package: on the effects of
 30-year family specific soil cultures on the germination, growth, biomass
 and survival of plant species from those plant families. Dataset includes
 raw species responses to soil treatments, along with phylogenetic distance
 estimates and soil chemistry distances separating the plant family beds
 used in the experiments. See README for more details and
 metadata.Mehrabietal_psf30yrcultures.csv
DOI: 10.5061/dryad.k2q52
title: Data from: Neighbouring-group composition and within-group relatedness drive extra-group paternity rate in the European badger (Meles meles)

description: Extra-group paternity (EGP) occurs commonly among group-living mammals and
 plays an important role in mating systems and the dynamics of sexual
 selection; however, socio-ecological and genetic correlates of EGP have
 been underexplored. We use 23 years of demographic and genetic data from a
 high-density European badger (Meles meles) population, to investigate the
 relationship between the rate of EGP in litters and mate availability,
 mate incompatibility and mate quality (heterozygosity). Relatedness
 between within-group assigned mothers and candidate fathers had a negative
 quadratic effect on EGP, whereas the number of neighbouring-group
 candidate fathers had a linear positive effect. We detected no effect of
 mean or maximum heterozygosity of within-group candidate fathers on EGP.
 Consequently, EGP was associated primarily with mate availability, subject
 to within-group genetic effects, potentially to mitigate mate
 incompatibility and inbreeding. In badgers, cryptic female choice,
 facilitated by superfecundation, superfoetation and delayed implantation,
 prevents males from monopolizing within-group females. This resonates with
 a meta-analysis in group-living mammals, which proposed that higher rates
 of EGP occur when within-group males cannot monopolize within-group
 females. In contrast to the positive meta-analytic association, however,
 we found that EGP associated negatively with the number of within-group
 assigned mothers and the number of within-group candidate fathers;
 potentially a strategy to counter within-group males committing
 infanticide. The relationship between the rate of EGP and socio-ecological
 or genetic factors can therefore be intricate, and the potential for
 cryptic female choice must be accounted for in comparative studies.
description: Annavi et al datafile
 JEB
DOI: 10.15468/dl.jrbag6
title: Occurrence Download

description: A dataset containing 641 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physalis pruinosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 641 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000972-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.