cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.59kv753
title: Data from: Correlation of native and exotic species richness: a global meta-analysis finds no invasion paradox across scales

description: Support for the “biotic resistance hypothesis,” that species-rich
 communities are more successful at resisting invasion by exotic species
 than are species-poor communities, has long been debated. It has been
 argued that native-exotic richness relationships (NERR) are negative at
 small spatial scales and positive at large scales, but evidence for the
 role of spatial scale on NERR has been contradictory. However, no formal
 quantitative synthesis has previously examined whether NERR is
 scale-dependent across multiple studies, and previous studies on NERR have
 not distinguished spatial grain and extent, which may drive very different
 ecological processes. We used a global systematic review and hierarchical
 mixed-effects meta-analysis to provide a comprehensive quantitative
 assessment of the patterns of NERR over a range of spatial grain sizes and
 spatial extents, based on 204 individual cases of observational
 (non-experimental) NERRs from 101 publications. We show that NERR was
 indeed highly scale-dependent across studies and increased with the log of
 grain size. However, mean NERR was not negative at any grain size,
 although there was high heterogeneity at small grain sizes. We found no
 clear patterns of NERR across different spatial extents, suggesting that
 extent plays a less important role in determining NERR than does grain,
 although there was a complex interaction between extent and grain size.
 Almost all studies on NERR were conducted in North America, western
 Europe, and a few other regions, with little information on tropical or
 Arctic regions. We did find that NERR increased northward in temperate
 regions and also varied with longitude. We discuss possible explanations
 for the patterns we found, and caution that our results do not show that
 invasive species are benign or have no negative consequences for
 biodiversity preservation. This study represents the first global
 quantitative analysis of scale-based NERR and casts doubt on the existence
 of an "invasion paradox" of negative NERR at small scales and
 positive correlations at large scales in non-experimental studies.
description: Systematic Review
 DatabaseInformation from papers
 in the Systematic review, including grain, extent, habitat type, type of
 research, and lat/long.DataS1_SystematicReviewDatabase.csvMeta-analysis DatabaseAll data extracted from papers used in the meta-analysis. R code for the analysis used with these data is uploaded separately.DataS2_MetaAnalysisDatabase.csvR Code for the Meta-analysisThis is the R code that was used to analyze the data in the Data2MetaAnalysisDataBase fileRCodeS2_MetaAnalysis.RExperimental Studies DatabaseData from papers that carried out experiments; not used in the meta-analysis except for calculating weighted mean and CI mentioned in the DiscussionDataS3_ExperimentalStudiesDatabase.csv
DOI: 10.5061/dryad.m4m9v
title: Data from: A long-term evaluation of applied nucleation as a strategy to facilitate forest restoration

description: Applied nucleation is a restoration technique that seeks to facilitate
 woody plant establishment by attracting birds or other animals that may
 introduce seeds of dispersal-limited species. In 1991, an experimental
 test of applied nucleation was initiated in an abandoned landfill in New
 Jersey, USA. Trees and shrubs were planted into 16 10 × 10-m plots,
 covering less than 3% of the 6 ha site. In 2010-2011, we sampled the plant
 community to test the impact of the treatments on forest cover and plant
 biodiversity. Site-wide forest cover increased substantially in the 19
 years since planting from none to 59%. The original planted plots had
 significantly higher stem density, particularly of bird-dispersed species,
 than unplanted areas. Species composition outside the planted plots was
 dominated by the wind-dispersed Fraxinus americana and several
 small-seeded bird-dispersed species, but there were few species indicative
 of later successional stages. The expected model of successional
 development via the nucleation model - that rates of colonization would be
 highest near plantings and that forest cover would spread outward from
 established clusters - was not supported after this time span. Given the
 site's isolation from potential sources of woody propagules, the
 experimental treatments may not have been enough to overcome many
 species' dispersal limitation. Regardless of the mechanism, however,
 the treatments transformed the once essentially treeless site into a
 densely wooded habitat, and did so at a rate faster than other
 descriptions of reforestation following disturbances or land-use changes
 in the region. Despite the relatively low species richness of the
 community, this experiment demonstrated that reforestation of even
 severely degraded habitat can be achieved with minimal management after
 site preparation and cluster plantings.
description: Plot
 locationsGPS-located latitude and
 longitude of the locations of planted clusters. All data is in Zone
 18N.Trees in planted
 plotsTrees sampled in planted
 plotsTrees in
 TransectsTrees outside planted
 plots, sampled along transects between plots.
DOI: 10.5061/dryad.60f62
title: Data from: Downregulation of the evolutionary capacitor Hsp90 is mediated by social cues

description: The relationship between robustness and evolvability is a long-standing
 question in evolution. Heat shock protein 90 (HSP90), a molecular
 chaperone, has been identified as a potential capacitor for evolution,
 since it allows for the accumulation and release of cryptic genetic
 variation, and also for the regulation of novel genetic variation through
 transposon activity. However, to date, it is unknown whether Hsp90
 expression is regulated upon demand (i.e. when the release of cryptic
 genetic variation is most needed). Here, we show that Hsp90 has reduced
 transcription under conditions where the mobilization of genetic variation
 could be advantageous. We designed a situation that indicates a stressful
 environment but avoids the direct effects of stress, by placing untreated
 (focal) red flour beetles, Tribolium castaneum, into groups together with
 wounded conspecifics, and found a consistent reduction in expression of
 two Hsp90 genes (Hsp83 and Hsp90) in focal beetles. We moreover observed a
 social transfer of immunity in this non-eusocial insect: there was
 increased activity of the phenoloxidase enzyme and downregulation of the
 immune regulator, imd. Our study poses the exciting question of whether
 evolvability might be regulated through the use of information derived
 from the social environment.
description: Supplementary
 DataRaw data for
 figures
DOI: 10.5061/dryad.8338
title: Data from: Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

description: Genomes of animals as different as sponges and humans show conservation of
 global architecture. Here we show that multiple genomic features including
 transposon diversity, developmental gene repertoire, physical gene order,
 and intron-exon organization are shattered in the tunicate Oikopleura,
 belonging to the sister group of vertebrates and retaining chordate
 morphology. Ancestral architecture of animal genomes can be deeply
 modified and may therefore be largely nonadaptive. This rapidly evolving
 animal lineage thus offers unique perspectives on the level of genome
 plasticity. It also illuminates issues as fundamental as the mechanisms of
 intron gain.
description: Denoeud-Science2010_4genes_aa_probcons_gblocksAmino acid concatenation of the 4 most conserved mitocondrial genes (COX1, COX2, COX3, CYTB) for 60 metazoans.Denoeud-Science2010_4genes_aa_probcons_gblocks_CAT-GTRBayesian consensus tree obtained under the CAT-GTR mixture model implemented in Phylobayes using the amino acid alignment of the 4 most conserved mitochondrial genes (COX1, COX2, COX3, CYTB).
DOI: 10.15468/dl.3xex85
title: Occurrence Download

description: A dataset containing 1345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Iochroma arborescens",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1345 records from 149 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000929-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f78b1
title: Data from: Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts

description: Social insect sex and caste ratios are well-studied targets of
 evolutionary conflicts, but the heritable factors affecting these traits
 remain unknown. To elucidate these factors, we carried out a short-term
 artificial selection study on female caste ratio in the ant Monomorium
 pharaonis. Across three generations of bidirectional selection, we
 observed no response for caste ratio, but sex ratios rapidly became more
 female-biased in the two replicate high selection lines and less
 female-biased in the two replicate low selection lines. We hypothesized
 that this rapid divergence for sex ratio was caused by changes in the
 frequency of infection by the heritable bacterial endosymbiont Wolbachia,
 because the initial breeding stock varied for Wolbachia infection, and
 Wolbachia is known to cause female-biased sex ratios in other insects.
 Consistent with this hypothesis, the proportions of Wolbachia-infected
 colonies in the selection lines changed rapidly, mirroring the sex ratio
 changes. Moreover, the estimated effect of Wolbachia on sex ratio (~13%
 female bias) was similar in colonies before and during artificial
 selection, indicating that this Wolbachia effect is likely independent of
 the effects of artificial selection on other heritable factors. Our study
 provides evidence for the first case of endosymbiont sex ratio
 manipulation in a social insect.
description: Appendix
 S2Data for all colonies
 used in the study. Columns: "Colony_ID"; "Generation"
 = 0-3 "Group" = High/Low/NA for colonies in the High and Low
 selection lines as well as initial colonies that were not selection;
 "Group2" = High1, High2, Low1, Low2, NA, specifying which
 replicate group colonies were in; "Replicate" = 1,2,0 redundant
 with Group2; "Parent" = YES/NO for whether colonies were
 selected as parents for the next generation; "workers",
 "gynes", "males" = the total number of workers, gynes,
 and males produced; "survived" = YES/NO, whether the colony
 survived to produce any individuals; "reproduced" = YES/NO,
 whether the colony produced any gynes or males.Supporting Information
 2.txtAppendix
 S3Complete annotated R
 script to reproduce the results and graphs.Supporting Information
 3.txt
DOI: 10.5061/dryad.d22bq
title: Data from: Transcriptional response of Hoxb genes to retinoid signalling is regionally restricted along the neural tube rostrocaudal axis

description: During vertebrate neural development, positional information is largely
 specified by extracellular morphogens. Their distribution, however, is
 very dynamic due to the multiple roles played by the same signals in the
 developing and adult neural tissue. This suggests that neural progenitors
 are able to modify their competence to respond to morphogen signalling and
 autonomously maintain positional identities after their initial
 specification. In this work, we take advantage of in vitro culture systems
 of mouse neural stem/progenitor cells (NSPCs) to show that NSPCs isolated
 from rostral or caudal regions of the mouse neural tube are differentially
 responsive to retinoic acid (RA), a pivotal morphogen for the
 specification of posterior neural fates. Hoxb genes are among the best
 known RA direct targets in the neural tissue, yet we found that RA could
 promote their transcription only in caudal but not in rostral NSPCs.
 Correlating with these effects, key RA-responsive regulatory regions in
 the Hoxb cluster displayed opposite enrichment of activating or repressing
 histone marks in rostral and caudal NSPCs. Finally, RA was able to
 strengthen Hoxb chromatin activation in caudal NSPCs, but was ineffective
 on the repressed Hoxb chromatin of rostral NSPCs. These results suggest
 that the response of NSPCs to morphogen signalling across the rostrocaudal
 axis of the neural tube may be gated by the epigenetic configuration of
 target patterning genes, allowing long-term maintenance of intrinsic
 positional values in spite of continuously changing extrinsic signals.
description: Supplementary dataset
 1SUPPORTING DATA FOR FIG.
 1 AND FIG. S1A, S1D.Supplementary dataset
 2SUPPORTING DATA FOR FIG.
 2 AND FIG. S1B, S1C, S1F.Supplementary dataset
 3SUPPORTING DATA FOR FIG.
 S2 AND FIG. S3.Supplementary dataset
 4SUPPORTING DATA FOR FIG.
 3.Supplementary dataset
 5SUPPORTING DATA FOR FIG.
 S5.Supplementary dataset
 6SUPPORTING DATA FOR FIG.
 4 AND FIG. 5.
DOI: 10.5061/dryad.20r4r
title: Data from: Herbivore impacts on marsh production depend upon a compensatory continuum mediated by salinity stress

description: Plant communities are disturbed by several stressors and they are expected
 to be further impacted by increasing anthropogenic stress. The
 consequences of these stressors will depend, in part, upon the ability of
 plants to compensate for herbivory. Previous studies found that herbivore
 impacts on plants can vary from negative to positive because of
 environmental control of plant compensatory responses, a.k.a. the
 Compensatory Continuum Hypothesis. While these influential studies
 enhanced our appreciation of the dynamic nature of plant-herbivore
 interactions, they largely focused on the impact of resource limitation.
 This bias limits our ability to predict how other environmental factors
 will shape the impact of herbivory. We examined the role of salinity
 stress on herbivory of salt marsh cordgrass, Spartina foliosa, by an
 herbivore previously hypothesized to influence the success of restoration
 projects (the scale insect, Haliaspis spartinae). Using a combination of
 field and mesocosm manipulations of scales and salinity, we measured how
 these factors affected Spartina growth and timing of senescence. In
 mesocosm studies, Spartina overcompensated for herbivory by growing taller
 shoots at low salinities but the impact of scales on plants switched from
 positive to neutral with increasing salinity stress. In field studies of
 intermediate salinities, scales reduced Spartina growth and increased the
 rate of senescence. Experimental salinity additions at this field site
 returned the impact of scales to neutral. Because salinity decreased scale
 densities, the switch in impact of scales on Spartina with increasing
 salinity was not simply a linear function of scale abundance. Thus, the
 impact of scales on primary production depended strongly upon
 environmental context because intermediate salinity stress prevented plant
 compensatory responses to herbivory. Understanding this context-dependency
 will be required if we are going to successfully predict the success of
 restoration efforts and the ecological consequences of anthropogenic
 disturbances.
description: Salinity, scale density,
 and Spartina performance during field and mesocosm manipulations of scale
 insects and soil salinityEach tab in the excel
 file contains data for a separate component from one of the three
 experiments. The 2011 and 2012 field experiments were conducted in
 Sweetwater Marsh. The 2011 mesocosm experiment was conducted at the San
 Diego State University Coastal Marine Institute and
 Laboratory.DataforDepository.xlsx
DOI: 10.5061/dryad.8rt51j0
title: Data from: Size-assortative choice and mate availability influences hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)

description: Anthropogenic hybridization of historically isolated taxa has become a
 primary conservation challenge for many imperiled species. Indeed,
 hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)
 poses a significant challenge to red wolf recovery. We considered 7
 hypotheses to assess factors influencing hybridization between red wolves
 and coyotes via pair-bonding between the two species. Because long-term
 monogamy and defense of all-purpose territories are core characteristics
 of both species, mate choice has long-term consequences. Therefore, red
 wolves may choose similar-sized mates to acquire partners that behave
 similarly to themselves in use of space and diet. We observed multiple
 factors influencing breeding pair formation by red wolves and found that
 most wolves paired with similar-sized conspecifics and wolves that formed
 congeneric pairs with non-wolves (coyotes and hybrids) were mostly female
 wolves, the smaller of the two sexes. Additionally, we observed that lower
 red wolf abundance relative to non-wolves and the absence of helpers
 increased the probability that wolves consorted with non-wolves. However,
 successful pairings between red wolves and non-wolves was associated with
 wolves that maintained small home ranges. Behaviors associated with
 territoriality are energetically demanding and behaviors (e.g., aggressive
 interactions, foraging, and space use) involved in maintaining territories
 are influenced by body size. Consequently, we propose the hypothesis that
 size disparities between consorting red wolves and coyotes influence
 positive assortative mating and may represent a reproductive barrier
 between the 2 species. We offer that it may be possible to maintain wild
 populations of red wolves in the presence of coyotes if management
 strategies increase red wolf abundance on the landscape by mitigating key
 threats, such as human-caused mortality and hybridization with coyotes.
 Increasing red wolf abundance would likely restore selection pressures
 that increase mean body and home-range sizes of red wolves and decrease
 hybridization rates via reduced occurrence of congeneric pairs.
description: wolf_pairing_dataFile contains pairing events, body measurements, and home range data
DOI: 10.5061/dryad.37k44
title: Data from: Restoration of endangered fen communities: the ambiguity of iron-phosphorus binding and phosphorus limitation

description: 1.Low phosphorus (P) availability limits plant biomass production in fens,
 which is a prerequisite for the persistence of many endangered plant
 species. We hypothesized that P limitation is linked to soil iron (Fe)
 content and soil Fe:P ratios as iron compounds provide binding sites for
 dissolved P, presumably reducing P availability to plants. 2.We sampled 30
 fens in a trans-European field survey to determine how soil Fe pools
 relate to pools of P and Fe-bound P, and we measured vegetation P uptake
 and N:P ratio to assess where P limitation occurs. Next, we determined P
 uptake by Carex rostrata in experimental fen mesocosms to investigate
 interactive effects of soil Fe- and P pools (and -NDASH-fractions) and
 water levels (drained or rewetted). 3.The field survey revealed that soil
 P pools correlate positively with soil Fe pools, regardless of fen
 degradation level, location, or sampling depth. Moreover, soil Fe- and P
 pools correlated positively with P uptake by the vegetation and negatively
 with vegetation N:P ratios. Generally, N:P ratios dropped below 10 g g−1
 whenever thresholds of 15 mmol Fe L−1 soil and 3.3 mmol P L−1 soil were
 exceeded. Endangered fen species mainly thrived in Fe- (and thus P-) poor
 fens. 4.The mesocosm experiment further showed that interactions between
 water levels and P pools determined plant P uptake: although fen rewetting
 led to an overall increase in P uptake, plants that had grown on drained
 Fe-rich soils with large acid-extractable P pools (&gt;1.6 mmol Pacid
 L−1) could still sequester large quantities of P. Soil Fe:P ratio had no
 effect on P uptake. 5.Synthesis and applications. Our findings have
 important implications for the management and restoration of endangered
 fen communities. We demonstrated the existence of an iron-phosphorus
 (Fe-P) binding ambiguity in fens: large Fe pools “trap” mobile P, thereby
 enhancing overall P availability to plants rather than diminishing it. For
 P limitation we suggest an empirical threshold of &lt; 3.3 mmol P L−1
 soil, which is mainly found in Fe-poor fens. Restoring fens by rewetting
 increases the relative availability of P and may not always result in
 favourable conditions for endangered fen communities. Rewetting of drained
 fens is most likely to be successful if soil P and Fe pools are well below
 3.3 mmol L−1 and 15 mmol L−1 respectively.
description: Emsens et al.
 DatafileThis file contains data
 of the field survey, vegetation relevees and the mesocosm experiment (3
 tabs).Emsens et al.
 Data.xlsx
DOI: 10.5061/dryad.d4q54
title: Data from: Routine habitat switching alters the likelihood and persistence of infection with a pathogenic parasite

description: 1.Animals switch habitats on a regular basis, and when habitats vary in
 suitability for parasitism, routine habitat switching alters the frequency
 of parasite exposure and may affect post-infection parasite proliferation.
 However, the effects of routine habitat switching on infection dynamics
 are not well understood. 2.We performed infection experiments, behavioural
 observations, and field surveillance to evaluate how routine habitat
 switching by adult alpine newts (Ichthyosaura alpestris) influences
 infection dynamics of the pathogenic parasite, Batrachochytrium
 dendrobatidis (Bd). 3.We show that when newts are exposed to equal total
 doses of Bd in aquatic habitats, differences in exposure frequency and
 post-exposure habitat alter infection trajectories: newts developed more
 infections that persisted longer when doses were broken into multiple,
 reduced-intensity exposures. Intensity and persistence of infections was
 reduced among newts that were switched to terrestrial habitats following
 exposure. 4.When presented with a choice of habitats, newts did not avoid
 exposure to Bd, but heavily infected newts were more prone to reduce time
 spent in water. 5.Accounting for routine switching between aquatic and
 terrestrial habitat in the experiments generated distributions of
 infection loads that were consistent with those in two populations of wild
 newts. 6.Together, these findings emphasize that differential habitat use
 and behaviours associated with daily movement can be important ecological
 determinants of infection risk and severity.
description: Data Analysis R
 scriptR script containing data
 formatting, and models for analysis of experiment 1 and experiment 2
 dataCombined Experiment 2017
 code.RExperiment 1
 dataInfection data produced
 from our first experiment that tested the effect of exposure frequency and
 post-exposure habitat switching in the absence of
 choice.IoZ.2013.raw.data.csvExperiment 2 cumulative dataData produced from our second experiment that tracked newts in aquatic and terrestrial habitats while exposing them to varying concentration of in aquatic habitats. Data contains cumulative measures (pooled across all days) of aquatic and terrestrial habitat use as well as Bd infections exhibited at the end of the experiment.Experiment.2.data.totals.csvExperiment 2 data - By phaseData produced from our second experiment that tracked newts in aquatic and terrestrial habitats while exposing them to varying concentration of in aquatic habitats. Data were averaged over days for phase 1 and phase 2.Experiment.2.data.PhaseTotals.csvExperiment 2 daily dataData produced from our second experiment. Individual data on habitat use for each day of the experiment, as well as Bd infections exhibited at the end of the experiment.Experiment.2.data.daily.csvSpain and UK field datainfection loads of positive samples collected from our field surveillance.Daversa.etal.2017.field.data.csv