cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.u8ncmf
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cliftonia monophylla",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001116-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9sm68
title: Data from: Carrying capacity in a heterogeneous environment with habitat connectivity

description: A large body of theory predicts that populations diffusing in
 heterogeneous environments reach higher total size than if non-diffusing,
 and, paradoxically, higher size than in a corresponding homogeneous
 environment. However, this theory and its assumptions have not been
 rigorously tested. Here, we extended previous theory to include
 exploitable resources, proving qualitatively novel results, which we
 tested experimentally using spatially diffusing laboratory populations of
 yeast. Consistent with previous theory, we predicted and experimentally
 observed that spatial diffusion increased total equilibrium population
 abundance in heterogeneous environments, with the effect size depending on
 the relationship between r and K. Refuting previous theory, however, we
 discovered that homogeneously distributed resources support higher total
 carrying capacity than heterogeneously distributed resources, even with
 species diffusion. Our results provide rigorous experimental tests of new
 and old theory, demonstrating how the traditional notion of carrying
 capacity is ambiguous for populations diffusing in spatially heterogeneous
 environments.
description: DATA_Zhang et al
 EcoLettData for Fig 4, 5,
 6
DOI: 10.15468/dl.garfga
title: Occurrence Download

description: A dataset containing 512 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Culicoides"
 ]
}

 The dataset includes 512 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001117-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5089j74
title: Data from: Genetic quality affects the rate of male and female reproductive ageing differently in Drosophila melanogaster

description: Males and females often maximize fitness by pursuing different
 reproductive strategies, with males commonly assumed to benefit more from
 increased resource allocation into current reproduction. Such investment
 should trade-off with somatic maintenance and may explain why males
 frequently live shorter than females. It also predicts that males should
 experience faster reproductive ageing. Here we investigate if reproductive
 ageing and lifespan respond to condition differently in male and female
 Drosophila melanogaster, as predicted if sexual selection has shaped male
 and female allocation patterns. We manipulate condition through genetic
 quality, by comparing individuals inbred or outbred for a major autosome.
 While genetic quality had a similar effect on condition in both sexes,
 condition had a much larger general effect on male than female
 reproductive output, as expected when sexual selection on vigour acts more
 strongly on males. We find no differences in reproductive ageing between
 the sexes in low condition, but in high condition reproductive ageing is
 relatively faster in males. No corresponding sex-specific change was found
 for lifespan. The sex difference in reproductive ageing appearing in high
 condition was due specifically to a decreased ageing rate in females,
 rather than any change in males. Our results suggest that females age
 slower than males in high condition primarily because sexual selection has
 favoured sex differences in resource allocation under high condition, with
 females allocating relatively more towards somatic maintenance than males.
description: LifespanLifespan data from D. melanogaster (the Dahomey laboratory-adapted population), measured in vials. Numerical columns are days since start of experiment and their content is number of deaths since previous column.ViabilityEgg-to-adult viability data from D. melanogaster (the Dahomey laboratory-adapted population), measured in vials. Focal F is number of eclosed females and Focal M number of eclosed males. Ebony is number of eclosed competitor flies.Reproductive OutputData on reproductive output as number of eclosed offspring from D. melanogaster (the Dahomey laboratory-adapted population), measured in vials. The output in each vial is the sum of focal and ebony flies eclosed for each week. Numbers in column headings represents weeks since start of experiment. NA represents no counting due to all focal flies being deceased. For week 9 all ebony competitors for the male focals were at least 200. The number of offspring eclosed came from a number of parents in the vial recorded in the Lifespan file for focal flies and the Competitors file for ebony competitors.Reproductive_Output.csvCompetitorsNumber of ebony competitor flies alive (Drosophila melanogaster, Damohey lab-adapted population) for measurement of reproductive output.
DOI: 10.5061/dryad.84t42
title: Data from: Do pathogens limit the distributions of tropical trees across a rainfall gradient?

description: 1. Organisms are adapted to particular habitats; consequently, community
 composition changes across environmental gradients, enhancing regional
 diversity. In Panama, a rainfall gradient correlates with the spatial
 turnover of tree species. While strong evidence suggests that tree species
 common in the wetter forests are excluded from the drier forests by
 seasonal drought, the factor(s) excluding drought-tolerant species, common
 in the drier forests, from the wetter forests remain ambiguous. 2. Here,
 we show that seedlings were significantly more likely to suffer
 pathogen-caused damage and mortality in the wetter forest. While seedlings
 of dry- and wet-forest species were equally likely to suffer pathogen
 attack, seedlings of dry-forest species were significantly more likely to
 die when attacked and tended to suffer more pathogen-caused mortality
 overall. Furthermore, seedlings of dry-forest species suffered
 pathogen-caused mortality in the forest in which they do not naturally
 occur and in which conspecific and/or congeneric adults are absent or
 rare, indicating that some pathogens are relatively widespread and/or are
 capable of damaging multiple host species. 3. Synthesis. Elevated risk of
 pathogen-caused damage and mortality in the wetter forests and a greater
 impact to host fitness from pathogen attack for seedlings of dry-forest
 species suggest that pathogens may enhance regional forest diversity by
 contributing to changes in tree species composition via the exclusion of
 dry-forest tree species from the wetter forests. This study highlights a
 potentially widespread and under explored mechanism by which pathogens
 shape plant communities at the landscape scale. An understanding of how
 species’ distributions are shaped by the interplay between abiotic and
 biotic factors is essential for conservation biology.
description: DoPathogensLimitTreeDistributions_ArchivedData
DOI: 10.5061/dryad.1v035
title: Data from: Biological invasion modifies the co-occurrence patterns of insects along a stress gradient

description: Biological invasions have become one of the most important drivers of
 biodiversity loss and ecosystem change world-wide. However, it is still
 unclear how invasions may interact with local abiotic stressors, which are
 expected to increase as global change intensifies. Furthermore, we know
 little about the response to biological invasions of insects, despite
 their disproportionate contribution to global animal biodiversity. The aim
 of the present work is to investigate the impact of an invasive aquatic
 insect on the co-occurrence patterns of native species of insects along a
 salinity gradient, and determine which assembly rules are driving these
 patterns. First, we characterised the habitat specialisation and
 functional niches of each species from physiological and biological
 traits, respectively, and their degree of overlap. Second, we used field
 data to compare the co-occurrence patterns of native and invasive species
 in invaded and non-invaded areas of southern Iberia and northern Morocco.
 Finally, we tested if habitat filtering or niche differentiation assembly
 rules mediate their co-occurrence. In non-invaded areas, habitat filtering
 drives habitat segregation of species along the salinity gradient, with a
 lower contribution of niche differentiation. The presence of the invasive
 insect modifies the distribution and co-occurrence patterns of native
 species. In invaded areas, niche differentiation seems to be the main
 mechanism to avoid competition among the invasive and native species,
 enabling coexistence and resource partitioning. The combined study of
 functional niche similarity and abiotic stressor tolerance of invasive and
 native species can improve our understanding of the effects of invasive
 species along abiotic stress gradients. This approach may increase our
 capacity to predict the outcomes of biological invasion in a global change
 context.
description: Data Carbonell et
 alCompressed file
 containing 7 archives: environmental and biological data from invaded and
 non-invaded areas (original dataset); environmental and biological data
 from invaded area (to be used for data analysis along with the R script);
 environmental and biological data from non-invaded area (to be used for
 data analysis along with the R script); physiological and biological
 traits of corixids and their categories (to be used for data analysis
 along with the R script); affinity values of species for each trait
 category (to be used for data analysis along with the R script),
 physiological and biological traits of corixids and their categories
 (original dataset); document with detailed archives
 description.
DOI: 10.5061/dryad.589t0
title: Data from: Behaviour-related DRD4 polymorphisms in invasive bird populations

description: It has been suggested that individual behavioural traits influence the
 potential to successfully colonize new areas. Identifying the genetic
 basis of behavioural variation in invasive species thus represents an
 important step towards understanding the evolutionary potential of the
 invader. Here, we sequenced a candidate region for neophilic/neophobic and
 activity behaviour – the complete exon 3 of the DRD4 gene – in 100
 Yellow-crowned bishops (Euplectes afer) from two invasive populations in
 Spain and Portugal. The same birds were scored twice for activity
 behaviour while exposed to novel objects (battery or slice of apple) in
 captivity. Response to novel objects was repeatable (r = 0.41) within
 individuals. We identified two synonymous DRD4 SNPs that explained on
 average between 11% and 15% of the phenotypic variance in both
 populations, indicating a clear genetic component to the
 neophilic/neophobic/activity personality axis in this species. This
 consistently high estimated effect size was mainly due to the repeated
 measurement design, which excludes part of the within-individual
 nongenetic variance in the response to different novel objects. We suggest
 that the alternative alleles of these SNPs are likely introduced from the
 original population and maintained by weak or antagonistic selection
 during different stages of the invasion process. The identified genetic
 variants have not only the potential to serve as genetic markers of the
 neophobic/neophilic/activity personality axis, but may also help to
 understand the evolution of behaviour in these invasive bird populations.
description: Genotypes and phenotypes
 of Euplectes aferThe data file lists
 genotypes, behavioural phenotypes and relevant cofactors of the Spanish
 and Portuguese study populations of Yellow-crowned bishops (Euplectes
 afer).Euplectes_afer_genotypes_phenotypes.txt
DOI: 10.5061/dryad.fc546
title: Data from: Phage loss and the breakdown of a defensive symbiosis in aphids

description: Terrestrial arthropods are often infected with heritable bacterial
 symbionts which may themselves be infected by bacteriophages. However,
 what role, if any, bacteriophages play in the regulation and maintenance
 of insect-bacteria symbioses is largely unknown. Infection of the aphid
 Acyrthosiphon pisum by the bacterial symbiont Hamiltonella defensa confers
 protection against parasitoid wasps, but only when H. defensa is itself
 infected by the phage APSE. Here we use a controlled genetic background
 and correlation-based assays to show that loss of APSE produces up to
 seven- fold increases in the intra-aphid abundance of H. defensa. APSE
 loss is also associated with severe deleterious effects on aphid fitness:
 aphids infected with H. defensa lacking APSE have a significantly delayed
 onset of reproduction, lower weight at adulthood, and half as many total
 offspring as aphids infected with phage-harbouring H. defensa, indicating
 that phage loss can rapidly lead to the breakdown of the defensive
 symbiosis. Our results overall indicate that bacteriophages play critical
 roles in both aphid defence and the maintenance of heritable symbiosis.
description: APSElossaphidfitnessTable2Fitness data (time to first reproduction, fresh weight at time of first reproduction, and offspring production by cohorts of four aphids) in Acyrthosiphon pisum clonal lines sharing the same aphid genotype and Hamiltonella defensa strain, with (a1a-5a+) and without (a1a-5aX) bacteriophage APSE.phageAPSElossbacterialtitresfigure1Quantitative PCR data for Hamiltonella defensa dnaK and APSE gene P28 in experimental lines sharing the same aphid genotype (1a, 1b and 1d) and genotypically diverse clonal lineages (1c).correctedphageAPSElossbacterialtitresfigure1.xlsx
DOI: 10.5061/dryad.1rc0v
title: Data from: Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold

description: Maturation is a critical developmental process, and the age and size at
 which it occurs have important fitness consequences. Although maturation
 is remarkably variable, certain mechanisms, including a minimum size or
 state threshold, are proposed to underlie the process across a broad
 diversity of taxa. Recent evidence suggests that thresholds may themselves
 be developmentally plastic, and in the crustacean Daphnia pulex it is
 unclear whether maturation follows a threshold or is a gradual process
 more akin to a rate. Changes in gene expression across four instars before
 and during maturation were compared in a cDNA microarray experiment.
 Developmental stage was treated statistically both as a discontinuous and
 a continuous variable, to determine whether genes showed gradual or
 discrete changes in expression. The continuous analysis identified a
 greater number of genes with significant differential expression (45) than
 the discontinuous analysis (11). The majority of genes, including those
 coding for histones, factors relating to transcription and cell cycle
 processes, and a putative developmental hormone showed continuous
 increases or decreases in expression from the first to the fourth instar,
 suggestive of a prolonged and gradual maturation process. Three genes
 coding for a fused Vitellogenin/super-oxide dismutase showed increases in
 expression following the second instar and coincided with the posited
 maturation threshold, but even their expression increased in a continuous
 fashion.
description: JEB_12624_Dpulex-maturation_limma-analysisR script that runs continuous and discontinuous limma analysis, generates heatmap and plots profiles of transcriptional changes across development. Requires pair files, available from ArrayExpress accession number E-MTAB-3388, as well as the limma_coefficients_for-plots.txt tablelimma_coefficients_for-plotsTable modified from output of the R Script, allowing visualisation of changing patterns of gene expression across development. Requires the R script JEB_12624_Dpulex-maturation_limma-analysis.R
DOI: 10.5061/dryad.2815c
title: Data from: Predators indirectly induce stronger prey through a trophic cascade

description: Many prey species induce defences in direct response to predation cues.
 However, prey defences could also be enhanced by predators indirectly via
 mechanisms that increase resource availability to prey, e.g. trophic
 cascades. We evaluated the relative impacts of these direct and indirect
 effects on the mechanical strength of the New Zealand sea urchin Evechinus
 chloroticus. We measured crush-resistance of sea urchin tests (skeletons)
 in (i) two marine reserves, where predators of sea urchins are relatively
 common and have initiated a trophic cascade resulting in abundant food for
 surviving urchins in the form of kelp, and (ii) two adjacent fished areas
 where predators and kelps are rare. Sea urchins inhabiting protected rocky
 reefs with abundant predators and food had more crush-resistant tests than
 individuals on nearby fished reefs where predators and food were
 relatively rare. A six-month long mesocosm experiment showed that while
 both food supply and predator cues increased crush-resistance, the
 positive effect of food supply on crush-resistance was greater. Our
 results demonstrate a novel mechanism whereby a putative morphological
 defence in a prey species is indirectly strengthened by predators via
 cascading predator effects on resource availability. This potentially
 represents an important mechanism that promotes prey persistence in the
 presence of predators.
description: morphology_datasetThis file contains three datasets which were used in the analysis of the manuscript: 1) data on crushing resistance, test thickness and spine length for sea urchins collected inside and outside of marine reserves in north-eastern New Zealand, 2) data on crushing resistance, test thickness and spine length for juvenile sea urchins within the 6 month mesocosm experiment and, 3) porosity data collected from individuals examined under a scanning electron microscope.
DOI: 10.5061/dryad.98f8c
title: Data from: Hydrocarbon divergence and reproductive isolation in Timema stick insects

description: Background: Individuals commonly prefer certain trait values over others
 when choosing their mates. If such preferences diverge between
 populations, they can generate behavioral reproductive isolation and
 thereby contribute to speciation. Reproductive isolation in insects often
 involves chemical communication, and cuticular hydrocarbons, in
 particular, serve as mate recognition signals in many species. We combined
 data on female cuticular hydrocarbons, interspecific mating propensity,
 and phylogenetics to evaluate the role of cuticular hydrocarbons in
 diversification of Timema walking-sticks. Results: Hydrocarbon profiles
 differed substantially among the nine analyzed species, as well as between
 partially reproductively-isolated T. cristinae populations adapted to
 different host plants. In no-choice trials, mating was more likely between
 species with similar than divergent hydrocarbon profiles, even after
 correcting for genetic divergences. The macroevolution of hydrocarbon
 profiles, along a Timema speciesphylogeny, fits best with a punctuated
 model of phenotypic change concentrated around speciation events,
 consistent with change driven by selection during the evolution of
 reproductive isolation. Conclusion: Altogether, our data indicate that
 cuticular hydrocarbon profiles vary among Timema species and populations,
 and that most evolutionary change in hydrocarbon profiles occurs in
 association with speciation events. Similarities in hydrocarbon profiles
 between species are correlated with interspecific mating propensities,
 suggesting a role for cuticular hydrocarbon profiles in mate choice and
 speciation in the genus Timema.
description: Mating_ProportionsMating proportions within and between Timema speciesHydrocarbon_DataCuticular hydrocarbon values for Timema individuals
DOI: 10.5061/dryad.84bp7
title: Data from: Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient

description: Critical thermal limits are thought to be correlated with the elevational
 distribution of species living in tropical montane regions, but with upper
 limits being relatively invariant compared to lower limits. To test this
 hypothesis, we examined the variation of thermal physiological traits in a
 group of terrestrial breeding frogs (Craugastoridae) distributed along a
 tropical elevational gradient. We measured the critical thermal maximum
 (CTmax; n = 22 species) and critical thermal minimum (CTmin; n = 14
 species) of frogs captured between the Amazon floodplain (250 m asl) and
 the high Andes (3800 m asl). After inferring a multi-locus species tree,
 we conducted a phylogenetically informed test of whether body size, body
 mass, and elevation contributed to the observed variation in CTmax and
 CTmin along the gradient. We also tested whether CTmax and CTmin exhibit
 different rates of change given that critical thermal limits (and their
 plasticity) may have evolved differently in response to different
 temperature constraints along the gradient. Variation of critical thermal
 traits was significantly correlated with species’ elevational midpoint,
 their maximum and minimum elevations, as well as the maximum air
 temperature and the maximum operative temperature as measured across this
 gradient. Both thermal limits showed substantial variation, but CTmin
 exhibited relatively faster rates of change than CTmax, as observed in
 other taxa. Nonetheless, our findings call for caution in assuming
 inflexibility of upper thermal limits, and underscore the value of
 collecting additional empirical data on species’ thermal physiology across
 elevational gradients.
description: MCC_treeMaximum Clade Credibility tree for 22 species included in this study, based on a multilocus species tree obtained with *BEAST. The node values include Bayesian posterior probabilities and the bars indicate 95% High Posterior Density (HPD) intervals. (Included as Supplementary Figure S2.)SpeciesTree_MCC.tree