cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.895b2
title: Data from: Personality composition is more important than group size in determining collective foraging behaviour in the wild

description: Describing the factors that shape collective behaviour is central to our
 understanding of animal societies. Countless studies have demonstrated an
 effect of group size in the emergence of collective behaviours, but
 comparatively few have accounted for the composition/diversity of
 behavioural phenotypes, which is often conflated with group size. Here, we
 simultaneously examine the effect of personality composition and group
 size on nest architecture and collective foraging aggressiveness in the
 social spider Stegodyphus dumicola. We created colonies of two different
 sizes (10 or 30 individuals) and four compositions of boldness (all bold,
 all shy, mixed bold and shy, or average individuals) in the field and then
 measured their collective behaviour. Larger colonies produced bigger
 capture webs, while colonies containing a higher proportion of bold
 individuals responded to and attacked prey more rapidly. The number of
 attackers during collective foraging was determined jointly by composition
 and size, although composition had an effect size more than twice that of
 colony size: our results suggest that colonies of just 10 bold spiders
 would attack prey with as many attackers as colonies of 110 ‘average’
 spiders. Thus, personality composition is a more potent (albeit more
 cryptic) determinant of collective foraging in these societies.
description: Keiser and Pruitt -
 Composition and size ESMThe data associated with
 collective behavior assays. Three response variables (latency to emerge
 from the colony retreat, latency to attack the prey stimulus, number of
 attackers) in response to two independent variables: colony personality
 composition and colony size.
DOI: 10.5061/dryad.8b203
title: Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively

description: Transcription factor binding to the surface of DNA regulatory regions is
 one of the primary causes of regulating gene expression levels. A
 probabilistic approach to model protein–DNA interactions at the sequence
 level is through position weight matrices (PWMs) that estimate the joint
 probability of a DNA binding site sequence by assuming positional
 independence within the DNA sequence. Here we construct conditional PWMs
 that depend on the motif signatures in the flanking DNA sequence, by
 conditioning known binding site loci on the presence or absence of
 additional binding sites in the flanking sequence of each siteʼs locus.
 Pooling known sites with similar flanking sequence patterns allows for the
 estimation of the conditional distribution function over the binding site
 sequences. We apply our model to the Dorsal transcription factor binding
 sites active in patterning the Dorsal–Ventral axis of Drosophila
 development. We find that those binding sites that cooperate with nearby
 Twist sites on average contain about 0.5 bits of information about the
 presence of Twist transcription factor binding sites in the flanking
 sequence. We also find that Dorsal binding site detectors conditioned on
 flanking sequence information make better predictions about what is a
 Dorsal site relative to background DNA than detection without information
 about flanking sequence features.
description: Sequence
 DataSequence data of known
 binding sites for Dorsal transcription factors, and sequence data of known
 CRMs (see README file inside the folder).sequenceData.tar.gzhttps://github.com/jacobclifford/MIBBSMIBBS, Mutual Information Between Binding Sites, is a set of programs that generate all the figures for our Physical Biology paper, where the current program settings and input data are the same values as used in our Physical Biology paper. The git project contains a configure script to automatically compile our C/C++ code regardless of platform (see the README file in the MIBBS directory on github). Once one executes the configure script and runs make, then run masterscript.sh, which will create all eps files for all figures (see the README for necessary dependency programs, such as GNU Scientific Library and matlab (matlab is not necessary if one wishes to generate figures using some other utility)).
DOI: 10.5061/dryad.gq716
title: Data from: Sexual signals for the colour-blind: cryptic female mantids signal quality through brightness

description: 1. Cryptic coloration may evolve in response to selective pressure imposed
 by predators, yet effective intraspecific communication may require some
 level of detectability. This creates a tension between the benefits of
 sexually selected visual traits and the predatory costs imposed by greater
 conspicuousness, and little is known about how this tension may be
 ameliorated in highly cryptic species. 2. We explore these competing
 demands in the false garden mantid Pseudomantis albofimbriata, a
 colour-blind and seemingly cryptic insect. We use reflectance spectrometry
 and receptor-noise modelling to characterize the conspicuousness of mantid
 body regions in the visual systems of mates (mantids), as well as
 potential predators (birds) and prey (bees). We then use condition
 manipulation and conspecific choice tests to further explore the colour
 traits of interest. 3. Based on visual modelling, we find that male
 mantids are inconspicuous to conspecifics, prey and predators – that is,
 they are chromatically and achromatically cryptic. In contrast, female
 mantids are chromatically cryptic to all potential receivers, but their
 abdomens are achromatically conspicuous. Our food manipulation experiment
 shows that females in good condition (and therefore with more eggs) have
 brighter abdomens than females in poor condition. Choice assays show male
 mantids are consistently attracted to females bearing brighter abdomens.
 4. Our results reveal brightness-mediated sexual signalling in a
 colour-blind and classically cryptic insect. By communicating in the only
 visual channel available to them, female mantids are conspicuously
 signalling their quality to mates, while potentially minimizing their
 conspicuousness to predators and prey. Furthermore, by signalling with
 only a single body region, female mantids are apparently using coincident
 disruptive coloration to further decrease detectability to potential
 eavesdroppers. 5. Our data reveal a novel example of the way in which the
 trade-off between sexual selection for conspicuousness and natural
 selection for crypsis may be mediated in a visual signalling system. Such
 signals may be common in apparently cryptic species, and this study once
 again demonstrates the importance of analysing visual signals beyond the
 capacity of human vision.
description: Choice
 testsData from conspecific
 choice experimentchoice_tests.csvCondition and brightnessData from female condition/brightness experimentcondition_brightness.csvVisual modellingData from visual modelling of mantid body regionsvisual_modelling.csv
DOI: 10.5061/dryad.pm86c
title: Data from: Spatial autocorrelation in fitness affects the estimation of natural selection in the wild

description: 1. Natural selection is typically estimated in the wild using Lande and
 Arnold's multiple regression approach. Despite its utility for
 evolutionary ecologists, this method is subject to the classical
 assumptions of multiple regressions, which could result in potential
 analytical problems. In particular, spatial autocorrelation in fitness
 violates the assumption of residuals independence. Although widespread in
 the wild, the consequences of this effect have yet to be investigated in
 the context of Lande and Arnold's regression and resulting selection
 estimation. 2. Here we first described four spatially explicit models that
 allow to control for spatial autocorrelation in residuals of the Lande and
 Arnold's regression: a generalized least square (GLS) model with a
 distance-based exponential covariance function, two simultaneous
 autoregressive models (SAR, the lagged-response model (SAR-lag) and the
 spatial error model (SAR-err)) and a 5-step procedure using the principal
 coordinates of neighbour matrices (PCNM) method based on the extraction of
 spatial descriptors. We then compared the four spatially explicit models
 of selection to non-spatial models for three life-history traits recorded
 over 6 years in a wild blue tit (Cyanistes caeruleus) population. We also
 compared the performance of the four spatially explicit models of
 selection using a simulation approach. 3. Our analyses revealed strong
 spatial autocorrelation in residuals of selection models, which was
 completely described by the two SAR and the PCNM models, while only
 partially described by the GLS model. The magnitude of selection gradients
 and differentials decreased systematically in the 4 spatially explicit
 models while the degree of fit of these models increased (except for the
 GLS model). Moreover, we showed using simulations that the selection
 coefficients extracted from the SAR-lag model were systematically biased
 compared to those extracted from the GLS, SAR-err and PCNM models. 4. We
 hereby showed that spatial autocorrelation in fitness can severely affect
 selection differentials and gradients, even at a relatively small spatial
 scale. By using geostatistical models such as PCNM or SAR-err models, it
 is possible to control for this spatial autocorrelation. Finally, since
 spatial autocorrelation is closely linked to spatial environmental
 variation, this approach can also be used to explore environmental
 components of covariance between fitness and traits.
description: Blue Tits data set from
 2008 to 2013Please see the
 README.txt fileMarrot_Garant_Charmantier2015.xlsx
DOI: 10.5061/dryad.pj763
title: Data from: Regional diversity reverses the negative impacts of an alien predator on local species-poor communities

description: Species diversity is often an implicit source of biological insurance for
 communities against the impacts of novel perturbations, such as the
 introduction of an invasive species. High environmental heterogeneity
 (e.g., a mountainous gradient) is expected to beget greater regional
 species diversity and variation in functional traits related to
 environmental tolerances. Thus, heterogeneous metacommunities are expected
 to provide more tolerant colonists that buffer stressed local communities
 in the absence of dispersal limitation. We tested the hypothesis that
 importation of a regional zooplankton pool assembled from a diverse array
 of lakes and ponds lessens the impacts of a novel predator on local
 species-poor alpine communities by increasing response diversity (i.e.,
 diversity of tolerances to environmental change) as mediated by variation
 in functional traits related to predator evasion. We also tested if
 impacts varied with temperature, as warming may modify (e.g., dampen or
 amplify) invasion effects. An eight-week factorial experiment ([fishless
 vs. introduced Oncorhynchus mykiss (rainbow trout)] x [ambient temperature
 vs. heated] x [local vs. local + regional species pool]) was conducted
 using thirty-two 1000 L mesocosms. Associations between experimental
 treatments and species functional traits were tested by RLQ and
 fourth-corner analyses. Although the introduced predator suppressed local
 species richness and community biomass, colonization by several montane
 zooplankters reversed these negative effects, resulting in increased
 species diversity and production. Invasion resistance was unaffected by
 higher temperatures, which failed to elicit any significance impacts on
 the community. We discovered that the smaller body sizes of imported
 species drove functional overcompensation (i.e., increased production) in
 invaded communities. The observed ecological surprise showed how
 regionally sourced biodiversity from a highly heterogeneous landscape can
 offset, and even reverse, the local negative impacts of an invasive
 species. Further, prey body size was found to be a key species trait
 mediating the ecological impacts of the aquatic invasive predator. Our
 study highlights the novel application of a functional approach to
 understanding the impacts of biological invasions, using species traits
 that pertain directly to potential responses to exotic species.
description: Organism concentrations
 in mesocosm tanksConcentrations of
 zooplankton species (see Table 1 for species codes), Chaoborus larvae, and
 total chlorophyll (phytoplankton and periphyton) in experimental mesocosms
 (treatments noted) on each sampling date. Available data presented as
 micrograms/L.Dryad.Loewen_and_Vinebrooke.Ecol.2016.Org_conc_in_mesos.csv
DOI: 10.5061/dryad.3sq24
title: Data from: A stoichiometric perspective of the effect of herbivore dung on ecosystem functioning

description: Ungulate herbivores play a prominent role in maintaining the tree–grass
 balance in African savannas. Their top-down role through selective feeding
 on either trees or grasses is well studied, but their bottom-up role
 through deposition of nutrients in dung and urine has been overlooked.
 Here, we propose a novel concept of savanna ecosystem functioning in which
 the balance between trees and grasses is maintained through stoichiometric
 differences in dung of herbivores that feed on them. We describe a
 framework in which N2-fixing trees and grasses, as well as ungulate
 browsing and grazing herbivores, occupy opposite positions in an
 interconnected cycle of processes. The framework makes the testable
 assumption that the differences in dung N:P ratio among browsers and
 grazers are large enough to influence competitive interactions between
 N2-fixing trees and grasses. Other key elements of our concept are
 supported with field data from a Kenyan savanna.
description: Nitrogen and phosphorus
 concentrations in forage and herbivore dungThe data file lists the
 nitrogen and phosphorus concentrations of the forage and herbivore dung
 used in Figure 1 in the paper. The data file consists of 3 sheets. Sheet 1
 is the meta data explaining the column names in sheet 2 and 3. Sheet 2
 contains the forage nutrient data of 4 N-fixing tree species (i.e., Acacia
 (Senegalia) brevispica, A. mellifera, Acacia (Vachellia) drepanolobium,
 and A. gerrardii) and 4 C4-grass species (i.e., Brachiaria lachnantha,
 Pennisetum mezianum, P. stramineum, and Themeda triandra). Sheet 3
 contains the dung nutrient data of 5 browser species (i.e., Guenther’s
 dikdik, eland, giraffe, greater kudu and Thomson’s gazelle) and 4 grazer
 species (African buffalo, Burchell’s zebra, Grevy’s zebra, and common
 warthog).Forage and herbivore dung
 nutrients.xlsx
DOI: 10.5061/dryad.467r0
title: Data from: Covariance among premating, postcopulatory and viability fitness components in Drosophila melanogaster and their influence on paternity measurement

description: In polyandrous mating systems, male fitness depends on success in
 premating, postcopulatory, and offspring viability episodes of selection.
 We tracked male success across all of these episodes simultaneously, using
 transgenic Drosophila melanogaster with ubiquitously expressed green
 fluorescent protein (i.e., GFP) in a series of competitive and
 non-competitive matings. This approach permitted us to track
 paternity-specific viability over all life stages and to distinguish true
 competitive fertilization success from differential early offspring
 viability. Relationships between episodes of selection were generally not
 present when paternity was measured in eggs, however positive correlations
 between sperm competitive success and offspring viability became
 significant when paternity was measured in adult offspring. Additionally,
 we found a significant male × female interaction on hatching success and a
 lack of repeatability of offspring viability across a focal male's
 matings, which may underly the limited number of correlations found
 between episodes of selection.
description: DrogeYoung2012_EpisodesDryadDataDrogeYoung_CompatibilityDryadDataThis file includes all data collected in the laboratory experiment assessing male and female contribution to offspring viability (experiment one in the publication). Data was collected by E.M. Droge-Young, M.K. Manier, S. Lüpold and S. Pitnick; additional questions should be directed to E.M. Droge-Young (emdroge@syr.edu). Data are in csv. format. Empty cells represent missing data (e.g., missing body size) whereas 0 is an informative value (e.g., 0% of eggs hatched) Specific variable information: Copulation duration is measured in minutes Hatch success represents the proportion of eggs that successfully hatched after at least 24 hours Development time is an average for each mating measured in days Posthatching viability represents the proportion of hatched offspring that successfully eclose as adults Thorax length is measured in millimeters
DOI: 10.5061/dryad.t31q738
title: Data from: Temperature drives diversification in a model adaptive radiation

description: The warmer regions harbor more species, attributable to accelerated
 speciation and increased ecological opportunities for coexistence. While
 correlations between temperature and energy availability and habitat area
 have been suggested as major drivers of these biodiversity patterns,
 temperature can theoretically also have direct effects on the evolution of
 diversity. Here we experimentally studied the evolution of diversity in a
 model adaptive radiation of the bacterium Pseudomonas fluorescens across a
 temperature gradient. Diversification increased at higher temperatures,
 driven by both faster generation of genetic variation and stronger
 diversifying selection. Specifically, low temperatures could limit the
 generation of diversity, suggested by the observation that supply of
 genetic variation through immigration increased diversity at low, but not
 high temperatures. The two major determinants of mutation supply,
 population size and mutation rate, both showed a positive temperature
 dependence. Stronger diversifying selection in warmer environments was
 suggested by promoted coexistence, and further explicitly inferred by the
 ability of evolved phenotypes to invade the ancestral type from rare. We
 discussed possible physiological and environmental mechanisms underlying
 the findings, most of which are likely to be general.
description: Raw
 dataRaw data for Figure
 1-3raw.data.procb.xlsx
DOI: 10.5061/dryad.3qp36g8
title: Data from: When is the best time to flower and disperse? a comparative analysis of plant reproductive phenology in the Mediterranean

description: 1. The phenology of organisms corresponds to the temporal match between
 the components of their life cycle and the seasonal distribution of
 resources and hazards. Flowering has been extensively studied to describe
 the reproductive phenology of plants, but in comparison, other key events
 for reproductive success such as the seed maturation period and the time
 of seed dispersal have been considerably less investigated. 2. This study
 describes the temporal sequence of onset of flowering and seed dispersal,
 and the time necessary to mature seeds in 138 species growing in the
 strongly seasonal climate of Mediterranean southern France. Data for the
 three traits were compiled from several original surveys to characterize
 the reproductive phenology of 47 annual, 67 perennial herbaceous and 24
 low stature woody species. The timing of these three phases was assessed
 in relation to local climatic conditions, and the degree to which they
 were coordinated was tested. 3. All three phenological traits spanned a
 wide range of values from early spring to late summer. Annuals flowered
 slightly earlier than perennials but the largest difference between these
 groups was found for the seed maturation period, which was much shorter in
 annuals. This resulted in earlier dispersal dates in these species, which
 occurred before periods of high water deficit. Significant positive
 correlations were found between onset of flowering, onset of seed
 dispersal, and seed maturation period. This suggests a consistent pattern
 of coordination between the different phases of reproductive phenology
 across species. 4. Our results show that while the time slot for flowering
 appears restricted to periods with adequate temperature and water
 availability for most species, the seed maturation period and dispersal
 phase can occur during periods of substantial water deficit, at least for
 perennials. They also suggest that the different species can be arrayed
 along a fast-slow continuum based on reproductive events, from early
 flowering species with short seed maturation and early dispersal to late
 flowering species with long seed maturation and late dispersal. Whether
 this relates to the postulated fast-slow continuum identified for the
 functioning of vegetative organs is a promising avenue for future
 research.
description: Dataset_When is the best
 time to flower and disperseData used in "When
 is the best time to flower and disperse? A comparative analysis of plant
 reproductive phenology in the Mediterranean". It combines estimated
 means and standard errors of onset of flowering, onset of seed dispersal
 and seed maturation period for 138 plant species growing in the
 Mediterranean region of southern France.
DOI: 10.5061/dryad.6d2ps7s7
title: Data from: Noise pollution alters ecological services: enhanced pollination and disrupted seed dispersal

description: Noise pollution is a novel, widespread environmental force that has
 recently been shown to alter the behavior and distribution of birds and
 other vertebrates, yet whether noise has cumulative, community-level
 consequences by changing critical ecological services is unknown. Herein,
 we examined the effects of noise pollution on pollination and seed
 dispersal and seedling establishment within a study system that isolated
 the effects of noise from confounding stimuli common to human-altered
 landscapes. Using observations, vegetation surveys and pollen transfer and
 seed removal experiments, we found that effects of noise pollution can
 reverberate through communities by disrupting or enhancing these
 ecological services. Specifically, noise pollution indirectly increased
 artificial flower pollination by hummingbirds, but altered the community
 of animals that prey upon and disperse Pinus edulis seeds, potentially
 explaining reduced P. edulis seedling recruitment in noisy areas. Despite
 evidence that some ecological services, such as pollination, may benefit
 indirectly due to noise, declines in seedling recruitment for key dominant
 species like P. edulis may have dramatic long-term effects on ecosystem
 structure and diversity. Because the extent of noise pollution is growing,
 this study emphasizes that investigators should evaluate the ecological
 consequences noise alongside other human-induced environmental changes
 that are reshaping human-altered landscapes worldwide.
description: Francis_etal_2012ProcB_pollination_dataFrancis_etal_2012ProcB_SeedRemoval_dataFrancis_etal_2012ProcB_Seedling_data