cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h2m12
title: Data from: Habitat heterogeneity favors asexual reproduction in natural populations of grassthrips

description: Explaining the overwhelming success of sex among eukaryotes is difficult
 given the obvious costs of sex relative to asexuality. Different studies
 have shown that sex can provide benefits in spatially heterogeneous
 environments under specific conditions, but whether spatial heterogeneity
 commonly contributes to the maintenance of sex in natural populations
 remains unknown. We experimentally manipulated habitat heterogeneity for
 sexual and asexual thrips lineages in natural populations and under
 seminatural mesocosm conditions by varying the number of hostplants
 available to these herbivorous insects. Asexual lineages rapidly replaced
 the sexual ones, independently of the level of habitat heterogeneity in
 mesocosms. In natural populations, the success of sexual thrips decreased
 with increasing habitat heterogeneity, with sexual thrips apparently only
 persisting in certain types of hostplant communities. Our results
 illustrate how genetic diversity-based mechanisms can favor asexuality
 instead of sex when sexual lineages co-occur with genetically variable
 asexual lineages.
description: meadows_alldataThis file contains the number of field-collected thrips of each species and sex in the different experimental plots, as well as the cover of each Poaceae species.FitnessAssays_All_DataThis file contains the number of thrips counted in the experimental mesocosms. Sheets 1 and 4 contain fitness assays on different plant species that were used for Figure 1 of the manuscript. Sheets 2 and 3 contain adaptation assays, measured as numbers of offspring for a single, isolated female of asexual (sheet 2) or sexual (sheet 3) female. These data were used in Figure 3 of the manuscript.Mesocosms_elegans_rufusThis file contains the results of the competition experiment used in Figure 2 of the manuscript
DOI: 10.5061/dryad.fg220
title: Data from: Faunal response to sea-level and climate change in a short-lived seaway: Jurassic of the Western Interior, USA

description: Understanding how regional ecosystems respond to sea-level and
 environmental perturbations is a main challenge in palaeoecology. Here we
 use quantitative abundance estimates, integrated within a sequence
 stratigraphic and environmental framework, to reconstruct benthic
 community changes through the 13 myr history of the Jurassic Sundance
 Seaway in the western United States. Sundance Seaway communities are
 notable for their low richness and high dominance relative to most areas
 globally in the Jurassic, and this probably reflects steep temperature and
 salinity gradients along the 2000 km length of the Seaway that hindered
 colonization of species from the open ocean. Ordination of samples shows a
 main turnover event at the Middle–Upper Jurassic transition, which
 coincided with a shift from carbonate to siliciclastic depositional
 systems in the Seaway, probably initiated by northward drift from
 subtropical latitudes to more humid temperate latitudes, and possibly
 global cooling. Turnover was not uniform across the onshore–offshore
 gradient, but was higher in offshore environments. The higher resilience
 of onshore communities to third-order sea-level fluctuations and to the
 change from a carbonate to a siliciclastic system was driven by a few
 abundant eurytopic species that persisted from the opening to the closing
 of the Seaway. Lower stability in offshore facies was instead controlled
 by the presence of more volatile stenotopic species. Such increased
 onshore stability in community composition contrasts with the
 well-documented onshore increase in taxonomic turnover rates, and this
 study underscores how ecological analyses of relative abundance may
 contrast with taxonomically based analyses. We also demonstrate the
 importance of a stratigraphic palaeobiological approach to reconstructing
 the links between environmental and faunal gradients, and how their
 evolution through time produces local stratigraphic changes in community
 composition.
description: Danise & Holland - R
 script - 1 nMDS & clusterScript to perform NMDS
 ordination and cluster analysis. NOTE: run the scripts in the same order
 in which they are numbered (1 to 3) in order to be able to produce all the
 figures of the paper.Danise & Holland - R
 script - 2 Diversity facies & biofaciesScript to perform
 diversity analysesDanise & Holland - R
 script - 3 Similarity measuresScript to perform
 similarity analysisDanise & Holland -
 DatasetDataset.csvDanise & Holland - Dataset propertiesDataset - prop.csv
DOI: 10.15468/dl.rktxxv
title: Occurrence Download

description: A dataset containing 1458 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calibrachoa parviflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1458 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000858-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4q6f1
title: Data from: Independence among physiological traits suggests flexibility in the face of ecological demands on phenotypes

description: Phenotypic flexibility allows animals to adjust their physiology to
 diverse environmental conditions encountered over the year. Examining how
 these varying traits covary gives insights into potential constraints or
 freedoms that may shape evolutionary trajectories. In this study we
 examined relationships among hematocrit, baseline corticosterone
 concentration, constitutive immune function and basal metabolic rate in
 red knot Calidris canutus islandica individuals subjected to
 experimentally manipulated temperature treatments over an entire annual
 cycle. If covariation among traits is constrained, we predict consistent
 covariation within and among individuals. We further predict consistent
 correlations between physiological and metabolic traits if constraints
 underlie species level patterns found along the slow-fast pace-of-life
 continuum. We found no consistent correlations among hematocrit, baseline
 corticosterone concentration, immune function and basal metabolic rate
 either within or among individuals. This provides no evidence for
 constraints limiting relationships among these measures of the
 cardiovascular, endocrine, immune and metabolic systems in individual red
 knots. Rather, our data suggest that knots are free to adjust individual
 parts of their physiology independently. This makes good sense if one
 places the animal within its ecological context where different aspects of
 the environment might put different pressures on different aspects of
 physiology.
description: Physiological
 dataPhysiological data taken
 from individual birds over an annual cycle. The birds were part of a year
 long experiment and this file contains experimental and temporal
 categories as well as physiological variables.Buehleretal2012JEBdataset.xls
DOI: 10.5061/dryad.kh657
title: Data from: Decomposition of coarse woody debris in a long-term litter manipulation experiment: a focus on nutrient availability

description: 1.The majority of aboveground carbon in tropical forests is stored in
 wood, which is returned to the atmosphere during decomposition of coarse
 woody debris. However, the factors controlling wood decomposition have not
 been experimentally manipulated over time scales comparable to the length
 of this process. 2.We hypothesized that wood decomposition is limited by
 nutrient availability and tested this hypothesis in a long-term litter
 addition and removal experiment in a lowland tropical forest in Panama.
 Specifically, we quantified decomposition using a 15 year chronosequence
 of decaying boles, and measured respiration rates and nutrient limitation
 of wood decomposer communities. 3.The long-term probability that a dead
 tree completely decomposed was decreased in plots where litter was
 removed, but did not differ between litter addition and control
 treatments. Similarly, respiration rates of wood decomposer communities
 were greater in control treatments relative to litter removal plots;
 litter addition treatments did not differ from either of the other
 treatments. Respiration rates increased in response to nutrient addition
 (nitrogen, phosphorus, and potassium) in the litter removal and addition
 treatments, but not in the controls. 4.Established decreases in
 concentrations of soil nutrients in litter removal plots and increased
 respiration rates in response to nutrient addition suggest that reduced
 rates of wood decomposition after litter removal were caused by decreased
 nutrient availability. The effects of litter manipulations differed
 directionally from a previous short-term decomposition study in the same
 plots, and reduced rates of bole decomposition in litter removal plots did
 not emerge until after more than 6 years of decomposition. These
 differences suggest that litter-mediated effects on nutrient dynamics have
 complex interactions with decomposition over time.
description: Data for logistic
 regression of complete bole decomposition over 15 yearsThe data are described
 in an internal readme file.LitterTreat_logistic_regression.xlsxComparison of removed and retained bolesBoles were removed from the logistic regression analysis and the removed/retained boles are compared heredead_compare_excludedboles.xlsxWood respiration rates before NPK treatmentpretreat_wood_respiration.xlsxWood respiration after NPK treatmentHere are the wood respiration rates, change in wood respiration rates from average pretreatment respiration, and PCA axes values for boles that were treated with both water and NPK to test for nutrient limitationNPKaddition_wood_respiration.xlsxnutrient concentrationsThe concentrations of a variety of nutrients in the boles that were then assessed for differences in respiration in response to either NPK or water addition. Average concentrations are given in a table in text of the relevant manuscript.nutrient_concentrations.xlsx
DOI: 10.5061/dryad.v2v83
title: Data from: Changing drivers of species dominance during tropical forest succession

description: 1. Deterministic theories predict that local communities assemble from a
 regional species pool based on niche differences, thus by plant functional
 adaptations. We tested whether functional traits can also explain patterns
 in species dominance among the suite of co-occurring species. 2. We
 predicted that along a gradient of secondary succession the main driver of
 species dominance changes from environmental filtering in the relatively
 harsh (dry and hot) early successional conditions, towards increased
 competitive interactions and limiting similarity in later successional
 conditions (when light is limited). 3.We used the Kurtosis (K) (a measure
 of peakedness) of the functional trait distribution of secondary forest
 communities in high-diversity tropical rainforest in Chiapas, Mexico. The
 forests ranged 1 to 25 years in age, and we used 8 functional leaf traits
 related to a plants’ carbon, water and heat balance. We calculated the
 functional trait distribution based on species dominance, where trait
 values were weighted by species’ relative basal area, as well as based on
 species presence, all species counting once. “K-ratio” was subsequently
 computed by dividing kurtosis based on species dominance by kurtosis based
 on species presence. If the K-ratio is high, the dominant species are
 functionally similar and we interpreted this as environmentally driven
 functional convergence allowing species to become dominant. If the K-ratio
 is small, dominant species are a functionally dissimilar subset of the
 species present and we interpreted this as competitively driven functional
 divergence allowing species to become dominant. 4. We found that in early
 succession dominant species represent a functionally narrow subset of
 species with similar traits and in late succession dominant species
 increasingly represent a wide subset of the species present. This trend
 was found for traits that reflect photosynthetic performance and light
 capture, and indicates increased competition for light with succession. No
 trend was found for traits that indicate defense against herbivory,
 suggesting no successional changes in herbivore pressure. 5. Synthesis.
 This is one of the first studies showing that drivers of species dominance
 change along a gradient of secondary succession. During the early
 successional time window we evaluated, the importance of environmental
 filtering as a driving force fades away rapidly, and the importance of
 niche partitioning for species dominance starts to emerge.
description: Dryad-files1This file contains the values of kurtosis (Pearson's measure of kurtosis) that were used to describe the functional trait distributions of the secondary forests based on different functional traits. For information on how these values were calculated see methods of the main manuscript.
DOI: 10.5061/dryad.1m2p3
title: Data from: RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells

description: The Golgi apparatus has many important physiological functions, including
 sorting of secretory cargo and biosynthesis of complex glycans. These
 functions depend on the intricate and compartmentalized organization of
 the Golgi apparatus. To investigate the mechanisms that regulate Golgi
 architecture, we developed a quantitative morphological assay using three
 different Golgi compartment markers and quantitative image analysis, and
 performed a kinome- and phosphatome-wide RNAi screen in HeLa cells.
 Depletion of 159 signaling genes, nearly 20% of genes assayed, induced
 strong and varied perturbations in Golgi morphology. Using bioinformatics
 data, a large regulatory network could be constructed. Specific
 subnetworks are involved in phosphoinositides regulation, acto-myosin
 dynamics and mitogen activated protein kinase signaling. Most gene
 depletion also affected Golgi functions, in particular glycan
 biosynthesis, suggesting that signaling cascades can control glycosylation
 directly at the Golgi level. Our results provide a genetic overview of the
 signaling pathways that control the Golgi apparatus in human cells.
description: Single-cell high-content
 dataset - Golgi reference setRaw features and SVM
 features (phenotypic features) for each channel of each cell in the Golgi
 reference setGolgiRef_Cell_features.txtSingle-cell high-content dataset - Kinome and phosphatome setRaw features and SVM features (phenotypic features) for each channel of each cell in the kinome and phosphatome setKinome_Cell_features.txt
DOI: 10.5281/zenodo.18382566
title: Tandem repeat (TR) catalogs identified in 13 species using mreps, T-REKS, and TRASH
DOI: 10.5281/zenodo.18382565
title: Tandem repeat (TR) catalogs identified in 13 species using mreps, T-REKS, and TRASH
DOI: 10.5061/dryad.kk71t
title: Data from: Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content

description: A comprehensive and meaningful phylogenetic hypothesis for the
 commercially important coffee genus (Coffea) has long been a key objective
 for coffee researchers. For molecular studies, progress has been limited
 by low levels of sequence divergence, leading to insufficient topological
 resolution and statistical support in phylogenetic trees, particularly for
 the major lineages and for the numerous species occurring in Madagascar.
 We report here the first almost fully resolved, broadly sampled
 phylogenetic hypothesis for coffee, the result of combining
 genotyping-by-sequencing (GBS) technology with a newly developed,
 lab-based workflow to integrate short read next-generation sequencing for
 low numbers of additional samples. Biogeographic patterns indicate either
 Africa or Asia (or possibly the Arabian Peninsula) as the most likely
 ancestral locality for the origin of the coffee genus, with independent
 radiations across Africa, Asia, and the Western Indian Ocean Islands
 (including Madagascar and Mauritius). The evolution of caffeine, an
 important trait for commerce and society, was evaluated in light of our
 phylogeny. High and consistent caffeine content is found only in species
 from the equatorial, fully humid environments of West and Central Africa,
 possibly as an adaptive response to increased levels of pest predation.
 Moderate caffeine production, however, evolved at least one additional
 time recently (between 2 and 4 Mya) in a Madagascan lineage, which
 suggests that either the biosynthetic pathway was already in place during
 the early evolutionary history of coffee, or that caffeine synthesis
 within the genus is subject to convergent evolution, as is also the case
 for caffeine synthesis in coffee versus tea and chocolate.
description: GBS data
 C49N4ACXX_3_fastq.gzGBS data file (Illumina
 reads) for Coffea speciesC49N4ACXX_3_fastq.gz
DOI: 10.5061/dryad.j327n
title: Data from: Little impact of over-winter parasitism on a free-ranging ungulate in the high Arctic

description: 1.Macroparasites have a central place in wildlife ecology because they
 have the potential to regulate host populations through effects on
 reproduction and/or survival. However, there remains a paucity of studies
 that have demonstrated the regulatory role of these parasites in
 free-ranging animals. 2.Previous work on Svalbard reindeer demonstrated
 that the experimental removal of the parasitic gastrointestinal nematode
 Ostertagia gruehneri transmitted in summer, improved reindeer fecundity,
 and that the species was capable of mediating a density-dependent
 reduction in fecundity. 3.The main coexisting parasitic nematode in the
 system, Marshallagia marshalli, exhibits a contrasting life-history with
 low abundances in summer and an increase during the winter. Here, we
 examine the impact of this over-winter infection on fitness of female
 reindeer in the same population. 4.Worm burdens were removed at the start
 of the winter in October using a novel delayed-release anthelmintic bolus.
 Body mass and pregnancy rates were recorded for animals recaptured five
 (February) and seven (April) months later. The sub-set of treated animals
 recaptured in February was treated again with anthelmintic to remove newly
 acquired nematodes. The experiment was replicated over six winters
 (2006/7-2011/12) with a total of 343 recaptures, comprising 145 individual
 animals. 5.We found little effect of anthelmintic treatment on reindeer
 body mass or pregnancy rates during the winter, suggesting that nematode
 infection during this time does not significantly affect fitness of
 Svalbard reindeer. 6.Our studies are consistent with marked virulence
 nutritional trade-offs in this system and highlights the need to integrate
 studies of parasite co-infection, inter-specific competition and community
 ecology to understand parasite impacts on hosts.
description: body mass and pregnancy
 in relation to parasite treatmentone row per observation.
 Each row is a captured individual. an individual may appear more then
 once. Columns provide data on date of capture, treatment, body mass,
 pregnancy status. Description of the variables is in the READ ME
 fileCarlsson_FE-2017-00463_Capture_data_Dryad.csvParasite intensities in relation to anthelminitic treatment in reindeerone row per observation. Each row is a separate individual. Columns provide date of culling, treatment group, age and various measures of the abundance of the different stages of the two main parasites. See READ ME file for definitions of the variablesCarlsson_FE-2017-00463_parasite_data_Dryad.csv
DOI: 10.5061/dryad.ch304
title: Data from: Topical vancomycin reduces the cerebrospinal fluid shunt infection rate: a retrospective cohort study

description: Object: Despite many efforts at reduction, cerebrospinal fluid (CSF) shunt
 infections are a major cause of morbidity in shunt surgery, occurring in
 5-15% of cases. To attempt to reduce the shunt infection rate at our
 institution, we added topical vancomycin (intrashunt and perishunt) to our
 existing shunt infection prevention protocol in 2012. Methods: We
 performed a retrospective cohort study comparing all shunted patients in
 January 2010 to December 2011 without vancomycin (control group, 263
 procedures) to all patients who underwent shunt surgery between April 2012
 and December 2015 with vancomycin (intervention group, 499 procedures).
 Results: The overall shunt infection rate significantly decreased from
 6.8% (control group) to 3.0% (intervention group) (p = 0.023, absolute
 risk reduction 3.8%, relative risk reduction 56%). Multivariate logistic
 regression analysis confirmed that the addition of topical vancomycin
 showed that cases treated under a protocol of topical vancomycin were
 associated with a decreased shunt infection rate (odds ratio [OR] 0.49 95%
 CI 0.25-0.998; p=0.049). Age &lt; 1 year was associated with an
 increased risk of infection (OR) 4.41, 95% CI 2,10-9,26; p=0.001). Time
 from surgery to infection was significantly prolonged in the intervention
 group (p=0.001). Conclusion: Adding intraoperative vancomycin to a shunt
 infection prevention protocol significantly reduces CSF shunt infection
 rate.
description: Database shunt
 infections 2010-2015, without identifiersFull database without
 direct identifiers (see readme file)database shuntinfections
 2010-2015 without identifiers.csv
DOI: 10.5061/dryad.46pg9
title: Data from: Enhanced ecosystem functioning following stream restoration: the roles of habitat heterogeneity and invertebrate species traits

description: 1. Habitat restoration is increasingly undertaken in degraded streams and
 rivers to help improve biodiversity and ecosystem functioning. Follow-up
 assessments focused on outcomes for biodiversity have often found scant
 evidence for recovery, thus raising concerns about the efficacy of habitat
 restoration for improving ecological integrity. However, responses of
 other ecological variables, such as ecosystem process rates and the
 functional trait composition of biological assemblages, have been little
 assessed. 2. We assessed how the restoration of habitat heterogeneity
 affected multiple functional parameters in 20 boreal stream reaches
 encompassing both more and less extensively restored sites, as well as
 channelised and natural reference sites. We further assessed relationships
 between our parameters and a fluvial geomorphic measure of habitat
 heterogeneity. 3. Leaf decomposition was positively related to habitat
 heterogeneity. This was associated with shifts in the functional
 composition of detritivore assemblages, with the most obligate litter
 consumers more prominent in reaches showing higher habitat heterogeneity.
 The deposition of fine particulate organic matter was consistently higher
 in restored than channelised sites, and was positively related to the
 heterogeneity gradient. Algal biomass accrual per unit area did not vary
 either with restoration or the heterogeneity gradient. 4. Synthesis and
 applications: Our findings demonstrate that restoration of river habitat
 heterogeneity can enhance retention and decomposition of organic matter,
 key ecosystem processes underpinning ecosystem functioning and service
 delivery. Significantly, enhanced litter decomposition was linked with a
 change in the functional composition rather than diversity of detritivore
 assemblages. Future evaluation of the success of habitat restorations
 should incorporate quantification of ecosystem processes and the
 functional traits of biota, in addition to measures of fluvial
 geomorphology and the more traditional biotic metrics, to facilitate a
 more comprehensive and mechanistic assessment of ecological responses.
description: Detritivore
 diversityInvertebrate
 detrititovre diversity in leaf-litter bags.Leaf litter
 decompositionLeaf litter mass loss
 values.