cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.b5h9ug
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fabiana viscosa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 35 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000916-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m317q
title: Data from: Genetic diversity of Bartonella quintana in macaques suggests zoonotic origin of trench fever

description: Bartonella quintana is a bacterium that causes a broad spectrum of
 diseases in humans including trench fever. Humans were previously
 considered to be the primary, if not the only, reservoir hosts for B.
 quintana. To identify the animal reservoir and extend our understanding of
 the ecological and evolutionary history of B. quintana, we examined blood
 samples from macaques and performed multilocus sequence typing (MLST)
 analysis. We demonstrated the prevalence of B. quintana infection was
 common in macaques from main primate centres in mainland China. Overall,
 18.0% (59/328) of rhesus macaques and 12.7% (39/308) of cynomolgus
 macaques were found to be infected with B. quintana by blood culture
 and/or polymerase chain reaction. The infection was more frequently
 identified in juvenile and young monkeys compared with adult animals. In
 contrast with the relatively low level of sequence divergence of B.
 quintana reported in humans, our investigation revealed much higher
 genetic diversity in nonhuman primates. We identified 44 new nucleotide
 variable sites and 14 novel sequence types (STs) among the B. quintana
 isolates by MLST analysis. Some STs were found only in cynomolgus
 macaques, while some others were detected only in rhesus macaques,
 suggesting evidence of host-cospeciation, which were further confirmed by
 phylogenetic analysis and Splits decomposition analysis. Our findings
 suggest that trench fever may primarily be a zoonotic disease with
 macaques as the natural hosts.
description: Data Accessibility for
 Molecular EcologyThe uploaded file
 inlcudes all the data associated with each blood sample, including
 species, origin of sample, results of bacterial culture and Bartonella DNA
 detection, as well as GenBank accession numbers associated with the
 MLST.
DOI: 10.5061/dryad.mp40j
title: Data from: Recovery of benthic marine communities from the end-Permian mass extinction at the low-latitudes of Eastern Panthalassa

description: Based on the quantitative community analysis using species-level
 identifications, we track the restoration of benthic ecosystems after the
 end-Permian mass extinction throughout the Lower Triassic of the western
 USA. New data on the palaeoecology of the Thaynes Group and Sinbad
 Formation are provided, which fill a gap between the recently studied
 palaeoecology of the Griesbachian–Dienerian Dinwoody Formation and the
 Spathian Virgin Formation. In the Sinbad Formation and Thaynes Group, 17
 species (12 genera) of bivalves, 7 species and genera of gastropods and 2
 species and genera of brachiopods are recognized. The new bivalve genus
 Confusionella (Pteriidae) is described. A comprehensive review of the
 whole Lower Triassic succession of benthic ecosystems of the western USA
 indicates that mid- and inner shelf environments show incipient recovery
 signals around the Griesbachian–Dienerian transition, during the Smithian
 and, most profound, during the early Spathian. Ecological data from
 youngest strata of the Dinwoody Formation as well as stratigraphic ranges
 of species suggest that the late Dienerian was likely a time interval of
 environmental stress for benthic ecosystems. Despite some evidence for
 short-term environmental disturbances (e.g. shift of dominant taxa,
 transient drop in alpha-diversity) during the Smithian–Spathian
 transition, benthic ecosystems did not show any notable taxonomic turnover
 at that time, in contrast to the major crisis that affected ammonoids and
 conodonts. Whereas alpha-diversity of benthic communities generally
 increased throughout the Early Triassic, beta-diversity remained low,
 which reflects a persistently wide environmental range of benthic species.
 This observation is in accordance with a recently proposed model that
 predicts a time lag between increasing within-habitat diversity
 (alpha-diversity) and the onset of taxonomic differentiation between
 habitats (beta-diversity) during biotic recoveries from mass extinction
 events. The observation that beta-diversity had not significantly
 increased during the Early Triassic might also provide an explanation for
 the comparably sluggish increase in benthic diversity during that time,
 which has previously been attributed to persistent environmental stress.
description: Early Triassic
 ecosystems of the Western U.S.Data file containing
 full sample and abundance list of benthic macrofossils of the Thaynes
 Group and the Sinbad Formation (Lower Triassic), benthic associations, and
 alpha and beta diversity calculations.HOFMANN_etal_Palaeontology_supplement.xls
DOI: 10.5061/dryad.6cv06
title: Data from: Evidence of a component Allee effect driven by predispersal seed predation in a plant (Pedicularis rex, Orobanchaceae)

description: A small or sparse population may suffer a reduction in fitness due to
 Allee effects. Here we explored effects of plant density on pollination,
 reproduction and predation in the alpine herb Pedicularis rex over two
 years. We did not detect a significant difference in pollination rate or
 fecundity (fruit set and initial seed set) before predation between sparse
 and dense patches in either year, indicating no pollination-driven Allee
 effect. However, dense patches experienced significantly fewer attacks by
 predispersal seed predators in both years, resulting in a significantly
 decreased realized fecundity (final seed set) and suggesting a component
 Allee effect driven by predispersal seed predation. Predation-driven Allee
 effects have been predicted by many models and demonstrated for a range of
 animals, but there is scant evidence for such effects in plants. Our study
 provides strong evidence of a component Allee effect driven by predation
 in a plant species.
description: raw
 data
DOI: 10.5061/dryad.k1f73
title: Data from: Intermediate habitat associations by hybrids may facilitate genetic introgression in a songbird

description: Hybridization or the interbreeding of genetically discrete populations or
 species can occur where ranges of genetically distinct units overlap.
 Golden-winged warblers Vermivora chrysoptera, a species that has been in
 steady decline for decades, highlight the potential population-level
 consequences of hybridization. A major factor implicated in their decline
 is hybridization with their sister species, the blue-winged warbler
 Vermivora cyanoptera, which has likely been exacerbated by historic and
 current land-use practices. We examined habitat associations of
 golden-winged and blue-winged warblers, phenotypic hybrids, and cryptic
 hybrids (i.e. mismatch between plumage phenotype and genotype as
 identified by mitochondrial DNA) in an area of relatively recent range
 overlap and hybridization in northern New York, USA. To explore the
 robustness of these results, we then compared the patterns from New York
 with habitat associations from the central Pennsylvanian Appalachian
 Mountains where blue-winged warblers either do not occur or are in very
 low abundance, yet cryptic golden-winged warbler hybrids are present. From
 2008 to 2011, we captured 122 birds in New York and 28 in Pennsylvania and
 collected blood samples, which we used to determine maternal ancestry. For
 each bird captured, we measured territory-level (50-m radius circles)
 habitat, and later used remote-sensing data to quantify habitat on the
 territories and in surrounding areas (100-, 250-, and 500-m radius
 circles). In New York, golden-winged warblers occupied structurally
 heterogeneous territories surrounded by homogeneously structured,
 contiguous deciduous forest, far from urban areas. Blue-winged warblers
 showed opposite associations, and hybrids’ habitat associations were
 typically intermediate. In Pennsylvania, the habitat associations of
 golden-winged warblers and their cryptic hybrids were remarkably similar
 to those in New York. These findings suggest that patterns of habitat
 occupancy by hybrids may promote contact with golden-winged warblers and
 thus likely facilitate genetic introgression, even in areas where the
 parental species are not sympatric.
description: JAV-00771_New_York_dataJAV-00771_Pennsylvania_data
DOI: 10.5061/dryad.bj3tt
title: Data from: Gypsy moth herbivory induced volatiles and reduced parasite attachment to cranberry hosts

description: Interactions between species can have cascading effects that shape
 subsequent interactions. For example, herbivory can induce plant defenses
 that affect subsequent interactions with herbivores, pathogens,
 mycorrhizae, and pollinators. Parasitic plants are present in most
 ecosystems, and play important roles in structuring communities. However,
 the effects of host herbivory on parasitic plants, and the potential
 mechanisms underlying such effects, are not well known. We conducted a
 greenhouse study to ask whether gypsy moth (Lymantria dispar) damage, host
 cultivar, and their interaction affected preference of the stem parasite
 dodder (Cuscuta spp.) on cranberry hosts (Vaccinium macrocarpum). We then
 assessed the mechanisms that could underlie such effects by measuring
 induced changes in phytohormones and secondary compounds. We found that
 damage by gypsy moths delayed dodder attachment by approximately 0.3 days
 when dodder stems were added 2 days after damage, and reduced attachment
 by more than 50% when dodder stems were added 1 week after host plant
 damage. Gypsy moth damage significantly increased jasmonic acid (JA)
 levels, total volatile emissions, and the flavonol, quercetin aglycone,
 suggesting possible mechanisms underlying variation in dodder ability to
 locate or attach to hosts. Dodder preference also differed between
 cranberry cultivars, with the highest attachment on the cultivar that had
 significantly lower levels of total volatile emissions and total phenolic
 acids, suggesting that volatile composition and phenolics may mediate
 dodder preference. Our results indicate that herbivory can reduce
 subsequent attachment by a highly damaging parasitic plant, demonstrating
 the potential importance of early damage for shaping subsequent species
 interactions.
description: Tjiurutue.etal.Oecologia.2017.Metadata.These are data from a manipulative experiment asking how damage by gypsy moths on cranberry affected attachment by a parasitic plant, dodder, as well as induced chemical defenses (phytohormones, volatiles and phenolics) that could be mechanisms mediating these interactions. The attachment and chemistry were assessed in two separate, parallel experiments in the greenhouse in Amherst, MA, USA in 2011. There is one worksheet for each of these responses (the 3 chemicals plus dodder attachment) and a worksheet describing all the variables.Tjiurutue.etal.Oecologia.2017Metadata..xlsx
DOI: 10.5061/dryad.nh597
title: Data from: Optimal group size in a highly social mammal

description: What are the costs and benefits for animals living in groups of different
 sizes? Balancing the trade-offs between within-group competition (which
 favors smaller groups) and between-group competition (which favors larger
 groups) suggests that intermediate-sized groups may be best, yet empirical
 support for this prediction has largely been lacking. Using long-term data
 on wild baboons, we provide novel evidence that individuals living in
 intermediate-sized groups have energetically optimal space-use strategies
 and lower glucocorticoid (stress hormone) concentrations than individuals
 in either large or small groups. Our results offer new insight into the
 costs and benefits of group living.
description: Annual home range and
 foraging predictorsExcel file containing
 data on group ID, hydrological year, average group size, cumulative
 rainfall, rainfall evenness, average maximum temperature, percent time
 foraging, and annual home range size. These data were used to determine
 the predictors of the proportion of time foraging and the predictors of
 annual home range size. See manuscript for more
 information.fGC and daily travel
 distance dataExcel file containing
 data on group ID, fGC concentrations, and daily travel distance. These
 data were used to determine whether daily travel distance predicted fGC
 concentrations. See manuscript for more information.Monthly fGC
 predictorsExcel file containing
 data on group ID, temporal sequence, group size, cumulative rainfall,
 average maximum temperature, and fGC concentrations. These data were used
 to determine the predictors of fGC concentrations. See manuscript for more
 information.Monthly ranging pattern
 predictorsExcel file containing
 data on group ID, temporal sequence, group size, cumulative rainfall,
 average maximum temperature, evenness of space use, home range size, and
 average daily travel distance. These data were used to determine the
 predictors of monthly ranging patterns. See manuscript for more
 information.
DOI: 10.5061/dryad.kr856
title: Data from: Evolution of a predator-induced, nonlinear reaction norm

description: Inducible, anti-predator traits are a classic example of phenotypic
 plasticity. Their evolutionary dynamics depend on their genetic basis, the
 historical pattern of predation risk that populations have experienced and
 current selection gradients. When populations experience predators with
 contrasting hunting strategies and size preferences, theory suggests
 contrasting micro-evolutionary responses to selection. Daphnia pulex is an
 ideal species to explore the micro-evolutionary response of anti-predator
 traits because they face heterogeneous predation regimes, sometimes
 experiencing only invertebrate midge predators and other times
 experiencing vertebrate fish and invertebrate midge predators. We explored
 plausible patterns of adaptive evolution of a predator-induced
 morphological reaction norm. We combined estimates of selection gradients
 that characterize the various habitats that D. pulex experiences with
 detail on the quantitative genetic architecture of inducible morphological
 defences. Our data reveal a fine scale description of daphnid defensive
 reaction norms, and a strong covariance between the sensitivity to cues
 and the maximum response to cues. By analysing the response of the
 reaction norm to plausible, predator-specific selection gradients, we show
 how in the context of this covariance, micro-evolution may be more uniform
 than predicted from size-selective predation theory. Our results show how
 covariance between the sensitivity to cues and the maximum response to
 cues for morphological defence can shape the evolutionary trajectory of
 predator-induced defences in D. pulex.
description: HRBC23Data Daphnia pulex
 reaction normSupplementary Table
 1Supplementary Table
 2
DOI: 10.5061/dryad.hn20p
title: Data from: Sublingual immunotherapy (SLIT) for house dust mites does not prevent new allergen sensitization and bronchial hyper-responsiveness in allergic rhinitis children

description: Introduction: The aim of this study is to identify the effects of
 sublingual immunotherapy (SLIT) on immunologic parameters and
 bronchial-hyper-responsiveness in children with allergic rhinitis to
 house-dust mite (HDM), through long-term follow-up cohort. Methods: Among
 the Allergic Rhinitis Cohort Study for Kids, pediatric patients who
 visited the hospital for rhinitis symptoms and proven allergy to HDM
 through skin prick test were studied. In this cohort, 37 patients received
 SLIT more than 3-years (SLIT group), and 184 patients received only
 pharmacologic therapy (non-SLIT group) were included in this study. The
 results of skin prick test, eosinophil percent and count, total
 immunoglobulin E (IgE), and bronchial provocation test at initial and
 3-year followed-up were compared in the two groups. Results: After 3 year
 follow-up, only the serum eosinophil percent decreased more significantly
 in SLIT group than that in the non-SLIT group. New-sensitization rate
 other than HDM between SLIT and non-SLIT group did not show any
 significant differences. The distribution of sensitized allergen other
 than HDM showed increasing tendency after 3 years in both groups. Older
 age and a small number of sensitized allergen affected the improvement of
 bronchial hyper-responsiveness regardless of SLIT. Conclusion: HDM SLIT in
 allergic rhinitis children for 3 years in Korea does not affect prevention
 of new sensitization and poly-sensitization rate increment, and
 improvement of bronchial hyper-responsiveness.
description: ARCO kids &
 SLIT_sensitivity change_SPSSSPSS file used in this
 present study. Several variables were categorized into numerical
 values.ARCO kids &
 SLIT_sensitivity change_raw dataFinal dataset used in
 this present study
DOI: 10.5061/dryad.sg4n7kb
title: Data from: Biofilm inhibition and pathogenicity attenuation in bacteria by Proteus mirabilis

description: Biofilms play an important role in the antibiotic resistance of encased
 bacteria, and their formation was regulated by quorum sensing (QS).
 Inhibiting the QS system may therefore degrade the integrity of a biofilm
 and expose the bacterial pathogens within it to the deleterious effects of
 molecules such as antibiotics. Moreover, the use of QS inhibitors (QSIs)
 may provide a novel approach for treating bacterial infections of
 aquacultures. In the present study, the bacterium Proteus mirabilis was
 identified as a potential producer of QSIs. Varying concentrations
 (0.1-1.1%) of filtrates prepared from the culture of P. mirabilis
 inhibited biofilm formation by the pathogens Pseudomonas aeruginosa,
 Vibrio harveyi, and Staphylococcus aureus by as much as 58.9%, 41.5%, and
 41.9%, respectively. These filtrates as well as the crude aqueous extracts
 prepared from them increased the sensitivities of pathogens to the
 inhibitory effects of kanamycin. The filtrates also showed pathogenicity
 attenuation potential in P. aeruginosa by decreasing the production of
 virulence factors. Moreover, the filtrates did not influence the
 planktonic growth of these pathogens. The results indicate that P.
 mirabilis may act as a nonspecific (or broad-spectrum) inhibitor of
 biofilm formation that will help control infectious diseases that
 adversely affect the aquaculture industry.
description: Raw
 DataThe Raw Data including 4
 tables (Table 1-4) and 3 figures (Figs. 2, 5 and 6) in the
 paper.Raw
 data.zip
DOI: 10.5061/dryad.7536h67
title: Data from: Elevated CO2 and water addition enhance nitrogen turnover in grassland plants with implications for temporal stability

description: Temporal variation in soil nitrogen (N) availability affects growth of
 grassland communities that differ in their use and reuse of N. In a
 seven-year-long climate change experiment in a semiarid grassland, the
 temporal stability of plant biomass production varied with plant N
 turnover (reliance on externally acquired N relative to internally
 recycled N). Species with high N turnover were less stable in time
 compared to species with low N turnover. In contrast, N turnover at the
 community level was positively associated with asynchrony in biomass
 production, which in turn increased community temporal stability. Elevated
 CO2 and summer irrigation, but not warming, enhanced community N turnover
 and stability, possibly because treatments promoted greater abundance of
 species with high N turnover. Our study highlights the importance of plant
 N turnover for determining the temporal stability of individual species
 and plant communities affected by climate change.
description: Species and community
 dataThe excel spreadsheet
 has four tabs. The first tab (Data by year) contains data at the community
 level that was collected in different years. These data include 15N
 recovery (as shown in Figure 1 and Figure S3), nitrogen content in
 different plant parts (shown in Figure S1 and S4) and resorption
 efficiency (shown in Figure S7). The second tab (Community data) contains
 measurements at the community level including shoot biomass (averaged
 across years), community stability of plant biomass production, the
 parameter values from equation 2, including community N turnover, and
 community 15N atom% measured in different years, used for equation 2.
 These data are shown in Figure 3, Figure 5, Figure S2, and Figure S6). The
 third tab (Species data), contains the same data as the Community data,
 but now at the species level (shown in Figure 2 and Figure S5). The fourth
 tab contains the meta data.Dryad
 data.xlsx
DOI: 10.5061/dryad.8j1hb
title: Data from: A treefrog with reproductive mode plasticity reveals a changing balance of selection for non-aquatic egg-laying

description: Non-aquatic reproduction has evolved repeatedly, but the factors that
 select for laying eggs on land are not well understood. The treefrog
 Dendropsophus ebraccatus has plasticity in reproductive mode, laying eggs
 that successfully develop in or out of water. This permits the first
 experimental comparison of the selective agents that shape adult
 oviposition behavior and embryo developmental capacity. I quantified the
 sources and strength of arboreal and aquatic egg mortality, how mortality
 varies with weather patterns, and assessed 39 years of daily rainfall
 patterns to infer historic levels of egg mortality and effects of climate
 change on the selective balance between aquatic and non-aquatic egg
 deposition. Aquatic predators and desiccation were the strongest selective
 agents in water and air, respectively. Egg mortality varied with weather
 such that aquatic oviposition was advantageous when rainfall was low, but
 laying eggs out of water increased survival when rainfall was high.
 Additionally, I found that since 1972 there have been significant changes
 in the patterns of rainfall in central Panama, which has altered the
 selective landscape acting on egg-laying behavior. This work provides
 insight into both the evolution and maintenance of adaptive phenotypic
 plasticity as well as historic and current selection on reproduction.
description: TerrAqEggs_DRYADThe data in this file are from an experiment conducted in the fall of 2010 in Gamboa, Panama. The experiment used naturally laid egg masses of the treefrog Dendropsophus ebraccatus, which were then placed above or below the surface of the water and placed inside a small cage to exclude predators or were left exposed to predators. Survival and developmental stage were recorded after 24 and 48 hours, as well as the amount of rainfall that fell, the mean and max temperature and minimum humidity during the preceeding 24 hours.PredictedBreeding_DRYADThe data in this file were generated from an R script that estimated the mortality of D. ebraccatus eggs that would have been laid between 1972-2010. The script used the experimental data in TerrAqEggs_DRYAD.csv to create functions of aquatic and terrestrial egg mortality based on the rain falling on eggs during the 48 h post-oviposition (figures 1D-F of the ms). Combining these functions, specific to each pond used in the study, egg mortality was estimated for each rainstorm 5mm or greater between 1972-2010 (data available from the Smithsonian Tropical Research Institute, as described above).ACP.rain.summary_DRYADThe data in this file are summarized rainfall data for each year between 1972-2010. Rainfall data are from the Panama Canal Authority weather station in Gamboa, Panama, and are freely available for download from the Smithsonian Tropical Research Institute. For the purposes of analyses, I defined the rainy season as May 15-November 15.