cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2hf38
title: Data from: Sensitivity of marine protected area network connectivity to atmospheric variability

description: International efforts are underway to establish well-connected systems of
 marine protected areas (MPAs) covering at least 10% of the ocean by 2020.
 But the nature and dynamics of ocean ecosystem connectivity are poorly
 understood, with unresolved effects of climate variability. We used
 40-year runs of a particle tracking model to examine the sensitivity of an
 MPA network for habitat-forming cold-water corals in the northeast
 Atlantic to changes in larval dispersal driven by atmospheric cycles and
 larval behaviour. Trajectories of Lophelia pertusa larvae were strongly
 correlated to the North Atlantic Oscillation (NAO), the dominant pattern
 of interannual atmospheric circulation variability over the northeast
 Atlantic. Variability in trajectories significantly altered network
 connectivity and source–sink dynamics, with positive phase NAO conditions
 producing a well-connected but asymmetrical network connected from west to
 east. Negative phase NAO produced reduced connectivity, but notably some
 larvae tracked westward-flowing currents towards coral populations on the
 mid-Atlantic ridge. Graph theoretical metrics demonstrate critical roles
 played by seamounts and offshore banks in larval supply and maintaining
 connectivity across the network. Larval longevity and behaviour mediated
 dispersal and connectivity, with shorter lived and passive larvae
 associated with reduced connectivity. We conclude that the existing MPA
 network is vulnerable to atmospheric-driven changes in ocean circulation.
description: RSOS160494_Python_CodePython scripts for the particle tracking model and data processing.
DOI: 10.5061/dryad.b5np1
title: Data from: Pollinator interactions with yellow starthistle (Centaurea solstitialis) across urban, agricultural, and natural landscapes

description: Pollinator-plant relationships are found to be particularly vulnerable to
 land use change. Yet despite extensive research in agricultural and
 natural systems, less attention has focused on these interactions in
 neighboring urban areas and its impact on pollination services. We
 investigated pollinator-plant interactions in a peri-urban landscape on
 the outskirts of the San Francisco Bay Area, California, where urban,
 agricultural, and natural land use types interface. We made standardized
 observations of floral visitation and measured seed set of yellow
 starthistle (Centaurea solstitialis), a common grassland invasive, to test
 the hypotheses that increasing urbanization decreases 1) rates of bee
 visitation, 2) viable seed set, and 3) the efficiency of pollination
 (relationship between bee visitation and seed set). We unexpectedly found
 that bee visitation was highest in urban and agricultural land use
 contexts, but in contrast, seed set rates in these human-altered
 landscapes were lower than in natural sites. An explanation for the
 discrepancy between floral visitation and seed set is that higher plant
 diversity in urban and agricultural areas, as a result of more introduced
 species, decreases pollinator efficiency. If these patterns are consistent
 across other plant species, the novel plant communities created in these
 managed landscapes and the generalist bee species that are favored by
 human-altered environments will reduce pollination services.
description: Leong_YSTbees_dataField data was collected in Contra Costa County, California in 2011.
DOI: 10.5061/dryad.52n11
title: Data from: Get smart: native mammal develops toad-smart behavior in response to a toxic invader

description: Although invasive species can cause major declines in native populations,
 some individuals in a native population are better equipped to deal with
 the threat than others. Existing trait variation—especially in highly
 flexible behavioral traits—may thus buffer populations and allow natural
 selection to proceed. Cane toads (Rhinella marina) have caused dramatic
 declines in native Australian predators, which unwittingly attack the
 poisonous toads. The northern quoll (Dasyurus hallucatus) is one such
 predator, with declines and local extinction of quoll populations
 typically occurring rapidly after toads arrive. Despite this, some quoll
 populations persist in areas where toads have been present for ≥70 years.
 Here, we compare northern quolls from toad-infested and toad-free areas to
 test whether this persistence is enabled by behavioral traits. We
 demonstrate that northern quolls from long-term toad-infested areas have
 indeed become “toad-smart,” spending significantly less time investigating
 a toad compared with a control prey item, and limiting this investigation
 time to investigatory rather than attacking behavior. By contrast, quolls
 from toad-naive populations vary in their response to toads, with many
 exhibiting attack behavior. These results demonstrate that behavioral
 variation exists within naive populations and the few persisting northern
 quoll populations in toad-infested areas have naturally developed
 toad-smart behavior. Population modeling suggests this behavior likely
 persists across generations. Although the mechanism is unknown, the
 observed shift in toad-smart behavior may be due to rapid adaption, and if
 so could become a vital tool for conserving this endangered species.
description: Experiment
 DataResults from the toad
 response experiment from quolls from toad-infested or toad-free areas of
 northern Australia. Data is the time spent investigating and attack type
 for both dead adult toads and dead adult mice.toaddata.csvExperiment AnalysisR code for analysis of data file Experimental Data.experiment.analysis.RNorthern quoll population modelR code to preform individual-based northern quoll population model and population viability analysis.quoll.pop.model.R
DOI: 10.5061/dryad.0t667
title: Data from: Susceptibility of Macrosiphum euphorbiae to the parasitoid Aphidius ervi: larval development depends on host aphid genotype

description: The potato aphid, Macrosiphum euphorbiae Thomas (Hemiptera: Aphididae:
 Macrosiphini), is a common polyphagous aphid in Europe and North America.
 However, the factors influencing potato aphid dynamics and susceptibility
 to natural enemies are largely undescribed, particularly in relation to
 facultative endosymbiotic bacteria, which can provide protection against
 parasitism and disease in some aphid species. This study investigated
 whether potato aphid susceptibility to one of its principal natural
 enemies, the parasitoid Aphidius ervi Haliday (Hymenoptera: Braconidae:
 Aphidiinae), varied in relation to aphid genotype and/or endosymbiont
 presence. Parasitism and aphid fitness assays were conducted on clonal
 lineages of aphids, harbouring their natural endosymbiont infections,
 collected over 3 years from separate geographic locations. Parasitized
 aphids were dissected to quantify parasitoid oviposition, larval
 development, and mummification. Amongst the 19 clonal lines of M.
 euphorbiae tested, seven aphid genotypes were identified, and 11 lines
 harboured one or both of the facultative endosymbionts Hamiltonella
 defensa Moran et al. and Regiella insecticola Moran et al.; H. defensa
 infections were associated exclusively with two of the seven M. euphorbiae
 genotypes. Parasitism resistance was detected in clonal lines belonging to
 a single aphid genotype and resulted from failure of parasitoid eggs to
 develop into larvae rather than failure of the parasitoid to oviposit.
 Contrary with studies of several other aphid species, there was little
 evidence that H. defensa provided strong protection to M. euphorbiae from
 parasitism by A. ervi. Furthermore, there were no clear fitness costs to
 the aphid associated with parasitism resistance or with H. defensa
 infection. The two M. euphorbiae genotypes in which H. defensa occurred,
 which included the resistant genotype, exhibited faster development,
 higher survival, and greater fecundity than the other five aphid
 genotypes. These findings suggest that biological control of M. euphorbiae
 using A. ervi alone could exacerbate pest problems by selecting for the
 fittest parasitism-resistant genotypes.
description: M. euphorbiae fitness
 and parasitism resistance dataSheets 1 and 2 give the
 results of performance (fitness) assays on 10 clonal lines of M.
 euphorbiae. 'Rm' is the intrinsic rate of population increase,
 given by 0.738(ln Md) / T where T is the pre-reproductive period and Md is
 the number of offspring produced in the time equivalent to the
 pre-reproductive period. 'Event' indicates whether an individual
 was alive (0) or dead (1) at a time equal to twice the pre-reproductive
 period. Sheets 3 and 4 give the data for the host acceptability and
 suitability experiments, where 'Count' is the number of aphids
 in which an egg or larva was found, or the number of mummies formed, for
 that replicate.
DOI: 10.5061/dryad.80f293g
title: Data from: Social living simultaneously increases infection risk and decreases the cost of infection

description: Elevated parasite infection risk is considered to be a near universal cost
 of social living. However, living in groups may also provide benefits that
 reduce the negative impacts of infection. These potential ‘tolerance’
 benefits of living socially are theoretically possible, but have rarely
 been described. In this study, we used an anthelmintic treatment
 experiment in wild Grant’s gazelles (Nanger granti), who are commonly
 infected with gastrointestinal nematodes (GIN), to show that social living
 confers both costs and benefits related to GIN parasitism. We show that
 although larger group size increases GIN infection risk, a key cost of GIN
 infection – the suppression of food intake − is simultaneously moderated
 by living in larger groups. Our findings help illuminate the complex role
 parasites play in the evolution of host social behavior.
description: Group Size-GIN
 datasetSee associated ReadMe
 filegroupsize.gin.csvGroup Size-Feeding datasetsee associated ReadMe filegroupsize.feed.csv
DOI: 10.5061/dryad.7nb81
title: Data from: The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees

description: Quantitative genetic analysis is often fundamental for understanding
 evolutionary processes in wild populations. Avian populations provide a
 model system due to the relative ease of inferring relatedness amongst
 individuals through observation. However, extra-pair paternity (EPP)
 creates erroneous links within the social pedigree. Previous work has
 suggested this causes minor underestimation of heritability if paternal
 misassignment is random and hence not influenced by the trait being
 studied. Nevertheless, much literature suggests numerous traits are
 associated with EPP and the accuracy of heritability estimates for such
 traits remains unexplored. We show analytically how non-random pedigree
 errors can influence heritability estimates. Then, combining empirical
 data from a large great tit (Parus major) pedigree with simulations, we
 assess how heritability estimates derived from social pedigrees change
 depending on the mode of the relationship between EPP and the focal trait.
 We show that the magnitude of the underestimation is typically small
 (&lt;15%). Hence, our analyses suggest that quantitative genetic
 inference from pedigrees derived from observations of social relationships
 are relatively robust; our approach also provides a widely-applicable
 method for assessing the consequences of non-random EPP.
description: Pedigree
 DataThe .Rdata file
 containing two objects. 'ped' contains the full pedigree, with
 the columns of id (unique individual identity), dam (the mother), dad (the
 social father), sire (the genetic father), long (longitude position of
 brood), lat (latitude position of brood), brood (unique ID of the brood
 the individual was born in), year (the year the individual was born).
 'males' contains all the males that could have potentially been
 the genetic sires of offspring for each year and includes columns of id
 (unique ID corresponding to the 'ped' dataframe), year (the year
 this ID could have sired genetic offspring), brood (the brood that this
 male was identified at this year - also corresponds to 'ped'
 dataframe), lat (latitude to brood position), long (longitude of brood
 position). The R script for simulating additional pedigrees using this
 data but with different parameters is included in the manuscript
 Supplementary Information.ped_and_males.RData
DOI: 10.15468/dl.wcv86q
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Histioteuthis atlantica",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 10",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 220 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001147-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.k53b7
title: Data from: Tropical forest restoration: fast resilience of plant biomass contrasts with slow recovery of stable soil C stocks

description: 1. Due to intensifying human disturbance, over half of the world’s
 tropical forests are reforested or afforested secondary forests or
 plantations. Understanding the resilience of carbon (C) stocks in these
 forests, and estimating the extent to which they can provide equivalent
 carbon (C) sequestration and stabilization to the old growth forest they
 replace, is critical for the global C balance. 2. In this study, we
 combined estimates of biomass C stocks with a detailed assessment of soil
 C pools in bare land, Eucalyptus plantation, secondary forest, and natural
 old-growth forest after over 50 years of forest restoration in a degraded
 tropical region of South China. We used isotope studies, density
 fractionation and physical fractionation to determine the age and
 stability of soil C pools at different soil depths. 3. After 52 years, the
 secondary forests had equivalent biomass C stocks to natural forest,
 whereas soil C stocks were still much higher in natural forest (97.42 t
 ha-1) than in secondary forest (58.75 t ha-1) or Eucalyptus plantation
 (38.99 t ha-1) and lowest in bare land (19.9 t ha-1). Analysis of δ13C
 values revealed that most of the C in the soil surface horizons in the
 secondary forest was new C, with a limited increase of more recalcitrant
 old C, and limited accumulation of C in deeper soil horizons. However,
 occlusion of C in microaggregates in the surface soil layer was similar
 across forested sites, which suggests that there is great potential for
 additional soil C sequestration and stabilization in the secondary forest
 and Eucalyptus plantation. 4. Collectively, our results demonstrate that
 reforestation on degraded tropical land can restore biomass C and surface
 soil C stocks within a few decades, but much longer recovery times are
 needed to restore recalcitrant C pools and C stocks at depth. Repeated
 harvesting and disturbance in rotation plantations had a substantial
 negative impact on the recovery of soil C stocks. We suggest that current
 calculations of soil C in secondary tropical forests (e.g. IPCC Guidelines
 for National Greenhouse Gas Inventories) could overestimate soil C
 sequestration and stabilization levels in secondary forests and
 plantations.
description: SoilfractionsdataThe raw data for the paperRcode for the LME analysisLandUse script.R
DOI: 10.5061/dryad.rm082
title: Data from: Dopaminergic lesions of the dorsolateral striatum in rats increase delay discounting in an impulsive choice task

description: Dysregulated dopamine transmission in striatal circuitry is associated
 with impulsivity. The current study evaluated the influence of
 dopaminergic inputs to the dorsolateral striatum on impulsive choice, one
 aspect of impulsive behavior. We implemented an operant task that measures
 impulsive choice in rats via delay discounting wherein intracranial
 self-stimulation (ICSS) was used as the positive reinforcer. To do so,
 rats were anesthetized to allow implanting of a stimulating electrode
 within the lateral hypothalamus of one hemisphere and bilateral dorsal
 striatal injections of the dopaminergic toxin, 6-OHDA (lesioned) or its
 vehicle (sham). Following recovery, rats were trained in a delay
 discounting task wherein they selected between a small ICSS current
 presented immediately after lever pressing, and a large ICSS current
 presented following a 0 to 15s delay upon pressing the alternate lever.
 Task acquisition and reinforcer discrimination were similar for lesioned
 and sham rats. All rats exhibited an initial preference for the large
 reinforcer, and as the delay was increased, preference for the large
 reinforcer was decreased indicating that the subjective value of the large
 reinforcer was discounted as a function of delay time. However, this
 discounting effect was significantly enhanced in lesioned rats for the
 longer delays. These data reveal a contribution of dopaminergic inputs to
 the dorsolateral striatum on impulsive choice behavior, and provide new
 insights into neural substrates underlying discounting behaviors.
description: Delay discounting raw
 dataRaw data for the delay
 discounting manuscript.Data for repository 2.6.15
 vF.xlsx
DOI: 10.5061/dryad.48jg20v0
title: Data from: Population structure and migration pattern of a conifer pathogen, Grosmannia clavigera, as influenced by its symbiont the mountain pine beetle

description: We investigated the population structure of Grosmannia clavigera (Gc), a
 fungal symbiont of the mountain pine beetle (MPB) that plays a crucial
 role in the establishment and reproductive success of this pathogen. This
 insect–fungal complex has destroyed over 16 million ha of lodgepole pine
 forests in Canada, the largest MPB epidemic in recorded history. During
 this current epidemic, MPB has expanded its range beyond historically
 recorded boundaries, both northward and eastward, and has now reached the
 jack pine of Alberta, potentially threatening the Canadian boreal forest.
 To better understand the dynamics between the beetle and its fungal
 symbiont, we sampled 19 populations in western North America and genotyped
 individuals from these populations with eight microsatellite markers. The
 fungus displayed high haplotype diversity, with over 250 unique haplotypes
 observed in 335 single spore isolates. Linkage equilibria in 13 of the 19
 populations suggested that the fungus reproduces sexually. Bayesian
 clustering and distance analyses identified four genetic clusters that
 corresponded to four major geographical regions, which suggested that the
 epidemic arose from multiple geographical sources. A genetic cluster north
 of the Rocky Mountains, where the MPB has recently become established,
 experienced a population bottleneck, probably as a result of the recent
 range expansion. The two genetic clusters located north and west of the
 Rocky Mountains contained many fungal isolates admixed from all
 populations, possibly due to the massive movement of MPB during the
 epidemic. The general agreement in north–south differentiation of MPB and
 G. clavigera populations points to the fungal pathogen’s dependence on the
 movement of its insect vector. In addition, the patterns of diversity and
 the individual assignment tests of the fungal associate suggest that
 migration across the Rocky Mountains occurred via a northeastern corridor,
 in accordance with meteorological patterns and observation of MPB movement
 data. Our results highlight the potential of this pathogen for both
 expansion and sexual reproduction, and also identify some possible
 barriers to gene flow. Understanding the ecological and evolutionary
 dynamics of this fungus–beetle association is important for the modelling
 and prediction of MPB epidemics.
description: GC293-dataThis is a microsatellite data set of 8 loci for the fungus Grosmannia clavigera. Cokumn A contains the strain code, column B represents the sampling location, while columns C-R have the raw data of fragment size.
DOI: 10.5061/dryad.576m2
title: Data from: Cytoskeletal stability and metabolic alterations in primary human macrophages in long-term microgravity

description: The immune system is one of the most affected systems of the human body
 during space flight. The cells of the immune system are exceptionally
 sensitive to microgravity. Thus, serious concerns arise, whether space
 flight associated weakening of the immune system ultimately precludes the
 expansion of human presence beyond the Earth's orbit. For human space
 flight, it is an urgent need to understand the cellular and molecular
 mechanisms by which altered gravity influences and changes the functions
 of immune cells. The CELLBOX-PRIME (= CellBox-Primary Human Macrophages in
 Microgravity Environment) experiment investigated for the first time
 microgravity-associated long-term alterations in primary human
 macrophages, one of the most important effector cells of the immune
 system. The experiment was conducted in the U.S. National Laboratory on
 board of the International Space Station ISS using the NanoRacks
 laboratory and Biorack type I standard CELLBOX EUE type IV containers.
 Upload and download were performed with the SpaceX CRS-3 and the Dragon
 spaceship on April 18th, 2014 / May 18th, 2014. Surprisingly, primary
 human macrophages exhibited neither quantitative nor structural changes of
 the actin and vimentin cytoskeleton after 11 days in microgravity when
 compared to 1g controls. Neither CD18 or CD14 surface expression were
 altered in microgravity, however ICAM-1 expression was reduced. The
 analysis of 74 metabolites in the cell culture supernatant by GC-TOF-MS,
 revealed eight metabolites with significantly different quantities when
 compared to 1g controls. In particular, the significant increase of free
 fucose in the cell culture supernatant was associated with a significant
 decrease of cell surface-bound fucose. The reduced ICAM-1 expression and
 the loss of cell surface-bound fucose may contribute to functional
 impairments, e.g. the activation of T cells, migration and activation of
 the innate immune response. We assume that the surprisingly small and
 non-significant cytoskeletal alterations represent a stable "steady
 state" after adaptive processes are initiated in the new microgravity
 environment. Due to the utmost importance of the human macrophage system
 for the elimination of pathogens and the clearance of apoptotic cells, its
 apparent robustness to a low gravity environment is crucial for human
 health and performance during long-term space missions.
description: Data sets for
 figuresThe file contains three
 tables which list the single datapoints, means, standard errors and
 samples sizes that underlie the graphs shown in the paper. The first table
 contains the data of the cell numbers, the cell areas and the quantitation
 of the investigated molecules by immunofluorescence. It refers to figures
 4-7 and 10. The second table contains the data of the qualitative rating
 of the cytoskeletal architecture in figure 8. The third table lists the
 metabolomics data which are shown in figures 9 and 10.Data sets
 PONE-D-17-01917.xlsx
DOI: 10.15468/dl.4wbpj6
title: Occurrence Download

description: A dataset containing 26079603 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 26079603 records from 1712 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004534-250227182430271/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.