cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hj627cr
title: Data from: Evaluating the taxa that provide shared pollination services across multiple crops and regions

description: Many pollinator species visit multiple crops in multiple regions, yet we
 know little about their pollination service provisioning at local and
 regional scales. We investigated the floral visitors (n = 13,200), their
 effectiveness (n = 1718 single visits) and response to landscape
 composition across three crops avocado, mango and macadamia within a
 single growing region (1 year), a single crop (3 years) and across
 different growing regions in multiple years. In total, eight wild visitor
 groups were shared across all three crops. The network was dominated by
 three pollinators, two bees (Apis mellifera and Tetragonula spp.) and a
 fly, Stomorhina discolour. The visitation network for the three crops was
 relatively generalised but with the addition of pollen deposition data,
 specialisation increased. Sixteen managed and wild taxa were consistently
 present across three years in avocado, yet their contribution to annual
 network structure varied. Node specialisation (d’) analyses indicated many
 individual orchard sites across each of the networks were significantly
 more specialised compared to that predicted by null models, suggesting the
 presence of site-specific factors driving these patterns. Identifying the
 taxa shared across multiple crops, regions and years will facilitate the
 development of specific pollinator management strategies to optimize crop
 pollination services in horticultural systems.
description: Text files containing R
 scriptIndividual files contain
 R code for analyses relating to research questions in this
 articlerscript.txtfiles.zipIndividual data filesContains individual data files used in the analysis of research questions in this article.data_csv_files.zip
DOI: 10.5061/dryad.nf481q8
title: Data from: Fire history and plant community composition outweigh decadal multi‐factor global change as drivers of microbial composition in an annual grassland

description: Soil microbial communities regulate and respond to key biogeochemical
 cycles and influence plant community patterns. However, microbial
 communities also respond to disturbance events, motivating an assessment
 of the relative roles of decadal multi-factor global change, disturbance,
 and plant community structure on microbial community responses. We used
 high-throughput amplicon sequencing to characterize the diversity and
 composition of bacterial and fungal communities in bulk soil (0–7 cm)
 collected in 2014 from the Jasper Ridge Global Change Experiment, a
 full-factorial field experiment in which ambient and elevated levels of
 nitrogen deposition (+7 g N m-2 yr-1 calcium nitrate), CO2 concentration
 (+275 ppm), temperature (+1–2 ºC), and precipitation (+50% volume with +3
 weeks duration) were applied to a California annual grassland from 1998 to
 2014. We used linear mixed-effects modeling to test for the effects of
 global change on microbial diversity (observed richness, Shannon index).
 We also used generalized dissimilarity modeling (GDM) to study controls on
 compositional dissimilarity in fungal and bacterial communities. Bacterial
 community composition was best explained by exposure to fires in 2003 and
 2011, whereas fungal community composition was best explained by plant
 community composition. The richness of fungi increased under elevated
 nitrogen deposition; bacterial diversity metrics decreased under warmer
 temperatures. Interactions between global change factors were
 statistically insignificant or weak. Synthesis. Our results indicate that
 even on decadal timescales, the effects of fire history and plant
 community composition on bacterial and fungal community composition,
 respectively, outweigh the effects of multi-factor global change.
 Furthermore, global change factors have mostly additive effects on
 microbial diversity patterns. Our results show that highly variable
 mediators such as fire history and plant community composition limit the
 generalizability of soil microbial responses to long-term global change.
description: dataThis folder contains all
 of the data used in the analysis of soil microbial communities in the
 Jasper Ridge Global Change Experiment by Qin et al. The manuscript
 associated with this data was accepted by the Journal of Ecology on August
 28, 2019. See the README file for more information.
DOI: 10.5061/dryad.n17dg25
title: Data from: Stress coping and evolution of aerobic exercise performance: corticosterone levels in voles from a selection experiment

description: The locomotor performance achieved in a challenging situation depends not
 only on physiological limitations, such as the aerobic exercise capacity,
 but also on behavioral characteristics, such as adequate stress coping.
 The stress response is mediated largely by the
 hypothalamic-pituitary-adrenal (HPA) axis, through modulated release of
 glucocorticoids. We used a unique experimental evolution model system to
 test a hypothesis that evolution of an increased aerobic exercise
 performance can be facilitated by modification of the
 glucocorticoid-related stress coping mechanisms. Bank voles (Myodes
 glareolus) from "aerobic" (A) lines, selected for 22 generations
 for high maximum swim-induced rate of oxygen consumption (VO2swim),
 achieved a 64% higher VO2swim than those from unselected, control (C)
 lines. The temporal pattern of exercise during the swimming trial also
 evolved, and the A-line voles achieved VO2swim later in the course of the
 trial, which indicates a modification in the stress response
 characteristics. Both VO2swim and the average metabolic rate measured
 during the trial tended to increase with baseline corticosterone level,
 and decreased with the post-exercise level. Thus, increased baseline
 corticosterone level promotes high metabolic performance, but a high
 corticosterone response to swimming acts as an inhibitor rather than
 stimulator of intense activity. However, neither of the corticosterone
 traits differed between the A-selected and control lines. Thus, the
 experiment did not provide evidence that evolution of increased aerobic
 performance is facilitated by modification of the glucocorticoid levels.
 The results, however, do not exclude a possibility that other aspects of
 the HPA axis function evolved in response to the selection.
description: Descriptive
 statisticsThis file contains tales
 of descriptive statistics (arithmetic means and standard deviations) of
 values relevant to the tests performed on bank voles from two groups: 1)
 all animals that completed the swimming trial as a part of the selection
 procedure in generations 22 and 23; and 2) animals involved in the
 corticosterone study.MLip_swim_Suppl_descriptive-2019-08-28.docxSAS Software CodesThis file contains SAS 9.4 Software Codes for the saturated and final ANCOVA Mixed models used to analyze the data from 1) all bank voles that completed the swimming trial as a part of selection procedure in generations 22 and 23; and 2) bank voles involved in the corticosterone study.MLip_swim_Suppl_SAS-codes-2019-08-28.docxRaw DataThis is a database containing raw data collected from bank voles involved in the corticosterone study. It is compatible with the statistical models presented in the file containing SAS software codes.MLip_swim_Suppl_database_20190828.xlsx
DOI: 10.5061/dryad.nd1bh1t
title: Data from: Fungicide suppression of flight performance in the honey bee (Apis mellifera) and its amelioration by quercetin

description: As a managed agricultural pollinator, the western honey bee Apis mellifera
 frequently encounters agrochemicals as contaminants of nectar and pollen.
 One such contaminant, the fungicide boscalid, is applied at bloom in
 orchards for fungal floral pathogen control. As an inhibitor of complex II
 in the mitochondrial electron transport chain of fungi, boscalid can
 potentially interfere with high energy-demanding activities of bees,
 including flight. We designed an indoor flight treadmill to evaluate
 impacts of ingesting boscalid and/or quercetin, a ubiquitous phytochemical
 in bee food that also affects mitochondrial respiration. Boscalid reduced
 the wing-beat frequencies of foragers during flight but did not alter the
 duration of flight. At the colony level, boscalid ingestion may thereby
 affect overall health by reducing forager efficiency. Consumption of
 quercetin, by contrast, led to higher adenosine triphosphate levels in
 flight muscles and a higher wing-beat frequency. Consuming the two
 compounds together increased wing beat frequency, demonstrating a hitherto
 unrecognized mechanism by which dietary phytochemicals may act to
 ameliorate toxic effects of pesticides to promote honey bee health. In
 carrying out this work, we also introduce two methodological improvements
 for use in testing for pesticide effects on flight capacity—a
 “force-feeding” to standardize flight fuel supply and a novel indoor
 flight treadmill.
description: ATP concentraion data
 CD-QC-ATP-0826_20190902Data for ATP
 concentration in flight muscles of foragersData_flight
 performanceFlight performance data
 of honey bees
DOI: 10.5061/dryad.7sm50ft
title: Data from: Meat ants cut more trail shortcuts when facing long detours

description: Engineered paths increase efficiency and safety but also incur
 construction and maintenance costs, leading to a trade-off between
 investment and gain. Such a trade-off is faced by Australian meat ants,
 which create and maintain vegetation-free trails between nests and food
 sources, and thus their trails are expected to be constructed selectively.
 To test this, we placed an artificial obstacle consisting of 300 paper
 grass blades between a sucrose feeder and the colony, flanked by walls of
 either 10 or 80cm length. To exploit the feeder, ants could detour around
 the walls or take a direct route by traversing through the obstacle. We
 found that, when confronted with a long alternative detour, 75% of
 colonies removed more grass blades and ants were also 60% more likely to
 traverse the obstacle instead of detouring. An analysis of cut patterns
 revealed that ants did not cut randomly, but instead concentrated on
 creating a trail to the food source. Meat ants were thus able to
 collectively deploy their trail clearing efforts in a directed manner when
 detour costs were high, and rapidly established cleared trails to the food
 source by focussing on completing a vertically aligned trail which is then
 followed by the ants.
description: ESM1_data_handling_protocolThis protocol leads through all analysis steps and results presented in the manuscript. It contains commentary, but has not been optimised for legibility.ESM2_raw_dataRaw data collected during the study.ESM3_cut patternsSimplified representations of all cut patterns created by ants.ESM4_ant movementSimplified representation of cut patterns overlaid with path trajectories of ants.ESM5_AntTrackerCode of the program used to track ants traversing the obstacle.
DOI: 10.5061/dryad.q0m0d84
title: Data from: Capture from the wild has long-term costs on reproductive success in Asian elephants

description: Capturing wild animals is common for conservation, economic, or research
 purposes. Understanding how capture itself affects lifetime fitness
 measures is often difficult because wild and captive populations live in
 very different environments and there is a need for long-term life-history
 data. Here we show how wild-capture influences reproduction in 2685 female
 Asian elephants (Elephas maximus) used in the timber industry in Myanmar.
 Wild-caught females demonstrated a consistent reduction in breeding
 success relative to captive-born females, with significantly lower
 lifetime reproduction probabilities, lower breeding probabilities at peak
 reproductive ages, and a later age of first reproduction. Furthermore,
 these negative effects lasted for over a decade, and there was a
 significant influence on the next generation: wild-caught females had
 calves with reduced survival to age 5. Our results suggest that
 wild-capture has long-term consequences for reproduction, which is
 important not only for elephants, but also for other species in captivity.
description: Lahdenpera_etal_analysesThis zipped folder contains 5 files, 4 .RData files and 1 .R script. These files enable the reader to view and plot data that are used in the manuscript entitled "Capture from the wild has long-term costs on reproductive success in Asian elephants".
DOI: 10.5061/dryad.130n95t
title: Data from: Plant-soil-foliage feedbacks on seed germination and seedling growth of an invasive plant Ageratina adenophora

description: Some exotic plants become invasive because they partially release from
 soil-borne enemies and thus benefit from the positive plant-soil feedbacks
 (PSFs) in the introduced range. However, these reports that have focused
 only on PSFs may exaggerate the invader’s competitiveness. Here, we
 conducted a series of plant-soil-foliage feedbacks (PSFFs) experiments in
 a greenhouse to determine the consequences of above- and belowground
 feedback on the early growth stages of an invasive plant, Ageratina
 adenophora. Surprisingly, most feedbacks from aboveground (mature leaves
 and leaf litter) had negative effects on A. adenophora’s seed germination
 and seedling growth. With increased invasion time, a more diverse fungal
 community (e.g., Didymella) or/and more virulent fungi (e.g., Fusarium)
 developed aboveground and partially contributed to this negative feedback,
 particularly in leaf litter. Interestingly, the adverse effects can be
 weakened by microbes from the rhizosphere soil, particularly those from
 sites with 80 years of invasion, indicating that the pathogenic microbes
 aboveground, as well as the counteraction of beneficial microbes
 belowground against pathogenic microbes aboveground, were enhanced with
 increased invasion time. These novel findings emphasize the important role
 of leaf feedback in the evaluation of plant invasiveness, and its
 commonness and significance remain to be explored in other invasive
 systems.
description: raw data for all three
 experimentsraw
 data.xlsx
DOI: 10.5061/dryad.p40r314
title: Data from: Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

description: The genus Phytophthora comprises many economically and ecologically
 important plant pathogens. Hybrid species have previously been identified
 in at least six of the 12 phylogenetic clades. These hybrids can
 potentially infect a wider host range and display enhanced vigour compared
 to their progenitors. Phytophthora hybrids therefore pose a serious threat
 to agriculture as well as to natural ecosystems. Early and correct
 identification of hybrids is therefore essential for adequate plant
 protection but this is hampered by the limitations of morphological and
 traditional molecular methods. Identification of hybrids is also important
 in evolutionary studies as the positioning of hybrids in a phylogenetic
 tree can lead to suboptimal topologies. To improve the identification of
 hybrids we have combined genotyping-by-sequencing (GBS) and genome size
 estimation on a genus-wide collection of 614 Phytophthora isolates.
 Analyses based on locus- and allele counts and especially on the
 combination of species-specific loci and genome size estimations allowed
 us to confirm and characterize 27 previously described hybrid species and
 discover 16 new hybrid species. Our method was also valuable for species
 identification at an unprecedented resolution and further allowed correct
 naming of misidentified isolates. We used both a concatenation- and a
 coalescent-based phylogenomic method to construct a reliable phylogeny
 using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species
 were subsequently connected to their progenitors in this phylogenetic
 tree. In this study we demonstrate the application of two validated
 techniques (GBS and flow cytometry) for relatively low cost but high
 resolution identification of hybrids and their phylogenetic relations.
description: locdatasel contains data
 about the exported loci output file from GIbPSs;
 it describes properties of the loci within the currently exported subset
 of data. locdatasel.txt
 locdatasel.txt
 
 locdata contains
 data about the exported loci Output from GIbPSs; this
 file has the same format and contains the same variables as locdatasel.txt
 except count_maj. locdata.txt
DOI: 10.5061/dryad.f28b4m6
title: Data from: Early stage prion assembly involves two subpopulations with different quaternary structures and a secondary templating pathway

description: The dynamics of aggregation and structural diversification of misfolded,
 host-encoded proteins in neurodegenerative diseases are poorly understood.
 In many of these disorders, including Alzheimer’s, Parkinson’s and prion
 diseases, the misfolded proteins are self-organized into conformationally
 distinct assemblies or strains. The existence of intrastrain structural
 heterogeneity is increasingly recognized. However, the underlying
 processes of emergence and coevolution of structurally distinct assemblies
 are not mechanistically supported. Here, we show that early prion
 replication generates two subsets of structurally different assemblies by
 two sequential processes of formation, regardless of the strain
 considered. The first process corresponds to a quaternary structural
 convergence, by reducing the parental strain polydispersity to generate
 small oligomers. The second process transforms these oligomers into larger
 ones, by a secondary autocatalytic templating pathway requiring the prion
 protein. This pathway provides first mechanistic insights into prion
 structural diversification, a key determinant for prion adaptation and
 toxicity.
description: Igel-Egalon et al raw
 dataRaw data from figures
 1,2,3,4,6,7 as excel filesIgel_data.zip
DOI: 10.5061/dryad.m27m0b4
title: Data from: Data sharing, management, use, and reuse: practices and perceptions of scientists worldwide

description: Background: With data becoming a centerpiece of modern scientific
 discovery, data sharing by scientists is now a crucial element of
 scientific progress. This article aims to provide an in-depth examination
 of the practices and perceptions of data management, including data
 storage, data sharing, and data use and reuse by scientists around the
 world. Methods: The Usability and Assessment Working Group of DataONE, an
 NSF-funded environmental cyberinfrastructure project, distributed a survey
 to a multinational and multidisciplinary sample of scientific researchers
 in a two-waves approach in 2017-2018. We focused our analysis on examining
 the differences across age groups, sub-disciplines of science, and sectors
 of employment. Findings: Most respondents displayed what we describe as
 high and moderate risk data practices by storing their data on their
 personal computer, departmental servers or USB drives. Respondents
 appeared to be satisfied with short-term storage solutions; however, only
 half of them are satisfied with available mechanisms for storing data
 beyond the life of the process. Data sharing and data reuse were viewed
 positively: over 85% of respondents admitted they would be willing to
 share their data with others and said they would use data collected by
 others if it could be easily accessed. A vast majority of respondents felt
 that the lack of access to data generated by other researchers or
 institutions was a major impediment to progress in science at large, yet
 only about a half thought that it restricted their own ability to answer
 scientific questions. Although attitudes towards data sharing and data use
 and reuse are mostly positive, practice does not always support data
 storage, sharing, and future reuse. Assistance through data managers or
 data librarians, readily available data repositories for both long-term
 and short-term storage, and educational programs for both awareness and to
 help engender good data practices are clearly needed.
description: ThirdSciSurveyResults of the Third Scientists Survey, DataONE U&A WG
DOI: 10.5061/dryad.6pt46j0
title: Data from: Differential impact of severe drought on infant mortality in two sympatric neotropical primates

description: Extreme climate events can have important consequences for the dynamics of
 natural populations, and severe droughts are predicted to become more
 common and intense due to climate change. We analysed infant mortality in
 relation to drought in two primate species (white-faced capuchins, Cebus
 capucinus imitator, and Geoffroy's spider monkeys, Ateles geoffroyi)
 in a tropical dry forest in north-western Costa Rica. Our survival
 analyses combine several rare and valuable long-term data sets, including
 long-term primate life-history, landscape-scale fruit abundance, food-tree
 mortality, and climate conditions. Infant capuchins showed a threshold
 mortality response to drought, with exceptionally high mortality during a
 period of intense drought, but not during periods of moderate water
 shortage. In contrast, spider monkey females stopped reproducing during
 severe drought, and the mortality of infant spider monkeys peaked later
 during a period of low fruit abundance and high food-tree mortality linked
 to the drought. These divergent patterns implicate differing physiology,
 behaviour, or associated factors in shaping species-specific drought
 responses. Our findings link predictions about the Earth’s changing
 climate to environmental influences on primate mortality risk and thereby
 improve our understanding of how the increasing severity and frequency of
 droughts will affect the dynamics and conservation of wild primates.
description: capuchin-survival.csv Survival data and environmental covariates for infant capuchins.   spider-survival.csv Survival data and environmental covariates for infant spider monkeys.   tree-survival.csv Survival data and environmental covariates for primate fruit trees.   model-survival R script that fits mixed effect Cox proportional hazards models to the capuchin and spider monkey survival data, and binomial GLMMs to the tree survival data.   README Text file that describes the variables in each of the CSV files.