cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fs8sb1g
title: Data from: Betweenness centrality as predictor for forces in granular packings

description: A load applied to a jammed frictional granular system will be localized
 into a network of force chains making inter-particle connections
 throughout the system. Because such systems are typically
 under-constrained, the observed force network is not unique to a given
 particle configuration, but instead varies upon repeated formation. In
 this paper, we examine the ensemble of force chain configurations created
 under repeated assembly in order to develop tools to statistically
 forecast the observed force network. In experiments on a gently suspended
 2D layer of photoelastic particles, we subject the assembly to hundreds of
 repeated cyclic compressions. As expected, we observe the non-unique
 nature of the force network, which differs for each compression cycle, by
 measuring all vector inter-particle contact forces using our open source
 PeGS software. We find that total pressure on each particle in the system
 correlates to its betweenness centrality value extracted from the
 geometric contact network. Thus, the mesoscale network structure is a key
 control on individual particle pressures.
description: Cyclic uniaxial
 compression, 29 particles, run 1Positions and weighted
 adjacency matrices for 29 particles under cyclic compression. See readme
 for details.29Particles_Run1.zipCyclic uniaxial compression, 29 particles, run 2Positions and weighted adjacency matrices for 29 particles under cyclic compression. See readme for details.29Particles_Run2.zipCyclic uniaxial compression, 824 particles, run 1Positions and weighted adjacency matrices for 824 particles under cyclic compression. See readme for details.824Particles_Run1.zipCyclic uniaxial compression, 824 particles, run 2Positions and weighted adjacency matrices for 824 particles under cyclic compression. See readme for details.824Particles_Run2.zip
DOI: 10.5061/dryad.224rg77
title: Data from: Carbon debt of field-scale Conservation Reserve Program grasslands converted to annual and perennial bioenergy crops

description: Over 5 million ha of US Conservation Reserve Program (CRP) grasslands have
 been converted to annual crops since 2000, driven mainly by demand for
 corn grain ethanol. Much of the soil carbon sequestered under CRP is lost
 upon conversion, creating a "carbon debt" that is presumed to be
 repaid by future greenhouse gas (GHG) savings from ethanol's
 substitution for petroleum. Model simulations, extrapolations, and
 national statistics rather than direct measurements have been used thus
 far to estimate the long-term global warming impact (GWI) of such
 conversions. Here we report measured GWIs for three 22 year-old CRP
 grassland fields and three conventionally tilled agricultural (AGR) fields
 (11–17 ha) converted to either annual no-till corn or perennial cellulosic
 (switchgrass or restored prairie) bioenergy crops. We assessed GWIs for
 each field over eight years using whole-system life cycle analysis (LCA)
 by measuring: a) greenhouse gas fluxes via eddy covariance and static
 chamber methodologies, b) farming operations and agronomic inputs, and c)
 the fossil fuel offset by ethanol use. Payback times were much longer than
 those estimated by prior modeling efforts. After 8 years, cumulative GWIs
 of switchgrass, restored prairie, and corn at the CRP grasslands were,
 respectively, -2.6±4.0, 6.9±3.6 and 85.2±5.1 Mg CO2-equivalent ha-1. The
 switchgrass system had repaid its carbon debt by year eight and the
 restored prairie will have likely repaid by year ten; however, the no-till
 corn system appears likely to require &gt;300 years. The same
 bioenergy crops grown on former agricultural lands, with no sequestered
 carbon lost on conversion, repaid their carbon debts within two years.
 Results indicate that GWI estimates and carbon debt payback times due to
 conversion of CRP lands to annual bioenergy crops have been substantially
 underestimated by current models.
description: Global warming impact
 (GWI) of anual and perennial bioenergy cropsThe data are collected
 from field experiments at the W.K. Kellogg Biological Station (KBS)
 Long-Term Ecological Research (LTER) site of the Michigan State University
 from 2009 through 2016. The file contains annual CO2-equivalent balances
 of net ecosystem C exchange (measured using eddy covariance), N2O and CH4
 fluxes (measured using chamber methodology), grain yield and/or biomass
 weighed from entire field and CO2-equivalent emissions due to farming
 operations and agronomic inputs. These data were used to compute fossil
 fuel offset credit, global warming impact (GWI) and emission reduction
 relative to lifecycle greenhouse gas emissions of gasoline (fossil fuel)
 for each bioenergy system.Abraha_2019_ERL_CarbonDebt.xlsx
DOI: 10.5061/dryad.nt511dp
title: Data from: The role of ecotype-environment interactions in intraspecific trophic niche partitioning subsequent to stocking

description: Worldwide, stocking of fish represent a valuable tool for conservation and
 maintenance of species exploited by recreational fishing. Releases of
 hatchery-reared fish are more and more recognized to have numerous
 demographic, ecological and genetic impacts on wild populations. However,
 consequences on intraspecific trophic relationships have rarely been
 investigated. In this study, we assessed the impacts of supplementation
 stocking and resulting introgressive hybridization on the trophic niches
 occupied by stocked, local and hybrid Lake Trout (Salvelinus namaycush)
 within populations of piscivorous and planktivorous ecotypes stocked from
 a wild piscivorous source population. We compared trophic niches using
 stable isotope analysis (δ13C and δ15N) and trophic position among the
 three genetic origins. Putative genetic effects were tested with
 phenotype-genotype association of “life history” ecological traits (body
 size, growth rate, condition index and trophic niche) and genotypes
 (RADseq SNP markers) using redundant discriminant analysis (RDA). Results
 showed that sympatry resulting from the stocking of contrasting ecotypes
 is a risk factor for niche partitioning. Planktivorous populations are
 more susceptible to niche partitioning, by competitive exclusion of the
 local fish from a littoral niche to an alternative pelagic/profundal
 niche. Observed niche partitioning is probably a manifestation of
 competitive interactions between ecotypes. Our results emphasize that
 ecotypic variation should be considered for more efficient management and
 conservation practices and in order to mitigate negative impact of
 supplementation stocking.
description: R script - Stable
 isotope analysesThis file provides all
 the R codes (scripts) necessary to conduct preliminary and statistical
 analysis on stable isotopes data for this article. The README file
 provides a general description of the script.R_script_Morissette_et_al_2019_Ecol-Apps.RStable isotope raw dataThis file provides all of the stable isotope raw data used in this article. The README file is including a complete description of datasets.Raw_data.zipGenotype-phenotype association by RDAThis file provides all the all R codes (scripts) as well as the description of provided raw data to run the genotype-phenotype association analysis realized using a redundancy analysis (RDA) in this article. See the README file for further information.RDA_data_and_codes.zip
DOI: 10.5061/dryad.hr5t61c
title: Data from: Microbial communities in hummingbird feeders are distinct from floral nectar and influenced by bird visitation

description: Human provisioning can shape resource availability for wildlife, but
 consequences for microbiota availability and exchange remain relatively
 unexplored. Here, we characterized microbial communities on bills and
 fecal material of two hummingbird species and their food resources,
 including hummingbird feeders and floral nectar. We experimentally
 manipulated bird visitation to feeders and examined effects on feeder
 microbial communities and sucrose solutions. Birds, feeders, and flowers
 hosted distinct bacterial and fungal communities. Flowers and feeders
 hosted remarkably different bacterial communities; Proteobacteria
 comprised over 80% of flower bacteria but feeders contained high relative
 abundance of Proteobacteria, Firmicutes and Actinobacteria. Birds hosted
 both bacterial taxa commonly found in other bird taxa, novel genera
 including Zymobacter [Proteobacteria], and Ascomycete fungi. In feeders,
 bird-visited and unvisited solutions both accumulated abundant microbial
 populations that changed solution pH and bird visitation rates, but
 microbial composition was largely determined by visitation treatment. Our
 results reveal that feeders host abundant microbial populations, including
 some bird-associated microbial taxa. Microbial taxa in feeders were
 primarily non-pathogenic bacteria and fungi but differ substantially from
 those in floral nectar. These results demonstrate that human provisioning
 influences microbial intake by free-ranging hummingbirds; however, it is
 unknown how these changes impact hummingbird gastrointestinal flora or
 health.
description: Feeder observation and
 chemical dataData on visitation to
 feeders and feeder chemical parametersFeeder_observations.csvFeeder plating dataData on CFU density of culturable microoganisms from hummingbird feedersVannetteHummingbird16S16S data from hummingbird bill, fecal, feeder and flower samplesBacteria_Bioinformatics_Hummingbird ProjectVannetteHummingbirdITSRaw ITS2 reads from Hummingbird bill, fecal, feeder and flower samples.Fungi_Bioinformatics_Hummingbird Project
DOI: 10.5061/dryad.39gq16q
title: Data from: Sink limitation of plant growth determines treeline in the arid Himalayas

description: 1. Understanding what determines the high elevation limits of trees is
 crucial for predicting how treelines may shift in response to climate
 change. Treeline formation is commonly explained by a low-temperature
 restriction of meristematic activity (sink limitation) rather than carbon
 assimilation (source limitation). In arid mountains, however, trees face
 simultaneously low temperature and drought, both potentially restricting
 their growth and thus setting range limits. However, the mechanisms of
 treeline formation in high arid mountains are largely unknown. 2. We
 studied Myricaria elegans, one of the world’s highest growing
 winter-deciduous woody species, endemic to the arid Himalayas. We
 hypothesized that the upper elevation limit of Myricaria is associated
 with low-temperatures during the early growing season affecting earlywood
 formation, while later in the season drought is constraining earlywood
 maturation and latewood formation. 3. To test this hypothesis, we studied
 the quantitative anatomy of tree rings at different developmental stages
 across the entire species elevation range (3200-4400 m). We also explored
 daily stem increment and rehydration rates, seasonal dynamics of
 non-structural carbohydrates and stable C isotopes as a proxy for possible
 drought constraints. 4. Both earlywood and latewood increments decreased
 towards the treeline, while NSC in leaves, twigs and stem sapwood did not
 change, indicating a sink limitation as a main driver of the treeline. At
 treeline, low temperatures restricted earlywood formation more than
 latewood formation. Treeline individuals had – compared to individuals
 from lower elevations – smaller and fewer earlywood vessels, frequent
 frost rings and shorter periods with positive daily increments, but
 comparable night-time stem rehydration rates and latewood density. All
 these results suggest a sink limitation as a main mechanism behind the
 treeline formation in high arid mountains. 5. In the arid Himalayas, the
 treeline is set by the drastic growth reduction (sink limitation) caused
 by low temperature and short growing season under otherwise sufficient
 carbon and water supply. Spring freezing and high summer temperatures
 further constrain stem increment at treeline. The mean 6.9 °C temperature
 during the growing season places the Myricaria treeline within the thermal
 range of other high elevation treelines worldwide and support a common
 mechanism of alpine treeline formation.
description: Dolezal_Func.Ecology_DataThe file provides data on Myricaria elegans radial stem growth, stem sapwood, branch and leaf non-structural carbohydrates and leaf nutrient concentrations from different elevations in Ladakh, NW Himalayas, India.
DOI: 10.5061/dryad.485b1c3
title: Data from: Tibial nerve decompression for the prevention of the diabetic foot: a cost-utility analysis using Markov model simulations.

description: Objective: To determine whether tibial neurolysis performed as a surgical
 intervention for patients with diabetic neuropathy and superimposed tibial
 nerve compression in the prevention of the diabetic foot is cost effective
 when compared to the current prevention program. Design: A baseline
 analysis was built on a five-year model to determine the cumulative
 incidence of foot ulcers and amputations with each strategy. Subsequently,
 a cost-effectiveness analysis and cohort-level Markov simulations were
 conducted with a model composed of 20 six-month cycles. A sensitivity
 analysis was also performed. Setting: A Markov model was used to simulate
 the effects of standard prevention compared to tibial neurolysis on the
 long-term costs associated with foot ulcers and amputations. This model
 included eight health states. Participants: Each cohort includes simulated
 patients with diabetic neuropathy at different levels of risk of
 developing foot ulcers and amputations. Primary and secondary outcome
 measures: The primary outcome was the long-term trends concerning the
 development of ulcers and amputations with each strategy. The secondary
 outcome measures were quality adjusted life years (QALYs); incremental
 cost-effectiveness; and net monetary benefits of the optimal strategy.
 Results: When compared to standard prevention, for a patient population of
 10,000, surgery prevented a simulated total of 1,447 ulcers and 409
 amputations over a period of 5 years. In a subsequent analysis that
 consisted of 20 six-month cycles (10 years), the incremental cost of
 tibial neurolysis compared to current prevention was $12,772.28; the
 incremental effectiveness was 0.41 QALYs; and the incremental
 cost-effectiveness ratio (ICER) was $31,330.78. Survival was 73% for those
 receiving medical prevention compared to 95% for those undergoing surgery.
 Conclusion: These results suggest that among patients with diabetic
 neuropathy and superimposed nerve compression, surgery is more effective
 at preventing serious comorbidities and is associated with a higher
 survival over time. It also generated greater long-term economic benefits.
description: Transition
 ProbabilitiesTransition probabilities
 used to conduct a baseline analysis as well as cohort-level Markov
 simulations.Tibial Neurolysis Markov
 Model (discounted)TreeAge decision tree
 used for a cost-effectiveness analysis and cohort-level Markov
 simulations.
DOI: 10.5061/dryad.37qv5rd
title: Data from: Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient

description: Background. Effective biodiversity monitoring is fundamental in tracking
 changes in ecosystems as it relates to commercial, recreational, and
 conservation interests. Current approaches to survey coral reef ecosystems
 center on the use of indicator species and repeat surveying at specific
 sites. However, such approaches are often limited by the narrow snapshot
 of total marine biodiversity that they describe and are thus hindered in
 their ability to contribute to holistic ecosystem-based monitoring. In
 tandem, environmental DNA (eDNA) and next-generation sequencing
 metabarcoding methods provide a new opportunity to rapidly assess the
 presence of a broad spectrum of eukaryotic organisms within our oceans,
 ranging from microbes to macrofauna. Methods. We here investigate the
 potential for rapid universal metabarcoding surveys (RUMS) of eDNA in
 sediment samples to provide snapshots of eukaryotic subtropical
 biodiversity along a depth gradient at two coral reefs in Okinawa, Japan
 based on 18S rRNA. Results. Using 18S rRNA metabarcoding, we found that
 there were significant separations in eukaryotic community assemblages (at
 the family level) detected in sediments when compared across different
 depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was
 observed across operational taxonomic units assigned to the class
 Demospongiae (sponges), the most diverse class (contributing 81% of
 species) within the phylum Porifera; the oldest metazoan phylum on the
 planet. However, zonation was not observed across the class Anthozoa
 (i.e., anemones, stony corals, soft corals, and octocorals), suggesting
 that the former may serve as a better source of indicator species based on
 sampling over fine spatial scales and using this universal assay.
 Furthermore, despite their abundance on the examined coral reefs, we did
 not detect any octocoral DNA, which may be due to low cellular shedding
 rates, assay sensitivities, or primer biases. Discussion. Overall, our
 pilot study demonstrates the importance of exploring depth effects in eDNA
 and suggest that RUMS may be applied to provide a baseline of information
 on eukaryotic marine taxa at coastal sites of economic and conservation
 importance.
description: Raw .fastq sequence
 files for PeerJ submission "Digging for DNA at depth: rapid universal
 metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity
 across a depth gradient"Raw .fastq 18S rRNA
 sequences for sediment samples collected at two coral reefs in Okinawa,
 Japan.PeerJ
 Raw Data Submission.zip
DOI: 10.5061/dryad.9g91451
title: Data from: Climate will increasingly determine post-fire tree regeneration success in low-elevation forests, Northern Rockies, USA

description: Climate change is expected to cause widespread shifts in the distribution
 and abundance of plant species through direct impacts on mortality,
 regeneration, and survival. At landscape scales, climate impacts will be
 strongly mediated by disturbances, such as wildfire, which catalyze shifts
 in species distributions through widespread mortality and by shaping the
 post‐disturbance environment. We examined the potential for regional
 shifts in low‐elevation tree species in response to wildfire and climate
 warming in low‐elevation, dry mixed‐conifer forests of the northern Rocky
 Mountains, USA. We analyzed interactions among climate and wildfire on
 post‐fire tree seedling regeneration 5–13 yr post‐fire at 177 sites burned
 in 21 large wildfires during two years with widespread regional burning.
 We used generalized additive mixed models to quantify how the density of
 Douglas‐fir and ponderosa pine seedlings varied as a function of climate
 normals (30‐yr mean temperature, precipitation, soil moisture, and
 evapotranspiration) and fire (tree survivorship, burn severity, and seed
 source availability). Mean summer temperature was the most important
 predictor of post‐fire seedling densities for both ponderosa pine and
 Douglas‐fir. Seed availability was also important in determining
 Douglas‐fir regeneration. As mean summer temperature continues to
 increase, however, seed availability will become less important for
 determining post‐fire regeneration. Above a mean summer temperature of
 17°C, Douglas‐fir regeneration is predicted to be minimal regardless of
 how close a seed source is to a site. The majority (82%) of our sampled
 sites are predicted to exceed a mean summer temperature of 17°C by
 mid‐century, suggesting significant declines in seedling densities and
 potential forest loss. Our results highlight mechanisms linking climate
 change to shifts in the distribution of two widely dominant tree species
 in western North America. Under a warming climate, we expect post‐fire
 tree regeneration in these low‐elevation forests to become increasingly
 unsuccessful. Such widespread regeneration failures would have important
 implications for ecosystem processes and forest resilience, particularly
 as wildfires increase in response to climate warming.
description: Kemp_et_al_2019_Ecosphere_DataCodeThis archive contains the data and R scripts needed to reproduce the results from: Kemp KB, Higuera PE, Morgan P, Abatzoglou JT. 2019. Climate will increasingly determine post-fire tree regeneration success in low-elevation forests, Northern Rockies, USA. Ecosphere 10(1):e02568. 10.1002/ecs2.2568
DOI: 10.5061/dryad.bm1j1c7
title: Data from: Sperm competition accentuates selection on ejaculate attributes

description: Ejaculate attributes are important factors driving the probability of
 fertilizing eggs. When females mate with several males, competition
 between sperm to fertilize eggs should accentuate selection on ejaculate
 attributes. We tested this hypothesis in the North African houbara bustard
 (Chlamydotis undulata undulata) by comparing the strength of selection
 acting on two ejaculate attributes when sperm from single males or sperm
 from different males were used for insemination. In agreement with the
 prediction, we found that selection on ejaculate attributes was stronger
 when sperm of different males competed for egg fertilization. These
 findings provide the first direct comparison of the strength of selection
 acting on ejaculate attributes under competitive and non-competitive
 fertilizations, confirming that sperm competition is a major selective
 force driving the evolution of ejaculate characteristics.
description: Dataset for selection
 analyses on ejaculate attributesThe excel file contains
 two worksheets. The first one, called "Dataset", contains the
 table used for the selection analyses on ejaculate attributes described in
 the manuscript. The second one, called "Variables", provides the
 name and a short description for each variable included in the
 dataset.Vuarin et
 al_dataset.xlsx