cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.vtzxr2
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Lao People’s Democratic Republic",
 "TaxonKey is Ichthyophis"
 ]
}

 The dataset includes 48 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002590-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8w610
title: Predator group composition indirectly influences food web dynamics through predator growth rates

description: Considerable theoretical work predicts that intraspecific trait variation
 can have profound ecological consequences by altering species
 interactions. Because of their high flexibility, behavioral traits may be
 especially relevant in mediating how species respond to one another, thus
 affecting food web dynamics and ecosystem functioning. However, empirical
 evidence supporting this idea is limited. Here we generated predator
 groups where we manipulated the composition of behavioral types within the
 groups to assess effects on predator growth rates, prey communities, basal
 resources and ecosystem functioning in replicated outdoor ponds. Using
 European perch (Perca fluviatilis), we created three types of predator
 groups where all individuals expressed either bold or shy phenotypes, or
 individuals were a mix of the two behavioral types. Bold perch grew faster
 in mixed groups, indicating that predator growth depends both on each
 individual’s behavioral type and that of its group members. However, there
 was no evidence that the behavioral composition of perch directly altered
 the dynamics of lower trophic levels. Instead, final perch biomass, not
 behavioral composition, had the strongest influence on lower trophic
 levels. Thus, the central question may not be whether predator behavior
 matters at all for trophic dynamics, but rather when behavioral effects
 will predominate over effects of other influences such as predator biomass
 variation.
DOI: 10.15468/dl.jcj7cs
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Centrolobium microchaete",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 215 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002592-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.wpzgmsbk6
title: Banks grass mite (Acari: Tetranychidae) suppression may add to the benefit of drought-tolerant corn hybrids exposed to water-stress

description: Spider mite (Acari: Tetranychidae) outbreaks are common on corn grown in
 the arid West. Hot and dry conditions reduce mite development time,
 increase fecundity, and accelerate egg hatch. Climate change is predicted
 to increase drought incidents and produce more intense temperature
 patterns. Together, these environmental shifts may cause more frequent and
 severe spider mite infestations. Spider mite management is difficult as
 many commercially-available acaricides are ineffective due to the
 development of resistance traits in field mite populations. Therefore,
 alternative approaches to suppress outbreaks are critically needed.
 Drought-tolerant plant hybrids alleviate the challenges of growing crops
 in water-limited environments; yet, it is unclear if drought-tolerant
 hybrids exposed to water-stress affects mite outbreaks under these
 conditions. We conducted a greenhouse experiment to evaluate the effect of
 drought-tolerant corn hybrids on Banks grass mite, a primary pest of corn,
 under optimal irrigation and water-stress irrigation. This was followed by
 a 2-year field study investigating the effect of drought-tolerant corn
 hybrids exposed to the same irrigation treatments on Banks grass mite
 artificially infested on hybrids and resident spider mite populations.
 Results showed that water-stressed drought-tolerant hybrids had
 significantly lower Banks grass mite and resident spider mite populations
 than water-stressed drought-susceptible hybrids. Interestingly,
 water-stressed drought-tolerant hybrids had equal Banks grass mite
 populations to drought-susceptible and drought-tolerant hybrids under
 optimal irrigation. We posit that planting drought-tolerant hybrids may
 suppress spider mite outbreaks in water-challenged areas.
description: Banks grass mite egg and motile densities in the greenhouse
 experiment were Log<sub>x</sub> transformed before analyses to
 correct for heterogeneous variances and non-normal distribution. For the
 field experiment, resident spider mite motiles, and egg densities were
    transformed before analyses. Conversely, densities of Banks grass mite motiles, and eggs, as well as leaf temperature were Log<sub>x</sub> transformed before analyses to correct for heterogeneous variances and non-normal distribution. Data for testing differences between hybrids within each seed company were Log<sub>x</sub> transformed to correct for heterogeneous variances and non-normal distribution. Data were analyzed using JMP (version 9.3; SAS Institute Inc., Cary, NC, USA).
DOI: 10.5061/dryad.2jm63xsn0
title: Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America

description: Isthmian Central America (ICA) is one of the most biodiverse regions in
 the world, hosting an exceptionally high number of species per unit area.
 ICA was formed &lt; 25 million years ago and, consequently, its biotic
 assemblage is relatively young and derived from both colonization and in
 situ diversification. Despite intensive taxonomic work on the local fauna,
 the potential forces driving genetic divergences and ultimately speciation
 in ICA remain poorly studied. Here, we used a landscape genetics approach
 to test whether isolation by distance, topography, habitat suitability, or
 environment drive the genetic diversity of the regional frog assemblage.
 To this end, we combined data on landscape features and mitochondrial DNA
 sequence variation for nine co-distributed amphibian species with
 disparate life histories. In five species, we found that at least one of
 the factors tested explained patterns of genetic divergence. However,
 rather than finding a general pattern, our results revealed idiosyncratic
 responses to historical and ecological processes, indicating that
 intrinsic life-history characteristics may determine the effect of
 different drivers of isolation on genetic divergence in ICA. Our work also
 suggests that the convergence of several factors promoting isolation among
 populations over a heterogeneous landscape might maximize genetic
 differentiation despite short geographical distances. In conclusion,
 abiotic factors and geographical features have differentially affected the
 genetic diversity across the regional frog assemblage. Much more complex
 models (i.e. considering multiple drivers), beyond simple vicariance of
 Caribbean and Pacific lineages are needed to better understand the
 evolutionary history of ICA’s diverse biotas.
DOI: 10.15468/dl.yjxudb
title: Occurrence Download

description: A dataset containing 537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-107.61672 -19.76346,-26.38328 -19.76346,-26.38328 12.76346,-107.61672 12.76346,-107.61672 -19.76346))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Virola duckei"
 ]
}

 The dataset includes 537 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002593-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7h2
title: Effectiveness of orally-delivered double-stranded RNA on gene silencing in the stinkbug Plautia stali

description: The stinkbug Plautia stali shows high sensitivity to RNAi with
 injected dsRNA but very low sensitivity to RNAi with orally-delivered
 dsRNA.
description: The detail of the methods are described in the paper. See
 it.
DOI: 10.5061/dryad.8gtht76mz
title: Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change

description: “Evolve and resequence” (E&R) studies combine experimental
 evolution and whole-genome sequencing to interrogate the genetics
 underlying adaptation.  Due to ease of handling, E&R work
 with asexual organisms like bacteria can employ optimized experimental
 design, with large experiments and many generations of
 selection.  By contrast, E&R experiments with sexually
 reproducing organisms are more difficult to implement, and design
 parameters vary dramatically among studies. Thus, efforts have been made
 to assess how these differences, such as number of independent replicates,
 or size of experimental populations, impact inference. We add to this work
 by investigating the role of time sampling – the number of discrete
 timepoints sequence data is collected from evolving populations. Using
 data from an E&R experiment with outcrossing Saccharomyces
 cerevisiae in which populations were sequenced 17 times over ~540
 generations, we address the following questions: (i) do more timepoints
 improve the ability to identify candidate regions underlying selection?
 And (ii) does high-resolution sampling provide unique insight into
 evolutionary processes driving adaptation? We find that while time
 sampling does not improve the ability to identify candidate regions,
 high-resolution sampling does provide valuable opportunities to
 characterize evolutionary dynamics. Increased time sampling reveals three
 distinct trajectories for adaptive alleles: one consistent with classic
 population genetic theory (i.e. models assuming constant selection
 coefficients), and two where trajectories suggest more context-dependent
 responses (i.e. models involving dynamic selection coefficients). We
 conclude that while time sampling has limited impact on candidate region
 identification, sampling 8 or more timepoints has clear benefits for
 studying complex evolutionary dynamics.
description: Data is from an evolve and resequence experimental
 featuring <i>Saccharomyces cerevisiae. </i>Briefly, 12
 populations were exposed to an outcrossing regime and allowed to evolve
 for 540 generations. Samples were taken from each population at 17
 timepoints for DNA sequencing. Details for population maintenance and
 sequencing can be found in the manuscript entitled "Increased time
 sampling in an evolve-and-resequence experiment with outcrossing
 <i>Saccharomyces cerevisiae</i> reveals multiple paths of
 adaptive change" published in Molecular Ecology.  This entry includes
 a SNP table, haplotype frequency tables, and tables with various
 statistical results (See ReadMe file for details).
DOI: 10.5061/dryad.mkkwh70xn
title: Decreasing effects of precipitation on grassland spring phenology in temperate China

description: Vegetation phenology is highly sensitive to climate change. The timing of
 spring phenology in temperate grasslands is primarily regulated by
 temperature and precipitation. This study aims to study whether the
 primary factor regulating vegetation phenology changed under ongoing
 climate change and its underlying mechanisms. In this study, we extracted
 Start of Season (SOS) dates using five standard methods from
 satellite-derived Normalized Difference Vegetation Index (NDVI) data and
 determined the primary regulating factor for spring phenology using
 partial correlation analysis.
description: We used the satellite Normalized Difference Vegetation Index
 (NDVI) records by NASA’s GIMMS group from 1982-2015. This NDVI dataset has
 been produced at a spatial resolution of 8 km and a time resolution of 15
 days. In order to remove the disturbing artifacts, we
 defined that no spring phenological events occurred before air temperature
 surpassed 0 ℃ for 5 consecutive days (Cong<i> et al.</i>,
 2012). In addition, we excluded pixels where mean annual NDVI value was
 below 0.1. Croplands were removed from the data in order to avoid the
 anthropogenic influences in the data. We used in the Vegetation Map of the
 People’s Republic of China the same resolution as was used in the NDVI
 images and then removed the pixels marked as croplands. Extracting dates
 of phenological spring events took place in two steps.
 First, we used one of five filter functions at a time to smooth
 the NDVI series, since in those series there are always some abnormal
 values due to atmospheric interference. Then we interpolated the daily
 values between the biweekly observations, because a biweekly resolution is
 too coarse to estimate dates of spring phenological events. Finally, we
 defined a threshold value of NDVI for identifying the date of the spring
 phenological events. To illustrate the methods used in extracting the SOS
 dates, we chose one pixel in a meadow steppe and used three filter methods
 as an example (Figure S2). Five methods, each characterized by its filter
 function and the corresponding threshold, were used for extracting the
 dates of start of season at each pixel from the NDVI: Gaussian, Spline,
 Polyfit, HANTS, and Timesat-SG. After we got the SOS from each method, we
 used the mean value of five different methods to represent the SOS date at
 each pixel.
DOI: 10.5061/dryad.9kd51c5fd
title: Highly mobile seed predators contribute to interisland seed dispersal within an oceanic archipelago

description: Long-distance dispersal (LDD) is an essential event for species
 colonization and expansion in oceanic island ecosystems. Endozoochory by
 birds is an important factor promoting the LDD of plant seeds, but its
 contribution to interisland seed dispersal is still unclear. Here, we show
 possible seed dispersal by a seed predator pigeon, the Japanese wood
 pigeon Columba janthina, among oceanic islands in the Izu archipelago,
 Japan. Although some previous studies showed that most seeds swallowed by
 this pigeon are crushed, intact seeds were found in 44.5% of pigeon feces,
 indicating the contribution of these birds to seed dispersal. Seasonal
 population fluctuations and movements by pigeons between neighbouring
 islands which are 4 km apart by pigeons can promote interisland seed
 dispersal. We found seeds from fruiting trees not located on the islands
 where the pigeon feces were collected, which could have been transported
 from another island. Although many tree species overlap their fruiting
 phenology with pigeon movement between islands, the seeds of only six
 species were dispersed by pigeons, and most of the dispersed seeds were
 from species with small seeds less than 1.5 mm in diameter. Seed
 consumption and frequent interisland movement of Japanese wood pigeons
 might homogenize the distribution of plants with small seeds among
 neighboring islands. In contrast, their intensive seed consumption might
 disturb the recruitment of plants with large seeds and make their
 expansion to other islands difficult. Such effects of mutualistic
 (dispersal) and antagonistic (predation) interactions with highly mobile
 seed predators may modify plant distributions and gene flow in oceanic
 archipelagos.
DOI: 10.5061/dryad.brv15dv7t
title: Water availability rather than temperature control soil fauna community structure and prey-predator interactions

description: The ongoing climate change may strongly impact soil biodiversity with
 cascading effects on the processes they drive. Thus, it is of prime
 interest to improve our knowledge about responses by soil organisms such
 as collembolans to expected shifts in environmental conditions by
 considering communities comprising both detritivores and predators. The
 aim of the present study was to evaluate how simulated climate change and
 predation under laboratory conditions alter a collembolan community. To
 infer the impact of climate change, we applied a decreased level of soil
 moisture (60% vs. 30% soil water holding capacity) and an increasing air
 temperature (15 °C vs. 25 °C) to a collembolan community constituted by
 four species (Folsomia candida, Protaphorura fimata, Proisotoma minuta and
 Mesaphorura macrochaeta) exhibiting distinct functional traits, e.g. body
 size and furca presence, in presence or absence of a predatory gamasid
 Acari (Stratiolaelaps scimitus) during two months in a microcosm
 experiment. We observed that decreasing soil moisture altered the
 collembolan community with species-specific responses. Interaction between
 soil moisture, temperature and predation indicates that low soil moisture
 reduced total collembolan abundance especially i) by suppressing the
 positive effect of increasing temperature and ii) by increasing the
 predatory control on collembolan abundance. These results highlight that
 soil moisture is the major driver of Collembola community and by
 consequence, a shift in climatic parameters with the ongoing climate
 change should strongly modify the Collembola community structure and the
 predator-prey interaction. Our findings are highly important since a
 strengthening of predation impact on Collembola prey could have major
 consequences on the whole soil food web being able to lead to a slowdown
 of key ecosystem processes they drive (e.g., litter decomposition and
 nutrient recycling). Finally, our study promotes the need to study more
 complex systems considering distinct soil-dwelling species, their
 functional traits and their trophic interactions to better predict the
 ecosystem responses to the ongoing climate change.
DOI: 10.5061/dryad.jq2bvq87d
title: Dataset for METAPOPGEN 2.0: a multi-locus genetic simulator to model populations of large size

description: Multi-locus genetic processes in subdivided populations can be complex and
 difficult to interpret using theoretical population genetics models.
 Genetic simulators offer a valid alternative to study multi-locus genetic
 processes in arbitrarily complex scenarios. However, the use of
 forward-in-time simulators in realistic scenarios involving high numbers
 of individuals distributed in multiple local populations is limited by
 computation time and memory requirements. These limitations increase with
 the number of simulated individuals. We developed a genetic simulator,
 MetaPopGen 2.0, to model multi-locus population genetic processes in
 subdivided populations of arbitrarily large size. It allows for spatial
 and temporal variation in demographic parameters, age structure, adult and
 propagule dispersal, variable mutation rates and selection on survival and
 fecundity. We developed MetaPopGen 2.0 in the R environment to facilitate
 its use by non-modeler ecologists and evolutionary biologists. We
 illustrate the capabilities of MetaPopGen 2.0 for studying adaptation to
 water salinity in the striped red mullet Mullus surmuletus.
description: This dataset contains the scripts and data to run the simulations
 presented in the paper, namely: the
 simulations used to validate MetaPopGen 2.0 against theoretical
 expectations (the Wright-Fisher model and the two-locus Slatkin
 model); the simulations used to compare the
 computation times of Nemo 2.2.0 and MetaPopGen 2.0;
 the simulations to study adaptation to water salinity in the
 striped red mullet Mullus surmuletus. Data
 structure: Dispersal_SC.RData # Dispersal
 probabilities for Mullus surmuletus, used in
 MullusSimulations.R IslandModelMetaPopGen.R # R code
 to run the island model simulation (section "Computation
 time") IslandModelNemo.ini # Ini file for Nemo
 2.2.0 to run the island model simulation (section "Computation
 time") MullusSimulations.R # R code to run the
 Mullus simulation (section "Example: adaptation to water salinity in
 the red mullet Mullus surmuletus")
 Salinity_data.RData # Salinity, used in
 MullusSimulations.R Simulation_parameters.RData #
 Other simulation parameters used in MullusSimulations.R
 SlatkinModel.R # R code to run the Slatkin model simulation
 (section "Theoretical validation")
 SlatkinModelFunctions.R # R functions to used in
 SlatkinModel.R WrightFisher.R # R code to run the
 Wright-Fisher model simulation (section "Theoretical
 validation")
DOI: 10.6086/d1vh5w
title: VISSIM and real-world eco-approach and departure comparison

description: In addition to providing safety and mobility benefits, Connected and
 Automated Vehicles (CAVs) have the potential to reduce fuel consumption
 and emissions. As new CAV applications are developed, it is valuable to
 estimate these potential environmental benefits, typically using vehicle
 activity data and emissions models. To date, most researchers in the U.S.
 have used the MOVES vehicle emissions model, developed and maintained by
 the U.S. Environmental Protection Agency (EPA). However, because MOVES
 uses a binning approach, it is likely underestimating the true energy and
 emissions savings that occur when CAV applications smooth traffic flow. To
 illustrate this problem, we measure and model the fuel consumption and CO2
 emissions for a real-world CAV application: Eco-Approach and Departure
 (EAD) at signalized intersections. First, a traffic simulation of the
 real-world corridor the experiments will be performed on was created.
 Next, the hardware needed to perform the real-world experiments was
 installed on the real-world corridor. Then, using the traffic simulation
 previously mentioned was used to mimic real-world testing of EAD in
 different traffic conditions. Finally, real-world EAD tests were performed
 on the real-world corridor where fuel consumption and carbon dioxide
 emissions was recorded. Real-world measurements are compared to a
 MOVES-based estimate, as well as to an estimate provided by the
 physical-based Comprehensive Modal Emissions Model (CMEM). Results show
 that MOVES consistently underestimates the energy and emissions benefits
 of the CAV application, primarily since the bin sizes in MOVES are too
 large to catch the nuances of traffic smoothing. On the other hand, CMEM
 provided a more accurate energy and emissions estimate, primarily since it
 uses analytical functions to model emissions and does not suffer from the
 same binning problem.
description: The data are output from PTV VISSIM via application programming
 interfaces (APIs). The files are in .csv format. The contents of each file
 include vehicle ID, vehicle speed (in mph), MOVES estimate of fuel
 consumption (in grams), and CMEM estimate of fuel consumption (in grams)
 on the basis of one simulation time step (1 Hz).
 Real-world data files are in .csv format. The contents of each
 file include vehicle speed (in mph), air/fuel ratio, mass air flow, fuel
 consumption (grams), vehicle speed from gps (in mph), CMEM estimate of
 fuel consumption (in grams), and MOVES estimate of fuel consumption (in
 grams) collected every second (1Hz).