cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7fh3800
title: Data from: (In)exhaustible suppliers for evolution? Epistatic selection tunes the adaptive potential of non-genetic inheritance

description: Non-genetic inheritance media, from methyl-accepting cytosines to culture,
 tend to 'mutate' more frequently than DNA sequences. Whether or
 not this makes them inexhaustible suppliers for adaptive evolution will
 depend on the effect of non-genetic mutations (hereafter epimutations) on
 fitness-related traits. Here we investigate how the magnitude of these
 effects might themselves evolve, specifically whether natural selection
 may set boundaries to the adaptive potential of non-genetic inheritance
 media due to their higher mutability. In our model, the genetic and
 epigenetic contributions to a non-neutral phenotype are controlled by an
 epistatic modifier locus, which evolves under the combined effects of
 drift and selection. We show that a pure genetic control evolves when the
 environment is stable, provided that the population is large, such that
 the phenotype becomes robust to frequent epimutations. When the
 environment fluctuates, however, selection on the modifier locus also
 fluctuates and can overall produce a large non-genetic contribution to the
 phenotype, especially when the epimutation rate matches the rate of
 environmental variation. We further show that selection on the modifier
 locus is generally insensitive to recombination, meaning it is mostly
 direct, i.e. not relying on subsequent effects in future generations.
 These results suggest that unstable inheritance media might significantly
 contribute to fitness variation of traits subject to highly variable
 selective pressures, but little to traits responding to scarcely variable
 aspects of the environment. More generally, our study demonstrates that
 the rate of mutation and the adaptive potential of any inheritance media
 should not be seen as independent properties.
description: rajon_charlat_2019.tar
DOI: 10.5061/dryad.9gg5rh3
title: Data from: Antagonistic selection and pleiotropy constrain the evolution of plant chemical defenses

description: When pleiotropy is present, genetic correlations may constrain the
 evolution of ecologically important traits. We used a quantitative
 genetics approach to investigate constraints on the evolution of secondary
 metabolites in a wild mustard, Boechera stricta. Much of the genetic
 variation in chemical composition of glucosinolates in B. stricta is
 controlled by a single locus, BCMA1/3. In a large-scale common garden
 experiment under natural conditions, we quantified fitness and
 glucosinolate profile in two leaf types and in fruits. We estimated
 genetic variances and covariances (the G-matrix) and selection on chemical
 profile in each tissue. Chemical composition of defenses was strongly
 genetically correlated between tissues. We found antagonistic selection
 between defense composition in leaves and fruits: compounds that were
 favored in leaves were disadvantageous in fruits. The positive genetic
 correlations and antagonistic selection led to strong constraints on the
 evolution of defenses in leaves and fruits. In a hypothetical population
 with no genetic variation at BCMA1/3, we found no evidence for genetic
 constraints, indicating that pleiotropy affecting chemical profile in
 multiple tissues drives constraints on the evolution of secondary
 metabolites.
description: READMESummary of each file,
 and header information.HPLCreaperCollects peak data from raw HPLC reports and adds the identifying sample number and metatdata.GS_datamergeMerges the output of HPLCreaper with data from a tab-delimited text file.GS_calcUses the output of GS_datamerge, which is raw amounts of glucosinolates, to calculate the concentrations and proportions of each compound.Covar_componentsWhen given phenotypic data, calculates covariance components by family, and tests for significance.Gmatrix_DFAUses data from GS_forG.txt. Estimates a G-matrix using the covariances of family means. Compares the predicted response to selection with and without genetic covariances, using bootstrapping and discriminant function analysis to test for statistical significance.Perm_selgradsPerforms a permutation test to compare selection gradients for two specific traits.GS_forGA tab-delimited text file containing phenotypic data for experimental individuals.2015_stg_GSIncludes glucosinolate data for plants from the 2015 cohort, which had early stage data available.FamilyLSmeansLS means for each family for glucosinolates, survival traits, and herbivory.
DOI: 10.5061/dryad.1gm77f6
title: Data from: Number of neighbors instead of group size significantly affects individual vigilance levels in large animal aggregations

description: The group size effect states that animals living in groups gain
 anti-predator benefits through reducing vigilance levels as group size
 increases. A basic assumption of group size effect is that all individuals
 are equally important for a focal individual, who may adjust its vigilance
 levels according to social information acquired from them. However, some
 studies have indicated that neighbors pose greater influences on an
 individual’s vigilance decisions than other group members, especially in
 large aggregations. Vigilance has also been found to be directed to both
 predators (anti-predation vigilance) and conspecifics (social vigilance).
 Central individuals might rely more on social vigilance than peripheral
 individuals. To test these hypotheses, we examined the effects of flock
 size, number of neighbors and position within a flock on vigilance and
 competition of greater white-fronted goose (Anser albifrons) that form
 large foraging flocks in winter, controlling the effects of other
 variables (group identity, winter period, and site). We found that
 individual vigilance levels were significantly affected by number of
 neighbors and position within a flock, whereas flock size showed no
 effect. Individuals devoted a large component of vigilance to nearby flock
 mates. Central individuals directed a relatively larger proportion of
 vigilance to monitor neighbors than peripheral ones, indicating that
 central individuals more relied on social information acquired from
 neighbors, possibly caused by the more blocked visual field of central
 individuals. Moreover, some social vigilance may function as conducting or
 preventing agonistic interactions since competition intensity was
 positively correlated with number of neighbors. Our study therefore
 demonstrate that the number of neighbors is more important than group size
 in determining individual vigilance in large animal groups. Further
 studies are still needed to unravel which neighbors pose greater influence
 on individual vigilance, and the factors that influence individuals to
 acquire information from their neighbors to adjust vigilance behaviors.
description: Data_JAB
DOI: 10.5061/dryad.6hj0824
title: Data from: Restoration potential of threatened ecosystem engineers increases with aridity: broad scale effects on soil nutrients and function

description: Species extinctions alter ecosystem services, and the magnitude of this
 impact is likely to change across environmental gradients. In Australia,
 soil-disturbing mammals that are now considered ecologically extinct are
 thought to be important ecosystem engineers. Previous studies have
 demonstrated microsite-level impacts of reintroduced soil-disturbing
 mammals on soil functions, but effects are yet to be tested across larger
 scales. Further, it is unclear how impacts vary across environmental
 gradients and if the restoration potential of reintroductions changes with
 climate. We examined the effects of soil-disturbing mammal reintroductions
 across a large rainfall gradient in Australia to test the hypothesis that
 ecosystem engineering effects on soil function depend on climate. We
 compared soil labile carbon, available nitrogen and the activity of four
 enzymes associated with nutrient cycling in three microsite types with and
 without soil-disturbing mammals in five sites along a large rainfall
 gradient (166-870 mm). Soil enzyme activity was greatest in the presence
 of soil-disturbing mammals and increased with rainfall, but soil available
 carbon and nitrogen varied across the gradient and among microsites.
 Microsite effects were often stronger than any effects of soil-disturbing
 mammals, with soil beneath vegetated patches (shrubs and trees) having
 greater enzyme activity, carbon and nitrogen than bare soils. However,
 soil-disturbing mammals homogenised nutrient distributions across
 microsites. The impacts of soil-disturbing mammals on soil function
 previously detected at micro-scales was detected at a landscape-scale.
 However, the overall effects of soil-disturbing mammals on soil functions
 varied with productivity (rainfall). The context of soil-disturbing mammal
 reintroductions is thus likely to be critical in determining their
 effectiveness in restoring soil function.
description: Soil nutrients with and
 without digging mammalsThe file includes
 various data on the studied sites. There file contains data of the studied
 reserves' biotic (vegetation) and abiotic (climate) attributes, their
 history and the reintroduced mammals. The file also contains information
 on the studied sites' soil properties: labile carbon, available
 nitrogen and microbial enzyme activities.dataDryad_ODeckerEcography.xlsx
DOI: 10.5061/dryad.8dm275k
title: Data from: Correlates of alternative migratory strategies in western bluebirds

description: Partial migration occurs when only some animals in a population migrate.
 While evidence suggests that migratory strategies are partially controlled
 by genes, individual and environmental conditions which alter the
 cost‐benefit trade‐off of migration among individuals are also likely to
 play a role. Three hypotheses have been advanced to explain
 condition‐dependent partial migration: the arrival time, dominance, and
 body size hypotheses. In this study, we asked whether these hypotheses
 explained differences in migratory strategy among individuals in a
 partially migratory population of western bluebirds (Sialia mexicana)
 breeding in southern British Columbia, Canada. We used stable hydrogen
 isotope signatures in claw tissue to determine migratory strategy of
 individual bluebirds, and examined patterns of migration at both
 individual and population levels. The proportion of resident bluebirds
 varied significantly over the three years of the study, and across study
 sites. Several migrants switched to the resident strategy between years;
 however, we found no evidence of strategy switching in the opposite
 direction. Young birds were significantly more likely to be resident than
 older birds, a pattern which could arise if early arrival is particularly
 important for birds obtaining a territory for the first time. Furthermore,
 young females were the most likely of all sex‐age classes to be resident,
 which may reflect a survival advantage of residency for young females.
 Finally, birds mated assortatively by migratory strategy and isotopic
 evidence suggests that members of a pair often wintered in the same place.
 Our results provided no support for the dominance or body size hypotheses,
 and only limited support for the arrival time hypothesis in bluebirds.
 However, taken together, we suggest that our findings indicate that social
 factors may influence migratory strategies in this system.
description: Known Origin
 BirdsClaw isotope values for
 known migrant and resident bluebirds used in
 assignment.Migratory
 StrategyClaw hydrogen isotope
 values and individual data (sex, age, size, etc.) for all captured
 bluebirds.PairsData for all pairs with
 claw hydrogen isotope values for both males and
 females.Hydrogen Isotope
 StandardsRepeated measurements of
 hydrogen isotope signatures of standards.
DOI: 10.5061/dryad.q0k4q3c
title: Data from: Tau protein as a diagnostic marker for diffuse axonal injury

description: Background: Diffuse axonal injury (DAI) is difficult to identify in the
 early phase of traumatic brain injury (TBI) using common diagnostic
 methods. Tau protein is localized specifically in nerve axons. We
 hypothesized that serum level of tau can be a useful biomarker to diagnose
 DAI in the early phase of TBI. Methods & Results: We measured
 serum tau levels in 40 TBI patients who were suspected of DAI within 6
 hours after TBI to evaluate the accuracy of the tau level as a diagnostic
 marker for DAI. Diagnosis of DAI was confirmed according to magnetic
 resonance imaging (MRI) findings. The serum tau level in the DAI group
 (n=13) was significantly higher than that in the non-DAI group (n=27) (DAI
 vs. non-DAI, 25.3 [0 to 99.1] pg/mL vs. 0 [0 to 44.4] pg/mL, P=0.03)). A
 receiver-operating characteristic curve to evaluate the diagnostic ability
 of serum tau level within 6 hours for DAI showed an area under the curve
 of 0.690 with 74.1% for sensitivity and 69.2% for specificity. Serum tau
 level was not significantly higher in unfavorable outcome group (Glasgow
 Outcome scale [GOS] score=1-3 at hospital discharge) compared with
 favorable outcome group (GOS score=4-5) (P=0.19). Conclusions: Tau protein
 may be a useful biomarker for diagnosis of DAI in the early phase of TBI.
description: data set
 tauThe detailed data of
 patients in this study.
DOI: 10.5061/dryad.9p7t664
title: Data from: A nation-wide survey of neonicotinoid insecticides in agricultural land with implications for agri-environment schemes

description: 1. Neonicotinoids are the most widely used class of insecticides globally.
 However, the link between farming practices and the extent of
 contamination of soils and crops by neonicotinoid insecticides, as well as
 and the extent of such contamination in organic fields and ecological
 focus areas (EFAs) are currently unclear. 2. We measured the
 concentrations of five neonicotinoid insecticides (imidacloprid,
 clothianidin, thiamethoxam, thiacloprid, acetamiprid) in 702 soil and
 plant samples in 169 cultivated fields and EFAs from 62 conventional,
 integrated production and organic farms distributed over the entire
 lowland of Switzerland. 3. We detected neonicotinoids in 93% of organic
 soils and crops, and more than 80% of EFA soils and plants – two types of
 arable land supposedly free of insecticides. We also tested 16 samples of
 organic seeds, of which 14 were positive for neonicotinoids. 4. Finally,
 we calculated hazard quotients (HQs) and potentially affected fractions
 for 72 beneficial and 12 pest species. Under a field-realistic scenario,
 we found that between 5.3 and 8.6% of above-ground invertebrate species
 may be exposed to lethal concentrations of clothianidin, and 31.6 to 41.2%
 to sublethal concentrations, in “integrated production” and conventional
 fields. We also found that 1.3 to 6.8% (up to 12.5% based on HQs) of the
 beneficial invertebrate species may be exposed to sublethal concentrations
 of neonicotinoids in EFAs and organic fields. In contrast, no pest species
 would be exposed to lethal concentrations, even under a worst-case
 scenario. 5. Synthesis and applications. Our study suggests that diffuse
 contamination by neonicotinoids may harm a significant fraction of
 non-target beneficial species. The use of neonicotinoids on crops may
 threaten biodiversity in refuge areas, while also potentially jeopardizing
 the practice of organic farming by impeding the biological control of
 pests. Based on our results, we call for a reduction in the dispersion and
 overuse of neonicotinoid insecticides in order to prevent any detrimental
 effects on biodiversity and ecosystem services associated with
 agroecosystems.
description: Raw
 databaseConcentrations of the
 five NNIs in soil, plant and organic seeds samples and associated location
 (GPS), slope, watershed and date of sampling.JAPPL-2018-01037_R2_Raw_database.xlsxR codeR script for all the analyses conducted in this study.JAPPL-2018-01037_R2_R_code.R
DOI: 10.5061/dryad.7qm13nn
title: Data from: Association between restless legs syndrome and other movement disorders

description: Objectives. The present review focuses on the possible association between
 restless legs syndrome and movement disorders, including Parkinson’s
 disease, other parkinsonian syndromes, essential tremor, choreic and
 dystonic syndromes, Tourette’s syndrome and heredodegenerative ataxias.
 Methods. Review of PubMed Database from 1966 to September 2018 and
 identification of references of interest for the topic. Meta-analysis of
 eligible studies on the frequency of RLS in Parkinson’s disease patients
 and controls using the Meta-DiSc1.1.1 software and using the PRISMA
 guidelines. Results and conclusions. Although there are substantial
 clinical, neuroimaging, neuropathological and genetic differences between
 RLS and Parkinson’s disease, many reports describe a higher than expected
 prevalence of RLS in patients with Parkinson’s disease, when compared both
 with the general population or with matched control groups; several
 studies have also suggested that RLS could be an early clinical feature of
 Parkinson’s disease. RLS symptoms are very frequent in multiple system
 atrophy, essential tremor, Tourette’s syndrome, Friedreich ataxia, and
 spinocerebellar ataxia type 3 (SCA3) as well. Finally, possible genetic
 links between Parkinson’s disease and RLS (the presence of allele 2 of the
 complex microsatellite repeat Rep1 within the alpha-synuclein gene
 promoter) and between Tourette’s syndrome and RLS (several variants in the
 BTBD9 gene) have been reported in two case-control association studies,
 although these data, based on preliminary data with small sample sizes,
 need to be replicated in further studies.
description: RLS-OTHER
 MD-NEUROLOGY-SUPPLEMENTARY MATERIAL-REVISED-2Supplementary data from
 the article association between restless legs syndrome and other movement
 disorders (Hortensia Alonso-Navarro MD PhD, Elena García-Martín MD PhD,
 José A.G. Agúndez MD PhD, Félix Javier Jiménez-Jiménez MD
 PhD
DOI: 10.6084/m9.figshare.31158187
title: <b>Landslide-Debris_Flow_Chain_Simulation_Data</b>

description: This data consists of all the raw data used for landslide-debris flow hazard simulation.
DOI: 10.6084/m9.figshare.31158187.v1
title: <b>Landslide-Debris_Flow_Chain_Simulation_Data</b>

description: This data consists of all the raw data used for landslide-debris flow hazard simulation.
DOI: 10.5061/dryad.qf0k11c
title: Data from: A functional diversity approach of crop sequences reveals that weed diversity and abundance show different responses to environmental variability

description: 1. Combining several crop species and associated agricultural practices in
 a crop sequence has the potential to control weed abundance while
 promoting weed diversity in arable fields. However, how the variability of
 environmental conditions that arise from crop sequences affects weed
 diversity and abundance remains poorly understood, with most studies
 to-date simply opposing weed communities in monoculture and in crop
 rotation. Here, we describe crop sequences along gradients of disturbance
 and resource variability using a crop functional trait and associated
 agricultural practices. We tested the hypothesis that variability of
 disturbances reduces weed abundance while variability of resources
 promotes weed diversity. 2. We used functional Hill’s numbers to compute
 crop sequence functional diversity based on sowing date, herbicide
 spectrum and crop height - these are the respective proxies of disturbance
 timings, disturbance types and light availability. Using a large-scale
 weed monitoring database, we assessed crop sequence diversity for 1045
 crop sequences of five consecutive cropping seasons. We computed weed
 richness and abundance at pluri-annual (pool of weeds observed across five
 cropping seasons) and annual (pool of weeds observed during a winter
 cereal cropping season preceded by five cropping seasons) scales. We also
 accounted for herbicide and tillage intensities to test whether management
 intensity affects the response of weed diversity and abundance to crop
 sequence diversity. 3. At the pluri-annual scale, weed richness increased
 with the diversity of crop height and sowing date while weed abundance
 decreased with sowing date diversity. Annual weed richness decreased with
 sowing date diversity while annual weed abundance poorly relied on crop
 sequence diversity. 4. Synthesis and applications. This study establishes
 a scientific basis for designing crop sequences according to specific weed
 management goals. We show that farmers may enhance arable weed diversity
 on a pluri-annual scale by sequentially sowing crop species that differ in
 their competitive ability and sowing date. They may also achieve a better
 control of weed abundance by increasing the diversity of crop sowing dates
 across the crop sequence.
description: Weeds diversity, weed
 abundance and crop sequences diversityThis file describes weed
 richness and abundance as well as crop sequence diversity and management
 intensity for around 200 arable fields monitored in French between 2002
 and 2010. We computed the diversity and abundance of weeds for both
 pluri-annual (i.e. five consecutive cropping seasons) and annual (i.e.
 winter cereal cropping season) species pools. Annual species pools were
 monitored at the beginning of a cropping season (T1) or at the middle
 (T2), both in presence or absence of herbicide sprayed.data.xlsx
DOI: 10.5061/dryad.nb20b4g
title: Data from: Using river color to predict Amazonian floodplain forest avifauna in the world’s largest black-water river basin

description: Despite the importance of rivers in Amazonian biogeography, avian
 distribution patterns in river-created habitats (i.e., floodplain forest)
 have been sparsely addressed. Here we explore geographic variation in
 floodplain forest avifauna, specifically regarding one of the most
 striking aspects of the Amazon: the diversity of river “colors” (i.e.,
 types, based on the color of the water). We sampled the avifauna at 30
 sites, located in 17 different rivers (nine black- and eight white-water),
 in the Rio Negro basin, northwestern Brazil. Our sampling comprised ten
 15-min point-counts per site, distributed every 500-1000m along the river.
 We recorded a total of 352 bird species, many of which occurred in both
 river types. Although bird species richness was similar among rivers, we
 found significant differences in species composition. Nearly 14 percent of
 the species were significantly associated with one of the two river types.
 Most floodplain forest specialists occurred predominantly in white-water
 rivers, whereas species that are typically associated with white-sand
 habitats occurred in black-water. Despite significant distinctions between
 river types, occurrence patterns and levels of habitat association
 differed among indicator species and may vary in the same species
 throughout its global distribution. There were also “intermediate”
 avifaunas in some of our sites, suggesting continuous parameters that
 characterize river types are structuring species turnover. The water
 color-based classification of Amazonian rivers represent a simple and
 powerful predictor of the floodplain forest avifauna, offering a
 stimulating starting point for understanding patterns of floodplain avian
 distributions and for prioritizing conservation efforts in these
 overlooked habitats.
description: point_counts_coordinatesList of point-counts where bird species were sampled at river sites. File includes attributes description in a separate sheet.bird_species_detectionsData-base of records of bird species detections at river sites. File includes attributes descriptions in a separate sheet.