cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d24pj
title: Data from: Comparative impacts of aboveground and belowground enemies on an invasive thistle

description: 1. Most research examining how herbivores and pathogens affect performance
 of invasive plants focuses on aboveground interactions. Although
 important, the role of belowground communities remains poorly understood,
 and the relative impact of aboveground and belowground interactions is
 still debated. As well, most studies of belowground interactions have been
 carried out in controlled environments, so little is known about the role
 of these interactions under natural conditions or how these relationships
 may change across a plant’s range. 2. Using the invasive plant Cirsium
 arvense, we performed a reciprocal transplant experiment to test the
 relative impacts of above- and belowground interactions at three sites
 across a 509 km latitudinal gradient in its invaded range in Ontario,
 Canada. At each site, C. arvense seedlings were protected with above-
 and/or belowground exclosures in a factorial design. 3. Plant performance
 (biomass, height, stem thickness, number of leaves, length of longest
 leaf, maximum rhizome length) was greatest when both above- and
 belowground exclosures were applied and lowest when no exclosures were
 applied. When only one type of exclosure was applied, biomass generally
 improved more with belowground exclosures than with aboveground
 exclosures. 4. Synthesis: Despite site-to-site differences in foliar
 damage, root damage, and mesofaunal populations, belowground interactions
 generally had a greater negative impact on performance than aboveground
 herbivory alone. These results stress the importance of including both
 aboveground enemy interactions and plant-soil interactions in studies of
 plant community dynamics and invader performance.
description: Nunes and Kotanen Ecol
 Evol 2017
DOI: 10.5061/dryad.7980
title: Data from: Life-history QTLs and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis

description: Plants must precisely time flowering to capitalize on favorable
 conditions. Although we know a great deal about the genetic basis of
 flowering phenology in model species under controlled conditions, the
 genetic architecture of this ecologically-important trait is poorly
 understood in non-model organisms. Here, we evaluated the transition from
 vegetative growth to flowering in Boechera stricta, a perennial relative
 of Arabidopsis thaliana. We examined flowering time QTLs using 7,920
 recombinant inbred individuals, across seven lab and field environments
 differing in vernalization, temperature, and photoperiod. Genetic and
 environmental factors strongly influenced the transition to reproduction.
 We found directional selection for earlier flowering in the field. In the
 growth chamber experiment, longer winters accelerated flowering, whereas
 elevated ambient temperatures delayed flowering. Our analyses identified
 one large effect QTL (nFT), which influenced flowering time in both
 experiments and the probability of flowering in the field. In Montana,
 homozygotes for the native allele at nFT showed a selective advantage of
 6.6%. Nevertheless, we found relatively low correlations between flowering
 times in the field and the growth chambers. Additionally, we detected
 flowering-related QTLs in the field which were absent across the full
 range of laboratory conditions, thus emphasizing the need to conduct
 experiments in natural environments.
description: field
 dataFamily level means for
 traits measured in the common garden site in Montana.growth chamber
 dataFamily level means for
 flowering time and leaf number at flowering in all growth chambers, and
 averaged across growth chambers.
DOI: 10.5061/dryad.jf5jv
title: Data from: Estimating animal density without individual recognition using information derivable exclusively from camera traps

description: 1. Efficient and reliable methods for estimating animal density are
 essential to wildlife conservation and management. Camera trapping is an
 increasingly popular tool in this area of wildlife research , with further
 potential arising from technological improvements, such as video recording
 functions that allow for behavioural observation of animals. This
 information may be useful in the estimation of animal density, even
 without individual recognition. Although several models applicable to
 species lacking individual markings (i.e. unmarked populations) have been
 developed, a methodology incorporating behavioural information from videos
 has not yet been established. 2. We developed a likelihood-based model:
 the random encounter and staying time (REST) model. It is an extension of
 the random encounter model (REM) by Rowcliffe et al. (2008). The REST
 model describes the relationship among staying time, trapping rate, and
 density, which is estimable using a frequentist or Bayesian approach. We
 tested the reliability and feasibility of the REST model using Monte Carlo
 simulations. We also applied the approach in the African rainforest and
 compared the results with those of a line-transect survey. 3. The
 simulations showed that the REST model provided unbiased estimates of
 animal density. Even when animal movement speeds varied among individuals,
 and when animals travelled in pairs, the model provided unbiased density
 estimates. However, the REST model was vulnerable to unsynchronized
 activity patterns among individuals. Moreover, it is necessary to use a
 camera model with a fast and reliable infrared sensor, and to set the
 camera trap’s parameters appropriately (i.e. video length, delay period).
 The field survey showed that the staying time of two ungulate species in
 the African rainforest exhibited good fit with a temporal parametric
 distribution, and the REST model provided density estimates consistent
 with those of a line-transect survey. 4. Synthesis and applications. The
 random encounter and staying time (REST) model provides better efficiency
 and higher feasibility than the random encounter model in estimating
 animal density without individual recognition. Careful application of the
 REST model should provide the potential to estimate density of many
 ground-dwelling vertebrates lacking individually recognizable markings,
 and thus should be an effective method for population monitoring.
description: Data from: Estimating
 animal density without individual recognition using information derivable
 exclusively from camera traps, Nakashima, Yoshihiro, Fukasawa, Keita,
 Samejima, HiromitsuNakashima_JAPPL_2017.csv
DOI: 10.5061/dryad.p64s1hh
title: Data from: Transgenerational effects and acclimation affect dispersal in guppies

description: 1. Evolutionary theory predicts that intergenerational environmental
 fluctuations lead to transgenerational effects where offspring phenotypes
 are matched to conditions experienced by previous generations. However, in
 fluctuating environments, transgenerational effects can be detrimental by
 causing mismatches between ancestral and offspring environments.
 Acclimation in offspring could alleviate these negative effects.2. We
 determined whether the interaction between transgenerational effects and
 acclimation affects locomotor performance and dispersal in guppies
 (Poecilia reticulata). In a fully factorial experiment, we tested the
 interaction between ancestral (22 or 30°C for 6-8 generations),
 acclimation (22 or 30°C for 4 weeks), and acute test temperatures (2-5
 temperatures across 18-34°C). We predicted that matching ancestral and
 acclimation temperatures to acute environmental temperature maximizes
 physiological capacities (swimming performance [U crit ] and metabolic
 enzyme activities), and dispersal in an artificial stream. Alternatively,
 when ancestral and acute temperatures were mismatched, we predicted that
 thermal acclimation compensates for this mismatch by shifting performance
 curves. Finally, we hypothesised that physiological capacities are
 positively related to dispersal. We measured dispersal as a combination of
 traits characterising the departure and transient phases of dispersal
 (time taken to leave the introductory pool, voluntary speed against the
 current, number of dispersal decisions taken) in an 8 m artificial stream.
 3. As hypothesised, U crit was greatest when ancestral, acclimation, and
 acute temperatures matched. Cold acclimation reduced the decrement in U
 crit resulting from a mismatch between ancestral and acute test
 temperatures. In both sexes, the interaction between ancestral and
 acclimation temperatures determined U crit, but not metabolic enzyme
 activities, and it affected the number of dispersal decisions in males
 only. Contrary to our hypothesis, physiological capacities did not
 constrain dispersal. Males were more likely to initiate dispersal when the
 acute temperatures mismatched their ancestral temperature. After
 initiating dispersal, males moved at a greater voluntary speed and made
 more dispersal decisions in environments matching their ancestral
 environment. 4. Our findings imply that although the interaction between
 transgenerational effects and acclimation modulates locomotor capacities,
 these relationships do not necessarily translate to all ecologically
 relevant locomotor tasks. Instead, sex-specific life history traits such
 as lifespan are more likely to influence dispersal, and males in
 particular may initiate dispersal to escape sub-optimal conditions.
description: Full dataset of
 physiological and ecological measurements.This file includes the
 full dataset of physiological and ecological measurements conducted on
 guppies from all combinations of ancestral, acclimation and acute thermal
 treatments.LeRoy&Seebacher_2018_FE.xlsx
DOI: 10.5061/dryad.331f7
title: Data from: Clinical study reports of randomised controlled trials: an exploratory review of previously confidential industry reports

description: Objective: To explore the structure and content of a non-random sample of
 clinical study reports (CSRs) to guide clinicians and systematic
 reviewers. Search strategy: We searched public sources and lodged Freedom
 of Information requests for previously confidential CSRs primarily written
 by industry for regulators. Selection criteria: CSR reporting sufficient
 information for extraction (“adequate”). Primary outcome measures:
 Presence and length of essential elements of trial design and reporting
 and compression factor (ratio of page length for CSR compared to its
 published counterpart in a scientific journal). Data extraction: data were
 extracted on standard forms and cross-checked for accuracy. Results: We
 assembled a population of 78 CSRs (covering 90 RCTs; 144,610 pages total)
 dated 1991-2011 of 14 pharmaceuticals. Report synopses had a median length
 of 5 pages, efficacy evaluation 13.5 pages, safety evaluation 17 pages,
 attached tables 337 pages, trial protocol 62 pages, statistical analysis
 plan 15 pages, and individual efficacy and safety listings had a median
 length of 447 and 109.5 pages, respectively. While 16 (21%) of CSRs
 contained completed case report forms, these were accessible to us in only
 one case (765 pages representing 16 individuals). Compression factors
 ranged between 1 and 8805. Conclusions: Clinical study reports represent a
 hitherto mostly hidden and untapped source of detailed and exhaustive data
 on each trial. They should be consulted by independent parties interested
 in a detailed record of a clinical trial, and should form the basic unit
 for evidence synthesis as their use is likely to minimize the problem of
 reporting bias. We cannot say whether our sample is representative and
 whether our conclusions are generalizable to an undefined and undefineable
 population of CSRs.
description: Data
 extractionAudited table of
 extracted and derived variables. Data were extracted on MS Word extraction
 tables. These tables were then brought into Microsoft Excel. Subsequently
 selected variables were audited (double-checked) and are presented in this
 Excel file. The Excel file contains multiple "sheets"
 (worksheets). Their contents are described in the readme
 file.
DOI: 10.5061/dryad.17s38
title: Data from: Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations

description: Predicting viral evolution has proven to be a particularly difficult task,
 mainly owing to our incomplete knowledge of some of the fundamental
 principles that drive it. Recently, valuable information has been provided
 about mutation and recombination rates, the role of genetic drift and the
 distribution of mutational, epistatic and pleiotropic fitness effects.
 However, information about the topography of virus' adaptive
 landscapes is still scarce, and to our knowledge no data has been reported
 so far on how its ruggedness may condition virus' evolvability. Here,
 we show that populations of an RNA virus move efficiently on a rugged
 landscape and scape from the basin of attraction of a local optimum. We
 have evolved a set of Tobacco etch virus genotypes located at increasing
 distances from a local adaptive optimum in a highly rugged fitness
 landscape, and we observed that few evolved lineages remained trapped in
 the local optimum, while many others explored distant regions of the
 landscape. Most of the diversification in fitness among the evolved
 lineages was explained by adaptation, while historical contingency and
 chance events contribution was less important. Our results demonstrate
 that the ruggedness of adaptive landscapes is not an impediment for RNA
 viruses to efficiently explore remote parts of it.
description: Raw fitness
 dataFitness are provided for
 the ancestral virus as well a to the two replicates of each evolutionary
 lineage relative to the 01001 genotype at the local fitness
 maximum.Fitness
 values.xlsxSummary of mutations
 found on each lineagePage 1 contains the
 nucleotide substitutions observed on each evolved lineage. Page 2 contains
 a schematic representation of mutations *fixed* on each lineage. Page 3
 contains the corresponding amino acid substitutions.
DOI: 10.5061/dryad.59kr65r
title: Data from: The importance of competition for light depends on productivity and disturbance

description: Eutrophication is a major cause of biodiversity loss. In grasslands this
 appears to occur due to asymmetric competition for light following the
 increases in aboveground biomass production. Here, we report the results
 of an experiment with five grass species that tests how well competitive
 outcomes can be predicted under a factorial combination of fertilized and
 disturbed (frequent cutting) conditions. Under fertile conditions our
 results confirm earlier success in predicting short-term competitive
 outcomes based on light interception in monocultures. This effect was
 maintained but weakened under less fertile conditions with competition
 becoming more symmetric. However, under disturbed conditions, competitive
 outcomes could not be predicted from differences in light interception in
 monocultures regardless of fertility. Our results support the idea that
 competition in grasslands shifts from symmetric to asymmetric as fertility
 increases but that disturbance destroys this relationship, presumably by
 preventing the development of differences in canopy structure and reducing
 competition for light.
description: Hautier_Disturbance_ZurichMono08: Monoculture biomass and light interception, June08: Mixtures biomas, pHNitrogen08: pH and nitrogen, Prediction08: Biomass and light ratio
DOI: 10.5061/dryad.0550m
title: Data from: Inducible versus constitutive social immunity: examining effects of colony infection on glucose oxidase and defensin-1 production in honeybees

description: Honeybees use a variety of defence mechanisms to reduce disease infection
 and spread throughout the colony. Many of these defences rely on the
 collective action of multiple individuals to prevent, reduce or eradicate
 pathogens—often referred to as ‘social immunity’. Glucose oxidase (GOX)
 and some antimicrobial peptides (e.g. defensin-1 or Def1) are secreted by
 the hypopharyngeal gland of adult bees on larval food for their antiseptic
 properties. Because workers secrete these compounds to protect larvae,
 they have been used as ‘biomarkers’ for social immunity. The aim of this
 study was to investigate if GOX and Def1 are induced after pathogen
 exposure to determine whether its production by workers is the result of a
 collective effort to protect the brood and colony in response to a
 pathogen challenge. Specifically, we quantified GOX and Def1 in honeybee
 adults before and after colony-level bacterial infection by American
 foulbrood ((AFB), Paenibacillus larvae). Overall, our results indicate
 that levels of GOX and Def1 are not induced in response to pathogenic
 infections. We therefore conclude that GOX and Def1 are highly
 constitutive and co-opted as mechanisms of social immunity, and these
 factors should be considered when investigating immunity at the individual
 and colony level in social insects.
description: Raw data for GOX
 enzymatic activity, and GOX and Def1 gene expressionThis excel file contains
 two sheets: (1) 'GOX_EnzymeActivity' contains the glucose
 oxidase activity values for the 3 replicates of all samples included in
 the study; (2) 'GeneExpression' contains gene expression values
 for the reference gene (Actin), GOX and Def1.Lopez-Uribe-GOX_Def1_RawData.xlsx
DOI: 10.5061/dryad.r774t76
title: Data from: Ecological sorting and character displacement contribute to the structure of communities of Clarkia species

description: Despite long‐standing interest in the evolutionary ecology of plants that
 share pollinators, few studies have explored how these interactions may
 affect communities during both community assembly (ecological sorting) and
 through ongoing, in situ evolution (character displacement), and how the
 effects of these interactions may change with community context. To
 determine if communities display patterns consistent with ecological
 sorting, we assessed the frequency of co‐occurrence of four species of
 Clarkia in the southern Sierra foothills (Kern County, CA, USA). To
 investigate potential character displacement, we measured
 pollination‐related traits on plants grown in a greenhouse common garden
 from seed collected in communities with one, two, or four Clarkia species.
 Among the four species of Clarkia in this region, the two species that are
 often found in multi‐species communities also co‐occur with one another
 more frequently than expected under a null model. This pattern is
 consistent with ecological sorting, although further investigation is
 needed to determine the role of pollinators in shaping community assembly.
 Patterns of trait variation in a common garden suggest that these two
 species have diverged in floral traits and converged in flowering time
 where they co‐occur, which is consistent with character displacement.
 Trait variation across community types also suggests that the process and
 outcome of character displacement may vary with community context. Because
 community context appears to affect both the direction and magnitude of
 character displacement, change in more species‐rich communities may not be
 predictable from patterns of change in simpler communities.
description: Common garden trait
 dataMeasures of floral and
 plant traits from 539 plants grown in a common garden. Blank cells
 indicate plants for which only plant level traits (height and date of
 first flower) were measured--floral traits were not measured on these
 plants.CG_All_Traits_Feb_2016.csvCo-occurrence dataData on species co-occurrence from the lower Kern River canyon and Oiler canyon. Any stop that contained multiple species is listed twice (e.g. if stop 1 contained C. xantiana and C. unguiculata, there are two separate entries in the file--stop 1: X and stop 1: U). Species were abbreviated as follows: C = Clarkia cylindrica, D = C. dudleyana, E = C. exilis, P = C. xantiana ssp. parviflora, S = C. speciosa, U = C. unguiculata, X = C. xantiana ssp. xantiana.Co_occurrence_data_long_canyons.csv
DOI: 10.5061/dryad.gb905
title: Data from: A hierarchical distance sampling model to estimate abundance and covariate associations of species and communities

description: Distance sampling is a common survey method in wildlife studies, because
 it allows accounting for imperfect detection. The framework has been
 extended to hierarchical distance sampling (HDS), which accommodates the
 modelling of abundance as a function of covariates, but rare and elusive
 species may not yield enough observations to fit such a model. We
 integrate HDS into a community modelling framework that accommodates
 multi-species spatially replicated distance sampling data. The model
 allows species-specific parameters, but these come from a common
 underlying distribution. This form of information sharing enables
 estimation of parameters for species with sparse data sets that would
 otherwise be discarded from analysis. We evaluate the performance of the
 model under varying community sizes with different species-specific
 abundances through a simulation study. We further fit the model to a
 seabird data set obtained from shipboard distance sampling surveys off the
 East Coast of the USA. Comparing communities comprised of 5, 15 or 30
 species, bias of all community-level parameters and some species-level
 parameters decreased with increasing community size, while precision
 increased. Most species-level parameters were less biased for more
 abundant species. For larger communities, the community model increased
 precision in abundance estimates of rarely observed species when compared
 to single-species models. For the seabird application, we found a strong
 negative association of community and species abundance with distance to
 shore. Water temperature and prey density had weak effects on seabird
 abundance. Patterns in overall abundance were consistent with known
 seabird ecology. The community distance sampling model can be expanded to
 account for imperfect availability, imperfect species identification or
 other missing individual covariates. The model allowed us to make
 inference about ecology of species communities, including rarely observed
 species, which is particularly important in conservation and management.
 The approach holds great potential to improve inference on species
 communities that can be surveyed with distance sampling.
description: Seabird distance
 sampling dataThis .R file contains
 all data to repeat the community distance sampling case study on seabird
 abundance and distribution off the mid-Atlantic coast presented in the
 associated paper. The data are in the form of a R list object; the R
 script to read in and analyze the data are part of the Supplement 2,
 available with the paper. The ReadMe file contains a detailed description
 of the data.sbdata.R