cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pp5qk07
title: Data from: Transcriptional remodeling upon light removal in a model cnidarian: losses and gains in gene expression

description: Organismal responses to light:dark cycles can result from two general
 processes: (i) direct response to light or (ii) a free-running rhythm
 (i.e., a circadian clock). Previous research in cnidarians has shown that
 candidate circadian clock genes have rhythmic expression in the presence
 of diel lighting, but these oscillations appear to be lost quickly after
 removal of the light cue. Here, we measure whole-organism gene expression
 changes in 136 transcriptomes of the sea anemone Nematostella vectensis,
 entrained to a light:dark environment and immediately following light cue
 removal to distinguish two broadly defined responses in cnidarians: light
 entrainment and circadian regulation. Direct light exposure resulted in
 significant differences in expression for hundreds of genes, including
 more than 200 genes with rhythmic, 24-hour periodicity. Removal of the
 lighting cue resulted in the loss of significant expression for 80% of
 these genes after one day, including most of the hypothesized cnidarian
 circadian genes. Further, 70% of these candidate genes were phase shifted.
 Most surprisingly, thousands of genes, some of which are involved in
 oxidative stress, DNA damage response, and chromatin modification, had
 significant differences in expression in the 24 hours following light
 removal, suggesting that loss of the entraining cue may induce a cellular
 stress response. Together, our findings suggest that a majority of genes
 with significant differences in expression for anemones cultured under
 diel lighting are largely driven by the primary photoresponse rather than
 a circadian clock when measured at the whole animal level. These results
 provide context for the evolution of cnidarian circadian biology and help
 to disassociate two commonly confounded factors driving oscillating
 phenotypes.
description: N. vectensis light
 removal experiment, raw all counts tableRaw tag-based sequencing
 data used as input file for DESeq2 meta-analysis. This data set was
 collected in the Reitzel Lab at the University of North Carolina at
 Charlotte in December, 2017. A description of the sampling protocol is
 given in the materials and methods section of the manuscript. Briefly, sea
 anemones were sampled at 4-hour intervals over a ~ 3 day period, pre- and
 post- light cue removal and during constant conditions for a total of 136
 samples. Columns correspond to single genes mapped to the Vienna
 Nematostella transcriptome, and each row corresponds to 1 individual (4
 reps per time point, 17 time points, 2 light
 treatments).all_counts_table.csvData1Data1 contains all raw Illumina sequencing files associated with diel-entrained subjects. File names contain information regarding treatment (LD), timepjoint (T#), and biological replicate (A-D).Data2Data2 contains all Illumina raw sequencing files associated with long-term constant darkness-entrained subjects. File names contain information regarding treatment (DD), timepjoint (T#), and biological replicate (A-D).
DOI: 10.5061/dryad.n66q0nv
title: Data from: What does urbanization actually mean? A review and framework for urban metrics in wildlife research

description: 1. Extensive research has demonstrated that urbanization strongly alters
 ecological processes, often perniciously. However, quantifying the
 magnitude of urban effects and determining how generalized they can be
 across systems depends on the ways in which urbanization is measured and
 modelled. 2. We coupled a formal literature survey with a novel conceptual
 framework to document and synthesize the myriad of metrics used to
 quantify urbanization. The framework enables clear cataloguing of urban
 metrics by identifying) the urban component measured, ii) the method of
 measurement, iii) the metric’s spatial scale, and iv) the metric’s
 temporal nature. Thus, the framework comprehensively captures the what,
 how, where, and when of urban metrics.3. We documented striking
 variability in urban metrics with respect to which urban components were
 measured as well as how, where, and when they were quantified. Overall,
 our survey revealed that they tended to be: i) be structurally-focused,
 ii) methodologically simplistic, iii) spatially variable, and iv)
 temporally static. 4. Synthesis and applications. Many metrics are used to
 quantify urbanization or “urban-ness”. The variation in urban metrics
 complicates the development of theory, comparisons of findings across
 studies, and the implementation of management and conservation actions. To
 pave a clear path forward for more efficient and policy-relevant urban
 research, we systematically organized urban metrics using a simple,
 flexible, and comprehensive framework. The framework clarifies what
 urbanization actually means in empirical practice and identifies several
 crucial areas for future research, including: i) systematic assessments of
 urban metrics across multiple scales, ii) an increased and judicious use
 of more complex urban metrics aimed at evaluating both mechanistic and
 broad-scale correlative ecological hypotheses, and iii) an increased
 emphasis on the socio-economic aspects of urban effects.
description: Table of urban
 metricsThe table lists 1,177
 urban metrics and their specific categorizations, collected from a survey
 of urban wildlife studies published between 2012 and 2016. Column
 abbreviations: com_type = component type; com_s_type = component subtype;
 meth_cat_con = whether method was categorical or continuous; prop_hr =
 ratio of metric spatial scale to species' typical home
 range.Moll_etal_JAE_urbanization_studies.csvStudies omitted from reviewThis table provides a list of studies that did not meet the criteria for review.Moll_etal_JAE_urbanization_omitted_studies.csv
DOI: 10.5061/dryad.2463f63
title: Data from: Meta-analysis of yield response of foliar fungicide-treated hybrid corn in the United States and Ontario, Canada

description: Background: Foliar fungicide applications to corn (Zea mays) occur at one
 or more application timings ranging from early vegetative growth stages to
 mid-reproductive stages. Previous studies indicated that fungicide
 applications are profitable under high disease pressure when applied
 during the tasseling to silking growth stages. Few comprehensive studies
 in corn have examined the impact of fungicide applications at an early
 vegetative growth stage (V6) compared to late application timings (VT) for
 yield response and return on fungicide investment (ROI) across multiple
 locations. Objective: Compare yield response of fungicide application
 timing across multiple fungicide classes and calculate the probability of
 positive ROI. Data sources: Data were collected specifically for this
 analysis using a uniform protocol conducted in 13 states in the United
 States and one province in Canada from 2014 - 2015. Synthesis methods:
 Data were subjected to a primary mixed-model analysis of variance.
 Subsequent univariate meta-analyses, with and without moderator variables,
 were performed using standard meta-analytic procedures. Follow-up power
 and prediction analyses were performed to aid interpretation and
 development of management recommendations. Results: Fungicide application
 resulted in a positive yield response in 68.2% of the 436 trial-studies.
 All three moderator variables tested (application timing, fungicide class,
 and disease base level), had a significant effect (=0.05) on the absolute
 difference in yield between fungicide treated and non-treated plots ( ¯D).
 Application timing influenced ¯D, with V6 + VT and the VT application
 timings resulting in greater yield responses than the V6 application
 timing alone. Fungicide formulations that combined demethylation inhibitor
 and quinone outside inhibitor fungicides significantly increased yield
 response. Conclusion: Foliar fungicide applications can increase corn
 grain yield. To ensure the likelihood of a positive ROI, farmers should
 focus on applications at VT and use fungicides that include a mix of
 demethylation inhibitor and quinone outside inhibitor active ingredients.
description: Raw Data for Corn
 Fungicide Meta-Analysis2019 CDWG Meta-Analysis
 FULL SET_METRICSAS Analysis of the Full
 Data Set k=4362019 CDWG Meta-Analysis
 QoI SET_METRICSAS Analysis of QoI data
 Only2019 CDWG Meta-Analysis
 DMI+QoI SET_METRICSAS Analysis of DMI+QoI
 data Only
DOI: 10.5061/dryad.j89p2tj
title: Data from: Responses of seedling growth and survival to post-germination cotyledon removal: an investigation among seven oak species

description: 1. Rodents regularly rely on emerged epicotyls to locate and remove
 cotyledons still containing valuable nutrients. However, the extent to
 which acorn characteristics influence tolerance to post-germination
 predation has received little attention. 2. Here, we investigated the
 impact of cotyledon removal following epicotyl emergence on seedling
 performance and survival of seven oak (Quercus) species. We imitated
 cotyledon predation at different stages of seedling establishment and
 development in order to detect effects on seedling height, leaf number,
 and tissue/component mass. 3. Seedling growth and survival were negatively
 affected by cotyledon loss regardless of oak species. However, these
 negative effects decreased as the epicotyl length at which cotyledons were
 removed increased. We also found that there was a threshold epicotyl
 length above which seedling survival and performance were relatively
 unaffected in white oak species compared to red oak species. 4. Following
 cotyledon removal, early germinating white oak (section Quercus) seedlings
 survived and/or grew better than the late germinating red oak (section
 Lobatae) seedlings. This was likely caused by a difference in dependence
 on cotyledon reserves, which ultimately affected the ability of seedlings
 to tolerate cotyledon removal. 5. Synthesis From an evolutionary
 perspective, this is likely to follow from the early germination in white
 oaks and the ability of seed consumers to locate young seedlings from the
 emerging epicotyls. Our study has implications for forest regeneration by
 suggesting additional opportunities for white oak species to establish
 following epicotyl emergence. Future studies should consider quantifying
 the rates of post-germination cotyledon loss.
description: Seedling removal-journal
 of Ecology
DOI: 10.5061/dryad.3b1rj70
title: Data from: Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards

description: Species abundance data are critical for testing ecological theory, but
 obtaining accurate empirical estimates for many taxa is challenging.
 Proxies for species abundance can help researchers circumvent time and
 cost constraints that are prohibitive for long-term sampling. Under simple
 demographic models, genetic diversity is expected to correlate with census
 size, such that genome-wide heterozygosity may provide a surrogate measure
 of species abundance. We tested whether nucleotide diversity is correlated
 with long-term estimates of abundance, occupancy, and degree of ecological
 specialization in a diverse lizard community from arid Australia. Using
 targeted sequence capture, we obtained estimates of genomic diversity from
 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb
 of DNA sequence per individual. We compared measures of individual
 heterozygosity to a metric of habitat specialization to ask whether
 ecological preference exerts a measurable effect on genetic diversity. We
 find that heterozygosity is significantly correlated with species
 abundance and occupancy, but not habitat specialization. Demonstrating the
 power of genomic sampling, the correlation between heterozygosity and
 abundance/occupancy emerged from considering just one or two individuals
 per species. However, genetic diversity does no better at predicting
 abundance than a single day of traditional sampling in this community. We
 conclude that genetic diversity is a useful proxy for regional-scale
 species abundance and occupancy, but a large amount of unexplained
 variation in heterozygosity suggests additional constraints or a failure
 of ecological sampling to adequately capture variation in true population
 size.
description: Matuwa lizard community
 data matrixMatrix of data for
 lizard species in the Matuwa community including genetic diversity,
 abundance, occupancy, body size, and a metric of habitat
 specialization.matuwa_community_data_matrix.csvMatuwa lizard community habitat meansMean habitat values for lizard species in the Matuwa community, including fourteen different variables describing microhabitat characteristics.species_habitat_means.csv
DOI: 10.5061/dryad.q2cc41c
title: Data from: A comparative morphometric study of sensory capacity in geometrid moths

description: Diet breadth and the degree of capital breeding have been established as
 major determinants of species-specific ecology of herbivorous insects. The
 relationship of these variables with sensory capacity, although allowing
 an array of hypotheses, has remained poorly studied, let alone in
 phylogenetically explicit multi-species comparisons. We contribute to
 filling this gap in a study of 60 species of geometrid moths (Lepidoptera:
 Geometridae), using adult head measures (eye size, antennal length and
 shape, forehead width) as indices of sensory capacity. When controlled for
 body size, eyes of capital breeding species were found to be smaller, and
 female antennae shorter, than in income breeders. Feathery (vs simple
 filiform) male antennae were more frequently present in the capital
 breeders and in larger species. Regarding diet breadth, generalist species
 were found to have relatively wider male foreheads than specialists. The
 results suggest that (a) breeding strategy rather than diet breadth
 predicts sensory capacity in geometrids, (b) capital breeding (vs income
 breeding) is related to low sensory capacity in females, and (c) in
 contrast, males of the capital breeding species have evolved towards
 elevated olfactory capacity.
description: Data used in Javoiš et
 al (Journal of Evolutionary Biology)Data set containing
 species used in the study of sensory capacity of geometrid moths. Data
 collected from lab, photo-based measurements and literature
 sources.javoiš_et_al_data.xls
DOI: 10.5061/dryad.92dj50c
title: Data from: Mortality versus survival in drought‐affected Aleppo pine forest depends on the extent of rock cover and soil stoniness

description: Drought-related tree mortality had become a widespread phenomenon in
 forests around the globe. Recent drought years led to 5-10% mortality in
 the semi-arid pine forest of Yatir (Israel). The distribution of dead
 trees was, however, highly heterogeneous with parts of the forest showing
 &gt;80% dead trees (D plots) and others with mostly live trees (L
 plots). At the tree level, visible stress was associated with low predawn
 leaf water potential at the dry season (-2.8 MPa, vs. -2.3 MPa in
 non-stressed trees), shorter needles (5.5 vs. 7.7 mm) and lower
 chlorophyll content (0.6 vs. 1 mg g-1 dw). Trends in tree ring widths
 reflected differences in stress intensity (30% narrower rings in stressed
 compared with unstressed trees), which could be identified 15-20 years
 prior to mortality. At the plot scale, no differences in topography, soil
 type, tree age, or stand density could explain the mortality difference
 between the D and L plots. It could only be explained by the higher
 surface rock cover and in stoniness across the soil profile in the L
 plots. Simple bucket model simulations using the site’s long-term
 hydrological data supported the idea that these differences could result
 in higher soil water concentration (m3/m3) in the L plots and extend the
 time above wilting point by several months across the long dry season.
 Accounting for subsurface heterogeneity is therefore critical to assessing
 stand level response to drought and projecting tree survival, and can be
 used in management strategies in regions undergoing drying climate trends.
description: Preisler et al. 2019_
 Climatic panel_Figure 1Climatic data and
 evapotranspiration recorded measured by the Yatir forest Eddy covariance
 flux towerPreisler et al. 2019_
 WP_figure 2Pre-dawn water potential
 measurements data from 5 seasons that were held at the trees in different
 stress stages. rainfall amount of the corresponding period is also
 notedPreisler et al. 2019_
 BAI-tree rings_Figure 3Tree ring data recorded
 from all tree in the study period for the period of 1972 to 2012. Annual
 rainfall for the same period is also notedPreisler et al. 2019_
 Stoniness and root density_Figure 4Root density and
 stoniness % measurements as obtained from the soil trenches in the Live
 and dead plotsPreisler et al. 2019_
 Bucket model results_Figure 5The bucket model
 simulation results output.
DOI: 10.5061/dryad.q499457
title: Data from: The possible role of ant larvae in the defence against social parasites

description: Temporary social parasite ant queens initiate new colonies by entering
 colonies of host species, where they begin laying eggs. As the resident
 queen can be killed during this process, host colonies may lose their
 entire future reproductive output. Selection thus favours the evolution of
 defence mechanisms, before and after parasite intrusion. Most studies on
 social parasites focus on host worker discrimination of parasite queens
 and their offspring. However, ant larvae can also influence brood
 composition by consuming eggs. This raises the question whether host
 larvae can aid in preventing colony takeover by consuming eggs laid by
 parasite queens. To test whether larvae could play a role in anti-parasite
 defence, we compared the rates at which larvae of a common host species,
 Formica fusca, consumed eggs laid by social parasite, non-parasite,
 nestmate, or conspecific non-nestmate queens. Larvae consumed social
 parasite eggs more than eggs laid by a heterospecific non-parasite queen,
 irrespective of the chemical distance between the egg cuticular profiles.
 Also, larvae consumed eggs laid by conspecific non-nestmate queens more
 than those laid by nestmate queens. Our study suggests that larvae may act
 as players in colony defence against social parasitism, and that social
 parasitism is a key factor shaping discrimination behaviour in ants.
description: Behavioural
 dataData of F. fusca larvae
 used in the experiments. File contains larvae colony information, sex of
 the larvae and whether they consumed an egg or not. Included also details
 of the eggs offered to larvae: the colony and species of
 eggs.Hatching
 dataThis data shows the
 hatching success of eggs of different Formica species used in the
 study.Egg size
 dataThis data contains
 measures of egg sizes of different Formica species used in this
 studyCHC data F.
 truncorumThis file contains the
 raw cuticular hydrocarbon peak areas of Formica truncorum eggs. Retention
 times and peak areas shown.Larva genotypes used for
 sexing F.fuscaThis file contains
 Formica fusca larval genotypes and allele frequencies over 8
 microsatellite loci used for sexingLarva genotypes
 F.fusca.xlsx
DOI: 10.5061/dryad.5072425
title: Data from: Adult nutritional stress decreases oviposition choosiness and fecundity in female butterflies

description: Despite the benefits of careful decision-making, not all animals are
 choosy. One explanation is that choosiness can cost time and energy and
 thus depend on nutrition. However, it is not clear how allocation to
 choosiness versus other components of life history shifts in the face of
 nutritional stress. We tested two hypotheses about the effects of
 nutritional stress on choosiness and other life history traits: 1) poor
 nutrition leads to compensatory shifts in life history strategy towards
 greater investment per offspring in terms of choosy oviposition behavior
 and egg resources, and 2) poor nutrition negatively affects a range of
 life history traits. Cabbage white butterfly (Pieris rapae) females were
 reared under low or high nutrition conditions during the larval and adult
 stage in a fully factorial design. Choosiness was quantified as avoidance
 of conspecific models during oviposition. Adult life history traits
 included egg number, egg size, and thorax protein. Females that
 experienced nutritional stress as adults were less choosy and less fecund,
 in support of the second hypothesis. Yet females that were stressed as
 larvae invested more in thorax muscle, consistent with the first
 hypothesis. Overall, adult nutritional stress decreased investment in
 multiple reproductive traits, including a behavioral trait, but larval
 stress increased investment in flight, potentially to disperse away from
 nutritionally poor environments.
description: Spermatophore counts of
 low and high larval nutrition femalesData set showing
 spermatophore counts for a subset of 10 adult females from each of the two
 larval treatments- low and high nutrition. These data are a different
 subset of individuals from the other two files.NutSpermatophoreData_1-30-19.csvThorax Protein Data (non-averaged between duplicates)Data set with thorax protein data, showing larval and adult treatment, batch, and the duplicate mg protein/g thorax values for all individuals included in the main study, plus ten "reference" females from each larval treatment.ThoraxProteinData.csvLife History DataData set with life history data for all individuals included in the main study. The data set includes adult and larval treatment and measured values for choosiness, fecundity, egg area in mm squared (measure of egg size), forewing length in mm (as a proxy for body size), and thorax protein in mg protein per g thorax. Thorax protein values in this file are the two replicate values from the ThoraxProtein file averaged together for each individual. All individuals in the study were female.MainData.csv