cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kk75k1p
title: Data from: The geographical variation of network structure is scale dependent: understanding the biotic specialization of host-parasitoid networks

description: Research on the structure of ecological networks suggests that a number of
 universal patterns exist. Historically, biotic specialization has been
 thought to increase towards the Equator. Yet, recent studies have
 challenged this view showing non-conclusive results. Most studies
 analysing the geographical variation in biotic specialization focus,
 however, only on the local scale. Little is known about how the
 geographical variation of network structure depends on the spatial scale
 of observation (i.e., from local to regional spatial scales). This should
 be remedied, as network structure changes as the spatial scale of
 observation changes, and the magnitude and shape of these changes can
 elucidate the mechanisms behind the geographical variation in biotic
 specialization. Here we analyse four facets of biotic specialization in
 host-parasitoid networks along gradients of climatic constancy,
 classifying the networks according to their spatial extension (local or
 regional). Namely, we analyse network connectance, consumer diet overlap,
 consumer diet breadth, and resource vulnerability at both local and
 regional scales along the gradients of both current climatic constancy and
 historical climatic change. While at the regional scale none of the
 climatic variables are associated to biotic specialization, at the local
 scale, network connectance, consumer diet overlap, and resource
 vulnerability decrease with current climatic constancy, whereas consumer
 generalism increases (i.e., broader diet breadths in tropical areas).
 Similar patterns are observed along the gradient of historical climatic
 change. We provide an explanation based on different beta-diversity for
 consumers and resources across the geographical gradients. Our results
 show that the geographical gradient of biotic specialization is not
 universal. It depends on both the facet of biotic specialization and the
 spatial scale of observation.
description: Table
 S7.Dataset_Geographical.varGeographical variation
 of Host-Parasitoid networks across two different spatial scales. The file
 contains for each network: geographical location, number of hosts, number
 of parasitoids, number of species, connectance, mean generality, mean
 vulnerability and parasitoid:host ratios. The environmental variables
 associated to each location are: mean annual temperature range, and past
 climatic-change. The source of the original paper where each network was
 extracted from is also provided.
DOI: 10.5061/dryad.8c4092n
title: Data from: Parental care and the evolution of terrestriality in frogs

description: Frogs and toads (Anura) exhibit some of the most diverse parental
 strategies in vertebrates. Identifying the evolutionary origins of
 parenting is fundamental to understanding the relationships between sexual
 selection, social evolution and parental care systems of contemporary
 Anura. Moreover, parenting has been hypothesized to allow the invasion of
 terrestrial habitats by the ancestors of terrestrial vertebrates. Using
 comprehensive phylogenetic analyses of frogs and toads based on data from
 over 1000 species that represent 46 out of 55 Anura families, we test
 whether parental care is associated with terrestrial reproduction and
 several life history traits. Here we show that both the duration of care
 and offspring protection by males and females have co-evolved with
 terrestrial reproduction. Sexual size dimorphism is also related to care,
 since large male size relative to female size is associated with increased
 paternal care. Furthermore, increased egg size and reduced clutch volume
 are associated with increased care in bivariate but not in multivariate
 analyses, suggesting that the relationships between care, egg size and
 clutch volume are mediated by terrestrial reproduction. Taken together,
 our results suggest that parenting by males and females has co-evolved,
 and complex parenting traits have evolved several times independently in
 Anura in response to breeding in terrestrial environments.
description: Vagi et al_S3
 Supplementary datadata
 fileVagi et al_S2
 Supplementary datareferences for
 datacomposite
 treecomposite phylogenetic
 tree (alternative tree in analyses)
DOI: 10.5061/dryad.c6c4bt8
title: Data from: Nitrous oxide (N2O) emissions from subsurface soils of agricultural ecosystems

description: Nitrous oxide (N2O) is a major greenhouse gas and cultivated soils are the
 most important anthropogenic source. N2O production and consumption are
 known to occur at depths below the A or Ap horizon but their magnitude in
 situ is largely unknown. At a site in SW Michigan USA we measured N2O
 concentrations at different soil depths and used diffusivity models to
 examine the importance of depth-specific production and consumption. We
 also tested the influence of crop and management practices on subsurface
 N2O production in 1) till vs. no-till, 2) a nitrogen fertilizer gradient,
 and 3) perennial crops including successional vegetation. N2O
 concentrations below 20 cm exceeded atmospheric concentrations by up to
 900 times, and profile concentrations increased markedly with depth except
 immediately after fertilization when production was intense in the surface
 horizon, and in winter, when surface emissions were blocked by ice.
 Diffusivity analysis showed that N2O production at depth was especially
 important in annual crops, accounting for over 50% of total N2O production
 when crops were fertilized at recommended rates. At nitrogen fertilizer
 rates exceeding crop need, subsurface N2O production contributed 25-35% of
 total surface emissions. Dry conditions deepened the maximum depth of N2O
 production. Tillage did not. In systems with perennial vegetation,
 subsurface N2O production contributed &lt;20% to total surface
 emissions. Results suggest that the fraction of total N2O produced in
 subsurface horizons can be substantial in annual crops, is low under
 perennial vegetation, appears to be largely controlled by subsurface
 nitrogen and moisture, and is insensitive to tillage.
description: dataset_n2o_subsurfaceContains concentrations of nitrous oxide (N2O) at different depths in soil profiles and measured N2O surface fluxes of three experiments at the Kellogg Biological Station (KBS) Long-term Ecological Research (LTER) site: LTER Main Cropping System Experiment (MCSE, in 2011), Monolith Lysimeters (in 2010-2011), and Resource Gradient Experiment (in 2011). Also includes additional MCSE treatments and well as concurrent concentrations and fluxes of carbon dioxide (CO2) and methane (CH4) for LTER MCSE and Monolith Lysimeters that are not analyzed in the publication.
DOI: 10.5061/dryad.5682v7j
title: Data from: Causes and short-term consequences of variation in milk composition in wild sheep

description: 1.Ecologists seek to understand the fitness consequences of variation in
 physiological markers, under the hypothesis that physiological state is
 linked to variability in individual condition and life history. 2.Thus,
 ecologists are often interested in estimating correlations between entire
 suites of correlated traits, or biomarkers, but sample size limitations
 often do not allow us to do this properly when large numbers of traits or
 biomarkers are considered. 3.Latent variables are a powerful tool to
 overcome this complexity. Recent statistical advances have enabled a new
 class of multivariate models – Multivariate Hierarchical Modeling (MHM)
 with latent variables − which allow to statistically estimate unstructured
 covariances/correlations among traits with reduced constraints on the
 number of degrees of freedom to account in the model. It is thus possible
 to highlight correlated structures in potentially very large numbers of
 traits. 4.Here, we apply MHM to evaluate the relative importance of
 individual differences and environmental effects on milk composition and
 identify the drivers of this variation. We ask whether variation in
 bighorn sheep milk affects offspring fitness. 5.We evaluate whether
 mothers show repeatable individual differences in the concentrations of 11
 markers of milk composition and we investigate the relative importance of
 annual variability, maternal identity and morphological traits in
 structuring milk composition. We then use variance estimates to
 investigate how a subset of repeatable milk markers influence lamb summer
 survival. 6.Repeatability of milk markers ranged from 0.05 to 0.64 after
 accounting for year‐to‐year variations. Milk composition was weakly but
 significantly associated with maternal mass in June and September, summer
 mass gain and winter mass loss. Variation explained by year‐to year
 fluctuations ranged from 0.07 to 0.91 suggesting a strong influence of
 environmental variability on milk composition. Milk composition did not
 affect lamb survival to weaning. 7.Using joint models in ecological,
 physiological or behavioural contexts has the major advantage of
 decomposing a (co)variance/correlation matrix while being estimated with
 fewer parameters than in a ‘traditional’ mixed‐effects model. The joint
 models presented here complement a growing list of tools to analyse
 correlations at different hierarchical levels separately and may thus
 represent a partial solution to the conundrum of physiological complexity.
description: Data on milk composition
 in bighorn sheepThis .csv file contains
 data to reproduce multivariate analyses of milk composition in bighorn
 sheep. We provided the R code to run most analyses in the article's
 Supplementary Material.tidy_milk.csv
DOI: 10.5061/dryad.5cv05bc
title: Data from: Temporal road closures improve habitat quality for wildlife

description: Increasing levels of human activity threaten wildlife populations through
 direct mortality, habitat degradation, and habitat fragmentation. Area
 closures can improve habitat quality for wildlife, but may be difficult to
 achieve where tourism or other economic drivers are a priority. Temporal
 closures that limit human use during specific times of day have potential
 to increase habitat quality for wildlife, while continuing to provide
 opportunities for human use. However, the effectiveness of daily temporal
 closures has not been tested. We assessed how implementation of a temporal
 road closure affected wildlife movements in Banff National Park. Parks
 Canada closed a popular 17 km stretch of road between 2000 and 0800 hours
 to improve habitat quality for wildlife. We assessed the effectiveness of
 the closure on nine mammal species using three sets of data: remote
 cameras, road surveys, and grizzly bear (Ursus arctos) GPS data. In all
 three analyses, wildlife detection rates on the road doubled during the
 closure while remaining unchanged in reference areas. Our strong and
 consistent results suggest temporal closures are an important conservation
 tool that can increase habitat quality for wildlife while minimizing
 effects on people.
description: Temporal Closure Data
 and R ScriptThree data sets (remote
 camera, grizzly bear GPS, road side observation surveys), associated read
 me files, and an R script for running analyses.TemporalClosuresDataDryad.zip
DOI: 10.5061/dryad.3tn78n2
title: Data from: Meta-analytic and economic approaches for evaluation of pesticide impact on Sclerotinia stem rot control and soybean yield in the North Central U.S.

description: As complete host resistance in soybean has not been achieved, Sclerotinia
 stem rot (SSR) caused by Sclerotinia sclerotiorum continues to be of major
 economic concern for farmers. Thus, chemical control remains a prevalent
 disease management strategy. Pesticide evaluations were conducted in
 Illinois, Iowa, Michigan, Minnesota, New Jersey, and Wisconsin from 2009
 to 2016, for a total of 25 site-years (n = 2057 plot-level data points).
 These studies were used in network meta-analyses to evaluate the impact of
 10 popular pesticide active ingredients, and seven common application
 timings on SSR control and yield benefit, compared to not treating with a
 pesticide. Boscalid and picoxystrobin frequently offered the best
 reductions in disease severity and best yield benefit (P &lt; 0.0001).
 Pesticide applications (one or two-spray programs) made during the bloom
 period provided significant reductions in disease severity index (DIX) (P
 &lt; 0.0001) and led to significant yield benefits (P = 0.0009). Data
 from these studies were also used in nonlinear regression analyses to
 determine the effect of DIX on soybean yield. A three-parameter logistic
 model was found to best describe soybean yield loss (pseudo-R2 = 0.309).
 In modern soybean cultivars, yield loss due to SSR does not occur until
 20-25% DIX, and considerable yield loss (-697 kg ha-1 or -10 bu a-1) is
 observed at 68% DIX. Further analyses identified several pesticides and
 programs that resulted in greater than 60% probability for return on
 investment under high disease levels.
description: Treatment Master
 List2009-16 NETWORK Meta
 Analysis_Dataset_without Non-treated
DOI: 10.5061/dryad.18516pq
title: Data from: Determinants of predation success: how to survive an attack from a rattlesnake

description: 1. The selection pressures that arise from capturing prey and avoiding
 predators are some of the strongest biotic forces shaping animal form and
 function. Examining how performance (i.e., athletic ability) affects the
 outcomes of encounters between free-ranging predators and prey is
 essential for understanding the factors that determine predation success
 rates and broad scale predator–prey dynamics, but quantifying these
 encounters in natural situations is logistically challenging. 2. The goal
 of our study was to examine the relationship between performance and
 predation success by studying natural predator-prey interactions in the
 field with minimal manipulation of the study subjects. 3. We used
 high-speed video recordings of free-ranging sidewinder rattlesnakes
 (predator, Crotalus cerastes) and desert kangaroo rats (prey, Dipodomys
 deserti) to study how performance at various stages of their encounters
 alters the outcome of their interactions. 4. We found that predation
 success depends on 1) whether the snake struck accurately, 2) if the
 strike was accurate, the reaction time of the kangaroo rat, and 3) if the
 kangaroo rat was bitten, the speed with which kangaroo rat dislodged the
 snake (i.e., the duration of fang contact). 5. The results of our study
 suggest that the role of performance in predator-prey interactions is
 complex, and both predator and prey can alter the outcome at multiple
 stages of an interaction.
description: Whitford et al
 Determinants of predation success datadata associated with
 Whitford et al 2019 "Determinants of predation success: how to
 survive an attack from a rattlesnake "Whitford et al Determinants of
 success data 11202018.csv
DOI: 10.5061/dryad.64964m0
title: Data from: A clinical decision support system learned from data to personalize treatment recommendations towards preventing breast cancer metastasis

description: Objective: A Clinical Decision Support System (CDSS) that can amass
 Electronic Health Record (EHR) and other patient data holds promise to
 provide accurate classification and guide treatment choices. Our objective
 is to develop the Decision Support System for Making Personalized
 Assessments and Recommendations Concerning Breast Cancer Patients (DPAC),
 which is a CDSS learned from data that recommends the optimal treatment
 decisions based on a patient’s features. Method: We developed a Bayesian
 network architecture called Causal Modeling with Internal Layers (CAMIL),
 and an algorithm called Treatment Feature Interactions (TFI), which learns
 from data the interactions needed in a CAMIL model. Using the TFI
 algorithm, we learned interactions for six treatments from the Lynn Sage
 Data Set (LSDS). We created a CAMIL model using these interactions,
 resulting in a DPAC which recommends treatments towards preventing 5-year
 breast cancer metastasis. Results: In a 5-fold cross-validation analysis,
 we compared the probability of being metastasis free in 5 years for
 patients who made decisions recommended by DPAC to those who did not.
 These probabilities are (the probability for those making the decisions
 appears first): chemotherapy (.938, .872); breast/chest wall radiation
 (.939, .902); nodal field radiation (.940, .784); antihormone (.941,
 .906); HER2 inhibitors (.934, .880); neadjuvant therapy (.931, .837). In
 an application of DPAC to the independent METABRIC dataset, the
 probabilities for chemotherapy were (.845, .788). Discussion: Patients who
 took the advice of DPAC had, as a group, notably better outcomes than
 those who did not. We conclude that DPAC is effective at amassing and
 analyzing data towards treatment recommendations. Some of the findings in
 DPAC are controversial. For example, DPAC says that chemotherapy increases
 the chances of metastasis for many node negative patients. This
 controversy shows the importance of developing a conclusive version of
 DPAC to ensure we provide patients with the best patient-specific
 treatment recommendations.
description: LSDS-5YDMThe Lynn Sage Data Base (LSDB) contains information about patients who came to the Lynn Sage Comprehensive Breast Center at Northwestern Memorial Hospital for care. The Northwestern Medicine Enterprise Data Warehouse (NMEDW) is a joint initiative across the Northwestern University Feinberg School of Medicine and Northwestern Memorial HealthCare, which maintains comprehensive data obtain from EHRs. Using the LSDB and the NMEDW, we curated a dataset named as the Lynn Sage Data Set with 5-year distant metastasis (LSDS-5YDM), which includes records on 6726 breast cancer patients including clinical features and distant metastasis. The records span 03/02/1990 to 07/28/2015.
DOI: 10.5061/dryad.910105r
title: Data from: Intraspecific variation in worker body size makes North American bumble bees (Bombus spp.) less susceptible to decline

description: Population declines have been documented in approximately one-third of
 bumble bee species. Certain drivers of these declines are known, however
 less is known about the interspecific trait differences that make certain
 species more susceptible to decline. Two traits, which have implications
 for responding to rapidly changed environments, may be particularly
 consequential for bumble bee populations: intraspecific body size
 variation and brain size. Bumble bee body size is highly variable and is
 likely adaptive at the colony level, and brain size correlates with
 cognitive traits (e.g. behavioral plasticity) in many groups. Trait
 variation and plasticity may buffer species against negative effects of
 rapidly changed environments. Using phylogenetically controlled analyses
 of 31 North American bumble bee species, we find higher intraspecific body
 size variation is associated with species having increased their relative
 abundance over time. However, this variation does not significantly
 interact with tongue length, another trait thought to influence bees’
 decline susceptibility. Head size, a proxy for brain size, is not
 correlated with change in relative abundance. Our results support the
 hypothesis that variation in body size makes species less susceptible to
 decline in rapidly altered environments and suggests that this variation
 is important to the success of bumble bee populations.
description: North American Bombus
 spp. DataIncluded in this data
 file are measurements of thorax width and head width, year of collection,
 latitude, and longitude per specimen.
DOI: 10.5061/dryad.37rp8r9
title: Data from: Functional consequences of morphologically plastic jaws in juvenile purple sea urchins

description: Morphological plasticity is a critical mechanism that animals use to cope
 with variation in resource availability. During periods of food scarcity,
 sea urchins demonstrate an increase in jaw length relative to test
 diameter. This trait is thought to be reversible and adaptive by yielding
 an increase in feeding efficiency. We directly test the hypotheses that
 (1) there are reversible shifts in jaw length to test diameter ratios with
 food abundance in individual urchins, and (2) these shifts alter feeding
 efficiency. Purple sea urchins, Strongylocentrotus purpuratus, were placed
 in either high or low food treatments for 3 months, after which treatments
 were switched for 2 additional months. Measurements of jaw length to test
 diameter ratios were significantly higher in low compared to high food
 urchins, but this was due to test growth in the high food treatments.
 Ratios of low food urchins did not change following a switch to high food
 conditions, indicating that this trait is not reversible. Relatively
 longer jaws were also not correlated with increased feeding efficiency. We
 argue that jaw length plasticity is not adaptive and is simply a
 consequence of exposure to high food availability, as both jaw and test
 growth halt when food is scarce.
description: urchin_data_deVriesWebbTaylorThis file contains the data for all of the analyses conducted in this manuscript, including urchin growth, jaw length, test diameter, and feeding efficiency, for the focal species, Strongylocentrotus purpuratus. For detailed descriptions of the data file, refer to the README file.
DOI: 10.5061/dryad.56451sc
title: Data from: Maternal effects obscure condition-dependent sex allocation in changing environments

description: Climate change increases environmental fluctuations which thereby impact
 population demography. Species with temperature-dependent sex
 determination may experience more extreme sex ratio skews, but this has
 not been considered in species with chromosomally-determined sex. However,
 anticipatory maternal effects cause lifelong physiological changes
 impacting sex ratios. Here we show, in mice, that more sons were born to
 mothers in good condition when their breeding environment matched their
 gestational environment, consistent with theoretical predictions, but
 mothers in mismatched environments have no condition sex-ratio
 relationship. Thus, the predicted effect of condition on sex ratio was
 obscured by maternal effects when the environment changed. This may
 explain extreme or unexpected sex ratio skews in reintroduced or
 translocated populations, and sex ratio skews may become more common and
 less predictable with accelerating environmental change.
description: Data for Maternal
 effects obscure condition-dependent sex allocation in changing
 environmentsData for Maternal
 effects obscure condition-dependent sex allocation in changing
 environmentsData.xlsx