cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m8413
title: Data from: Mixed assemblages of drilling predators and the problem of identity in the fossil record: a case study using the muricid gastropod Ecphora

description: Drillholes made by naticid and muricid gastropods are frequently used in
 evolutionary and ecological studies because they provide direct,
 preservable evidence of predation. The muricid Ecphora is common in many
 Neogene Atlantic Coastal Plain assemblages in the United States, but is
 frequently ignored in studies of naticid predation. We used a combination
 of Pliocene fossil, modern beach, and experimentally derived samples to
 evaluate the hypothesis that Ecphora was an important source of drillholes
 in infaunal bivalve prey shared with naticids. We focused on the large,
 thick-shelled venerid, Mercenaria, which is commonly drilled by naticids
 today. Laboratory experiments, modern beach samples, and the published
 literature confirm that naticids preferentially drill near the umbo
 (significant clumping of holes), show a significant correlation between
 prey size and predator size (estimated by outer borehole diameter), and
 prefer Mercenaria &lt;50 mm antero-posterior width when other prey are
 present. Fossil samples containing Ecphora (with or without other large
 muricids) show no drillhole site stereotypy (no significant clumping,
 greater variability in placement), no significant predator: prey size
 correlation, drilled prey shells larger than the largest modern naticids
 could produce in an experimental setting, and drillholes larger in
 diameter than those estimated for the largest Pliocene naticids, thus
 supporting our hypothesis. Substantial overlap in the placement of holes
 drilled by naticids and muricids, however, made identifying predators from
 drillhole position problematic. The lack of overlapping ranges of prey
 shell thickness between fossil and other samples precluded the use of
 drillhole morphology to establish predator identity (e.g., ratio of inner
 borehole diameter to outer borehole diameter, drillhole angle). Whereas
 the difficulty in determining predator identity from drillholes limits the
 types of analyses that can be reliably performed in mixed-predator
 assemblages, recognizing Ecphora as a prominent drilling predator creates
 the opportunity to investigate previously unrecognized questions.
description: Supplemental Figure 1:
 Regression lines for OBD versus A-P length.Regressions of outer
 borehole diameter (OBD) of predatory drill-holes on antero-posterior
 length (A-P length) of prey shells by locality (Pliocene and Recent). OBD
 is used as a proxy for predator size, therefore, plotting OBD by A-P
 length is used to detect significant relationships between predator and
 prey body size.Suppl Fig
 1.pdf
DOI: 10.5061/dryad.38d8k
title: Data from: Comparing the genetic architecture and potential response to selection of native and invasive populations of reed canary grass

description: Evolutionary processes such as migration, genetic drift, and natural
 selection are thought to play a prominent role in species invasions into
 novel environments. However, few empirical studies have explored the
 mechanistic basis of invasion in an evolutionary framework. One promising
 tool for inferring evolutionarily important changes in introduced
 populations is the genetic variance-covariance matrix (G matrix). G matrix
 comparisons allow for the inference of changes in the genetic architecture
 of introduced populations relative to their native counterparts that may
 facilitate invasion. Here, we compare the G matrices of reed canarygrass
 (Phalaris arundinacea L.) populations across native and invasive ranges,
 and between populations along a latitudinal gradient within each range. We
 find that the major differences in genetic architecture occur between
 populations at the Northern and Southern margins within each range, not
 between native and invasive populations. Previous studies have found that
 multiple introductions in introduced populations caused an increase in
 genetic variance on which selection could act. In addition, we find that
 differences in the evolutionary potential of Phalaris populations are
 driven by differences in latitude, suggesting that selection also shapes
 the evolutionary trajectory of invasive populations.
description: ReedCanaryDryadEmergence Time, tiller height at 78 days, tiller number at 78 days, above ground dry weight, root weight, and total dry weight for reed canarygrass clones grown in greenhouse conditions. Original plants collected from native European (Czech Republic and France) and invasive North American (Vermont and North Carolina) populations. For full description see Lavergne and Molofsky (2007).
DOI: 10.5281/zenodo.18381845
title: No molecular evidence for Muller's ratchet in mitochondrial genomes

description: This repository contains alignments used in the manuscript "No molecular evidence for Muller's ratchet in mitochondrial genomes".
DOI: 10.5061/dryad.5dr7b
title: Data from: Purple pitcher plant (Sarracenia rosea) dieback and partial community disassembly following experimental storm surge in a coastal pitcher plant bog

description: Sea-level rise and frequent intense hurricanes associated with climate
 change will result in recurrent flooding of inland systems such as Gulf
 Coastal pitcher plant bogs by storm surges. These surges can transport
 salt water and sediment to freshwater bogs, greatly affecting their
 biological integrity. Purple pitcher plants (Sarracenia rosea) are Gulf
 Coast pitcher plant bog inhabitants that could be at a disadvantage under
 this scenario because their pitcher morphology may leave them prone to
 collection of saline water and sediment after a surge. We investigated the
 effects of storm surge water salinity and sediment type on S. rosea
 vitality, plant community structure, and bog soil-water conductivity.
 Plots (containing ≥1 ramet of S. rosea) were experimentally flooded with
 fresh or saline water crossed with one of three sediment types (local,
 foreign, or no sediment). There were no treatment effects on soil-water
 conductivity; nevertheless, direct exposure to saline water resulted in
 significantly lower S. rosea cover until the following season when a
 prescribed fire and regional drought contributed to the decline of all the
 S. rosea to near zero percent cover. There were also significant
 differences in plant community structure between treatments over time,
 reflecting how numerous species increased in abundance and a few species
 decreased in abundance. However, in contrast to S. rosea, most of the
 other species in the community appeared resilient to the effects of storm
 surge. Thus, although the community may be somewhat affected by storm
 surge, those few species that are particularly sensitive to the storm
 surge disturbance will likely drop out of the community and be replaced by
 more resilient species. Depending on the longevity of these biological
 legacies, Gulf Coastal pitcher plant bogs may be incapable of fully
 recovering if they become exposed to storm surge more frequently due to
 climate change.
description: Abbott & Battaglia
 (2015) - Sarracenia rosea dataSarracenia rosea percent
 cover data.PLOS ONE Sarracenia rosea cover
 data for Dryad.xlsxAbbott & Battaglia
 (2015) - Plant community dataPlant community
 composition data (i.e., percent cover of each species encountered in all
 field plots throughout experiment).PLOS ONE Community composition
 data for Dryad.xlsxAbbott & Battaglia
 (2015) - Soil-water conductivity dataSoil-water conductivity
 data.PLOS
 ONE Soil-water conductivity data for
 Dryad.xlsx
DOI: 10.5281/zenodo.18381844
title: No molecular evidence for Muller's ratchet in mitochondrial genomes

description: This repository contains alignments used in the manuscript "No molecular evidence for Muller's ratchet in mitochondrial genomes".
DOI: 10.5061/dryad.j2c4g
title: Data from: Sharing detailed research data is associated with increased citation rate

description: Sharing research data provides benefit to the general scientific
 community, but the benefit is less obvious for the investigator who makes
 his or her data available. We examined the citation history of 85 cancer
 microarray clinical trial publications with respect to the availability of
 their data. The 48% of trials with publicly available microarray data
 received 85% of the aggregate citations. Publicly available data was
 significantly (p = 0.006) associated with a 69% increase in citations,
 independently of journal impact factor, date of publication, and author
 country of origin using linear regression. This correlation between
 publicly available data and increased literature impact may further
 motivate investigators to share their detailed research data.
description: Raw Citation Counts and
 CovariatesRaw bibliometric data
 used in the analysis, combining data extracted from Thomson ISI Web of
 Science, PubMed, the Ntzani and Ioannidis 2003 Lancet paper, and the
 author's own investigations.rawdata.csvStatistical analysis R scriptStatistical R script to compute analysis and graphics in the paper. Reads rawdata.csv as input.stats.RCohort Publication BibliographyA list of gene expression microarray study publications identified by Ntzani and Ioannidis from Lancet 2003 and used as our cohort for analysis.dataset_publication_list.txtLocations of Publicly Available Data for the CohortLocations of publicly available data for each of the gene expression microarray studies in our cohort.dataset_locations.txt
DOI: 10.5061/dryad.7q4r8
title: Data from: Female monkeys use both the carrot and the stick to promote male participation in intergroup fights

description: Group-level cooperation often poses a social dilemma in which joint action
 may be difficult to achieve. Theoretical models and experimental work on
 humans show that social incentives, such as punishment of defectors and
 rewarding of cooperators, can promote cooperation in groups of unrelated
 individuals. Here, we demonstrate that these processes can operate in a
 non-human animal species, and be used to effectively promote the
 production of a public good. We took advantage of the fact that intergroup
 fights in vervet monkeys (Chlorocebus aethiops pygerythrus) are
 characterized by episodes of intergroup aggression with pauses in-between.
 During pauses, females selectively groomed males that had participated in
 the previous aggressive episode, but aggressed male group members that had
 not. In subsequent (i.e. future) episodes, males who had received either
 aggression or grooming participated above their personal base-line level.
 Therefore, female–male aggression and grooming both appear to function as
 social incentives that effectively promote male participation in
 intergroup fights. Importantly, females stood to gain much from recruiting
 males as the probability of winning intergroup fights was dependent on the
 number of active participants, relative to the number of fighters in the
 opposing group. Furthermore, females appear to maximize the benefits
 gained from recruiting males as they primarily used social incentives
 where and when high-quality food resources, which are the resources
 primarily limiting to female fitness, were at stake.
description: Dataset1: Population
 level analysisDataset used (1) to
 determine if females who used social incentives were more likely to direct
 aggression at males who had recently defected, but groom males who had
 recently cooperated, and (2) if target males were more likely to
 participate after receiving social incentives than
 before.Dataset1.xlsxDataset2: Individual level analysesDataset used to test (1) if individual males were more likely to participate after receiving social incentives than before, and (2) if individuals who received social incentives participated above their personal base-line level (i.e. the proportion of aggressive episodes participated in during intergroup fights where they were not the male to receive social incentives).Dataset2.xlsxDataset3: spatio-temporal variability in the occurrence of social incentivesDataset used in the GLMM testing the spatio-temporal variability in the occurrence of social incentives (punishment and/or rewards). The summer season (when high quality fruits were available) was indexed by the NDVI, the birth season was indexed by the number of small infants (&lt;3 months old) in the group, and the mating season was a dichotomous variable. The spatial distribution of food in the different areas (mapping units) of each home range was determined by mapping the distribution of important tree species and monitoring their fruit abundance on a monthly basis.Dataset3.xlsx
DOI: 10.5061/dryad.5t19f
title: Data from: Can alternative mating tactics facilitate introgression across a hybrid zone by circumventing female choice?

description: Reproductive barriers and divergence in species’ mate recognition systems
 underlie major models of speciation. However, hybridization between
 divergent species is common, and classic mechanisms to explain permeable
 reproductive barriers rarely consider how an individual may attain
 reproductive success. Alternative mating tactics exist in various forms
 across animal taxa. Such tactics may allow poorer quality individuals to
 gain mating opportunities and facilitate introgression either through
 asymmetrical positive selection, or by circumventing female choice
 altogether in areas of secondary contact. One such tactic is satellite
 behaviour in frogs, where silent males perch near advertisers in an
 attempt to intercept females. To test whether such satellite male tactics
 are context-dependent and favoured by hybrids, we genotyped and quantified
 the morphology of 80 male spring peeper (Pseudacris crucifer) individuals
 involved in caller-satellite associations from a secondary contact zone
 between two intraspecific mitochondrial lineages. Irrespective of
 population, satellite behaviour was best predicted by size but not body
 condition. Within the contact zone, pure individuals showed a
 significantly greater probability of being active callers, whereas hybrids
 of one lineage were more likely to adopt the satellite tactic. We suggest
 that satellite behaviour in P. crucifer promotes introgression,
 breaks-down reproductive isolating barriers, and contributes to
 asymmetrical introgression in this secondary contact zone. Alternative
 mating tactics may thus be an underexplored but important alternative to
 oft-discussed causes of genetic discordance found in hybrid zones.
description: P. crucifer
 Caller-Satellite Genotypic and Morphological InformationStewart et al. JEB_
 DRYAD.xlsx
DOI: 10.5061/dryad.f5r3k
title: Data from: Effects of experimental warming on biodiversity depend on ecosystem type and local species composition

description: Climatic warming is a primary driver of change in ecosystems worldwide.
 Here, we synthesize responses of species richness and evenness from 187
 experimental warming studies in a quantitative meta-analysis. We asked 1)
 whether effects of warming on diversity were detectable and consistent
 across terrestrial, freshwater and marine ecosystems, 2) if effects on
 diversity correlated with intensity, duration, and experimental unit size
 of temperature change manipulations, and 3) whether these experimental
 effects on diversity interacted with ecosystem types. Using multilevel
 mixed linear models and model averaging, we also tested the relative
 importance of variables that described uncontrolled environmental
 variation and attributes of experimental units. Overall, experimental
 warming reduced richness across ecosystems (mean log-response ratio =
 –0.091, 95% bootstrapped CI: –0.13, –0.05) representing an 8.9% decline
 relative to ambient temperature treatments. Richness did not change in
 response to warming in freshwater systems, but was more strongly negative
 in terrestrial (–11.8%) and marine (–10.5%) experiments. In contrast,
 warming impacts on evenness were neutral overall and in aquatic systems,
 but weakly negative on land (7.6%). Intensity and duration of experimental
 warming did not explain variation in diversity responses, but negative
 effects on richness were stronger in smaller experimental units,
 particularly in marine systems. Model-averaged parameter estimation
 confirmed these main effects while accounting for variation in latitude,
 ambient temperature at the sites of manipulations, venue (field versus
 lab), community trophic type, and whether experiments were open or closed
 to colonization. These analyses synthesize extensive experimental evidence
 showing declines in local richness with increased temperature,
 particularly in terrestrial and marine communities. However, the more
 variable effects of warming on evenness were better explained by the
 random effect of site identity, suggesting that effects on species’
 relative abundances were contingent on local species composition.
description: Log response ratio
 effect sizes and covariates for meta-analysis.Log response ratio
 effect sizes of community-level diversity responses to experimental
 warming, with covariates extracted from the literature for for
 meta-analysis.oik.03688.csvoik.03688.metadataField names and descriptions for data file: Log response ratio effect sizes and covariates for meta-analysis.
DOI: 10.5061/dryad.jk2jm
title: Data from: Social setting, intuition and experience in laboratory experiments interact to shape cooperative decision-making

description: Recent studies suggest that cooperative decision-making in one-shot
 interactions is a history-dependent dynamic process: promoting intuition
 versus deliberation typically has a positive effect on cooperation
 (dynamism) among people living in a cooperative setting and with no
 previous experience in economic games on cooperation (history dependence).
 Here, we report on a laboratory experiment exploring how these findings
 transfer to a non-cooperative setting. We find two major results: (i)
 promoting intuition versus deliberation has no effect on cooperative
 behaviour among inexperienced subjects living in a non-cooperative
 setting; (ii) experienced subjects cooperate more than inexperienced
 subjects, but only under time pressure. These results suggest that
 cooperation is a learning process, rather than an instinctive impulse or a
 self-controlled choice, and that experience operates primarily via the
 channel of intuition. Our findings shed further light on the cognitive
 basis of human cooperative decision-making and provide further support for
 the recently proposed social heuristics hypothesis.
description: cooperation under time
 pressure vs time delay in IndiaThis sheet contains the
 data of the 1558 subjects who participated in our experiment investigating
 the effect of promoting intuition versus deliberation on cooperative
 decision-making in India.data_india.odsData India 20150409This file contains the data of the 450 participants of our experiment.
DOI: 10.5061/dryad.491d1
title: Data from: Stratified assessment of the role of inhaled hypertonic saline in reducing cystic fibrosis pulmonary exacerbations: a retrospective analysis

description: Objective: Limited data exist concerning the role of inhaled hypertonic
 saline (HS) in decreasing pulmonary exacerbations in cystic fibrosis (CF),
 especially as more advanced stages of CF lung disease were excluded in
 prior studies. Herein we retrospectively determined the efficacy of
 inhaled HS in reducing CF pulmonary exacerbations when stratified
 according to the severity of CF lung disease. Stratification was based on
 the framework of the Pulmonary Therapeutics Committee’s published
 gradation of obstructive lung physiology in CF, i.e., mild (FEV1 &gt;
 70%), moderate (FEV1 40-70%) and severe (FEV1 &lt; 40%) lung disease,
 respectively. Design: A retrospective review of the Port CF® database over
 a 3-year period performed at an academic CF care center. Results: 340
 pulmonary exacerbations were identified; inhaled HS was being used in 99
 of these cases. Univariate analysis demonstrated a significant reduction
 in pulmonary exacerbations only in mild obstruction (OR=0.09, CI
 0.01-0.81, p=0.012); however, multivariate logistic regression that
 adjusted for confounding variables showed a reduction in pulmonary
 exacerbations across the entire spectrum of obstructive lung disease when
 using inhaled HS i.e., mild obstructive CF lung disease (OR=0.17, CI
 0.05-0.58, p=0.004), moderate obstructive CF lung disease (OR=0.39, CI
 0.16-0.93, p=0.034), as well as severe obstructive CF lung disease
 (OR=0.02, CI 0.001-0.45, p=0.015). Moreover, inhaled HS appeared
 reasonably well tolerated across all stages of lung disease severity, and
 was discontinued in only 7% of cases (n=4) with severe lung disease.
 Conclusion: In this study, inhaled HS appeared to reduce pulmonary
 exacerbations in CF lung disease at all stages of obstruction. This
 underscores the importance of therapeutic inhaled HS in CF lung disease,
 regardless of severity of lung obstruction.
description: Role of inhaled
 hypertonic saline in cystic fibrosis - AppendixDryadAppendix.pdf
DOI: 10.5061/dryad.110s9
title: Data from: Evolution of the leaf economics spectrum in herbs: evidence from environmental divergences in leaf physiology across Helianthus (Asteraceae)

description: The leaf economics spectrum (LES) describes a major axis of plant
 functional trait variation worldwide, defining suites of leaf traits
 aligned with resource-acquisitive to resource-conservative ecological
 strategies. The LES has been interpreted to arise from leaf-level
 trade-offs among ecophysiological traits common to all plants. However, it
 has been suggested that the defining leaf-level trade-offs of the LES may
 not hold within specific functional groups (e.g., herbs) nor within many
 groups of closely-related species, which challenges the usefulness of the
 LES paradigm across evolutionary scales. Here we examine the evolution of
 the LES across 28 species of the diverse herbaceous genus Helianthus (the
 sunflowers), which occupies a wide range of habitats and climate variation
 across North America. Using a phylogenetic comparative approach, we find
 repeated evolution of more resource-acquisitive LES strategies in cooler,
 drier, and more fertile environments. We also find macroevolutionary
 correlations among LES traits that recapitulate aspects of the global LES,
 but with one major difference: leaf mass per area is uncorrelated with
 leaf lifespan. This indicates that whole-plant processes likely drive
 variation in leaf lifespan across Helianthus, rather than leaf-level
 trade-offs. These results suggest that LES patterns do not reflect
 universal physiological trade-offs at small evolutionary scales.
description: Dataset S1
 (source)Source site and USDA
 GRIN accession information for all populations used in this
 study.Dataset S2
 (data)Plant trait data and
 source site environmental data for all populations included in this
 study.