cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6djh9w0zj
title: Trade-offs between seed size and biotic interactions contribute to coexistence of co-occurring species that vary in fecundity

description: Despite theoretical advances, the ecological factors and functional traits
 that enable species varying in seed size and fecundity to coexist remain
 unclear. Given inherent fecundity advantages, why don’t small-seeded
 species dominate communities? In perennial grasslands, we evaluated
 whether small-seeded species are less tolerant of competition from the
 community dominant bunchgrass than large-seeded species but also less
 vulnerable to seed predation by mice. We also explored whether trade-offs
 involving competitive tolerance include two other functional traits,
 height and leaf mass per area (LMA). We added seeds of 17 forb species to
 plots where bunchgrass competition and rodent seed predation were
 manipulated across sites varying in bunchgrass productivity and thus
 competitive intensity. Seeds were added at densities mimicking
 interspecific variation in fecundity among target species. Standardizing
 for differences in fecundity (i.e. seed input; which enabled us to
 evaluate inherent interspecific differences in susceptibility to biotic
 interactions), bunchgrass competition more greatly reduced recruitment and
 establishment of small vs. large-seeded species, whereas rodent seed
 predation more greatly reduced the recruitment of large- versus
 small-seeded species. Plant height and LMA were unrelated to the
 competition effect size. Small-seeded species abundance decreased across
 sites increasing in bunchgrass productivity, whereas this was not the case
 for large-seeded species. For adult plants but not seedlings, community
 weighted functional trait means (CWM) for seed size, height, and LMA
 increased in plots with versus without bunchgrass competition and the CWM
 for seed size and height also increased at sites with greater bunchgrass
 productivity (for adults only). In contrast, rodent seed predation had no
 significant effects on CWM seed size. At the end of the experiment, adult
 abundance positively correlated with plant fecundity in plots lacking
 bunchgrass, indicating the inherent advantages accrued to high fecundity
 small-seeded species. However, with bunchgrass competition, abundances
 were equalized across species due to reduced competitive tolerance of high
 fecundity small-seeded species. Synthesis: Our results suggest that
 coexistence among subordinate forb species varying in seed size and
 fecundity is in-part due to a trade-off involving competitive tolerance
 and fecundity, mediated by seed size and associated functional traits.
description: Please see the associated paper for Methods.
description: Please see the Metadata tab in the data files for variable
 descriptions.
DOI: 10.5061/dryad.0gb5mkkzk
title: Within-crown variability in herbivore performance and leaf traits

description: Functional trait variation within individual plants is predicted to have
 important ecological consequences. However, our understanding of the
 sources contributing to subindividual trait heterogeneity, and the
 ramifications thereof, is poor. In a common garden, we sampled multiple
 genotypes of mature trembling aspen (Populus tremuloides) at different
 vertical crown levels and quantified the contributions of genetic, spatial
 and biotic (herbivory) factors to subindividual morphological and chemical
 leaf trait variance. Bioassays using gypsy moth (Lymantria dispar L.)
 caterpillars were conducted to study impacts of spatial and genotypic
 factors on insect performance. Crown position was the primary source of
 subindividual variation in leaf morphology and explained more of the
 variance in morphological traits than tree genotype. Effects of spatial,
 genetic and biotic factors on within-crown chemistry were highly
 compound-specific. For many compounds, changes in within-crown
 concentrations differed among genotypes, revealing that genotypic
 variation not only contributes to phytochemical diversity among
 individuals of the same population, but also affects subindividual
 chemical trait heterogeneity. For many defense related compounds, total
 within-crown variance itself differed among genotypes and was in many
 cases a heritable trait. Bioassays revealed that effects of crown position
 on caterpillar performance varied among tree genotypes and caterpillar
 sexes. We demonstrate that even relatively small trees can express subtle
 but distinct levels of within-crown leaf-trait variation. In aspen, this
 variation is shaped not only by spatial factors, but also by genetics and
 to a lesser degree by herbivory. Within-crown variation in defense
 chemistry might itself provide a defensive phenotype against herbivores
 and contribute to the biological diversity of canopy insect communities.
DOI: 10.5061/dryad.zpc866t6s
title: Cheilostome cyclostome assemblage 2020

description: Examining the supposition that local-scale competition drives
 macroevolutionary patterns has become a familiar goal in fossil
 biodiversity studies. But it is an elusive goal, hampered by inadequate
 confirmation of ecological equivalence and interactive processes between
 clades, patchy sampling, few comparative analyses of local species
 assemblages over long geologic intervals, and a dearth of appropriate
 statistical tools. We address these concerns by reevaluating one of the
 classic examples of clade displacement in the fossil record, in which
 cheilostome bryozoans surpass the once dominant cyclostomes. Here, we
 analyze a newly expanded and vetted compilation of 40,190 fossil species
 occurrences to estimate cheilostome and cyclostome patterns of species
 proportions within assemblages, global genus richness, and genus
 origination and extinction rates while accounting for sampling. Comparison
 of time series models using linear stochastic differential equations
 suggests that inter-clade genus origination and extinction rates are
 causally linked to each other in a complex feedback relationship rather
 than by simple correlations or unidirectional relationships, and that
 these rates are not causally linked to changing within-assemblage
 proportions of cheilostome versus cyclostome species.
description: See the main text, supplementary information of ms and READme and
 Rmarkdown files associated with these datafiles.
description: See the Readme file.
DOI: 10.5061/dryad.gxd2547jc
title: Data from: Intra-sexual selection: kin competition increases male-male territorial aggression in a monogamous cichlid fish

description: During intrasexual competition, individuals of the same sex compete for
 access to breeding sites and mating partners, often accompanied by
 aggressive behavior. Kin selection theory predicts different kin directed
 social interactions ranging from cooperation to aggression depending on
 the context and the resource in question. Kin competition reducing
 indirect fitness might be avoided by actively expelling relatives from
 territories and by showing higher aggression against kin. The West-African
 cichlid Pelvicachromis taeniatus is a monogamous cave breeder with males
 occupying and defending breeding sites against rivals. This species is
 capable of kin recognition and shows kin-preference during juvenile
 shoaling and mate choice. However, sub-adults of P. taeniatus seem to
 avoid the proximity of same-sex kin. In the present study, we examined
 territorial aggression of territory holders against intruding related and
 unrelated males as well as intruder’s behavior. We observed higher
 aggression among related competitors suggesting that related males are
 less tolerated as neighbors. Avoidance of intra-sexual competition with
 relatives might increase indirect fitness of males in monogamous species.
DOI: 10.5061/dryad.msbcc2fw8
title: Age-dependent phenological plasticity in a wild bird

description: Life-history traits are often plastic in response to environmental factors
 such as temperature or precipitation, and they also vary with age in many
 species. Trait variation during the lifetime could thus be partly driven
 by age-dependent plasticity in these traits. We study whether plasticity
 of a phenological trait – the egg-laying date – with respect to spring
 temperature, varies with age, and explore whether this variation relates
 to changes in breeding success throughout the life cycle. We use data from
 a four-decade long-term monitoring of a wild population of blue tits in
 Corsica to estimate age-dependent plasticity of reproductive phenology and
 annual reproductive success. We show that both laying date plasticity and
 annual reproductive success vary with age: young and old females are less
 plastic, and fledge fewer offspring, than middle-age females. Furthermore,
 in contrast to young and prime-age females, in old females fledging
 success does not depend on laying date. 5. Phenological plasticity is a
 major mechanism for coping with rapid environmental variation. Our results
 suggest that understanding its role in adaptation to climate change and
 population persistence requires integrating the age structure of the
 population.
description: See
 attached Bonamour_et_al_-_Age-dependent_plasticity_-_JAE_-_Archived_Data_Description.docx for additional information.
DOI: 10.5061/dryad.cz8w9gj1r
title: Scholastica survey 2020: The state of journal production and access

description: Responses from the 2020 survey "The State of Journal Production and
 Access" conducted by Scholastica.  “The State of Journal
 Production and Access” is a global survey that spans all scholarly
 publishing disciplines and welcomes feedback from publishing programs of
 all sizes. The survey representation has been wide-reaching with responses
 from members of scholarly publishing organizations in 26 countries in
 various roles, ranging from senior leaders to journal editors to technical
 staff. The goal of this survey is to help society and university journal
 publishers and stakeholders gauge the current state of production and
 access among independent publishing organizations and what they are
 prioritizing in the future. 
description: Collected via a Google form. Country and optional email address
 removed to avoid identifying respondents.
DOI: 10.5061/dryad.xgxd254dx
title: Data supporting Food web complexity weakens size-based constraints on the pyramids of life

description: Marine ecosystems are generally expected to have bottom-heavy trophic
 structure (more plants than animals) due to size-based constraints arising
 from increased metabolic requirements and inefficient energy transfer.
 However, size-based (allometric) approaches are often limited to confined
 trophic level windows where energy transfer is predicted by size alone,
 and are constrained to bottom-up control at steady state. In real food
 webs, energy flow is more complex and top-down processes can also shape
 trophic structure. We expand size-based theory to account for complex food
 webs, and show that moderate levels of food web connectance allow for
 inverted trophic structure more often than predicted, especially in marine
 ecosystems. Trophic structure inversion occurs due to incorporation of
 complex energy pathways and top-down effects on ecosystems. Our results
 suggest that marine ecosystems should be top-heavy, and observed
 bottom-heavy trophic structure may be a result of human defaunation of the
 ocean that has been more extreme than presently recognized.
description: This dataset is consists of the output of a static ecosystem
 model and literature based estimates of food web connectance.
description: These data are the output of a static ecosystem model. Model code
 is available at https://github.com/cbrockw/ecosystem_structure
DOI: 10.5061/dryad.8cz8w9gn6
title: The relationship between a combinatorial processing rule and a continuous mate preference function in an insect

description: Mate choice involves processing signals that can reach high levels of
 complexity and feature multiple components, even in small animals with
 tiny brains. This raises the question of whether and how such organisms
 deal with this complexity. One solution involves combinatorial processing,
 whereby different signal elements are processed as single units.
 Combinatorial processing has been described in several mammals and birds,
 and recently in a vibrationally signalling
 insect, Enchenopa treehoppers. Here, we ask about the
 relationship between combinatorial rules and mate preferences for
 continuously varying signal features. Enchenopa male
 advertisement signals are composed of two elements:
 a ‘whine’ followed by a set of pulses. The dominant
 frequency of the whine and element combination both matter to females. We
 presented synthetic signals varying in element order (natural
 [whine-pulses], reverse [pulses-whine]) and in frequency
 to Enchenopa females and recorded their responses. The
 reverse combination resulted in a decrease in attractiveness of the
 signals, and also slightly changed the shape of the preference for
 frequency. We found that females could be classified into
 three ‘types’: females with both a strong preference and a strong
 combinatorial rule, females with both a weak preference and weak rule and
 females with a strong preference but a weak rule. Our results suggest that
 in Enchenopa signal processing, the mate preference for
 a continuous signal feature ‘takes precedence’ over, but
 also interacts with, the combinatorial rule. The relationship between the
 preference and the rule could evolve to take different forms according to
 selection on mate choice decisions. We suggest that exploring the
 relationship between such preferences and rules in species with more
 complex signals will bring insight into the evolution of the
 multi-component communication systems.
description: Full methods described in the original article.
DOI: 10.5061/dryad.3tx95x6d9
title: Change in terrestrial human footprint drives continued loss of intact ecosystems

description: Human pressure mapping is important for understanding humanity's role
 in shaping Earth’s patterns and processes. Our ability to map this
 influence has evolved, thanks to powerful computing, earth observing
 satellites, and new bottom-up census and crowd-sourced data. Here, we
 provide the latest temporally inter-comparable maps of the terrestrial
 human footprint, and assessment of change in human pressure at global,
 biome, and ecoregional scales. In 2013, 42% of terrestrial Earth could be
 considered relatively free of direct anthropogenic disturbance, and 25%
 could be classed as ‘wilderness’ (the least degraded end of the human
 footprint spectrum). Between 2000 and 2013, 1.9 million km2 of
 land relatively free of human disturbance became highly modified. The
 majority of this occurred within tropical and subtropical grasslands,
 savannah, and shrubland ecosystems, but the rainforests of Southeast Asia
 also underwent rapid modification. Our results show that humanity’s
 footprint is eroding Earth’s last intact ecosystems, and greater efforts
 are urgently needed to retain them.
description: For full methodolgical details please see: Williams, B.A, Venter,
 O., Allan, J.R., Atkinson, S, Rehbein, J., Ward, M.S, Di Marco, M.,
 Grantham, H., Ervin, J., Goetz, S., Hansen, A.J., Hansen, M.C., Jantz, P.,
 Pillay, R., Rodríguez-Buriticá, S., Supples, C., Virnig, A.L.S., Watson,
 J.E.M., 2020. Change in terrestrial human footprint drives continued loss
 of intact ecosystems. One Earth, http://dx.doi.org/10.2139/ssrn.3600547
description: This repository contains the outputs detailing the area in each
 state, and the area that transitioned between each state (wilderness,
 intact, and highly modified) at the global, biome, ecoregional, and
 national scales from the Williams et al. 2020 analysis.
 The repository also includes the human footprint maps for the
 years 2000, 2005, 2010, and 2013 and all underlying code and data to
 re-create the human footprint maps.
DOI: 10.5061/dryad.rbnzs7h91
title: Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling

description: Deep neural networks (DNNs) are powerful machine learning models that are
 widely used for classification problems, and have been recently proposed
 for quartet tree phylogeny estimation (Survorov et al. Systematic Biology
 2020 and Zou et al. Molecular Biology and Evolution 2020). Here we present
 a study evaluating recently trained DNNs (from Zou et al., MBE 2020) in
 comparison to a collection of standard phylogeny estimation methods,
 including UPGMA, neighbor joining, maximum parsimony, and maximum
 likelihood, on a heterogeneous collection of 20-sequence datasets
 simulated under the same models that were used to train the DNNs, and also
 under similar conditions but with higher rates of evolution. Our study
 shows that using DNNs with quartet amalgamation (to combine quartet trees
 into a tree on the full dataset) is only more accurate than UPGMA, and
 otherwise is less accurate than all standard phylogeny estimation methods
 we explore (maximum likelihood, neighbor joining, and maximum parsimony).
 We further find that while DNNs can provide good quartet tree accuracy,
 some standard phylogeny estimation methods match or improve on DNNs for
 quartet accuracy, especially, but not exclusively, when used in a global
 manner (i.e., the tree on the full dataset is computed and then the
 induced quartet trees are extracted from the full tree). Thus, our study
 provides evidence that a major challenge impacting the utility of current
 DNNs for phylogeny estimation is their restriction to estimating quartet
 trees which must subsequently be combined into a tree on the full dataset:
 in contrast, global methods -- i.e., those that estimate trees from the
 full set of sequences -- are able to benefit from taxon sampling, and
 hence have higher accuracy on large datasets.
description: README README file for data and
 results datasets-results
 datasets-results.tar.gz
DOI: 10.5061/dryad.7sqv9s4qs
title: Invasive grass (Microstegium vimineum) indirectly benefits spider community by subsidizing available prey

description: 1. Invasive plant species cause a suite of direct, negative ecological
 impacts, but subsequent, indirect effects are more complex and difficult
 to detect. Where identified, indirect effects to other taxa can be
 wide-ranging and include ecological benefits in certain habitats or
 locations. 2. Here, we simultaneously examine the direct and indirect
 effects of a common, invasive grass species (Microstegium vimineum) on the
 invertebrate communities of understory deciduous forests in the eastern
 United States. To do this, we use two complementary analytic approaches to
 compare invaded and reference plots: 1) community composition analysis of
 understory arthropod taxa and 2) analysis of isotopic carbon and nitrogen
 ratios of a representative predatory spider species. 3. Invaded plots
 contained a significantly greater abundance of nearly all taxa, including
 predators, herbivores, and detritivores. Spider communities contained over
 seven times more individuals and exhibited greater species diversity and
 richness in invaded plots. 4. Surprisingly, however, the abundant
 invertebrate community is not nutritionally supported by the invasive
 plant, despite 100% ground cover of M. vimineum. Instead, spider isotopic
 carbon ratios showed that the invertebrate prey community found within
 invaded plots was deriving energy from the plant tissue of C3 plants and
 not the prevalent, aboveground M. vimineum.  5. Synthesis and
 applications. We demonstrate that invasive M. vimineum can create
 non-nutritional ecological benefits for some invertebrate taxa, with
 potential impacts to the nutritional dynamics of invertebrate-vertebrate
 food webs. These positive impacts, however, may be restricted to habitats
 that experience high levels of ungulate herbivory or reduced vegetative
 structural complexity. Our results highlight the importance of fully
 understanding taxon- and habitat-specific effects of invading plant
 species when prioritizing invasive species removal or management
 efforts.
DOI: 10.5061/dryad.qfttdz0f8
title: Virtual poster session student and observer data

description: COVID-19 presented the world with trauma and isolation, but many people,
 including educators, have offered bright spots of creativity and
 engagement. As we confronted these issues in our own ecology classroom, we
 sought solutions to carry-forward the learning objectives we set for our
 students in January 2020, yet encourage interaction with the sensitivity
 that a pandemic requires. In the rapid transition to online course
 delivery, we opted to retain the original end-of-semester poster project
 in our introductory ecology course. However, we experimented with a new
 virtual platform where students could disseminate their work and
 communicate with the community. In this paper, we discuss the Mozilla Hubs
 virtual reality platform that we used for our event. We also collected
 qualitative data to share the benefits and challenges of this experience
 felt by the students, the instructors, and external observers.
DOI: 10.5061/dryad.4f4qrfj95
title: Randomized trial of AKI alerts in hospitalized patients

description: Objective: To determine whether electronic health record (EHR) alerts for
 Acute Kidney Injury (AKI) would improve patient outcomes of mortality,
 dialysis and progression of AKI.  Design: Double-blinded,
 multicenter, parallel, randomized, controlled trial of an electronic AKI
 alert versus usual care (no alert). Participants were electronically
 identified and randomized via a best practice alert build using simple
 randomization with allocation concealment. Setting: Six diverse hospitals
 (four teaching and two non-teaching) ranging from small community
 hospitals to large tertiary care centers. Participants: 6,030 adult
 inpatients with AKI, as defined by the Kidney Disease: Improving Global
 Outcomes (KDIGO) creatinine criteria. Interventions: An
  EHR-based “pop-up” alert for AKI with an associated AKI order
 set upon provider opening of the patient’s medical record. Main Outcome
 Measures: A composite of AKI progression, receipt of dialysis, or death
 within 14 days of randomization. Pre-specified secondary outcomes included
 per-hospital outcome rates and rates of various AKI care
 practices.  Results: 6,030 patients were randomized over 22
 months. The primary outcome occurred in 653 (21.4%) patients in the alert
 group and 622 (20.9%) in the usual care group (relative risk 1.02, 95%
 confidence interval [CI] 0.93 to 1.13, p=0.67). Per-hospital analysis
 revealed worse outcomes in the two non-teaching hospitals (N=765, 13%),
 where alerts were associated with a relative risk of the primary outcome
 of 1.49 (95% CI, 1.12 to 1.98, p=0.006). More deaths (15.6% in the alert
 group vs. 8.6% in the usual care group) occurred at these centers
 (p=0.003). Certain AKI care practices were increased in the alert group
 but did not appear to mediate these outcomes. Conclusions: Alerts did not
 reduce rates of our primary outcome among hospitalized patients with
 AKI.  The overall lack of clinical benefit and signals of harm in
 non-teaching hospitals should lead to a re-evaluation of existing AKI
 alerting systems. Trial Registration:  ClinicalTrials.gov
 NCT02753751.
description: <strong>Time to Event Analysis Note</strong>: The
 "time_to" data reflects the time from randomization to the event
 of interest, discharge, or 14 days (whichever comes first). Be careful
 when analyzing this!  In the paper, we change this value to 14 for people
 who were discharged alive prior to day 14 without the event of interest.
 This assumes, for example, that if a patient was not dialyzed prior to
 their (alive) discharge on day 10 after randomization, they were not
 dialyzed at day 14 (a relatively safe assumption).  But we leave the data
 in more raw form in this dataset to facilitate other analyses.