cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sbcc2fr44
title: Data from: The fading of fear effects due to coral degradation is modulated by community composition

description: An increasing number of coral reefs throughout the world have become
 degraded as a result of climate change. This degradation has resulted in a
 significant decline in local biodiversity. Studies have shown that some
 fishes (non-responders) within these altered habitats are not able to
 adequately access olfactory cues, specifically chemical alarm cues that
 are crucial in mediating predation risk. We propose that the inability to
 access this crucial information is a potential mechanism for increased
 mortality of these species under natural conditions. However, we posit
 that the presence of certain key species (responders that are unaffected
 by degradation) may buffer the handicap of non-responders by providing an
 alternate source of information. To explore this hypothesis, we
 investigated if a high ratio of responders to non-responders could
 mitigate the impact of information loss for the affected species. Using
 mesocosms, we manipulated the ratio of two damselfish species, Pomacentrus
 chrysurus (responder) and P. moluccensis (non-responders), to determine if
 community composition can be predictive of information transfer about
 predation threats in nearby non-responder individuals. Our results
 indicate that the magnitude of fear effects seen in P. moluccensis exposed
 to a predator was proportional to the number of P. chrysurus present and
 consumed by the predator in the community. This indicates that P.
 chrysurus became the only functional source of predation-related
 information for P. moluccensis in degraded habitats. Our study provides
 evidence that the presence of non-affected species in the community
 provides a potential mechanism allowing increased resilience by affected
 species, therefore providing another example of the way biodiversity
 affects ecological resilience of species in changing ecosystems.
DOI: 10.5061/dryad.08kprr50h
title: Growth, metabolism, anatomy, behaviour, invertebrate drift

description: Adaptive trade-offs are fundamental mechanisms underlying phenotypic
 diversity, but the presence of generalizable patterns in multivariate
 adaptation and their mapping onto environmental gradients remain unclear.
 To understand how life-history affects multivariate trait associations, we
 examined relationships among growth, metabolism, anatomy and behaviour in
 rainbow trout juveniles from piscivore vs. insectivore ecotypes along an
 experimental gradient of food availability. We hypothesized that i)
 selection for larger size in piscivorous adults would select for higher
 juvenile growth at the cost of lower active metabolism; ii) elevated
 growth of piscivores would be supported by a greater productivity of their
 natal stream and more proactive foraging behaviours; and iii) general
 patterns of multivariate trait associations would match the predictions of
 the Pace-Of-Life Syndrome. Relative to insectivores, piscivorous fry
 showed a pattern of higher growth (+63%), maximum food intake (+33%),
 growth efficiency (+41%), and standard metabolic rate (SMR; +47%), but
 lower active metabolic capacity (maximum metabolic rate (MMR; -17%),
 aerobic scope (AS; -48%)), suggesting that faster piscivore growth is
 supported by greater food intake and digestive capacity but is traded-off
 against lower scope for active metabolism. A similar trade-off appeared
 among organ systems, with piscivorous fry exhibiting an 83% greater
 investment in average mass of organs associated with food consumption and
 processing (i.e. stomach and intestine), but an apparently smaller
 relative investment in organs involved in cardio-vascular or cognitive
 activities (heart and brain, respectively). Higher invertebrate drift in
 their natal rearing habitat, quicker behavioural transition to a novel
 food source and lower anxiety after a frightening event in piscivorous fry
 suggest that faster growth requires both proactive foraging behaviours and
 higher prey availability in the environment. Finally, the sampling of
 replicate insectivore populations confirmed their lower juvenile growth
 (-73% on average) and reduced environmental productivity of their natal
 streams (-45% lower drift abundance) relative to the piscivore ecotype.
 Our results suggest that selection for large adult body size influences
 selection on high juvenile growth, high basal metabolism and proactive
 behaviours, and that the intense phenotypic divergence between piscivorous
 and insectivorous rainbow trout may be constrained by environmental
 productivity.
DOI: 10.5061/dryad.jdfn2z38f
title: Top 100-Ranked Clinical Journals' Preprint Policies as of April 23, 2020

description: Objective: To determine the top 100-ranked (by impact factor) clinical
 journals' policies toward publishing research previously published on
 preprint servers (preprints).  Design: Cross sectional. Main
 outcome measures: Editorial guidelines toward preprints, journal rank by
 impact factor. Results: 86 (86%) of the journals examined will
 consider papers previously published as preprints (preprints), 13
 (13%) determine their decision on a case-by-case basis, and 1 (1%) does
 not allow preprints.  Conclusions: We found wide acceptance of
 publishing preprints in the clinical research community, although
 researchers may still face uncertainty that their preprints will be
 accepted by all of their target journals.
description: We examined journal policies of the 100 top-ranked clinical
 journals using the 2018 impact factors as reported by InCites Journal
 Citation Reports (JCR). First, we examined all journals with an impact
 factor greater than 5, and then we manually screened by title and category
 do identify the first 100 clinical journals. We included only those that
 publish original research. Next, we checked each journal's editorial
 policy on preprints. We examined, in order, the journal website, the
 publisher website, the Transpose Database, and the first 10 pages of a
 Google search with the journal name and the term "preprint." We
 classified each journal's policy, as shown in this dataset, as
 allowing preprints, determining based on preprint status on a case-by-case
 basis, and not allowing any preprints. We collected data on April 23,
 2020.  (Full methods can also be found in previously
 published paper.)
DOI: 10.5061/dryad.4xgxd256s
title: Data from: Urbanization and plant invasion alter the structure of litter microarthropod communities

description: Anthropogenic activity underpins the creation of urban ecosystems, often
 with introduced or invasive species playing a large role in structuring
 ecological communities. While the effects of urbanization on charismatic
 taxa such as birds, bees or butterflies have received much attention, the
 impacts on small and inconspicuous organisms remain poorly understood.
 Here, we assess how the community structure of leaf litter-inhabiting
 microarthropods in city parks varies along an urbanization gradient in
 Toronto, Canada. At each park, we established paired forest understory
 plots which were either dominated by native vegetation or dog-strangling
 vine (Vincetoxicum rossicum), an invasive species that is spreading
 throughout northeastern North America and abundant in urban areas. We
 compared microarthropod richness, abundance, and diversity in ecological
 traits between invaded and non-invaded plots as well as compositional
 dissimilarities among plots across the urbanization gradient. We recorded
 123 genera and found: i) there was a negative effect of urbanization on
 microarthropod richness and abundance but only in invaded plots; ii)
 richness and abundance increased continuously with urbanization in
 non-invaded plots, but peaked at intermediate urbanization levels in
 invaded plots; and iii) there was significant turnover with increasing
 urbanization, with distinct communities represented in highly urbanized
 areas compared to less urbanized areas, regardless of whether invaded. We
 also found litter microarthropod richness and abundance increased with
 soil ammonium and decreased with nitrate. These trends were especially
 strong for fungivorous microarthropods, however there was no relationship
 between soil nutrients and urbanization or invasion. Urbanization and
 biological invasion drive biodiversity change, and there is a need to
 disentangle these effects on ecological communities and related ecosystem
 processes. We show microarthropod communities change with urbanization,
 with the effects of invasion most prominent in non-urban areas. Here,
 there is high richness and abundance but low ecological trait diversity,
 possibly because certain feeding traits are excluded and others
 overrepresented. Understanding of urban ecological systems must include
 knowledge of the microarthropods that interact widely across food webs,
 form distinct communities in highly urban areas, and drive many of the
 important ecological functions upon which people in cities depend.
description: All information about collection and processing are included in
 the published manuscript that accompany these data.
description: Everything needed to interpret these data are included in the
 accompanying published manuscript.
DOI: 10.5061/dryad.h18931zhs
title: Nutritional constraints on brain evolution: sodium and nitrogen limit brain size

description: Nutrition has been hypothesized as an important constraint on brain
 evolution. However, it is unclear whether the availability of specific
 nutrients or the difficulty of locating high quality diets limits brain
 evolution, especially over long periods of time. We show that dietary
 nutrient content predicted brain size across 42 species of butterflies.
 Brain size, relative to body size, was associated with the sodium and
 nitrogen content of a species’ diet. There was no evidence that host plant
 apparency (measured by plant height) was related to brain evolution. The
 timing of diet shifts varied from 3.5 to 90 million years ago, but
 nutritional constraints did not lessen over time as species adapted to a
 diet. While nutrition was linked to overall brain volume, there was no
 evidence that nutrition was related to the relative size of individual
 brain regions. Lab rearing experiments confirmed the underlying assumption
 of most comparative studies that the majority of interspecific trait
 variation stems from species differences rather than an individual’s
 current developmental environment. This study highlights a novel role of
 sodium and nitrogen in brain evolution, which is additionally interesting
 given current anthropogenic change in the availability of these nutrients.
description: Brain volumes of 99 individuals of 42 species of butterflies
 collected around the United States. Brain mass of lab-reared individuals
 from four butterfly species. Please see methods of paper for additional
 details. 
description: Please see tab in excel file describing each column heading.
DOI: 10.5061/dryad.2z34tmpjm
title: Range-wide population structure of three tropical deepwater Eteline snappers across the Indo-Pacific basin

description: Deep-sea habitats may drive unique dispersal and demographic patterns for
 fishes, but population genetic analyses to address these questions have
 rarely been conducted for fishes in these environments. This study
 investigates the population structure of three tropical deepwater snappers
 of the genus Etelis that reside at 100 – 400 m depth, with broad and
 overlapping distributions in the Indo-Pacific. Previous studies showed
 little population structure within the Hawaiian Archipelago for two of
 these species: Etelis coruscans and E. carbunculus. Here we extend
 sampling to the entire geographic range of each species to resolve the
 population genetic architecture for these two species, as well as a
 recently proposed cryptic species (Etelis sp.). One goal was to determine
 whether deepwater snappers are more dispersive than shallow water fishes.
 A second goal was to determine whether submesophotic fishes have older,
 more stable populations than shallow reef denizens that are subject to
 glacial sea-level fluctuations. Both goals are pertinent to management of
 these valuable food fishes. A total of 1,153 specimens of E. coruscans
 from 15 geographic regions were analyzed, along with 1,064 specimens of E.
 carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions.
 The first two species were analyzed with mtDNA and 9 – 11 microsatellite
 loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a
 non-significant microsatellite global FST, but significant global mtDNA
 FST= 0.010 (P=0.0007), with isolation of the Seychelles in the western
 Indian Ocean, and intermittent signals of isolation for the Hawaiian
 Archipelago. Etelis carbunculus had a non-significant microsatellite
 global FST, and significant global mtDNA FST= 0.021 (P=0.0001), with low
 but significant levels of isolation for Hawaiʻi, and divergence between
 Tonga and Fiji. Etelis sp. had mtDNA FST= 0.018 (P=0.0005), with a strong
 pattern of isolation for both Seychelles and Tonga. Overall, we observed
 low population structure, shallow mtDNA coalescence, and isolation at the
 fringes of the Indo-Pacific basin in Hawaiʻi and the western Indian Ocean.
 While most shallow water species have population structure on the scale of
 biogeographic provinces, deepwater snapper populations are structured on
 the wider scale of ocean basins, more similar to pelagic fishes than to
 shallow water species. This population structure indicates capacity for
 widespread dispersal throughout the Indo-Pacific region.
description: The dataset includes the following, with a separate file for each
 of the three species in the study: Fasta files with
 mitochondrial cytochrome b (cytb) DNA sequences for each sample used in
 this study. Example Arlequin infiles with mitochondrial
 cytochrome b (cytb) DNA sequence data for each sample used in this
 study. Text files with microsatellite genotypes for
 each sample used in this study.
DOI: 10.5061/dryad.w3r2280np
title: Foraging behavior and extended phenotype independently affect foraging success in spiders

description: Multiple phenotypic traits often interact with each other to determine an
 individual’s fitness. Behavioral and extended phenotypic traits, such as
 architectural constructions, can contribute to fitness in an integrated
 way. The goal of this study was to understand how the interaction between
 behavioral and extended phenotypic traits can affect foraging success. We
 tested this question using black widow spiders, where spiders that are
 aggressive in a foraging context tend to build more gumfooted silk lines
 that aid in prey capture, while non-aggressive spiders build webs with
 fewer gumfooted lines. We repeatedly assessed behavior and web structure
 to quantify relationships between these traits, and then allowed spiders
 to forage for live prey on their own web or the web of a conspecific that
 differed in structure. Thus, we assessed how varying combinations of
 behavior and web structure affect foraging success, and if correlational
 selection might act on them. We confirmed that aggressiveness and number
 of gumfooted lines are positively correlated and found that capture
 success increased with both aggressiveness and the number of gumfooted
 lines. Yet, we did not find any evidence for correlational selection:
 aggressiveness and number of gumfooted lines appeared to affect foraging
 success independently of each other. These findings highlight that a
 correlation between traits that contribute towards the same ecological
 function does not necessarily imply correlational selection. Taking
 advantage of the experimental convenience afforded by extended phenotypic
 traits can provide insight into the functional consequences of phenotypic
 variation within and between individuals.
DOI: 10.5061/dryad.47d7wm3b5
title: Destabilizing effects on a classic tri-trophic oyster-reef cascade

description: How interactions among multiple predators affect the stability of trophic
 cascades is a topic of special ecological interest. To examine factors
 affecting the stability of the classic tri-trophic oyster reef cascade
 within a different context, configurations of three predators, including
 the Gulf toadfish, Gulf stone crab, and oystershell mud crab, were
 manipulated together with either oyster shell or limestone gravel
 substrate within a multiple predator effects (MPE) experiment.
 Additionally, a complimentary set of trait-mediated-indirect interaction
 (TMII) experiments examined the inhibition of oyster consumption relative
 to mud-crab size and top predator identity in the absence of other cues
 and factors. The classic tri-trophic cascade formed by the toadfish-mud
 crab-oyster configuration was potentially weakened by several interactions
 within the MPE experiment. Consumption of oysters and mud crabs by the
 intraguild stone crab was undeterred by the presence of toadfish. Although
 mud crab feeding was inhibited in the presence of both toadfish and stone
 crabs, estimated non-consumptive effects (NCEs) were weaker for stone
 crabs in the MPE experiment. Consequently, the total effect was
 destabilizing when all three predator species were together. Inhibition of
 mud crab feeding was inversely related to direct predation on mud crabs
 within the MPE experiment. Complimentary TMII experiments revealed greater
 inhibition of mud crab feeding in response to stone crabs under sparse
 conditions. TMII experiments also implied that inhibition of mud crab
 feeding could have largely accounted for NCEs relative to oysters within
 the MPE experiment, as opposed to interference by other mud crabs or top
 predators. An inverse relationship between mud crab size and NCE strength
 in the TMII experiment disclosed another potentially destabilizing
 influence on the tri-trophic-cascade. Finally, although habitat complexity
 generally dampened the consumption of oysters across MPE treatments,
 complex habitat promoted mud crab feeding in the presence of toadfish
 alone. This study underscores how ecological interactions can mediate
 trophic cascades and provides some additional insights into the trophic
 dynamics of oyster reefs for further testing under natural conditions.
description: Dataset established through compilations of laboratory
 experiments consisting of mesocosms comprising multiple predator species
 and juvenile oysters as prey - the response variables reflect predation
 mortality on the basal prey, juvenile oysters, and on the intermediate
 predator, the mud crab - files represent data for (1) multiple predator
 effect experiments and (2) for trait-mediated indirect effect (TMII)
 experiments.
description: Data files are uploaded as IBM SPSS files which can be viewed in
 flatfile or variable definition formats - the latter format provides
 metafile contextual information for the variables
DOI: 10.5061/dryad.w3r2280nq
title: Global annual soil respiration from 2000 to 2014

description: This dataset contains a product of annual global soil
 respiration from 2000 to 2014 at 1 km×1 km spatial resolution. A
 Matlab script (i.e., global_soil_respiration_calculation.m) for the
 calculation of global soil respiration is provided. More details on this
 dataset are presented in the manuscript titled “Spatial and temporal
 variations in global soil respiration and their relationships with climate
 and land cover”.
description: This dataset was derived
 using satellite remote sensing data, biome-specific statistical models,
 and 1,292 site years of globally-distributed <i>in-situ
 R</i><sub>s</sub> measurements. All data
 processing and statistical analyses were conducted using Matlab (The
 MathWorks, Natick, MA).
description: This dataset only contains soil respiration of vegetated regions
 and does not contain soil respiration of bare land.
DOI: 10.5061/dryad.95x69p8hc
title: Identification of seminal proteins related to the inhibition of mate searching in female crickets

description: In response to the reduction in fitness associated with sperm competition,
 males are expected to evolve tactics that hinder female remating. For
 example, females often display a post-mating reduction in their sexual
 receptivity that has been shown to be mediated by proteins contained in a
 male’s seminal fluid (sfps). However, although there has been
 comprehensive research on sfps in genetically well characterized species,
 few non-model species have been studied in such detail. We initially
 confirm that female Australian field crickets, Teleogryllus oceanicus, do
 display a significant reduction in their mate searching behavior 24 hours
 after mating. This effect was still apparent three days after mating but
 was entirely absent after one week. We then attempted to identify the sfps
 that might play a role in inducing this behavioral response. We identified
 two proteins, ToSfp022 and ToSfp011, that were associated with the
 alteration in female post-mating behavior. The knockdown of both proteins
 resulted in mated females that displayed a significant increase in their
 mate searching behaviors compared with females mated to males having the
 full compliment of seminal fluid proteins in their ejaculate. Our results
 indicate that the female refractory period in T. oceanicus likely reflects
 a sperm competition avoidance tactic by males, achieved through the action
 of male seminal fluid proteins.
DOI: 10.5066/p1c2xdvq
title: Morphometrics and Lipid Values from Four Diving Duck Species in San Francisco Bay

description: Winter body condition is an important driver of survival, reproductive output, and overall population health in waterfowl. Diving duck species utilize distinct habitats, exploit unique resources, and can collectively provide an integrated index of winter habitat quality. The San Francisco Bay (SFB) is the largest estuary on the west coast of North America, serving as critical wintering habitat for diving ducks in the Pacific Flyway. To evaluate diving duck response to SFB habitat quality, we compared annual and decadal structurally corrected measurements of total carcass lipid among canvasback, (Aythya valisineria), greater scaup, (Aythya marila), lesser scaup, (Aythya affinis), and ruddy duck, (Oxyura jamaicensis). Our findings help inform tidal restoration efforts in SFB.