cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tht76hf3r
title: Data for: Phenotypic plasticity increases exposure to extreme climatic events that reduce individual fitness

description: Climate models, and empirical observations, suggest that anthropogenic
 climate change is leading to changes in the occurrence and severity of
 extreme climatic events (ECEs). Effects of changes in mean climate on
 phenology, movement, and demography in animal and plant populations are
 well documented. In contrast, work exploring the impacts of ECEs on
 natural populations is less common, at least partially due to the
 challenges of obtaining sufficient data to study such rare events. Here,
 we assess the effect of changes in ECE patterns in a long-term study of
 great tits, near Oxford, over a 56-year period between 1965 and 2020. We
 document marked changes in the frequency of temperature ECEs, with cold
 ECEs being twice as frequent in the 1960s than at present, and hot ECEs
 being ~three times more frequent between 2010 and 2020 than in the 1960s.
 While the effect of single ECEs was generally quite small, we show that
 increased exposure to ECEs often reduces reproductive output, and that in
 some cases, the effect of different types of ECE is synergistic. We
 further show that long-term temporal changes in phenology, resulting from
 phenotypic plasticity, lead to an elevated risk of exposure to
 low-temperature ECEs early in reproduction, and hence suggest that changes
 in ECE exposure may act as a cost of plasticity. Overall, our analyses
 reveal a complex set of risks of exposure and effects as ECE patterns
 change and highlight the importance of considering responses to changes in
 both mean climate and extreme events. Patterns in exposure and effects of
 ECEs on natural populations remain underexplored and continued work will
 be vital to establish the impacts of ECEs on populations in a changing
 climate.
DOI: 10.5061/dryad.rn8pk0pgp
title: On the use of antibiotics in plasticity research: gastropod shells unveil a tale of caution

description: 1) Through phenotypic plasticity, individual genotypes can produce
 multiple phenotypes dependent on the environment. In the modern world,
 anthropogenic influences such as man-made pharmaceuticals are increasingly
 prevalent. They might alter observable patterns of plasticity and distort
 our conclusions regarding the adaptive potential of natural populations.
 2) Antibiotics are nowadays nearly ubiquitous in aquatic environments and
 prophylactic antibiotic use is also becoming more common to optimize
 animal survival and reproductive output in artificial settings. In the
 well-studied plasticity model system Physella acuta, prophylactic
 erythromycin treatment acts against gram-positive bacteria and thereby
 reduces mortality. 3) Here, we study its consequences for inducible
 defence formation in the same species. In a 2×2 split-clutch design, we
 reared 635 P. acuta in either the presence or absence of this antibiotic,
 followed by 28-day exposure to either high or low predation risk as
 perceived through conspecific alarm cues. 4) Under antibiotic treatment,
 risk-induced increases in shell thickness, a well-known plastic response
 in this model system, were larger and consistently detectable. Antibiotic
 treatment reduced shell thickness in low-risk individuals, suggesting that
 in controls, undiscovered pathogen infection increased shell thickness
 under low risk. Family variation in risk-induced plasticity was low, but
 the large variation in responses to antibiotics among families suggests
 different pathogen susceptibility between genotypes. Lastly, individuals
 that developed thicker shells had reduced total mass, which highlights
 resource trade-offs. 5) Antibiotics thus have the potential to uncover a
 larger extent of plasticity, but might counterintuitively distort
 plasticity estimates for natural populations where pathogens are a part of
 natural ecology.
description: This data originates from a laboratory study on
 <em>Physella acuta</em>. In a 2×2 split-clutch design, we
 reared 635 <em>P. acuta</em> in either the presence or absence
 of the antibiotic erythromycin, followed by 28-day exposure to either high
 or low predation risk as perceived through conspecific alarm cues. These
 individuals were then sampled at an age of 33 days. Detailed information
 on how this data was obtained and processed is contained in the
 corresponding manuscript.
description: R ( https://www.r-project.org/ ) RStudio ( https://posit.co ) Notepad++ ( https://notepad-plus-plus.org/ ) Microsoft Excel ( https://www.microsoft.com/en-us/microsoft-365/excel ) or LibreOffice Calc ( https://www.libreoffice.org/ ) Mozilla Firefox ( https://www.mozilla.org/en-US/firefox/new/ )
DOI: 10.5061/dryad.4mw6m90f8
title: Data for: Invasive investigation: Uptake and transport of L-leucine in the gill epithelium of crustaceans

description: Many aquatic species are well-known as extremely successful invaders. The
 green crab (Carcinus maenas) is an arthropod native to European waters;
 however, it is now known to be a globally invasive species. Recently it
 was discovered that C. maenas could transport nutrients in the form of
 amino acids across their gill from the surrounding environment, a feat
 previously thought to be impossible in arthropods. We compared the ability
 for branchial amino acid transport of crustaceans native to Canadian
 Pacific waters to that of the invasive C. maenas, determining if this was
 a novel pathway in an extremely successful invasive species or a shared
 trait among crustaceans. Active transport of L-leucine was exhibited in
 Carcinus maenas, Metacarcinus gracilis, Metacarcinus magister, and Cancer
 productus across their gill epithelia. C. maenas exhibited the highest
 maximum rate of branchial L-leucine transport at 53.7 ± 6.24 nmolg-1h-1,
 over twice the rate of two native Canadian crustaceans. We also examined
 the influence of feeding, gill specificity, and organ accumulation of
 L-leucine. Feeding events displayed a heavy influence on the branchial
 transport rate of amino acids, increasing L-leucine transport rates by up
 to 10-fold in C. maenas. L-leucine displayed a significantly higher
 accumulation rate in the gills of C. maenas compared to the rest of the
 body at 4.15 ± 0.78 nmolg-1h-1, with the stomach, hepatopancreas,
 eyestalks, muscle tissue, carapace, and heart muscle exhibiting
 accumulation under 0.15 nmolg-1h-1. For the first time, the novel
 transport of amino acids in Canadian native arthropods is described,
 suggesting that branchial amino acid transport is a shared trait among
 arthropods, contrary to existing literature. Further investigation is
 required to determine the influence of environmental temperature and
 salinity on transport in each species to outline any competitive
 advantages of the invasive C. maenas in a fluctuating estuarine
 environment.
DOI: 10.5061/dryad.pnvx0k6sn
title: Characterizing the diet of a threatened seabird, the Marbled Murrelet (Brachyramphus marmoratus), using high-throughput sequencing

description: Understanding prey consu­­mption patterns is critical to understanding the
 ways in which seabirds cope with a changing ocean. However, characterizing
 the dietary habitats of seabirds can be challenging. In this study, we
 investigated the diet of the Marbled Murrelet (Brachyramphus marmoratus)
 population that lives in waters off California, Oregon, and Washington,
 USA, using fecal DNA, custom metabarcoding, and high-throughput
 sequencing. Murrelets were captured at sea by dip-netting at night. Across
 this region, murrelets consumed highly diverse prey types including 17
 fish species and 10 invertebrate species, in accord with previous work
 indicating the species’ forage on a wide range of prey. Pacific Herring
 (Clupea pallasii) was the most common prey in Washington and Oregon
 (frequency of occurrence = 0.84 and 0.69, respectively), replaced
 by Northern Anchovy (Engraulis mordax) in California (frequency of
 occurrence = 0.77). In Oregon, where our sample size was
 sufficient, diet composition differed between the 2017 and 2018 breeding
 seasons, with an apparent decline in the proportional consumption of
 energy-dense prey. Common and energy-dense prey were consumed in equal
 proportions by males and females, perhaps because of foraging in the same
 habitat. Diet did not vary between breeders and non-breeders. Our study
 offers the first detailed report on the diet of adult Marbled Murrelets in
 waters where they are listed as Threatened by the US federal government.
 This indicates that managing fisheries and conserving spawning habitat for
 high-occurrence prey species could benefit murrelet populations.
description: We extracted DNA from the fecal material using QIAamp® DNA Stool
 Mini Kit and the QIAamp DNA Stool Mini Kit. For all cloacal swabs, we
 extracted genomic DNA using a QIAamp DNA Investigator Kit following the
 manufacturer’s protocol for buccal swab extraction. We quantified DNA
 concentration for all extractions using a qubit fluorometer and
 high-sensitivity assay. We amplified a fragment of the 16S gene in prey
 DNA using single primer PCR reactions for four primer sets: 16S (fish,
 Deagle et al. 2007), SQ16S (cephalopods), Cala16S (copepods and
 amphipods), and Mala16S (malacostracans). We used
 QIIME2 (Bolyen et al. 2019) for all filtering and processing of raw
 sequence data. We used the R package <em>vegan</em> (Oksanen
 et al. 2020) to calculate diversity metrics, frequency of occurrence,
 percent occurrence, and PERMANOVA tests.
description: R and .csv text reader
DOI: 10.5061/dryad.73n5tb321
title: Data from: Cadaveric emergency cricothyrotomy training for non-surgeons using a bronchoscopy-enhanced curriculum

description: Emergency cricothyrotomy training for non-surgeons providing critical care
 is important as rare “cannot intubate or oxygenate events” may occur
 multiple times in a provider’s career when surgical expertise is not
 immediately available. However, such training is highly variable and often
 infrequent so enhancing these experiences is important. Our study was
 performed after implementing a program to train non-surgeon providers on
 cadaveric donors. Standard training with an instructional video and live
 coaching was enhanced by bronchoscopic visualization of the trachea
 allowing participants to review their technique after performing scalpel
 and Seldinger-technique procedures, and to review their colleagues’
 technique on live video. Feasibility was measured through assessing
 helpfulness for trainees, cost, setup time, quality of images, and
 operator needs. Footage from the bronchoscopy recordings was analyzed to
 assess puncture-to-tube time and errors. Participants submitted pre- and
 post-session surveys assessing their levels of experience and gauging
 their confidence and anxiety with cricothyrotomies. We found our training
 program met feasibility criteria for low costs, setup time, and operator
 needs. Furthermore, all 24 participants rated the cadaveric session as
 helpful and demonstrated efficient technique by puncture-to-tube times.
 Bronchoscopy videos revealed that sharp instrument puncturing of the
 posterior tracheal wall was common and that improper tube placement
 occurred but was uncommon. Bronchoscopic enhancement was rated as quite or
 extremely helpful for visualizing the trachea and to assess depth of
 instrumentation. There was a significant increase in confidence and
 decrease in performance anxiety after the session. Our findings confirm
 that supplementing cadaveric emergent cricothyrotomy training programs
 with tracheal bronchoscopy is feasible, helpful to trainees, meets prior
 documented times for efficient technique, and detects technical errors
 that would have been missed in a standard training program. Bronchoscopic
 enhancement is a valuable addition to cricothyrotomy cadaveric training
 programs and may help avoid real-life complications.
description: 1. Video files created by Ambu® monitors 2.
 Data in excel table from individual trainee survey repsonses to
 questions.
description: Videos are best viewed on free VLC software (for MPEG files),
 Microsoft browsers (for Avi files), or free DICOM RadiAnt software (open
 source).
DOI: 10.5061/dryad.rn8pk0pgq
title: Environmental context and herbivore traits mediate the strength of associational effects in a meta-analysis of crop diversity

description: 1. Crop diversification offers a promising solution to meet expanding
 global food demands while maintaining ecosystem services. Diversification
 strategies that employ mixed planting to reduce pest damage (e.g.,
 intercropping), termed "associational effects” (AE) in the ecological
 literature, can decrease (associational resistance) or increase
 (associational susceptibility) herbivore abundance on a focal plant. While
 application of AE to agroecosystems typically reduces pest abundance, the
 range of outcomes varies widely. 2. We conducted a meta-analysis using 272
 estimates of insect herbivore abundance on crops neighbored by a
 conspecific or heterospecific from 44 studies undertaken on six
 continents. We focus on four agricultural crops well-represented from
 sites across the globe to test hypotheses related to understanding how
 herbivore traits (diet breadth, feeding guild, origin), plant traits (crop
 type, phylogenetic distance to neighbor), and environmental context
 (climate, experimental design) contribute to variation in the outcomes of
 associational effects. 3. Overall, bicultures provided a strong reduction
 of insect abundance on the focal crop. Climate and interactions between
 herbivore traits, particularly diet breadth and origin, and plant traits
 or environmental context mediated the strength of associational effects.
 4. Bicultures provided the strongest reductions in insect abundance at low
 latitudes and this effect decreased at higher latitudes, but only for
 insects with certain traits. Abundance of generalist herbivores and
 globally distributed pests tended to be most strongly negatively affected
 by bicultures, under certain contexts, whereas specialist herbivores and
 native pests were less affected by neighbors. 5. Synthesis and
 application. This meta-analysis highlights that variability in AE is
 determined in part by the interactive effects of herbivore traits and
 environmental context and provides guidance for incorporating beneficial
 ecological interactions into integrated pest management strategies.
description: Data for this meta-analysis were collected by extracting data
 from published primary research articles. No new data were collected for
 this study. Methods for the literature search, screening of papers,
 extration of response variables, moderators, and effect sizes are
 described in detail in the associated paper and supplemental
 materials.
description: Data were processed for analysis using R. The R scripts for
 processing the data are made available here.
DOI: 10.5061/dryad.905qfttqh
title: Origins of green turtle fishery bycatch in the Central Pacific revealed by mixed genetic markers

description: Longline fishing vessels, such as those that target tuna or billfish, also
 unintentionally catch endangered marine turtle species on the high seas.
 The stock composition of this bycatch is often unknown but potentially
 complex, with individuals coming from many possible origins on an
 ocean-basin scale. To better understand the stock composition of green
 turtle (Chelonia mydas) bycatch, we obtained 46 turtles, 27–78 cm in
 curved carapace length, caught by Hawaii- and American Samoa-based pelagic
 longline fishing vessels across large areas of the North- and
 South-central Pacific. We genotyped these at nine microsatellite loci and
 one mitochondrial DNA marker and used a baseline of 1,043 nesting female
 green turtles from beaches across the Pacific for population assignment
 and mixed-stock analysis. By analyzing both marker types jointly we were
 able to increase power and genetically resolve ten baseline stocks of
 nesting females with mean self-assignment and simulated accuracies of
 75–97%. Above the Equator, green turtle bycatch was composed mostly of
 individuals from Hawaiian and Eastern Pacific stocks, with a small number
 from the Western Pacific. Below the Equator, the most common stocks in the
 bycatch were from Australia and the Coral Sea, American Samoa and French
 Polynesia, and the Galápagos Islands. Overall, turtles originating from
 East, West, and Central Pacific breeding populations were major components
 of the bycatch, suggesting that the geographic ranges of these populations
 overlap across large tracts of ocean during the pelagic life history
 stages.
DOI: 10.5061/dryad.f1vhhmh1x
title: Data from: Density and root exudates mediate Arabidopsis response to copper

description: Premise of the study: Plants grown at high densities show
 increased tolerance to heavy metals for reasons that are not clear. A
 potential explanation is the release of citrate by plant roots, which
 binds metals and prevents uptake. Thus, pooled exudates at high plant
 densities could increase tolerance. We tested this exclusion facilitation
 hypothesis using mutants of Arabidopsis thaliana defective in citrate
 exudation. Methods: Wild type Arabidopsis and two allelic mutants
 for the Ferric Reductase Defective 3 (FRD3) gene were grown at four
 densities and watered with copper sulfate at four concentrations. Plants
 were harvested before bolting and dried. Shoot biomass was measured, and
 shoot material and soil were digested in nitric acid. Copper contents were
 determined by atomic absorption. Key results: In the highest
 copper treatment, density-dependent reduction in toxicity was observed in
 the wild type but not in FRD3 mutants. For both mutants, copper
 concentrations per gram biomass were up to seven times higher thanwild
 type plants, depending on density and copper treatment. In all genotypes,
 total copper accumulation was greater at higher plant densities. Plant
 size variation increased with density and copper treatment because of
 heterogeneous distribution of copper throughout the soil.
 Conclusions: These results support the hypothesis that citrate
 exudation is responsible for density-dependent reductions in toxicity of
 metals. Density-dependent copper uptake and growth in contaminated soils
 underscores the importance of density in ecotoxicological testing. In
 soils with a heterogenous distribution of contaminants, competition for
 non-toxic soil regions may drive size hierarchies and determine
 competitive outcomes. 
description: Biomass is for dry weight at harvest; copper concentrations were
 determined by atomic absorption following acid digestion of
 shoots.
description: # Data from: Density and root exudates mediate Arabidopsis response to
 copper Data provides the
 biomass of individual Arabidopsis thaliana plants from three varieties
 grown at four densities in the presence of various concentrations of
 copper in soil. ##### Description of the data and file structure Column A
 is the label of plant genotype: A = wild-type; B = frd3-3 mutant; C =
 frd3-1 mutant Column B is pot number Column C is replicate (1-4) Column D
 is density (no. of plants per pot = 1, 3, 5 or 7) Column E is the copper
 treatment level (micrograms per g in potting mix) Columns F-L are the dry
 mass of individual plants Column M is total micrograms of copper found
 after digestion of plant material (recovered from shoot mass)
 "." indicates values that were not collected. For example, at a
 plant density of 1, dry mass values for plants 2-7 will be absent
 (".").
DOI: 10.5061/dryad.9kd51c5nq
title: Climate warming alters the relative importance of plant root and microbial community in regulating the accumulation of soil microbial necromass carbon in a Tibetan alpine meadow

description: Climate warming is predicted to considerably affect variations in soil
 organic carbon (SOC), especially in alpine ecosystems. Microbial necromass
 carbon (MNC) is an important contributor to stable soil organic carbon
 pools. However, accumulation and persistence of soil MNC across a gradient
 of warming are still poorly understood. An eight-year field experiment
 with four levels of warming was conducted in a Tibetan meadow. We found
 that low-level (+0-1.5 ℃) warming mostly enhanced bacterial necromass
 carbon (BNC), fungal necromass carbon (FNC), and total MNC compared with
 control treatment across soil layers, while no significant effect was
 caused between high-level (+1.5-2.5 ℃) treatments and control treatments.
 The contributions of both MNC and BNC to soil organic carbon were not
 significantly affected by warming treatments across depths. Structural
 equation modeling analysis demonstrated that the effect of plant root
 traits on MNC persistence strengthened with warming intensity, while the
 influence of microbial community characteristics waned along with
 strengthened warming. Overall, our study provides novel evidence that the
 major determinants of MNC production and stabilization may vary with
 warming magnitude in alpine meadows. This finding is critical for updating
 our knowledge of soil carbon storage in response to climate warming.
DOI: 10.15468/dl.d7zecr
title: Occurrence Download

description: A dataset containing 365341 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aconitum"
 ]
}

 The dataset includes 365341 records from 1378 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002854-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tqbuwg
title: Occurrence Download

description: A dataset containing 511074 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.63396 4.59722,-75.70756 4.45693,-75.62262 4.28754,-75.46178 4.19594,-75.21864 4.29124,-75.19819 4.54445,-75.29739 4.65436,-75.46727 4.64378,-75.63396 4.59722))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 511074 records from 238 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012436-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jqw4dg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina euchus Cohen, 1961",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.949 -34.5253,17.9648 -34.5378,17.9648 -34.1504,17.8905 -34.1504,17.949 -34.5253))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012487-250525065834625/datasets/export for details.
DOI: 10.15468/dl.xeb57f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina euchus Cohen, 1961",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9945 31.4042,17.9648 31.4107,17.9648 28.8496,26.9648 28.8496,26.9648 31.9498,25.9351 32.1234,25.521 32.0431,25.1292 32.4448,23.62 32.6843,23.2184 33.1274,22.2555 33.4227,21.6592 33.4362,20.3254 32.9854,19.735 32.5293,19.425 31.8208,19.6247 31.1033,19.1159 30.7686,17.9945 31.4042))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012488-250525065834625/datasets/export for details.