cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8gtht76tq
title: Estimation of changes in behaviour of narwhals

description: Anthropogenic activities are increasing in the Arctic posing a threat to
 species with high seasonal site-fidelity, such as the narwhal Monodon
 monoceros. In this controlled sound exposure study, six narwhals were
 live-captured and instrumented with animal-borne tags providing movement
 and behavioural data, and exposed to 1) ship noise and 2) concurrent ship
 noise and airgun pulses.
description: The sound exposure program was
 operated from an offshore patrol vessel HDMS <em>Lauge</em>
 <em>Koch</em> equipped with a Reson Seabat 7160 multibeam echo
 sounder (MBES) (nominal operating frequency 41–47 kHz), that ran
 continuously. The airgun setup included a cluster of two Sercel G-guns
 (17.0 l (1040 in<sup>3</sup>) in total) towed at 6 m depth and
 operated at a mean pressure of 125 bar. The guns in the cluster were fired
 synchronously every 80 seconds during trials, lasting 3–8 hours, while the
 ship’s GPS navigation system recorded the location of every
 shot. Six male narwhals were live-captured
 in August 2018 in the Scoresby Sound fjord system in East Greenland. The
 data were collected using animal-borne AcousondeTM acoustic and
 orientation recorders and backpack FastLoc GPS-receivers (Wildlife
 Computers (Redmond, Seattle, WA, USA) collecting an unrestricted number of
 FastLoc snapshots through August 2018. Acousondes were set to collect
 triaxial acceleration and orientation (sf 100 Hz), depth (sf 10 Hz), and
 acoustics. Acoustics was sampled continuously with a 25 811 Hz sampling
 rate (HTI-96-MIN hydrophone, nominal sensitivity -201 dB re 1 V / μ Pa,
 preamp gain 14 dB, an anti-aliasing filter with 3-dB reduction at 9.2 kHz
 and 22-dB reduction at 11.1 kHz, 16-bit resolution).
 The dataset has been processed as follows: Time-depth records
 were down-sampled to 1 Hz and time-synchronized with GPS positions.
 Additional GPS positions were created for each second between successive
 positions through linear interpolation. Buzzes were used as a proxy for
 foraging attempts and were detected using a custom-written detector
 (Matlab, The MathWorks, Inc., Natick, MA, USA) and verified manually. When
 the sound source and animal were within line of sight (determined visually
 from maps showing the positions of the ships and whales aligned in time),
 distance between the whale and the sound source was determined for each
 second. The dataset is comprised of 6 columns: 1) Ind:
 unique name for individual whale, 2) Depth: depth (m), 3) GPS_time, 4)
 Buzz: 0 or 1. 1 indicates a start of buzz in that second, 0 indicates no
 buzz. Buzzes were detected as described above, 5) X: exposure value
 (1/distance between ship and whale km) during exposure to ship with
 concurrent airgun pulses, 6) P: exposure value (1/distance between ship
 and whale km) during exposure to ship.
description: Saved as tab-separated .txt file. Can be opened in any program
 recognising .txt.
DOI: 10.5061/dryad.hdr7sqvnt
title: Camponotus fellah cDNA lists for: Social isolation shortens lifespan through oxidative stress in ants

description: Social isolation negatively affects health, induces detrimental behaviors,
 and shortens lifespan in social species. Little is known about the
 mechanisms underpinning these effects because model species are typically
 short-lived and non-social. Using colonies of carpenter ant Camponotus
 fellah, we show that social isolation induces hyperactivity, alters
 space-use, and reduces lifespan via changes in the expression of genes
 with key roles in oxidation-reduction and an associated accumulation of
 reactive oxygen species. These physiological effects are localized to the
 fat body and oenocytes, which perform liver-like functions in insects. We
 use pharmacological manipulations to demonstrate that the
 oxidation-reduction pathway causally underpins the detrimental effects of
 social isolation on behavior and lifespan. These findings have important
 implications for our understanding of how social isolation affects
 behavior and lifespan in general.
description: # Camponotus fellah transcriptome for: Social isolation shortens lifespan
 through oxidative stress in ants Three Oxford Nanopore sequencing
 libraries were prepared from high molecular weight genomic DNA using the
 RAD002 kit and sequenced on a MinION Mark1-B on three rev D R9.4.1
 flowcells. Reads were basecalled using Guppy v2.1.3 (Oxford Nanopore
 Technologies) and assembled using wtdbg2. The assembly was then polished
 with Nanopore long reads using Medaka v0.6
 (https://github.com/nanoporetech/medaka), then with Illumina reads first
 using Pilon , and then using variants called by freebayes
 (https://github.com/ekg/freebayes) with variant quality scores greater
 than 30. Candidate annotations were generated using the hint-guided gene
 predictors Augustus and SNAP, genome-guided RNA-seq assembly from the
 Trinity assembler and PASA refinement tool, and liftover of NCBI RefSeq
 protein annotations from Camponotus floridanus using GenomeThreader .
 Augustus and SNAP were run through the MAKER pipeline with protein
 homology evidence from the NCBI RefSeq Nasonia vitripennis, Apis
 mellifera, Camponotus floridanus, and Ooceraea biroi proteomes and RNA-seq
 alignments. MAKER was run first using pre-packaged ab-initio models from
 Nasonia vitripennis for Augustus and from Apis mellifera for SNAP, then
 again with the same evidence but with ab-initio models retrained from the
 first round. All candidate gene models were then combined using
 EvidenceModeler with the above-described transcript and homologous protein
 alignments used as evidence. ## Description of the data and file structure
 A transcriptome file (fasta) and an annotation file (gtf).
DOI: 10.5061/dryad.5tb2rbp8x
title: Temperature and turbidity interact synergistically to alter anti-predator behaviour in the Trinidadian guppy

description: Due to climate change, freshwater habitats are facing increasing
 temperatures and more extreme weather that disrupts water flow. Together
 with eutrophication and sedimentation from farming, quarrying and
 urbanisation, freshwaters are becoming more turbid as well as warmer.
 Predators and prey need to be able to respond to one another adaptively,
 yet how changes in temperature and turbidity interact to affect
 predator-prey behaviour remains unexplored. Using a fully factorial
 design, we tested the combined effects of increased temperature and
 turbidity on the behaviour of guppy shoals (Poecilia reticulata) in the
 presence of one of their natural cichlid predators, the blue acara
 (Andinoacara pulcher). Our results demonstrate that the prey and predator
 were in closest proximity in warmer, turbid water, with an interaction
 between these stressors showing a greater than additive effect. There was
 also an interaction between the stressors in the inter-individual
 distances between the prey, where shoal cohesion increased with
 temperature in clear water, but decreased when temperature increased in
 turbid water. The closer proximity to predators and reduction in shoaling
 in turbid, warmer water may increase the risk of predation for the guppy,
 suggesting that the combined effects of elevated temperature and turbidity
 may favour predators rather than prey.
DOI: 10.5061/dryad.6hdr7sr5d
title: Data for: Bet-hedging via dispersal aids the evolution of plastic responses to unreliable cues

description: Adaptive plasticity is expected to evolve when informative cues predict
 environmental variation. However, plastic responses can be maladaptive
 even when those cues are informative, if prediction mistakes are shared
 across members of a generation. These fitness costs can constrain the
 evolution of plasticity when initial plastic mutants use cues of only
 moderate reliability. Here we model the barriers to the evolution of
 plasticity produced by these constraints and show that dispersal across a
 metapopulation can overcome them. Constraints are also lessened, though
 not eliminated, when plastic responses are free to evolve gradually and in
 concert with increased reliability. Each of these factors can be viewed as
 a form of bet-hedging: by lessening correlations in the fates of
 relatives, dispersal acts as diversifying bet-hedging, while producing
 submaximal responses to a cue can be understood as a conservative
 bet-hedging strategy. While poor information may constrain the evolution
 of plasticity, the opportunity for bet-hedging may predict when that
 constraint can be overcome. 
description: Contents include R scripts and simulation data only–no empirical
 data.
DOI: 10.5061/dryad.n8pk0p31b
title: Data for: ASC oligomer favors caspase-1 CARD domain recruitment after intracellular potassium efflux

description: Signaling through the inflammasome is important for the inflammatory
 response. Low concentrations of intracellular K+are associated with the
 specific oligomerization and activation of the NLRP3 inflammasome, a type
 of inflammasome involved in sterile inflammation. After NLRP3
 oligomerization, ASC protein binds and forms oligomeric filaments that
 culminate in large protein complexes named ASC specks. ASC specks are also
 initiated from different inflammasome scaffolds, such as AIM2, NLRC4 or
 Pyrin. ASC oligomers recruit caspase-1 and then induce its activation
 through interactions between their respective caspase activation and
 recruitment domains (CARD). So far ASC oligomerization and caspase-1
 activation are K+-independent processes. Here we found that, when there is
 low intracellular K+, ASC oligomers change their structure independently
 of NLRP3 and make the ASCCARD domain more accessible for the recruitment
 of the pro-caspase-1CARD domain. Therefore, conditions that decrease
 intracellular K+ not only drive NLRP3 responses but also enhance the
 recruitment of pro-caspase-1 CARD domain into the ASC specks.
description: Please see the README document and the accompanying published
 article: Fátima Martín-Sánchez, Vincent Compan, Alejandro Peñín-Franch,
 Ana Tapia-Abellán, Ana I. Gómez, María C. Baños-Gregori, Florian I.
 Schmidt, Pablo Pelegrín. ASC oligomer favors caspase-1CARD domain
 recruitment after intracellular potassium efflux. Journal of Cell Biology.
 2023. https://doi.org/10.1083/jcb.202003053
DOI: 10.5061/dryad.m37pvmd76
title: Data from: Environmental and climate variability drive population size of annual penaeid shrimp in a large lagoonal estuary

description: Species with short life spans frequently show a close relationship between
 population abundance and environmental variation making these organisms
 potential indicator species of climatic variability. White (Penaeus
 setiferus), brown (P. aztecus), and pink (P. duorarum) penaeid shrimp
 typically have an annual life history and are of enormous ecological,
 cultural, and economic value to the southeastern United States and Gulf of
 Mexico. Within North Carolina, all three species rely on the Pamlico
 Sound, a large estuarine system that straddles Cape Hatteras, one of the
 most significant climate and biogeographic breaks in the world, as a
 nursery area. These characteristics make penaeid species within the
 Pamlico Sound a critical species-habitat complex for assessing climate
 impacts on fisheries. However, a comprehensive analysis of the influence
 of the environmental conditions that influence penaeid shrimp populations
 has been lacking in North Carolina. In this study, we used more than 30
 years of data from two fishery-independent trawl surveys in the Pamlico
 Sound to examine the spatial distribution and abundance of adult brown,
 white, and pink shrimp and the environmental drivers associated with adult
 shrimp abundance and juvenile brown shrimp recruitment using numerical
 models. Brown shrimp recruitment models demonstrate that years with higher
 temperature, salinity, offshore windstress, and North Atlantic Oscillation
 phase predict increased abundance of juveniles. Additionally, models
 predicting adult brown, white, and pink shrimp abundance illustrate the
 importance of winter temperatures, windstress, salinity, the North
 Atlantic Oscillation index, and the abundance of spawning adult
 populations from the previous year on shrimp abundance. Our findings show
 a high degree of variability in shrimp abundance is explained by climate
 and environmental variation and indicate the importance of understanding
 these relationships in order to predict the impact of climate variability
 within ecosystems and develop climate-based adaptive management strategies
 for marine populations.
description: The dataset
 (<em>BrownShrimpModelDataFrameP120.csv</em>) represents the
 annual mean catch per unit effort (CPUE) for the tidal creek trawl survey
 (P120, 1986–2019) run by the North Carolina Division of Marine Fisheries
 (NC DMF) merged with environmental variables that were used in our model.
 The dataset (<em>SpatialModelDataSetP195.csv</em>) is CPUE
 data for each site, season, and year for the Pamlico Sound trawl survey
 (P195, 1987–2019) survey run by NC DMF. The datasets
 (<em>AdultBrownShrimpEnviroModel.csv,
 AdultWhiteShrimpEnviroModel.csv,
 AdultPinkShrimpEnviroModel.csv</em>) include estimates of the number
 of shrimp in Pamlico Sound derived from spatial models built using P195
 CPUE data merged with environmental variables that were used in our
 models.
description: These datasets are CSV files and are open-source.
DOI: 10.5061/dryad.w0vt4b8x1
title: Herbivory and nutrients shape grassland soil seed banks

description: Anthropogenic nutrient enrichment and shifts in herbivory can lead to
 dramatic changes in the composition and diversity of aboveground plant
 communities which, in turn, can alter cryptic biodiversity storage, seed
 banks, in the soil. We used data from seven Nutrient Network grassland
 sites on four continents, encompassing a range of climatic and
 environmental conditions, to test the joint effects of fertilization and
 aboveground mammalian herbivory on seed banks and on the similarity
 between aboveground plant communities and seed banks. Fertilization
 decreased plant species richness and diversity in seed banks, and
 homogenized composition between aboveground and seed bank communities.
 Fertilization increased seed bank abundance especially in the presence of
 herbivores, while this effect was smaller in the absence of herbivores.
 Our findings highlight that nutrient enrichment can weaken the temporal
 storage effect as a diversity maintaining mechanism and that herbivory
 needs to be considered when assessing nutrient enrichment effects on seed
 bank abundance. 
description: There are several datasets associated with this work.
 A dataset that contains plant community composition
 data, in two parts A seedbank dataset that was
 collected from sites, seeds were grown from the soil, counted and
 identified. An aboveground plant community dataset
 where plant cover was collected in m<sup>2</sup> quadrats. 
 Within these quadrats plants were identied to the lowest taxonomic unit,
 and then the percent cover was estimated 
 a plot information dataset that contains all the
 treatment data for each plot across all the sites in the
 experiment A dataset that contains biomass sorted to
 functional group for each plot in the dataset.  Biomass was collected in
 two 0.1 m<sup>2</sup> plots, combined, sorted to functional
 group (forbs, graminoids, legumes and litter), then scaled to the
 m<sup>2</sup> scale.
description: We use R and R Studio to run these files.  All are open
 source.
DOI: 10.5061/dryad.bg79cnpft
title: Bird count dataset for: Oiling threats to marine birds on Southern Vancouver Island, BC, Canada

description: We conducted year-round boat-based strip transect surveys in waters
 between Sidney, BC and Victoria, BC from November 2015 to August 2019 and
 examined seasonal variation in bird distribution and abundance. Our study
 area included parts of the Sidney Channel Important Bird Area, the Shoal
 Harbour and Victoria Harbour Migratory Bird Sanctuaries and the Chain
 Islets Ecological Reserve, adjacent to major shipping lanes, as well as
 ports and marinas. We report counts of Rhinoceros Auklet Cerorhinca
 monocerata, Common Murre Uria aalgae, Pigeon Guillemot Cepphus columba,
 Marbled Murrelet Brachyramphus marmoratus, and Ancient Murrelet
 Synthliboramphus antiquus.
description: We conducted year-round strip transect surveys of alcids on the
 ocean between Sidney and Victoria BC, Canada.  We counted birds out to
 150m and recorded time and location at 10 minute intervals.  We calculated
 mid points for the transect segment and report relative densities for each
 species at each centroid.
DOI: 10.5061/dryad.rn8pk0ph5
title: Drivers of soil organic carbon stock during tropical forest succession

description: Soil organic matter contributes to productivity in terrestrial ecosystems
 and contains more carbon than is found in the atmosphere. Yet, there is
 little understanding of soil organic carbon (SOC) sequestration processes
 during tropical forest succession, particularly after land abandonment
 from agriculture practices. Here we used vegetation and environmental data
 from two large-scale surveys covering a total landscape area of 20,000 ha
 in Southeast Asia to investigate the effects of plant species diversity,
 functional trait diversity, phylogenetic diversity, aboveground biomass,
 and environmental factors on SOC sequestration during forest succession.
 We found that functional trait diversity plays an important role in
 determining SOC sequestration across successional trajectories. Increases
 in SOC carbon storage were associated with indirect positive effects of
 species diversity and succession age via functional trait diversity, but
 phylogenetic diversity and aboveground biomass showed no significant
 relationship with SOC stock. Furthermore, the effects of soil properties
 and functional trait diversity on SOC carbon storage shift across
 elevation. Synthesis: Our results suggest that reforestation and
 restoration management practices that implement a trait-based approach by
 combining long-lived and short-lived species (conservative and acquisitive
 traits) to increase plant functional diversity could enhance SOC
 sequestration for climate change mitigation and adaptation efforts, as
 well as accelerate recovery of healthy soils.
DOI: 10.5061/dryad.fttdz08z5
title: Data from: DCMIP2016: The tropical cyclone test case

description: This paper describes and analyzes the Reed-Jablonowski (RJ) tropical
 cyclone (TC) test case used in the 2016 Dynamical Core Model
 Intercomparison Project (DCMIP2016). The intermediate complexity test case
 analyzes the evolution of a weak vortex into a TC in an idealized tropical
 environment. Simulations from 9 general circulation models (GCMs) that
 participated in DCMIP2016 are analyzed in this study at 50 km horizontal
 grid spacing, with 5 of these models also providing simulations at 25 km
 grid spacing for an analysis on the impact of finer grid spacing.
 Evolution of minimum surface pressure (MSP) and maximum 1 km azimuthally
 averaged wind speed (MWS), the wind-pressure relationship, radial profiles
 of wind speed and surface pressure, and wind composites are documented for
 all participating GCMs at both horizontal grid spacings. While results are
 generally similar between all models, some GCMs reach significantly higher
 storm intensities than others, ultimately impacting specific
 characteristics of their horizontal and vertical structure. TCs simulated
 at 25 km grid spacings retained these differences, but reach higher
 intensities and are more compact than their 50 km counterparts. These
 results indicate dynamical core choice is an essential factor in GCM
 development, and future work should be conducted to explore how specific
 differences within the dynamical core affect TC behavior in GCMs.
DOI: 10.5061/dryad.cz8w9gj7p
title: Recent origin and diversification accompanied by repeated host shifts of thallus-mining flies (Diptera: Agromyzidae) on liverworts and hornworts

description: Despite the vast diversity of phytophagous insects that feed on vascular
 plants (tracheophytes), insects that feed on bryophytes remain
 understudied. Agromyzidae, one of the most species-rich phytophagous
 clades in Diptera, consists mainly of leaf-mining species that feed on
 tracheophytes. However, a recent discovery of thallus-mining species on
 liverworts and hornworts within the Liriomyza group of Phytomyzinae
 provides an opportunity to study host shifts between tracheophytes and
 bryophytes. This study aimed to explore the origin and diversification of
 thallus-miners and estimate the pattern and timing of host shifts.
 Phylogenetic analysis of Phytomyzinae has revealed that the thallus-mining
 agromyzids formed a separate clade, which was sister to a fern
 pinnule-miner. The diversification of bryophyte-associated agromyzids
 since the Oligocene involved multiple host shifts across various bryophyte
 taxa. The diversification of the thallus-mining Phytoliriomyza may have
 occurred at the same time as the leaf-mining agromyzid flies on herbaceous
 plants, indicating a dynamic history of interactions between bryophytes
 and herbivores in angiosperms-dominated ecosystems.
DOI: 10.5061/dryad.0zpc86730
title: Data for: Vegetation and soil ecology of threatened Himalayan Trillium habitats in Kashmir, Himalaya

description: Understanding the vegetation and soil ecology of natural habitats
 harbouring threatened species is critical in conservation planning and
 restoration. The present study investigated the vegetation composition and
 soil physico-chemical attributes of natural habitats of Trillium
 govanianum – a threatened Himalayan endemic species. We laid 120 quadrats
 across eight randomly selected sites where the species was growing in the
 Kashmir Himalaya. We collected the soil samples from these sites and
 determined soil physico-chemical attributes using standard methods. Across
 all the sites, we found a total of 57 plant species with dominance of
 Rosaceae and Ranunculaceae. The IVI results revealed that Fragaria
 nubicola, Corydalis diphylla, Galium aparine, and Leucanthemum vulgare,
 were the dominant species in T. govanianum communities. The density,
 abundance and IVI of 3-leaf vegetative plants was higher than 1-leaf
 vegetative and 3-leaf reproductive plants across all the study sites. We
 found that T. govanianum alone forms 23.5 % positive, 0 negative, 76.4%
 random co-occurrences with other associated species in its community. Our
 results reveal that the variations in vegetation composition among the
 sites was influenced by differences in soil properties. Principal
 component analysis revealed that several soil parameters such as organic
 carbon, nitrogen, potassium, and sulphur were concentrated in five sites,
 namely Dara, Drung, Bangus, Gulmarg, and Doodhpathri, which also showed
 the highest density, frequency, and abundance of T. govanianum. Overall,
 our study contributes quantitative information on the vegetation and soil
 ecology of T. govanianum-assemblages, which in turn can help in developing
 conservation strategies for this threatened species, and its sustainable
 management and habitat restoration.
description: Data was collected by carrying out field surveys across the
 different sampling sites. The data was written on already prepared
 datasheets and arranged on spreadsheets for further ananlysis using
 different softwares.