cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63z3j
title: Data from: Behavioral diversity and biomechanical determinants of the outcome of a fish predator-prey interaction

description: Predator-prey interactions are ubiquitous and under strong selection
 because of the consequences experienced by both predator and prey if they
 lose the interaction. Biomechanics and behavior play important roles in
 the outcome of these interactions, but many studies focus on the prey,
 restrict the range of behaviors considered, and the role of prey boldness
 in the outcome is not understood. We used high-speed video to test for
 effects of multiple measures of performance and kinematics of both the
 predator and prey, and boldness of prey on the outcome of interactions
 between Pike Cichlids (Crenicichla) and Guppies (Poecilia reticulata). We
 found high variation in the behaviors employed during the predator-prey
 interactions, including in suction versus raptorial feeding, strike
 accuracy, and guppy responsiveness. We also found that predators moving
 relatively slower and prey moving relatively faster were more successful
 at consuming the prey and evading the predator, respectively. Prey that
 reacted farther from the predator were more likely to escape predation,
 but boldness of the prey did not affect the interaction. Our work suggests
 that a high level of variation in predator-prey interactions is
 widespread, even when strike and escape behaviors are stereotyped. We also
 showed that what both the predator and the prey do during an interaction
 are important in determining the outcome.
description: Data were collected from predator-prey interactions between
 Crenicichla pike cichlids and guppies (<em>Poecilia
 reticulata</em>). Interactions were video recorded in the lab at
 480fps. The head at eye level and snout of the cichlids and the snout of
 the guppies were tracked with DLTdv8a in MATLAB. MATLAB was used to fit
 quintic splines to the data to estimate velocity and acceleration.
 Kinematic data were collected in ImageJ, behavioral data were collected
 through video playback. Guppy boldness was quantified separately from
 video recordings at 30fps, as the time it took each guppy to exit a refuge
 box. See manuscript for additional details.
description: Data are in an excel spreadsheet (xlsx file) and can be openned
 in Excel or other spreadsheet software. One worksheet contains the data
 and another is a readme explaining each variable.
DOI: 10.5061/dryad.cnp5hqc9c
title: Data for: Isolation of targeted hypothalamic neurons for studies of hormonal, metabolic, and electrical regulation

description: All original data used in the study published in the Journal of Visualized
 Experiments entitled: "Isolation of Targeted Hypothalamic Neurons for
 Studies of Hormonal, Metabolic, and Electrical Regulation" by
 Kathera-Ibarra-Forzisi et al. are provided in this dataset.  Data
 are organized in sub-folders containing either confocal or bright-field
 images of primary hypothalamic neurons. The dataset does not contain
 analyses or measurements. For each figure of the paper, the data are
 organized in sub-folders corresponding to a specific experimental
 condition. The sub-folders are labeled with the corresponding figure
 number and the salient experimental conditions. For example, the
 sub-folder labeled "confocal images figure 3" contains all the
 original confocal images from which the representative images of the
 figure were chosen from. Likewise, the folder  "LepR+ figure
 3" contains all the images of neurons immunolabeled with LepR
 antibody.  Data can be used by a third party for verification
 purposes but cannot be used for publication. Abstract of the study: The
 hypothalamus regulates fundamental metabolic processes by controlling
 functions as varied as food intake, body temperature, and hormone release.
 As the functions of the hypothalamus are controlled by specific subsets of
 neuronal populations, the ability to isolate them provides a major tool
 for studying metabolic mechanisms. In this regard, the neuronal complexity
 of the hypothalamus poses exceptional challenges. For these reasons, new
 techniques, such as Magnetic-Activated Cell Sorting (MACS), have been
 explored. This paper describes a new application of magnetic-activated
 cell sorting (MACS) using microbead technology to isolate a targeted
 neuronal population from prenatal mice brains. The technique is simple and
 guarantees a highly pure and viable primary hypothalamic neuron culture
 with high reproducibility. The hypothalamus is gently dissociated, neurons
 are selectively isolated and separated from glial cells, and finally,
 using a specific antibody for a cell surface marker, the population of
 interest is selected. Once isolated, targeted neurons can be used
 to investigate their morphological, electrical, and endocrine
 characteristics and their responses in normal or pathological conditions.
 Furthermore, given the variegated roles of the hypothalamus in regulating
 feeding, metabolism, stress, sleep, and motivation, a closer look at
 targeted and region-specific neurons may provide insight into their tasks
 in this complex environment.
description: There are images of cells in culture taken under bright field or
 confocal microscopy.
description: Bright field images are in JPEG. confocal images are in Nikon ND2
 format and can be imported in ImageJ or read through other freely
 available software.
DOI: 10.5061/dryad.s7h44j1c7
title: Organismal effects of heat in a fixed ecological niche: Implications on the role of behavioral buffering in our changing world

description: Increasingly frequent and intense heatwaves generate new challenges for
 many organisms. Our understanding of the ecological predictors of thermal
 vulnerability is improving, yet, at least in endotherms, we are still only
 beginning to understand one critical component of predicting resilience:
 exactly how do wild animals cope with sub-lethal heat? In wild endotherms,
 most prior work focuses on one or a few traits, leaving uncertainty about
 organismal consequences of heatwaves. Here, we experimentally generated a
 2.8 °C heatwave for free-living nestling tree swallows
 (Tachycineta bicolor). Over a week-long period coinciding with the peak of
 post-natal growth, we quantified a suite of traits to test the hypotheses
 that (a) behavioral or (b) physiological responses may be sufficient for
 coping with inescapable heat. Heat-exposed nestlings increased panting and
 decreased huddling, but treatment effects on panting dissipated over time,
 even though heat-induced temperatures remained elevated. Physiologically,
 we found no effects of heat on: gene expression of three heat shock
 proteins in blood, muscle, and three brain regions; secretion of
 circulating corticosterone at baseline or in response to handling; and
 telomere length. Moreover, heat had a positive effect on growth and a
 marginal, but not significant, positive effect on subsequent recruitment.
 These results suggest that nestlings were generally buffered from
 deleterious effects of heat, with one exception: heat-exposed nestlings
 exhibited lower gene expression for superoxide dismutase, a key
 antioxidant defense. Despite this one apparent cost, our thorough
 organismal investigation indicates general resilience to a heatwave that
 may, in part, stem from behavioral buffering and acclimation. Our approach
 provides a mechanistic framework that we hope will improve understanding
 of species persistence in the face of climate change.
description: See manuscript.
DOI: 10.5061/dryad.t76hdr85r
title: Soil amendment with biochar and manure alters wood stake decomposition and fungal community composition

description: Biochar and manure can be used for sustainable land management.
 However, little is known about how soil amendments might affect surface-
 and below-ground microbial processes and subsequent wood decomposition. In
 a split-split-split plot design, we amended soil with two rates of manure
 (whole plot; 0 and 9 Mg ha-1) and biochar (split-plot; 0 and 10 Mg ha-1).
 Wood stakes of three species (hybrid poplar, triploid Populus tomentosa
 Carr.; aspen, Populus tremuloides Michx.; and pine, Pinus taeda L.) were
 placed in two positions (horizontally on the soil surface, and inserted
 vertically in the mineral soil), which served as a substrate for fungal
 growth. In 3 years, the decomposition rate (mass loss), moisture content,
 and fungal community (via high-throughput sequencing methods) of stakes
 were evaluated. Results indicated that biochar and/or manure increased the
 wood stake decomposition rates, moisture content, and operational
 taxonomic unit (OTU) abundance. However, the richness and diversity of
 fungi were dependent on wood stake position (surface &gt; mineral),
 species (pine &gt; the two Populus), and sample dates. This study
 highlights that soil amendment with biochar and/or manure can alter the
 fungal community, which in turn can enhance an important soil process
 (i.e., decomposition).
DOI: 10.5061/dryad.h44j0zpr8
title: Multi‐species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds

description: Aquatic environmental DNA is increasingly used for biodiversity
 monitoring, such as surveying threatened and invasive species.
 Mainstreaming these methods in practical applications, however, still
 requires significant standardisation and optimisation, namely regarding
 DNA capture methods. Here we evaluated how filter type (standard disc
 filters vs high-capacity capsules), number of sampling sites, volume of
 water filtered and environmental factors affected amphibian detection in
 Mediterranean temporary ponds. The study involved water filtering until
 clogging at one (capsules) and five (discs) sites from 16 small and
 shallow ponds, where three urodele and seven anuran species were recorded
 through sweep-netting and adult observations. Detection probabilities were
 estimated from site occupancy models based on replicate sampling and from
 an adaptation of time-to-detection models relating detection probability
 to volume of water filtered. Discs filtered relatively small volumes
 (15–1250 mL), with detection probabilities of the two abundant species
 (Pelobates cultripes, Hyla meridionalis) increasing rapidly with sample
 size and water volume, reaching almost perfect detection (0.95) at four
 and seven discs, and 420 mL and 1860 mL, respectively. However, reaching
 high detection probabilities for rare species (Pelodytes atlanticus,
 Pleurodeles waltl, Triturus pygmaeus) would require larger sampling effort
 than that used in our study. Despite filtering much larger volumes
 (600–5300 mL), filtering with capsules at a single site per pond provided
 lower detection probabilities for abundant species than filtering with
 discs at five sites. Rarer species showed no difference between methods,
 which may be due to small sample sizes and reduced statistical power for
 species with few detection. The effect of conductivity on species
 detectability was largely negative, while the influence of water clarity
 varied across species, and pH had no effects. Overall, our results suggest
 that eDNA amphibian surveys in Mediterranean temporary ponds need to
 consider filter clogging, heterogeneous DNA distribution, and highly
 conductive waters.
DOI: 10.5061/dryad.dv41ns241
title: What Darwin couldn't see: Island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species

description: Oceanic islands play a central role in the study of evolution and island
 biogeography. The Galapagos Islands are one of the most studied oceanic
 archipelagos but research has almost exclusively focused on terrestrial
 organisms compared to marine species. Here we used the Galapagos bullhead
 shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to
 examine evolutionary processes and their consequences for genetic
 divergence and island biogeography in a shallow-water marine species
 without larval dispersal. The sequential separation of individual islands
 from a central island cluster gradually established different ocean depths
 between islands that pose barriers to dispersal in H. quoyi.
 Isolation-by-resistance analysis suggested that ocean bathymetry and
 historical sea level fluctuations modified genetic connectivity. These
 processes resulted in at least three genetic clusters that exhibit low
 genetic diversity and effective population sizes that scale with island
 size and the level of geographic isolation. Our results exemplify that
 island formation and climatic cycles shape genetic divergence and
 biogeography of coastal marine organisms with limited dispersal comparable
 to terrestrial taxa. Because similar scenarios exist in oceanic islands
 around the globe our research provides a new perspective on marine
 evolution and biogeography with implications for the conservation of
 island biodiversity.
description: Tissue samples were collected from Galapagos bullhead sharks from
 six islands in the Galapagos archipelago and stored in 96% EtOH.
 DNA extraction, sequencing and SNP genotyping were conducted by
 Diversity Array Technologies (DArT, Canberra, Australia). Samples were
 processed using the proprietary DArT Pty Ltd analytical pipeline, which
 includes technical replicates from a subset of samples to assess
 genotyping reproducibility.
description: R software Packages: 
 radiator: https://thierrygosselin.github.io/radiator/ DartR: http://georges.biomatix.org/dartR
DOI: 10.5061/dryad.3j9kd51q5
title: Data for: Visualization of the hidden food sources of bass (Micropterus salmoides), crucian carp (Carassius carassius), and minnow (Zacco platypus) using 18S rRNA V9 primers on urban Singal Reservoir in Korea

description: Fish are the most important consumers in aquatic ecosystems, and the
 analysis of fish prey is very important for understanding their short-term
 feeding characteristics and the connectivity of food webs. In this study,
 DNA metabarcoding was used to identify the prey of the native fish
 species, Zacco platypus (the pale chub) and Carassius carassius, and an
 introduced species, Micropterus salmoides, in domestic lentic ecosystems.
 Prey community composition, selectivity index, prey diversity, and trophic
 level analyses were performed. The prey composition ratio analysis showed
 that in August 2020, 85.8% of M. salmoides’ prey was fish from the orders
 Cypriniformes and Perciformes, and in July 2021, 100% of M. salmoides’
 prey was zooplankton from the orders Anomopoda and Calanoida. Zooplankton
 was the main prey of Z. platypus collected in August 2020 (69.5%) and C.
 carassius collected in July 2021 (88.9%). The selectivity index analysis
 showed that the preferred prey of M. salmoides was fish from the order
 Cypriniformes, the preferred prey of Z. platypus was phytoplankton from
 the division Bacillariophyta, and the preferred prey of C. carassius was
 zooplankton from the order Cladocera. For the prey width analysis, C.
 carassius had the highest BI index value (0.8), followed by Z. platypus
 (0.29), while M. salmoides had BI index values of 0.09, 0.19, and 0.001,
 indicating low prey width. These results provide fundamental data on the
 utility of DNA metabarcoding for dietary studies of major fish species in
 lentic ecosystems and for analyzing food web connectivity based on major
 prey items.
description: fastq file name definitions : The first S and
 W of the fastq file refer to Stomach contents and Water, respectively, and
 in the case of S, the second name refers to the scientific name of each
 fish [ex) M: Micropterus salmoides, Z: <em>Zacco
 platypus</em>, C: <em>Carassius
 carassius</em>].<br>The next number represents the year and
 the next name represents the month. SM20A: August 2020
 Stomach contents of <em>Micropterus salmoides</em>
 SM20O: October 2020 Stomach contents of <em>Micropterus
 salmoides</em> SM21J: July 2021 Stomach contents
 of <em>Micropterus salmoides</em> SZ20A:
 August 2020 Stomach contents of <em>Zacco
 platypus</em> SC21J: July 2021 Stomach contents
 of <em>Carassius carassius</em> W20A:
 August 2020 Water eDNA W21J: July 2021 Water
 eDNA
DOI: 10.57745/n1msw1
title: eco2adapt_Soil MicroResp_T0_France

description: This dataset presents the results of soil CLPP (Community-Level Physiological Profile) analyses performed using the MicroResp™ technique for French LL (Bordeaux) (Time zero - October 2023 & June 2024)
DOI: 10.57745/pnj9qq
title: eco2adapt_Soil MicroResp_T0_France.tab

description: :unav
DOI: 10.6073/pasta/a9efc28195fae0657970ea2772832fcc
title: Georgia Salt Marsh: Soil Organic Carbon, Nitrogen, Bulk Density, Moisture, and Texture

description: As part of project predicting soil carbon at depth from that found at the surface using remote sensing, 28 soil cores were taken from six salt marshes along the Georgia coastline. Cores were taken as deep as possible (25 – 165 cm) and sectioned into 5 cm depths. Soils were analyzed for organic carbon (SOC), total nitrogen (N), bulk density (BD), and particle size (by horizon). Stable carbon isotopes were obtained in three marshes on Sapelo Island; a subset was also analyzed for radiocarbon.
DOI: 10.5061/dryad.x0k6djhqq
title: Data for: Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs

description: Studies investigating the evolution of flowering plants have long focused
 on isolating mechanisms such as pollinator specificity. Some recent
 studies have proposed a role for introgressive hybridization between
 species, recognizing that isolating processes such as pollinator
 specialization may not be complete barriers to hybridization. Occasional
 hybridization may therefore lead to distinct yet reproductively connected
 lineages. We investigate the balance between introgression and
 reproductive isolation in a diverse clade using a densely sampled
 phylogenomic study of fig trees (Ficus, Moraceae). Co-diversification with
 specialized pollinating wasps (Agaonidae) is recognized as a major engine
 of fig diversity, leading to about 850 species. Nevertheless, some studies
 have focused on the importance of hybridization in Ficus, highlighting the
 consequences of pollinator sharing. Here we employ dense taxon sampling
 (520 species) throughout Moraceae and 1,858 loci to investigate
 phylogenetic relationships and the prevalence of introgression among
 species throughout the history of Ficus. We present a well-resolved
 phylogenomic backbone for Ficus, providing a solid foundation for an
 updated classification. Our results paint a picture of phylogenetically
 stable evolution within lineages punctuated by occasional local
 introgression events likely mediated by local pollinator sharing,
 illustrated by clear cases of cytoplasmic introgression that have been
 nearly drowned out of the nuclear genome through subsequent lineage
 fidelity. The phylogenetic history of figs thus highlights that while
 hybridization is an important process in plant evolution, the mere ability
 of species to hybridize locally does not necessarily translate into
 ongoing introgression between distant lineages, particularly in the
 presence of obligate plant-pollinator relationships.
description: This dataset consists largely of DNA sequences and phylogenetic
 trees and networks. Sequences were all generated using Illumina
 instruments.
description: DNA sequence files are in FASTA format, and tree files are in
 Newick format. Both can be viewed with text editors or with specialized
 tree or alignment viewers. .Rdata files can be viewed
 with R. .xlsx files can be viewed with Microsoft
 Excel.
DOI: 10.5061/dryad.mkkwh715b
title: Data from: Positive plant diversity effects on soil microbial drought resistance are linked to variation in labile carbon and microbial community structure

description: Biodiversity loss and drought are substantially altering both above-and
 belowground terrestrial ecosystem functioning, but mechanistic
 understanding of plant diversity effects on the drought resistance of soil
 microbial biomass remains limited.  We designed a mesocosm
 experiment to examine drought resistance of soil microbial biomass along a
 plant species richness gradient (five plant species richness levels based
 on old-field communities). We calculated resistance of microbial biomass
 to drought and recorded key belowground properties which may influence
 microbial resistance to drought (i.e., microbial diversity, microbial
 community structure, soil carbon stocks and root biomass).  Plant
 species richness had a positive effect on microbial resistance to drought.
 Variation in microbial resistance to drought was linked to properties of
 the fungal community in ambient soil (Shannon diversity, arbuscular
 mycorrhizal fungal richness and abundance) but not soil bacterial
 diversity. Moreover, microbial resistance to drought increased with
 increasing root biomass and dissolved organic carbon recorded under
 ambient conditions.  These results highlight the importance of
 plant diversity for microbial biomass stability in our old-field study
 system with implications for biogeochemical cycling, and suggest that
 indirect effects of plant species richness on labile soil carbon and soil
 fungi may drive resistance of soil microbial biomass to drought.
DOI: 10.15468/dl.g58ttq
title: Occurrence Download

description: A dataset containing 98485 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.66387 29.21271,37.21232 29.21271,37.21232 48.03466,-7.66387 48.03466,-7.66387 29.21271))",
 "OccurrenceStatus is Present",
 "TaxonKey is Scyliorhinus canicula"
 ]
}

 The dataset includes 98485 records from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003438-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3ffbg79pv
title: National forest inventory data for a size-structured forest population model

description: In forest communities, light competition is a key process for community
 assembly. Species' differences in seedling and sapling tolerance to
 shade cast by overstory trees is thought to determine species composition
 at late-successional stages. Most forests are distant from these
 late-successional equilibria, impeding a formal evaluation of their
 potential species composition. To extrapolate competitive equilibria from
 short-term data, we therefore introduce the JAB model, a parsimonious
 dynamic model with interacting size-structured populations, which focuses
 on sapling demography including the tolerance to overstory competition. We
 apply the JAB model to a two-"species" system from temperate
 European forests, i.e. the shade-tolerant species Fagus sylvatica L. and
 the group of all other competing species. Using Bayesian calibration with
 prior information from external Slovakian national forest inventory (NFI)
 data, we fit the JAB model to short timeseries from the German NFI. We use
 the posterior estimates of demographic rates to extrapolate that F.
 sylvatica will be the predominant species in 94% of the competitive
 equilibria, despite only predominating in 24% of the initial states. We
 further simulate counterfactual equilibria with parameters switched
 between species to assess the role of different demographic processes for
 competitive equilibria. These simulations confirm the hypothesis that the
 higher shade-tolerance of F. sylvatica saplings is key for its long-term
 predominance. Our results highlight the importance of demographic
 differences in early life stages for tree species assembly in forest
 communities.
description: The data set is a curation of the German and the Slovakian
 NFIs.
description: R programming language and environment is needed to access the
 files.