cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76hdr7sxk
title: Ecological analysis of Pavlovian fear conditioning in rats

description: Pavlovian fear conditioning, which offers the advantage of simplicity in
 both the control of conditional and unconditional stimuli (CS, US)
 presentation and the analysis of specific conditional and unconditional
 responses (CR, UR) in a controlled laboratory setting, has been the
 standard model in basic and translational fear research. Despite 100 years
 of experiments, the utility of fear conditioning has not been
 trans-situationally validated in real-life contexts. We thus investigated
 whether fear conditioning readily occurs and guides the animal’s future
 behavior in an ecologically-relevant environment. To do so, Long-Evans
 rats foraging for food in an open arena were presented with a tone CS
 paired with electric shock US to their dorsal neck/body that instinctively
 elicited escape UR to the safe nest. On subsequent test days, the
 tone-shock paired animals failed to exhibit fear CR to the CS. In
 contrast, animals that encountered a realistic agent of danger (a looming
 artificial owl) paired with a shock, simulating a plausible predatory
 strike, instantly fled to the nest when presented with a tone for the
 first time. These results highlight the possibility of a nonassociative,
 rather than standard associative, fear process providing survival function
 in life-threatening situations that animals are likely to encounter in
 nature.
DOI: 10.15468/dl.bdsemc
title: Occurrence Download

description: A dataset containing 442 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Sceptridium"
 ]
}

 The dataset includes 442 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002945-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zs7h44j9p
title: Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

description: Polymorphisms have fascinated biologists for a long time, but their
 genetic underpinnings often remained elusive. Here, we aimed to uncover
 the genetic basis of the gold/dark polymorphism that is eponymous of Midas
 cichlid fish (Amphilophus spp.) adaptive radiations in Nicaraguan
 crater lakes. While most Midas cichlids are of the melanic “dark morph”,
 about 10% of individuals lose their melanic pigmentation during their
 ontogeny and transition into a conspicuous “gold morph”. Using a new
 haplotype-resolved long-read assembly we discovered an 8.2kb,
 transposon-derived inverted repeat in an intron of an undescribed
 gene, which we term goldentouch in reference to
 the Greek myth of King Midas. The gene goldentouch is
 differentially expressed between morphs, likely due to structural
 implications of inverted repeats in both DNA and RNA (cruciform and
 hairpin formation). The near-perfect association with the phenotype across
 several independent populations suggests that this insertion likely
 underlies this trans-specific, stable polymorphism.
DOI: 10.5061/dryad.7sqv9s4sv
title: Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer

description: A challenge in quantitative biology is to predict output patterns of gene
 expression from knowledge of input transcription factor patterns and from
 the arrangement of binding sites for these transcription factors on
 regulatory DNA. We tested whether widespread thermodynamic models could be
 used to infer parameters describing simple regulatory architectures that
 inform parameter-free predictions of more complex enhancers in the context
 of transcriptional repression by Runt in the early fruit fly embryo. By
 modulating the number and placement of Runt binding sites within an
 enhancer, and quantifying the resulting transcriptional activity using
 live imaging, we discovered that thermodynamic models call for
 higher-order cooperativity between multiple molecular players. This
 higher-order cooperativity capture the combinatorial complexity underlying
 eukaryotic transcriptional regulation and cannot be determined from
 simpler regulatory architectures, highlighting the challenges in reaching
 a predictive understanding of transcriptional regulation in eukaryotes and
 calling for approaches that quantitatively dissect their molecular nature.
description: Data were collected using fluorescent confocal microscopy as
 described in the Methods and Materials section of the main text, and
 processed using the image processing techniques described therein. The
 file 'compiledData.mat' represents the pre-and
 post-processed transcription data using the fitting schemes described in
 the main text. Data for the concentration of input transcription factors,
 Bicoid and Runt, are stored in 'Bicoid.mat' and
 'Runt.mat' respectively.
description: Data files are in MATLAB .mat file structures.
DOI: 10.5061/dryad.pnvx0k6nk
title: Can diet composition estimates using stable isotope analysis of feathers predict growth and condition in nestling mountain bluebirds (Sialia currucoides)

description: Insectivorous birds breeding in seasonal environments provision their
 dependent young during periods when prey diversity and abundance vary.
 Consequently, the composition and nutritional value of diets parents feed
 to their offspring may differ within and among broods, potentially
 affecting the condition of nestlings. In a population of mountain
 bluebirds (Sialia currucoides), we used two methods to estimate diet
 composition for individual nestlings: direct observation of provisioning
 using video recordings at 5 and 9 days post-hatch, and stable isotopes of
 the δ13C and δ15N in nestling feathers and prey followed by analysis with
 mixing models. We determined the macronutrient content (% fat and lean
 mass) and estimated the metabolized energy from each type of prey. We
 evaluated whether different methods of estimating diet composition would
 produce similar results, and if the types of prey nestlings ate at one or
 both ages affected their morphology, growth rates, or blood ketone
 concentration. We found that bluebirds fed their young 5 main types of
 prey: beetles, cicadas, grasshoppers, insect larvae, and spiders. Both
 observational and mixing model estimates of diet composition indicated
 that larvae are traded-off with grasshoppers, and that fewer larvae are
 provided to nestlings as the season progresses. In evaluating how diet
 influences individual growth and condition, estimates from direct
 observations had greater explanatory power than those from mixing models,
 indicating that diets rich in the most energy-dense prey (greatest fat
 content; cicadas and larvae) were associated with larger size and higher
 body condition, and faster rate of mass gain and growth of tarsus. Lower
 value prey had more limited, specific effects on nestlings, but may still
 be important dietary components. While isotopic methods produced estimates
 of diet composition that were generally informative, when applied to
 explain the growth and condition of nestlings they proved less
 useful. 
description: We studied mountain bluebirds breeding in nest boxes near
 Williams Lake, British Columbia, Canada (51°N, 122°W; 700 ‒ 1100 m a.s.l.;
 see O’Brien and Dawson, 2008 for further site details) in 2016. We
 measured the growth and condition of nestlings, and recorded provisioning
 by parents to determine what they ate on days 5 and 9 post-hatch. We
 collected feathers from nestlings and insects from the site to use for
 stable isotope analysis, to determine the isotopic ratios and
 concentration of C and N (δ<sup>13</sup>C,
 δ<sup>15</sup>N, [C], and [N]) in feather and prey samples.
 The isotopic signatures of feathers and prey were used in stable isotope
 mixing models to estimate the proportional contributions of different
 types of prey to the diets of nestlings.
DOI: 10.5061/dryad.jwstqjq9g
title: Occurrence patterns of crop-foraging sika deer distribution in an agriculture-forest landscape revealed by nitrogen stable isotopes

description: Conflicts arising from the consumption of anthropogenic foods by wildlife
 are increasing worldwide. Conventional tools for evaluating the spatial
 distribution pattern of large terrestrial mammals that consume
 anthropogenic foods have various limitations, despite their importance in
 management to mitigate conflicts. In this study, we examined the spatial
 distribution pattern of crop-foraging sika deer by performing nitrogen
 stable isotope analyses of bone collagen. We evaluated whether
 crop-foraging deer lived closer to agricultural crop fields during the
 winter and spring, when crop production decreases. We found that female
 deer in proximity to agricultural crop fields during the winter and spring
 were more likely to be crop-foraging individuals. Furthermore, the
 likelihood of crop consumption by females decreased by half as the
 distance to agricultural crop fields increased to 5-10 km. We did not
 detect a significant trend in the spatial distribution of crop-foraging
 male deer. The findings of spatial distribution patterns of crop-foraging
 female deer will be useful for the establishment of management areas, such
 as zonation, for efficient removal of them.
DOI: 10.5061/dryad.qv9s4mwfp
title: Survey of customers' perception and adoption with the mandatory plastic bag charging in Japan

description: We conducted a questionnaire survey of 218 persons of 10s to 60s in Japan
 via the internet from 11th to 14th, December 2020, and obtained 200 valid
 answers. We grouped the respondents according to the adoption of the
 reduction to use plastic bags; 100 of those answered that they have
 reduced to use plastic bags (Group 1), 100 of those answered no behavior
 changes with charging (Group 2). Questionnaire includes questions related
 to the attempt to reduce plastic shopping bags, observing others'
 behavior, reuse behavior, pro-environmental habit, environmental risk
 perception, and a sense of community. We asked the respondents to state to
 what extent they carry out or concerned about above questions with 5-point
 Likert scale from 1 (strongly disagree) to 5 (strongly agree).
DOI: 10.5061/dryad.8cz8w9gr3
title: Data from: Localized neighborhood species mingling is correlated with individual tree size inequality in natural forests in South China

description: Context: Numerous hypotheses such as Janzen–Connell and herd
 immunity effects have been proposed to explain the coexistence of diverse
 species in plant communities. However, these mechanisms for maintaining
 diversity have been studied primarily through the lens of species
 diversity, whereas tree size diversity or relationships between size and
 species diversity resulting from local interactions have rarely been
 investigated. Aims: We aimed to identify relationships between
 spatial species mingling and tree size inequality using extensive plot
 data from species-rich forest ecosystems. Methods: We applied
 neighborhood-based methods and explored relationships between spatial
 species mingling and size inequality indices in 22 large forest plots (30
 ha in total) in subtropical and tropical China. Results: Forest
 communities with low species mingling, or segregation of heterospecific
 trees, exhibited increased segregation of trees with dissimilar sizes. In
 most plots, large trees (e.g. dbh &gt; 30 cm) were extensively
 associated with high species mingling, and individual-tree neighborhood
 species and size diversity were closely correlated.
 Conclusion: Our findings suggest that both the spatial patterns
 of conspecific dispersal and neighborhood interactions play an important
 role in determining the spatial patterns of tree size and species
 diversity and eventually in shaping the structure of forest communities.
description: Twenty-two permanent plots
 (30 ha in total) were established in seven natural reserves located in
 different regions of South China, ranging from mid-subtropical to tropical
 monsoon climate zones. All the forest plots are protected natural mixed
 forests comprising diverse species and represent a variety of forest
 types, such as evergreen broad-leaved forests, mid-subtropical evergreen
 broad-leaved and coniferous forests, mid-subtropical evergreen and
 deciduous broad-leaved mixed forests, and tropical monsoon rainforests.
 Data from the fully mapped plots includes all live trees larger than 1 cm,
 and each individual tree was tagged, numbered, mapped and their species
 and diameters were recorded. Forest plot data are organized as follows:
 Number (individual tree number), x [m] and y [m] (tree coordinates), stem
 diameter at 1.3 m above soil level (dbh in cm) and species. For questions
 relating to the data please contact the authors.
DOI: 10.5061/dryad.tqjq2bw0p
title: Omnivory in predatory ladybird beetles is widespread and driven by an appetite for sterols

description: 1. Animals maintain physiological and behavioral systems that allow them
 to detect and consume specific macro- and micronutrients to maximize their
 fitness. One common physiological system is the nutrient-state-dependent
 or demand-driven appetite. These systems are well described for
 macronutrient regulation, but not for micronutrients. 2. Sterols are
 essential micronutrients that all animals need to survive. They are the
 backbone of many hormones, important in cell signaling, and an integral
 component of cell membranes. 3. Lady beetles are globally distributed
 predators of insect herbivores. Adult sevenspotted lady beetles maintain a
 state-dependent sterol appetite and consume plant tissues to obtain
 sterols, which improves their fitness. Additionally, sevenspotted lady
 beetles can detect sterols pre-ingestion. 4. We used lady beetle species
 distributed across the three clades of the Coccinellini to determine 1)
 whether other beetle species maintain a state-dependent sterol appetite,
 2) if sterol structure affects beetles’ state-dependent sterol appetite,
 and 3) whether lady beetles consume foliage in a sterol-state dependent
 manner. Additionally, we determined 1) what sensory organ beetle’s use to
 detect sterols, 2) their limit of detection, and 3) when during
 development their appetite manifests. 5. All six beetle species we tested
 maintained a state-dependent appetite for sterols. Sterol structure
 affected beetles’ propensity to feed on sterol-treated disks, indicating
 that the number and position of double bonds in sterol molecules affects
 beetles’ ability to detect or desire to feed on them. Only beetles in
 clade three fed on plant foliage in response to sterol-limitation. Few
 beetles in any clade that were supplemented with sterols consumed plant
 tissue. 6. Beetles’ appetite for sterols first appeared during the second
 larval stadium, and the rate of sterol consumption increased with age.
 Ablations of sensory organs revealed that beetles use their labial palps
 to detect sterols, and that they detect them at concentrations as low as
 1ppm. 7. These data demonstrate that lady beetles across the Coccinellini
 maintain a state-dependent appetite for an essential class of
 micronutrients. They also provide very strong evidence that lady beetles
 can taste sterols, raising the possibility that they maintain novel as-yet
 undescribed gustatory receptors for an essential class of lipids.
description: See associated mansucipt.
DOI: 10.5061/dryad.t4b8gtj36
title: Evaluation of lethal control of introduced sugar gliders

description: Lethal control of invasive mammalian predators can be controversial and is
 rarely a ‘silver bullet’ for conservation problems. Evaluating
 the efficacy of lethal control is important for demonstrating the benefits
 to threatened species are real and detecting unexpected perverse outcomes.
 We implemented a pilot study to evaluate if lethal control of introduced
 sugar gliders Petaurus breviceps can reduce the rate of nest predation on
 Tasmanian hollow nesting birds including swift parrots (Lathamus
 discolor). Using a before-after-control-impact design, we implemented a
 lethal control treatment whereby we attempted to remove sugar gliders from
 three treatment sites. In each time period across sites we monitored quail
 eggs in nest boxes to record predation, and used cameras to detect sugar
 gliders.We caught nine sugar gliders over three treatment sites. The model
 best supported by the data indicated an effect of site x time
 period on both egg survival and the rate of glider detection on cameras.
 There was no support for an effect of treatment on our data. We also
 recorded predation of a real swift parrot nest by sugar gliders at a
 treatment site where we recorded no predation of quail eggs. Our pilot
 study shows that at small scales, intensive lethal control of gliders
 yields low capture rates and no discernible effect on the metrics we
 measured. We conclude that alternative approaches to controlling the
 impact of sugar gliders, such as habitat protection, are critical in this
 study system before lethal control is widely implemented as a management
 tool.
DOI: 10.5061/dryad.6djh9w125
title: Flying over phylogeographic breaks by wind: Quaternary evolutionary history of a mountain aspen in southwestern China

description: The role of phylogeographic break and wind direction in the formation of
 plant genetic pattern has aroused increasing interest. Two phylogeographic
 breaks, MSD and TKL, existed in the Sino-Japanese floristic region have
 affected many plants, but there was no landscape genetic research across
 these two phylogeographic breaks. Here, we tested the internal and
 external factors that influence the phylogeographic pattern of Populus
 rotundifolia. Genetic variation was surveyed across 49 populations (567
 individuals) covering the Chinese range of P. rotundifolia, using 14 nSSRs
 and 4 cpDNA markers. Demographic and migration hypotheses were tested
 using coalescent-based approaches, and the current and past potential
 distributions were predicted using ecological niche modelling. The range
 and habitat of the western and eastern lineages barely overlap at present,
 and demographic inferences suggest a population expansion event of P.
 rotundifolia in 600 Ka. Based on two biogeographic barriers (MSD and TKL)
 and genetic variation pattern, P. rotundifolia was divided into three
 groups. The historical gene flow was detected in the central group with
 western and eastern respectively, indicating an obvious lineages admixture
 in the central. Moreover, the central part is also the intersection of
 East Asian monsoon and South Asian monsoon, and has the highest genetic
 diversity. The existing genetic distribution pattern of P. rotundifolia
 reflects the combined impacts of biogeographic history and biological
 traits.
DOI: 10.7291/d1d973
title: Weights of northern elephant seal weanlings from Año Nuevo Reserve

description: Long-term observations of foraging success at
 the population scale are key to understanding
 demographic and ecological patterns.  Northern elephant seals,
 Mirounga angustirostris, are capital breeders and the resources
 delivered to the pup during the 4-week lactation period are related to
 both the past foraging success of the mother and the future survival of
 the pup post-weaning.  We collected weight and basic morphometric
 data from more than 7,000 recently weaned elephant seals at the
 Año Nuevo colony in central California, USA beginning in 1976 and
 extending through the present.  This archive will be updated
 periodically as new data are collected. The PIs would like to be informed
 of manuscripts intended for publication that use this dataset. Depending
 on our level of interest and how much a paper depends on the data,
 co-authorship might be requested. Funding for this project was
 provided by a variety of public and private organizations
 including:  NSF, ONR, JIP, and the Moore, Packard and Sloan
 foundations (please consult PI's for a complete list). 
 Funding was also provided by generous donations to Año Nuevo
 Reserve and UC Santa Cruz.
description: Recently weaned northern elephant seals (<em>Mirounga
 angustirostris</em>) from the colony at UC Santa Cruz's Año
 Nuevo Reserve (San Mateo County, California, USA) were captured shortly
 after the departure of their mothers using a custom cone-shaped bag.  To
 obtain a direct weight measurement, each weanling was suspended from a
 scale hanging from a tripod.  Standard length and axillary girth were
 collected while the seal was physically restrained.  Sex was determined by
 rolling the weanling and observing the presence/absence of a penile
 opening.  The date of weaning for each seal was estimated from routine
 observations on the colony based on the presence/absence of the mother and
 the unique bleach mark on the pup/weanling.  If available, the
 mother's age was determined by querying the unique flipper tag of the
 mother in a separate database. Data collection was
 conducted by a large number of dedicated volunteers, undergraduates,
 graduate students, postdocs, and researchers; their efforts are greatly
 appreciated.
description: The table includes data starting in 1976.  Sample sizes varied
 widely across years and not all variables were collected in all
 years. Variables include:
 animalID: a unique animal identification number
 sex: direct observation ("M" = male, "F" =
 female, and blank = unknown) weighingdate:  date
 the weanling was weighed (YYYY-MM-DD format)
 weandate: estimated date the seal was weaned (YYYY-MM-DD
 format). Wt: weight of the weanling
 (kg). SL: standard length (cm).  The straight-line
 length from the tip of the nose to the tip of the tail
 AG: axillary girth (cm). momage: age of
 the weanling's mother (years)
DOI: 10.5061/dryad.c59zw3r86
title: Efficiency of antlion trap design and larval behavior in capture success

description: Traps constructed by an animal reduce the amount of energy required to
 seek prey. The main risk of trap-building predators is the greater
 uncertainty of encountering prey, owing to their immobility. Sometimes
 environmental characteristics do not allow them to build efficient traps,
 resulting in lower capture success. We observed prey escape, capture
 success, and behavior of two antlion species, Cueta lineosa, a habitat
 specialist, and Myrmeleon hyalinus, a generalist, building geometrically
 different traps. The traps of C. lineosa are elaborate and deep,
 consisting of two inverted cones, while M. hyalinus builds simple inverted
 cones. Prey escape was observed from traps with antlion larvae present and
 from artificially constructed traps without antlions. We used a 3D printer
 to create a replica model of both trap types, pressing the model onto the
 substrate surface to create a trap. The C. lineosa artificial trap slowed
 prey escape more effectively than the simpler artificial trap of M.
 hyalinus. Prey escape time was four times longer for two ant species and
 three times longer for woodlice from C. lineosa traps. Escape time also
 decreased with increasing prey length. We also found behavioral
 differences between these two antlion species. The behavior of M. hyalinus
 is much more efficient in catching prey than that of C. lineosa. The
 results indicates that both species are efficient trap-building predators;
 however, it appears that capture success depends not only on trap design
 but also on larval behavior.