cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3tx95x6cx
title: Data from: Tradeoffs affect the adaptive value of plasticity: Stronger cannibal-induced defenses incur greater costs in toad larvae

description: Adaptive developmental plasticity allows individuals to match their
 phenotype with their environment, which can increase fitness where threats
 are inconsistently present. Because adaptive traits are not ubiquitously
 nor infinitely plastic, tradeoffs between benefits and costs or limits are
 theoretically necessary to constrain plastic responses. Systems in which
 extreme risk can be reliably detected are ideal for investigating
 mechanisms that constrain plasticity, as even costly responses may be
 adaptive where risk is severe. Cane toads (Rhinella marina) are abundant
 in Australia and produce large clutches (frequently &gt;10,000 eggs),
 but asynchronous breeding and rapid development result in variable larval
 densities within breeding pools. In the field, we found that cannibalism
 by older cohorts often reduces the survival of conspecific eggs and newly
 hatched pre-feeding larvae (“hatchlings”) by &gt;99%, as feeding
 larvae (“tadpoles”) use chemical cues from the relatively immobile
 hatchlings to locate and consume them. After hatchlings become
 free-swimming, however, they are safe from cannibalism. Hatchlings can
 reduce this period of vulnerability by accelerating development when they
 detect conspecific tadpole cues. However, this developmental acceleration
 decreases initial tadpole mass, reduces subsequent survival, growth, and
 development, affects behavior, and compromises feeding structures.
 Reaction norms differ among clutches, and greater developmental
 acceleration is followed by greater impairment of larval function in
 plastic clutches, whereas nonresponsive clutches are unaffected by
 exposure to cannibal cues. More plastic clutches ultimately exhibit both
 poorer performance and greater variation among siblings in exposed and (to
 a lesser degree) control treatments. Variation among clutches in tadpole
 viability is driven by differences in plasticity rather than phenotype;
 fitness reductions are linked to developmental acceleration, not rapid
 development per se. Clutches with intrinsically slow pre-feeding
 developmental rates exhibit stronger acceleration (i.e., steeper reaction
 norms), but clutches with intrinsically rapid development reach
 invulnerable stages more quickly than those that accelerate development.
 As a result, high cannibalism risk may favor canalized rapid development
 rather than facultative developmental acceleration. Cannibalism plays an
 important role in the recruitment of this invasive species, and hatchling
 defenses against this threat demonstrate how the limits and tradeoffs
 associated with an inducible defense can favor canalized defenses over
 phenotypic plasticity.
description: Data collection methods are briefly described in each tab of the
 Excel document. See the associated manuscript for
 additional detail.
DOI: 10.5061/dryad.12jm63xvh
title: The population genomics of repeated freshwater colonizations by Gulf Pipefish

description: How organisms adapt to the novel challenges imposed by the colonization of
 a new habitat has long been a central question in evolutionary biology.
 When multiple populations of the same species independently adapt to
 similar environmental challenges, the question becomes whether the
 populations have arrived at their adaptations through the same genetic
 mechanisms. In recent years, genetic techniques have been used to tackle
 these questions by investigating the genome‐level changes underlying local
 adaptation. Here, we present a genomic analysis of colonization of
 freshwater habitats by a primarily marine fish, the Gulf pipefish
 (Syngnathus scovelli). We sample pipefish from four geographically
 distinct freshwater locations and use double‐digest restriction site
 associated DNA sequencing to compare them to 12 previously studied
 saltwater populations. The two most geographically distant and isolated
 freshwater populations are the most genetically distinct, although
 demographic analysis suggests that these populations are experiencing
 ongoing migration with their saltwater neighbours. Additionally, outlier
 regions were found genome‐wide, showing parallelism across ecotype pairs.
 We conclude that these multiple freshwater colonizations involve similar
 genomic regions, despite the large geographical distances and different
 underlying mechanisms. These similar patterns are probably facilitated by
 the interacting effects of intrinsic barriers, gene flow among populations
 and ecological selection in the Gulf pipefish.
description: These data were collected using double-digest restriction-site
 associated DNA sequencing (ddRADseq), as described in the paper published
 in Molecular Ecology.
DOI: 10.5061/dryad.8kprr4xkf
title: Data from: eDNA concentration, population size structure, and mark-recapture data

description: Organism abundance is a critical parameter in ecology, but its estimation
 is often challenging. Approaches utilizing eDNA to indirectly estimate
 abundance have recently generated substantial interest. However,
 preliminary correlations observed between eDNA concentration and abundance
 in nature are typically moderate in strength with significant unexplained
 variation. Here we apply a novel approach to integrate allometric scaling
 coefficients into models of eDNA concentration and organism abundance. We
 hypothesize that eDNA particle production scales non-linearly with mass,
 with scaling coefficients &lt; 1. Wild populations often exhibit
 substantial variation in individual body size distributions; we therefore
 predict that the distribution of mass across individuals within a
 population will influence population-level eDNA production rates. To test
 our hypothesis, we collected standardized body size distribution and
 mark-recapture abundance data using whole-lake experiments involving nine
 populations of brook trout. We correlated eDNA concentration with three
 metrics of abundance: density (individuals/ha), biomass (kg/ha), and
 allometrically scaled mass (ASM) (∑(individual mass0.73)/ha). Density and
 biomass were both significantly positively correlated with eDNA
 concentration (adj. r2 = 0.59 and 0.63, respectively), but ASM exhibited
 improved model fit (adj. r2 = 0.78). We also demonstrate how estimates of
 ASM derived from eDNA samples in ‘unknown’ systems can be converted to
 biomass or density estimates with additional size structure data. Future
 experiments should empirically validate allometric scaling coefficients
 for eDNA production, particularly where substantial intraspecific size
 distribution variation exists. Incorporating allometric scaling may
 improve predictive models to the extent that eDNA concentration may become
 a reliable indicator of abundance in nature.
description: Schnabel_input file is formatted to use the mrClosed() function
 from the Fisheries Stock Assessment package FSA in R.
 For other methods, refer to details in manuscript.
DOI: 10.5061/dryad.n2z34tmtj
title: Recurrent circuitry is required to stabilize piriform cortex odor representations across brain states

description: Pattern completion, or the ability to retrieve stable neural activity
 patterns from noisy or partial cues, is a fundamental feature of memory.
 Theoretical studies indicate that recurrently connected auto-associative
 or discrete attractor networks can perform this process. Although pattern
 completion and attractor dynamics have been observed in various recurrent
 neural circuits, the role recurrent circuitry plays in implementing these
 processes remains unclear. In recordings from head-fixed mice, we found
 that odor responses in olfactory bulb degrade under ketamine/ xylazine
 anesthesia, while responses immediately downstream, in piriform cortex,
 remain robust. Recurrent connections are required to stabilize cortical
 odor representations across states. Moreover, piriform odor
 representations exhibit attractor dynamics, both within and across trials,
 and these are also abolished when recurrent circuitry is eliminated. Here,
 we present converging evidence that recurrently-connected piriform
 populations stabilize sensory representations in response to degraded
 inputs, consistent with an auto-associative function for piriform cortex
 supported by recurrent circuitry.
description: These are processed and spike sorted recordings from olfactory
 bulb and piriform cortex under awake and anesthetized conditions.
 Documentation on the format of the files in this data can be found with a
 related dataset at
 https://crcns.org/data-sets/pcx/pcx-1/about-pcx-1
 MATLAB scripts that use this data to produce the figures in the
 associated paper can be found at
 https://github.com/FranksLab/eLife2020-recurrents-stabilize
DOI: 10.5061/dryad.dfn2z34z7
title: Taxonomy and relationships within polemonium foliosissimum (Polemoniaceae): Untangling a clade of colorful and gynodioecious herbs

description: New molecular and ecological data have necessitated taxonomic revisions of
 several species complexes within Polemonium (Polemoniaceae), including P.
 foliosissimum, an herbaceous perennial widespread in the Intermountain
 West of the United States. As currently circumscribed, P. foliosissimum is
 a highly polymorphic species of four taxonomic varieties. One of the most
 striking morphological traits of the species is its diversity in flower
 color, which is unusual for the genus. Several species have been proposed
 based on this variation in flower color. However, these names have been
 treated as infraspecific taxa because previous authors have concluded that
 the presence of micropollen grains throughout the geographic range of the
 species complex indicated partial hybrid sterility and therefore
 incomplete barriers to gene flow. However, recent evidence suggests that
 micropollen is instead due to a gynodioecious breeding system. Using 128
 nuclear loci and eight quantitative morphological traits, I clarify
 relationships and taxonomy within the species complex. I show that what is
 currently circumscribed as four varieties of P. foliosissimum represent
 five species that, in addition to differing in corolla color, differ in
 leaflet number, corolla size, and vegetative and floral pubescence. I
 propose a new species endemic to the White Mountains of southeastern
 Arizona, Polemonium apachianum. This study provides a new phylogenetic
 context and taxonomic circumscription to serve as a framework for future
 research on the evolution of floral color and sexual systems in a
 previously misunderstood but evolutionarily exciting system.
DOI: 10.5061/dryad.z34tmpg9v
title: Data from: Evolutionary patterns in the geographic range size of Atlantic Forest plants

description: Species’ geographic range size is arguably the single most important
 predictor of vulnerability to extinction and a key metric in ecology.
 Despite this, patterns of specific variation in range size and their
 underlying reasons are still poorly understood. For example, hypotheses on
 how evolutionary history affects range size have scarcely been tested. To
 address these questions, we focused on Brazil’s Atlantic Forest flora, one
 of the most species-rich in the world, relatively well-known and highly
 threatened. We investigated whether and how lineages’ diversification
 rate, number of species and age are associated with species’ geographic
 range size. We estimated the extent of occurrence and area of occupancy of
 each of 13,283 plant species native to the Atlantic Forest region based on
 over 500,000 unique records. We used phylogenetic least squares and
 logistic regressions to analyze how the predictors affect the geographic
 range size. On average, the higher the diversification rate and number of
 species in the lineage, the smaller the species range size and the higher
 the proportion of species with vulnerably small range size. Lineage age
 showed no clear effect on average range size. The results support our
 expectations that dynamics of diversification and taxonomic richness
 considerably affect the species range size. Finally, this work reveals
 poorly known patterns of range size variation and some of the mechanisms
 driving variation in range size and vulnerability to extinction.
DOI: 10.5061/dryad.bzkh18969
title: Data from: Characteristics of university students supported by counseling services: analysis of psychological tests and pulse rate variability

description: Objective Mental health is an essential issue during adolescence. The
 number of students who use counseling services is increasing in
 universities. We attempted to confirm the characteristics of the students
 who access counseling services using both psychological tests and pulse
 rate variability (PRV) for better support for students’ academic success.
 Methods We recruited the participants for this study from the students who
 had counseling sessions at Kanazawa University (Group S). As a control
 group, we also recruited students who had no experience in counseling
 services (Group H). We obtained health information from the database of
 annual health checkups. Participants received the Wechsler Adult
 Intelligence Scale (WAIS) III, Autism-Spectrum Quotient (AQ),
 Sukemune-Hiew (S-H) Resilience Test, and State-Trait Anxiety Inventory-JYZ
 (STAI). We also studied the SF-12v2 Health Survey. As a physiological
 test, we examined the spectral analyses of pulse rate variability (PRV) by
 accelerating plethysmography. We performed a linear analysis of PRV for
 LF, HF, and LF/HF as indexes of autonomic nervous function. We also
 conducted a non-linear analysis of PRV for the largest Lyapunov exponent
 (LLE). Additionally, we examined participants’ blood for autoantibodies
 against glutamate decarboxylase (GAD) 65. Results A total of 105 students
 participated in this study. Group S had 37 participants (Male: 26, Female:
 11), and Group H had 68 participants (Male: 27, Female 41). There were
 five males and one female who had diagnoses of autism spectrum disorder
 (ASD), and three males and no female with attention deficit hyperactivity
 disorder (ADHD) by medical institutes in Group S. Additionally, four males
 and two females had diagnoses of ASD with ADHD by medical institutes in
 Group S. A male with ASD in Group S had epilepsy. The students of Group S
 had characteristics as follows: 1) lower power of WMI despite high
 Full-Scale IQ, 2) higher ASD traits especially in Male, 3) lower
 resilience powers, 4) higher anxiety trait, 5) lower QOL in Role/social
 component in both Male and Female, 6) lower QOL in Mental component in
 Male 7) shifting of autonomic nervous balance toward higher sympathetic
 activity. Conclusion We could confirm the characteristics of students who
 visited counseling rooms for mental support. We also found gender
 differences in specificities of Group S. The educational system is
 changing rapidly to adjust social requests. These changes make conflict
 with the features of students of Group S. We should think about
 appropriate supports for the students who would pioneer the future of
 humanity.
DOI: 10.5061/dryad.gxd2547j1
title: Nest predation and adult mortality relationships with post-natal metabolic rates and growth among songbird species

description: Metabolism is thought to mediate the connection between environmental
 selection pressures and a broad array of life history tradeoffs, but tests
 are needed. High juvenile predation correlates with fast growth, which may
 be achieved via fast juvenile metabolism. Fast offspring metabolism and
 growth can create physiological costs later in life that should be
 minimized in species with low adult mortality. Yet, relations between
 juvenile metabolism and mortality at offspring versus adult stages are
 unexplored. We found that post-natal metabolism was correlated with adult
 mortality but not nest predation rates among 43 songbird species on three
 continents. Nest predation, but not adult mortality, explained additional
 variation in growth rates beyond metabolism. Our results suggest that
 metabolism may not be the mechanism underlying the relations between
 growth and mortality at different life stages.
DOI: 10.15468/dl.xm4wby
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Serbia",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((18.82718 46.00639,19.15633 43.40621,19.9889 42.52781,20.56976 41.75255,21.28616 42.11265,22.42852 42.25612,23.06747 43.15249,22.81576 44.61763,22.44788 44.79652,22.15745 44.64519,21.55722 45.19359,20.84083 45.77729,20.37614 46.22115,19.5823 46.24793,18.82718 46.00639))",
 "HasGeospatialIssue is false",
 "Month is one of (March, April, May)",
 "OccurrenceStatus is Present",
 "TaxonKey is Cinclus cinclus",
 "Year 2000-2026"
 ]
}

 The dataset includes 134 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002432-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1rn8pk0r7
title: Data from: Morphology and performance of the trap-jaw cheliceral strikes in spiders (Araneae, Mecysmaucheniidae)

description: Mecysmaucheniidae spiders have evolved ultra-fast cheliceral strikes four
 times independently. The mechanism for producing these high-speed strikes
 is likely due to a latch/spring system that allows for stored energy to be
 rapidly released. This study examines two different sister-lineages:
 Zearchaea has ultra-fast cheliceral strikes and Aotearoa, based on
 external morphology, is hypothesized to have slower strikes. Using
 high-speed videography, I gather kinematic data on each taxon and test the
 hypothesis that external morphology predicts cheliceral strike
 performance. Then, using histology and data from
 &[mu]-Computed-Technology scanning I ask whether internal muscle
 morphologies also correspond to performance differences. Results from
 high-speed video analysis reveal that Zearchaea sp. achieves peak angular
 velocities of 25.0 &[plusmn] 4.8 x 103 rad s-1 (mean
 &[plusmn] standard deviation) in durations of 0.0843
 &[plusmn] 0.017 ms. The fastest recorded strike had a peak angular
 and linear velocity of 30.8 x 103 rad s-1 and 18.2 m s-1, respectively.
 The slower striking sister-species, Aotearoa magna, was three orders of
 magnitude slower in velocity and longer in duration. Histology revealed
 sarcomere length differences, with some muscles specialized to be slow and
 forceful, and others to be fast and non-forceful. 3D printed models reveal
 structural differences that explain how the chelicerae hinge open and
 closed. Combining all of this evidence I put forth a hypothesis for the
 ultra-fast trap-jaw mechanism. This research documents the morphological
 shifts that accompany ultra-fast movements and result in increased
 rotation in joints and increased muscle specialization.
description: Data were collected using a high-speed video camera. Cheliceral
 strikes from individual videos were tracked using the 'point
 tool' in Fiji. Cheliceral displacement was fitted with a quintic
 spline and kinematic variables were calculated.
DOI: 10.5061/dryad.dv41ns1vq
title: Data from: COVID-19-related encephalopathy responsive to high doses glucocorticoids

description: One hundred twenty patients with coronavirus disease 2019 (COVID-19) were
 hospitalized in our intensive care unit, Geneva, Switzerland, between
 March 9 and April 16, 2020. We report the clinical evolution of 5
 consecutive patients intubated because of COVID-19– related acute
 respiratory distress syndrome, presenting with a pathologic recovery of
 consciousness, which was responsive to high-dose glucocorticoids. These
 patients all presented with angio-MRI signs of inflammation of CNS
 arteries, consistent with an endothelialitis rather than a vasculitis. The
 median time between COVID-19 first symptoms and intubation was 10 days
 (IQR 10–11 days). The clinical data, as well as biological and
 radiological data, were collected separately and analyzed as
 described in Supplemental tables 1 to 3.
description: All data were collected as described in the method section and
 the legend figures and tables. The missing data for some patients are
 described in the figures and tables. Supplemental
 data: Characteristic of
 patients (S1) Treatments and
 symptoms (S2) Laboratories Values
 (S3)
DOI: 10.5061/dryad.44j0zpcbq
title: Data from: Survival strategy of the endangered tree Acer catalpifolium Rehd., based on 13C fractionation

description: We conducted a field investigation and evaluation of 13C natural abundance
 to determine the growth habit and propagation strategy of Acer
 catalpifolium Rehd., a tree species native to China that is highly
 endangered. The results showed that A. catalpifolium is a K-selected
 strategist and pioneer species. Its narrow ecological range limits its
 geographical distribution, and poor fecundity limits its population size.
 The analysis of 13C natural abundance showed that A. catalpifolium does
 not use organic matter for reproduction when its stand volume is less than
 1.08×106 cm3 or it is less than 18.6 m tall, but it does use this strategy
 when it has a sufficient 1.08×106 cm3 stand volume or more or is taller
 than 18.6 m. If environmental conditions are not conducive (e.g., severe
 human disturbance, cliff edges, or fierce interspecific competition) to
 the continued growth of the tree, A. catalpifolium may allocate organic
 matter for reproduction. Human disturbance seems to promote the population
 expansion of A. catalpifolium. We provide our suggestions for the
 promotion and protection of A. catalpifolium as a species.
description: C-13, DBH and heights of <em>Acer catalpifolium
 </em>Rehd in  Sichuan Province, China.
DOI: 10.5061/dryad.cfxpnvx3d
title: Retention fraction of 15N-labelled deposited ammonium and nitrate in forests

description: The impacts of enhanced nitrogen (N) deposition on global forest carbon
 (C) sink and other ecosystem services may depend on whether N is deposited
 in reduced (mainly as ammonium) or oxidized forms (mainly as nitrate) and
 the subsequent fate of each. However, the fates of the two key reactive N
 forms and its contribution to forest C sink is unclear. We conducted
 ecosystem-scale paired 15N-labelling experiments in nine forests across
 China to quantify N retention fractions for both deposited
 ammonium and nitrate, including tropical and sub-tropical forests
 for the first time. By combining these results with four previous
 experiments from temperate Europe and North America, here we show that
 total ecosystem N retention is similar for ammonium and nitrate,
 but plants consistently take up more of the labelled
 nitrate  than ammonium  while soils
 retain more ammonium than nitrate. Nitrogen retention in plants
 and soils across sites is predicted by a combination of tree (NPP and
 woody biomass) and soil (organic layer mass and soil C/N ratios)
 variables. Greater proportions of deposited N are retained in N-limited
 ecosystems with low soil N availability and high soil C/N ratios. We
 estimate that N deposition-induced C sink in forests contributes more than
 20% of the total terrestrial C sink. Although less N is deposited in
 oxidized than reduced state, their total contributions to the global
 forest C sink are approximately equal due to more efficient use by trees
 of the oxidized than the reduced form. Our study demonstrates differential
 fates of reduced and oxidized N deposition that improves current
 understanding of the C-N interaction in forests and indicates a greater C
 sink attributable to atmospheric N deposition than previous estimates.
description: Nitrogen retention data is generated based on
 <sup>15</sup>N tracer experiments while N deposition is from
 model analysis.