cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7vsbxy
title: Occurrence Download

description: A dataset containing 386681 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-122.59179 46.53704,-121.01602 46.53704,-121.01602 48.50537,-122.59179 48.50537,-122.59179 46.53704))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 386681 records from 274 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002558-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7291/d11m38
title: Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability

description: Flexible resource investment is a risk-sensitive reproductive strategy
 where individuals trade resources spent on reproduction for basic
 metabolic maintenance and survival. This study examined morphological
 variation in herbivorous sea urchin grazers across a mosaic landscape of
 macroalgae-dominated habitats interspersed with patches of sea urchin
 barrens to determine whether sea urchins shift energy allocation in
 response to food limitation. Extensive underwater surveys of habitat
 attributes (e.g., sea urchin density, algae cover) were paired with
 detailed laboratory assays (e.g., sea urchin dissections) to determine how
 resource abundance affects energy allocation between reproductive capacity
 and body structure in the purple sea urchin, Strongylocentrotus
 purpuratus. We found that: (1) sea urchins had a more elongate jaw
 structure relative to body size in habitats void of macroalgae (i.e.,
 barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was
 lower in barrens and the barrens habitat was primarily comprised of
 encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index)
 and reproductive capacity (i.e., gonad index) were inversely related.
 These results suggest that sea urchins respond to macroalgae limited
 environments by shifting energy allocation between reproductive capacity
 and modifications of the foraging apparatus, which may explain the ability
 of sea urchins to persist in low resource
 environments.  
description: <strong>READ_ME</strong><br> This file explains
 all of the variables in each of the datasets required to conduct the
 analyses used in the manuscript, “Variation in purple sea urchin
 (Strongylocentrotus purpuratus) morphological traits in relation to
 resource availability.” These data were generated from benthic subtidal
 surveys led by Joshua G. Smith.
 <strong>Urchin_data.csv</strong><br> This data
 file contains information on habitat attributes and sea urchin
 morphometrics collected from benthic surveys along the Monterey Peninsula,
 CA, USA in the year 2017. All data reported are summarized at the size
 level, reported as mean values recorded from 1x1m quadrats.
 <strong>zone_data.csv</strong><br> This data
 file contains data summarized by test Log_TD for plotting the relationship
 between lantern length and gonad weight.
 <strong>Smith_raw_data_file.csv</strong><br>
 This data file contains unsummarized, raw sea urchin dissection
 data. <strong>Smith &
 Garcia.Rmd</strong><br> This file contains the code used to
 analyze the data in, “Variation in purple sea urchin (Strongylocentrotus
 purpuratus) morphological traits in relation to resource
 availability.”
DOI: 10.5061/dryad.41ns1rnc2
title: Effect of crosslinking modification with 4,4´-diphenylmethane diisocyanate (MDI) on physicochemical properties of peanut meal-based adhesives

description: The PM-based adhesives were prepared by crosslinking modification with
 diphenylmethane diisocyanate (MDI) as a crosslinking agent. The
 viscosity and water resistance of the modified PM-based adhesive were
 improved significantly, making it beneficial to the application of label
 industry. This paper investigated the properties of PM-based
 adhesives, including viscosity, solid content and water resistance time.
 Viscosity and solid content of the modified adhesives improved observably
 as MDI was introduced, and its water resistance time was up to 77 h when
 the modifier was added at 15% (based on PM), which met the industry
 requirements of Beer labels in China. In addition, FTIR and XRD
 were used to characterize the physical and chemical interactions in the
 cured adhesives. The thermal stability of the cured adhesives was
 determined by TGA, and SEM was used to observe the microstructure of the
 cured adhesives. The characterization and analysis results of the cured
 adhesives showed that incorporating MDI into the adhesives formed dense
 crosslinking structure because of chemical reactions between MDI and
 active groups on the PM protein molecules and introduced hydrophobic group
 into the adhesives, preventing water intrusion effectively, thus improving
 the water resistance of the cured adhesives. 
description: The Data is about the properties of peanut meal-based adhesives
 modified by 4,4´-diphenylmethane diisocyanate (MDI) , including the
 apparent viscosity, solid content, and water resistance duration, and the
 results obtained by FTIR, XRD, andTGAwere also presented.
DOI: 10.5061/dryad.jdfn2z38v
title: Wing: A suitable non-lethal tissue type for repeatable and rapid telomere length estimates in bats

description: Telomeres are used increasingly in ecology and evolution as biomarkers for
 ageing and environmental stress, and are typically measured from DNA
 extracted from non-lethally sampled blood. However, obtaining blood is not
 always possible in field conditions and only limited amounts can be taken
 from small mammals, such as bats, which moreover lack nucleated red blood
 cells and hence yield relatively low amounts of DNA. As telomere length
 can vary within species according to age and tissue, it is important to
 determine which tissues serve best as a representation of the organism as
 a whole. Here, we investigated whether wing tissue biopsies, a rapid and
 relatively non-invasive tissue collection method, could serve as a proxy
 for other tissues when measuring relative telomere length (rTL) in the
 Egyptian fruit bat (Rousettus aegyptiacus). Telomeres were measured from
 blood, brain, heart, kidney, liver lung, muscle and wing, and multiple
 wing biopsies were taken from the same individuals to determine
 intra-individual repeatability of rTL measured by using qPCR. Wing rTL
 correlated with rTL estimates from most tissues apart from blood. Blood
 rTL was not significantly correlated with rTL from any other tissue. Blood
 and muscle rTL were significantly longer compared with other tissues,
 while lung displayed the shortest rTLs. Individual repeatability of rTL
 measures from wing tissue was high (&gt;76%). Here we show the
 relationships between tissue telomere dynamics for the first time in a
 bat, and our results provide support for the use of wing tissue for rTL
 measurements.
description: Please see Materials & Methods of this paper for further
 details.
description: <strong>Individual_Tissues_DataDryad.csv</strong> Individual tissue z-score normalised telomere data.  <strong>Wing_Repeatability_DataDryad.csv</strong> Wing repeatability z-score normalised telomere data.
DOI: 10.5061/dryad.1jwstqjsq
title: Personality does not predict individual niche variation in a freshwater fish

description: Animal populations can exhibit considerable inter-individual variation in
 both behavioral traits and niche use, but the potential connections
 between these characteristics are rarely compared for the same
 individuals. We aimed to test whether behavioral syndromes were predictive
 of individual diet or microhabitat in a native New Zealand freshwater
 fish, Gobiomorphus cotidianus. We carried out laboratory behavioral assays
 and repeated habitat and diet measurement in a semi-natural mesocosm
 system. We found considerable repeatability in individual behavior,
 largely consistent with a proactive/reactive behavioral syndrome. We also
 found modest individual repeatability in microhabitat use and relatively
 strong individual specialization in diet. However, no measure of niche use
 in the mesocosms was significantly predicted by individual personality.
 Further studies of this type will be needed to assess whether links
 between individual behavior and resource use are more important in other
 species or ecological contexts.
description: Data consist of behavioural assays of individual common bullies
 followed by measures of habitat use and diet in pond mesocosms. Most data
 are stored as averages or aggregated data at the individual level, but for
 some measures (behavioural assays, refuge use, prey mass) additional data
 files are provided for calculation of repeatability. 
description: Methods and variables are explained in the related publication.
 Annotations in the R script explain and replicate the statistical
 analyses.
DOI: 10.5061/dryad.g4f4qrfnx
title: Tracking sickness effects on social encounters via continuous proximity-sensing in wild vampire bats

description: Sickness behaviors can slow the spread of pathogens across a social
 network. We conducted a field experiment to investigate how sickness
 behavior affects individual connectedness over time using a dynamic social
 network created from high-resolution proximity data. After capturing adult
 female vampire bats (Desmodus rotundus) from a roost, we created ‘sick’
 bats by injecting a random half of bats with the immune-challenging
 substance, lipopolysaccharide, while the control group received saline
 injections. Over the next three days, we used proximity sensors to
 continuously track dyadic associations between 16 ‘sick’ bats and 15
 control bats under natural conditions. Compared to control bats, ‘sick’
 bats associated with fewer bats, spent less time near others, and were
 less socially connected to more well-connected individuals (sick bats had
 on average a lower degree, strength, and eigenvector centrality).
 High-resolution proximity data allow researchers to flexibly define
 network connections (association rates) based on how a particular pathogen
 is transmitted (e.g., contact duration of &gt;1 vs &gt;60 minutes,
 contact proximity of &lt;1 vs &lt;10 meters). Therefore, we
 inspected how different ways of measuring association rates changed the
 observed effect of LPS. How researchers define association rates
 influences the magnitude and detectability of sickness effects on network
 centrality.
DOI: 10.5061/dryad.x3ffbg7gx
title: Data from: Olfactory testing in Parkinson’s disease & REM behavior disorder: a machine learning approach

description: Objective: We sought to identify an abbreviated test of impaired
 olfaction, amenable for use in busy clinical environments in prodromal
 (isolated REM sleep Behavior Disorder (iRBD)) and manifest Parkinson’s.
 Methods: 890 PD and 313 control participants in the Discovery
 cohort study underwent Sniffin’ stick odour identification assessment.
 Random forests were initially trained to distinguish individuals with poor
 (functional anosmia/hyposmia) and good (normosmia/super-smeller) smell
 ability using all 16 Sniffin’ sticks. Models were retrained using the top
 3 sticks ranked by order of predictor importance. One randomly selected
 3-stick model was tested in a second independent Parkinson’s dataset
 (n=452) and in two iRBD datasets (Discovery n=241;
 Marburg  n=37) before being compared to previously
 described abbreviated Sniffin’ stick combinations. Results: In
 differentiating poor from good smell ability, the overall area under the
 curve (AUC) value associated with the top 3 sticks (Anise, Licorice and
 Banana) was 0.95 in the development dataset (sensitivity:90%,
 specificity:92%, PPV:92%, NPV:90%). Internal and external validation
 confirmed AUCs≥0.90. The combination of 3-stick model determined poor
 smell and an RBD screening questionnaire score of ≥5, separated iRBD from
 controls with a sensitivity, specificity, PPV and NPV of 65%, 100%, 100%
 and 30%.  Conclusions: Our 3-Sniffin’-stick model holds
 potential utility as a brief screening test in the stratification of
 individuals with Parkinson’s and iRBD according to olfactory dysfunction.
 Classification of Evidence: This study provides Class III
 evidence that a 3-Sniffin’-stick model distinguishes individuals with poor
 and good smell ability and can be used to screen for individuals with
 iRBD.
DOI: 10.5061/dryad.nk98sf7rp
title: Polybrominated diphenyl ethers in human follicular fluid dysregulate mural and cumulus granulosa cell gene expression

description: Polybrominated diphenyl ethers (PBDEs), a major class of flame retardants
 incorporated into numerous consumer products, leach out into dust
 resulting in widespread exposure. There is evidence from in vitro and in
 vivo animal studies that PBDEs affect ovarian granulosa cell function and
 follicular development, yet human studies of their association with female
 infertility are inconclusive. Here, we tested the hypothesis that exposure
 to the PBDEs in follicular fluid is associated with dysregulation of gene
 expression in the mural and cumulus granulosa cells collected from women
 undergoing in vitro fertilization by intracytoplasmic sperm injection. The
 median concentration of the ∑10PBDEs detected in the follicular fluid
 samples (n=37) was 15.04 pg/g wet weight. RNA microarray analyses revealed
 that many genes were differentially expressed in mural and cumulus
 granulosa cells. Highest vs. lowest quartile exposure to the Σ10PBDEs or
 to two predominant PBDE congeners, BDE-47 or BDE-153, was associated with
 significant effects on gene expression in both cell types. Mural granulosa
 cells were generally more sensitive to PBDE exposure compared to cumulus
 cells. Overall, gene expression changes associated with BDE-47 exposure
 were similar to those for ∑10PBDEs but distinct from those associated with
 BDE-153 exposure. Interestingly, exposure to BDE-47 and ∑10PBDEs activated
 the expression of genes in pathways that are important in innate immunity
 and inflammation. To the best of our knowledge, this is the first
 demonstration that exposure to these environmental chemicals is associated
 with the dysregulation of pathways that play an essential role in
 ovulation.
description: Transcriptomic analysis of microarray gene expression data.
DOI: 10.5061/dryad.08kprr50x
title: Hippoglossus hippoglossus SNP data for coverage-based sex association

description: Changes in the genetic mechanisms that control sexual determination have
 occurred independently across the tree of life, and with exceptional
 frequency in teleost fishes. To investigate the genomic changes underlying
 the evolution of sexual determination, we sequenced a chromosome-level
 genome, multi-tissue transcriptomes, and population genomic data for the
 Atlantic Halibut (Hippoglossus hippoglossus), which has an XY/XX sex
 determination mechanism and has recently diverged from the Pacific Halibut
 (Hippoglossus stenolepis), which has a ZZ/ZW system. We used frequency and
 coverage-based population genomic approaches to identify a putative
 sex-determining factor, GSDF. We characterized regions with elevated
 heterozygosity and linkage disequilibrium indicating suppression of
 recombination across a recently formed sex chromosome. We detected
 testis-specific expression of GSDF, the sequence for which was highly
 conserved across flatfish. Based on evidence from genome-wide association,
 coverage, linkage disequilibrium, testis and brain transcriptomes, and
 sequence conservation with other flatfish, we propose a mechanism for the
 recent evolution of an XY sex-determination mechanism in Atlantic Halibut.
 A loss of function of the ancestral sex-determining gene DMRT1 in
 regulating the downstream gene GSDF likely enabled GSDF, or a proximal
 regulatory element, to become the primary sex-determining factor. Our
 results suggest changes to a small number of elements can have drastic
 repercussions for the genomic substrate available to sex-specific
 evolutionary forces, providing insight into how certain elements
 repeatedly evolve to control sex across taxa. Our chromosome-level
 assembly, multi-tissue transcriptomes, and population genomic data provide
 a valuable resource and understanding of the evolution of sexual systems
 in fishes.
description: SNP data were generated from RADseq reduced representation
 sequencing using the STACKS pipeline.
DOI: 10.5061/dryad.jdfn2z38w
title: Reduced stress defense responses contribute to the higher toxicity of a pesticide under warming

description: There is a pressing need to identify the molecular mechanisms underlying
 the, often magnifying, interactive effects between contaminants and
 natural stressors. We here test our hypothesis that lower general stress
 defense responses contribute to synergistic interactions between
 stressors. We focus on the widespread pattern that many contaminants are
 more toxic at higher temperatures. Specifically, we tested the effects of
 an environmentally realistic low-effect and high-effect concentration of
 the pesticide chlorpyrifos under warming at the gene expression level in
 the Northern house mosquito Culex pipiens molestus (Forskal, 1775). By
 applying the independent action model for combined stressors on RNA-seq
 data, we identified interactive gene expression patterns under combined
 exposure to chlorpyrifos and warming for general stress defense responses:
 protection of macromolecules, antioxidant processes, detoxification, and
 energy metabolism/allocation. Most of these general stress defense
 response genes showed upregulated antagonistic interactions, i.e. were
 less upregulated than expected under the independent action model. This
 indicates that when pesticide exposure was combined with warming the
 general stress defense responses were no longer buffering increased stress
 levels, which may contribute to a higher sensitivity to toxicants under
 warming. These upregulated antagonistic interactions were stronger for the
 high-effect chlorpyrifos concentration, indicating that exposure to this
 concentration under warming was most stressful. Our results highlight that
 quantitative analysis of the frequency and strength of the interaction
 types of general stress defense response genes, specifically focusing on
 antagonistic upregulations and synergistic downregulations, may advance
 understanding of how natural stressors modify the toxicity of
 contaminants.
description: Please see section '2. Materials and Methods' in the
 manuscript 'Reduced stress defense responses contribute to the higher
 toxicity of a pesticide under warming' in Molecular Ecology (Authors:
 Delnat V., Swaegers J., Asselman J. & Stoks R.).
description: Please read Delnat-et-al_Metadata.txt for more information about
 the uploaded files. Files with the extension .sf are text files which can
 be viewed with a text editor.
DOI: 10.5061/dryad.vq83bk3qx
title: Burying beetle parents adaptively manipulate information broadcast from a microbial community

description: Microbial volatiles provide essential information for animals, which
 compete to detect, respond to and perhaps control this information.
 Burying beetle parents have the opportunity to influence
 microbially-derived semiochemicals because they monopolize a small carcass
 for their family, repairing feeding holes and applying exudates that alter
 the microbial community. To study adaptive manipulation of microbial cues
 we integrated mechanistic and functional approaches. We contrasted Gas
 Chromatography, Mass Spectrometry (GC-MS) volatile profiles from carcasses
 that were or were not prepared by a resident pair of Nicrophorus
 orbicollis. Methyl thiocyanate (MeSCN), the primary attractant for burying
 beetles seeking a fresh carcass, was reduced 20-fold by carcass
 preparation, while dimethyl trisulfide (DMTS), which deters beetles, was
 increased 20-fold. These results suggest that parental care serves to make
 previously public information more private (crypsis, MeSCN) and to
 disinform rivals with a deterrent (DMTS). Functional tests in the field
 demonstrated that carcass preparation reduced discovery and use by
 congeners (three-fold) as well as by dipteran rivals. Because microbes and
 their chemicals influence nearly every aspect of animal ecology, animal
 manipulation of microbial cues may be as widespread as manipulation of
 their own signals.
DOI: 10.5061/dryad.sf7m0cg49
title: Ecological and social constraints combine to promote evolution of non-breeding strategies in clownfish

description: Individuals that forgo their own reproduction in animal societies
 represent an evolutionary paradox because it is not immediately apparent
 how natural selection can preserve the genes that underlie non-breeding
 strategies. Cooperative breeding theory provides a solution to the
 paradox: non-breeders benefit by helping relatives and/or inheriting
 breeding positions; non-breeders do not disperse to breed elsewhere
 because of ecological constraints. However, the question of why
 non-breeders do not contest to breed within their group has rarely been
 addressed. Here, we use a wild population of clownfish
 (Amphiprion percula), where non-breeders wait peacefully for years to
 inherit breeding positions, to show non-breeders will disperse when
 ecological constraints (risk of mortality during dispersal) are
 experimentally weakened. In addition, we show non-breeders will contest
 when social constraints (risk of eviction during contest) are
 experimentally relaxed. Our results show it is the combination of
 ecological and social constraints that promote the evolution of
 non-breeding strategies. The findings highlight parallels between, and
 potential for fruitful exchange between, cooperative breeding theory and
 economic bargaining theory: individuals will forgo their own reproduction
 and wait peacefully to inherit breeding positions (engage in cooperative
 options) when there are harsh ecological constraints (poor outside
 options) and harsh social constraints (poor inside options).