cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t7m7g
title: Data from: Red fluorescence of the triplefin Tripterygion delaisi is increasingly visible against background light with increasing depth

description: The light environment in water bodies changes with depth due to the
 absorption of short and long wavelengths. Below 10 m depth, red
 wavelengths are almost completely absent rendering any red-reflecting
 animal dark and achromatic. However, fluorescence may produce red
 coloration even when red light is not available for reflection. A large
 number of marine taxa including over 270 fish species are known to produce
 red fluorescence, yet it is unclear under which natural light environment
 fluorescence contributes perceptively to their colours. To address this
 question we: (i) characterized the visual system of Tripterygion delaisi,
 which possesses fluorescent irides, (ii) separated the colour of the
 irides into its reflectance and fluorescence components and (iii) combined
 these data with field measurements of the ambient light environment to
 calculate depth-dependent perceptual chromatic and achromatic contrasts
 using visual modelling. We found that triplefins have cones with at least
 three different spectral sensitivities, including differences between the
 two members of the double cones, giving them the potential for
 trichromatic colour vision. We also show that fluorescence contributes
 increasingly to the radiance of the irides with increasing depth. Our
 results support the potential functionality of red fluorescence, including
 communicative roles such as species and sex identity, and
 non-communicative roles such as camouflage.
description: Fluorescence matrix Td
 ID 450-1Fluorescence matrix Td
 ID 450-2Fluorescence matrix Td
 ID 741-1Fluorescence matrix Td
 ID 741-2Fluorescence matrix Td
 ID 775-1Fluorescence matrix Td
 ID 775-2Fluorescence matrix Td
 ID 793-1Fluorescence matrix Td
 ID 793-2Irradiance from 6 to 36m
 depth STARESOMean ocular media
 transmissionMSP data no unpaired
 DCMSP data with unpaired
 DCRaw MSP data with best
 matching template for Figure 2Reflectance curves for 8
 T delaisi irides
DOI: 10.5061/dryad.qg7kv6c
title: Data from: Insights into the roles of CMK-1 and OGT-1 in interstimulus interval-dependent habituation in Caenorhabditis elegans

description: Habituation is a ubiquitous form of non-associative learning observed as a
 decrement in responding to repeated stimulation that cannot be explained
 by sensory adaptation or motor fatigue. One of the defining
 characteristics of habituation is its sensitivity to the rate at which
 training stimuli are presented – animals habituate faster in response to
 more rapid stimulation. The molecular mechanisms underlying this
 interstimulus interval (ISI)-dependent characteristic of habituation
 remain unknown. In this article we use behavioral neurogenetic and
 bioinformatic analyses in the nematode Caenorhabiditis elegans to identify
 the first molecules that modulate habituation in an ISI-dependent manner.
 We show that the Caenorhabditis elegans orthologs of
 Ca2+/calmodulin-dependent kinases CaMK1/4, CMK-1, and O-linked
 N-acetylglucosamine (O-GlcNAc) transferase, OGT-1, both function in
 primary sensory neurons to inhibit habituation at short ISIs and promote
 it at long ISIs. In addition, both cmk-1 and ogt-1 mutants display a rare
 mechanosensory hyper-responsive phenotype, i.e. larger mechanosensory
 responses than wild-type. Overall, our work identifies two conserved genes
 that function in sensory neurons to modulate habituation in an
 ISI-dependent manner, providing the first insights into the molecular
 mechanisms underlying the universally observed phenomenon that habituation
 has different properties when stimuli are delivered at different rates.
description: Ardiel_etal_DryadDatacolumn 1 = plate ID column 2 = stimulus column 3 = reversal distance (mm) column 4 (if applicable) = reversal duration (sec)
DOI: 10.5061/dryad.fm278
title: Data from: Influences of environmental and spatial factors on genetic and epigenetic variations in Rhododendron oldhamii (Ericaceae)

description: Test of the relationship of genetic and particularly epigenetic variation
 with geographic isolation and environment is important to reveal potential
 environmental drivers for selection. Rhododendron oldhamii is widespread
 but inhabits fragmented subtropical forest landscapes and populations
 across its range may exhibit different levels of genetic and epigenetic
 structuring correlated to their environmental conditions. Here, we
 investigated the genetic and epigenetic variations and their ecological
 correlates in R. oldhamii. Genetic and epigenetic variations were surveyed
 using amplified fragment length polymorphism (AFLP) and
 methylation-sensitive amplification polymorphism (MSAP), respectively.
 Using variation partitioning by redundant analysis (RDA), we examined the
 pure and spatially-structured environmental effects and pure spatial
 factors on genetic and epigenetic variations among individuals collected
 from 18 localities across R. oldhamii distribution range in Taiwan. We
 found that environments compared to geographic isolation among sites
 explained more genetic and epigenetic variations. Patchy distribution of
 the contemporary R. oldhamii populations was revealed by correlograms with
 patch size of approximately around 20-30 km based on the total genetic and
 epigenetic data. Spatial variables derived from the method of principal
 coordinates of neighbor matrices (PCNM), including PCNM3, PCNM5, PCNM7 and
 PCNM8 representing biotic processes, such as individual dispersal, were
 found to be important influencing potentially adaptive genetic and
 epigenetic variations. Annual mean temperature, annual precipitation,
 precipitation of the warmest quarter, aspect, slope and soil moisture were
 the most important environmental variables influencing potentially
 adaptive genetic and epigenetic variations, and could be particularly
 important for the evolution of local adaptation in R. oldhamii.
description: R.oldhamii_AFLP and
 MSAPHere, we investigated
 the genetic and epigenetic variations and their ecological correlates in
 R. oldhamii. Genetic and epigenetic variations were surveyed using
 amplified fragment length polymorphism (AFLP) and methylation-sensitive
 amplification polymorphism (MSAP), respectively. For MSAP, we generated
 two binary matrices for analyses representing two informative patterns of
 methylation susceptible loci (i.e. MSAP-nonMeth for non-methylation and
 MSAP-Meth for methylation). In the MSAP-nonMeth dataset, the loci of
 methylation state (i) were coded with "1" and loci of
 methylation states (ii) and (iii) were coded with "0".
 Alternatively, the loci of methylation state (ii) were coded with
 "1" and loci of methylation states (i) and (iii) were coded with
 "0" in the MSAP-Meth dataset.
DOI: 10.5061/dryad.ps1931hb
title: Data from: Life history evolution in guppies VIII: the demographics of density regulation in guppies (Poecilia reticulata)

description: In prior research, we found the way guppy life histories evolve in
 response to living in environments with a high or low risk of predation is
 consistent with life history theory that assumes no density-dependence. We
 later found that guppies from high predation environments experience
 higher mortality rates than those from low predation environments, but the
 increased risk was evenly distributed across all age/size classes. Life
 history theory that assumes density-independent population growth predicts
 that life histories will not evolve under such circumstances, yet we have
 shown with field introduction experiments that they do evolve. However,
 theory that incorporates density regulation predicts this pattern of
 mortality can result in the patterns of life history evolution we had
 observed. Here we report on density manipulation experiments performed in
 populations of guppies from low predation environments to ask whether
 natural populations normally experience density regulation and, if so, to
 characterize the short term demographic changes that underlie density
 regulation. Our experiments reveal that these populations are density
 regulated. Decreased density resulted in higher juvenile growth, decreased
 juvenile mortality rates and increased reproductive investment by adult
 females. Increased density causes reduced offspring size, increased fat
 storage by adult females and increased adult mortality.
description: AdultFatThis file and all that follow represent the dependent variables collected on all seven of the density manipulation experiments included in this paper.growthmean growth of each mm size class in all seven experimentsNumberofOffspringfecundity of all preserved adult females from all seven experimentsOffspringSizemean size of offspring dissected from all females preserved at the end of the experimentsReproductiveAllocationreproductive allocation of all pregnant females preserved at the end of all experimentsSurvivalmean survival, by mm size class, in all seven experiments
DOI: 10.5061/dryad.nc584
title: Data from: Genealogy and demographic history of a widespread amphibian throughout Indochina

description: Relatively little is known about spatial patterns of cryptic diversity in
 tropical species and the processes that generate them. Few studies examine
 the geographic distribution of genetic lineages in Southeast Asia, an area
 hypothesized to harbor substantial cryptic diversity. We investigated the
 evolutionary history of Asian tree frogs of the Polypedates leucomystax
 complex (n = 172) based on 1800 bp of the mtDNA genes ND 1 and cytochrome
 b and tested hypotheses pertaining to climate, geology and dispersal
 patterns. Analyses revealed substantial genetic diversity and lineage
 divergence throughout the region with evidence for widespread sympatric
 lineages and a general north versus south clustering. Relaxed molecular
 clock analysis and tests for demographic expansion identified an initial
 cladogenesis during the Miocene with subsequent Plio–Pleistocene
 diversification, which corresponded to periods of increased aridity and
 the onset of monsoonal weather systems, respectively. Rates of
 diversification were relatively constant until the Early Pleistocene when
 rates increased exponentially. We found equivocal evidence for both
 isolation-by-distance and a potential role of some landscape features as
 partial barriers to dispersal. Finally, our analyses showed that
 divergence between insular and mainland populations occurred before Homo
 sapiens colonized Southeast Asia suggesting that historical human-mediated
 dispersal did not drive insular diversification. Our results suggested
 that demographic expansion in the Late Pleistocene resulted in widespread
 sympatric lineages in the P. leucomystax complex throughout southern China
 and Indochina, and further clarified the evolutionary history of lineages
 within P. leucomystax.
description: Supplementary
 Materials1.Appendix Showing
 collecting locality, latitude, longitude, field number, sequence ID,
 lineage, and GenBank accession numbers for all individuals used in this
 study.Primer information is shown in Supplementary Table
 1.
DOI: 10.5061/dryad.202fn
title: Data from: Na+ influx via Orai1 inhibits intracellular ATP induced mTORC2 signaling to disrupt CD4 T cell gene expression and differentiation

description: T cell effector functions require sustained calcium influx. However, the
 signaling and phenotypic consequences of non-specific sodium permeation
 via calcium channels remain unknown. α-SNAP is a crucial component of
 Orai1 channels, and its depletion disrupts the functional assembly of
 Orai1 multimers. Here we show that α-SNAP hypomorph, hydrocephalos with
 hopping gait, Napahyh/hyh mice harbor significant defects in CD4 T cell
 gene expression and Foxp3 regulatory T cell (Treg) differentiation.
 Mechanistically, TCR stimulation induced rapid sodium influx in
 Napahyh/hyh CD4 T cells, which reduced intracellular ATP, [ATP]i.
 Depletion of [ATP]i inhibited mTORC2 dependent NFB activation in
 Napahyh/hyh cells but ablation of Orai1 restored it. Remarkably, TCR
 stimulation in the presence of monensin phenocopied the defects in
 Napahyh/hyh signaling and Treg differentiation, but not IL-2 expression.
 Thus, non-specific sodium influx via bonafide calcium channels disrupts
 unexpected signaling nodes and may provide mechanistic insights into some
 divergent phenotypes associated with Orai1 function.
description: Miao et al_elife
 2017
DOI: 10.5061/dryad.t8n07
title: Data from: Clinical trial registration, reporting, publication and FDAAA compliance: a cross-sectional analysis and ranking of new drugs approved by the FDA in 2012

description: Objective: To evaluate clinical trial registration, reporting and
 publication rates for new drugs by: (1) legal requirements and (2) the
 ethical standard that all human subjects research should be publicly
 accessible to contribute to generalisable knowledge. Design:
 Cross-sectional analysis of all clinical trials submitted to the Food and
 Drug Administration (FDA) for drugs approved in 2012, sponsored by large
 biopharmaceutical companies. Data sources: Information from Drugs@FDA,
 ClinicalTrials.gov, MEDLINE-indexed journals and drug company
 communications. Main outcome measures: Clinical trial registration and
 results reporting in ClinicalTrials.gov, publication in the medical
 literature, and compliance with the 2007 FDA Amendments Acts (FDAAA),
 analysed on the drug level. Results: The FDA approved 15 drugs sponsored
 by 10 large companies in 2012. We identified 318 relevant trials involving
 99 599 research participants. Per drug, a median of 57% (IQR 32–83%) of
 trials were registered, 20% (IQR 12–28%) reported results in
 ClinicalTrials.gov, 56% (IQR 41–83%) were published, and 65% (IQR 41–83%)
 were either published or reported results. Almost half of all reviewed
 drugs had at least one undisclosed phase II or III trial. Per drug, a
 median of 17% (IQR 8–20%) of trials supporting FDA approvals were subject
 to FDAAA mandated public disclosure; of these, a median of 67% (IQR
 0–100%) were FDAAA-compliant. 68% of research participants (67 629 of
 99 599) participated in FDAAA-subject trials, with 51% (33 405 of 67 629)
 enrolled in non-compliant trials. Transparency varied widely among
 companies. Conclusions: Trial disclosures for new drugs remain below legal
 and ethics standards, with wide variation in practices among drugs and
 their sponsors. Best practices are emerging. 2 of our 10 reviewed
 companies disclosed all trials and complied with legal disclosure
 requirements for their 2012 approved drugs. Ranking new drugs on
 transparency criteria may improve compliance with legal and ethics
 standards and the quality of medical knowledge.
description: Aubagio_11.11.14Bosulif_11.11.14.xlsx companiesElelyso 11.11.14Eliquis 11.11.14Erivedge 11.11.14Inlyta 11.13.14MenHibrix_11.11.14Perjeta 11.20.14 companySignifor 200677Sirturo 11.20.14Stivarga 11.20.14.xlsx companiesStribild 11.11.14Xeljanz 11.20.14Zaltrap 11.20.14Zioptan 11.20.14
DOI: 10.5061/dryad.p57j80c4
title: Data from: Genetic monitoring and complex population dynamics: insights from a 12-year study of the Rio Grande silvery minnow

description: The endangered Rio Grande silvery minnow persists as a remnant population
 in a highly fragmented and regulated arid-land river system. The species
 is subject to dramatic fluctuations in density. Since 2003, the wild
 population has been supplemented by hatchery-reared fish. We report on a
 12-year (1999 – 2010) monitoring study of genetic diversity and effective
 population size (Ne) of wild and hatchery stocks. Our goals were to
 evaluate how genetic metrics responded to changes in wild fish density and
 whether they corresponded to the number and levels of diversity of
 hatchery-reared repatriates. Genetic diversity and all measures of Ne in
 the wild population did not correlate with wild fish density until
 hatchery supplementation began in earnest. Estimates of variance and
 inbreeding effective size were not correlated. Our results suggest
 source-sink dynamics where captive stocks form a genetically diverse
 source and the wild population behaves as a sink. Nevertheless, overall
 genetic diversity of silvery minnow has been maintained over the last
 decade and we attribute this to a well designed and executed propagation
 management plan. When multiple factors like environmental fluctuation and
 hatchery supplementation act simultaneously on a population,
 interpretation of genetic monitoring data may be equally complex and
 require considerable ecological data.
description: RGSM_dRYADMicrosatellite data for Rio Grande silvery minnow. Data file created in Excel with Microsatellite toolkit.
DOI: 10.5061/dryad.ns92q
title: Data from: Soil carbon response to woody plant encroachment: Importance of spatial heterogeneity and deep soil storage

description: 1. Recent global trends of increasing woody plant abundance in
 grass-dominated ecosystems may substantially enhance soil organic carbon
 (SOC) storage and could represent a strong carbon (C) sink in the
 terrestrial environment. However, few studies have quantitatively
 addressed the influence of spatial heterogeneity of vegetation and soil
 properties on SOC storage at the landscape scale. In addition, most
 studies assessing SOC response to woody encroachment consider only surface
 soils, and have not explicitly assessed the extent to which deeper
 portions of the soil profile may be sequestering C. 2. We quantified the
 direction, magnitude, and pattern of spatial heterogeneity of SOC in the
 upper 1.2 m of the profile following woody encroachment via
 spatially-specific intensive soil sampling across a landscape in a
 subtropical savanna in the Rio Grande Plains, USA, that has undergone
 woody proliferation during the past century. 3. Increased SOC accumulation
 following woody encroachment was observed to considerable depth, albeit at
 reduced magnitudes in deeper portions of the profile. Overall, woody
 clusters and groves accumulated 12.87 and 18.67 Mg C ha-1 more SOC
 compared to grasslands to a depth of 1.2 m. 4. Woody encroachment
 significantly altered the pattern of spatial heterogeneity of SOC to a
 depth of 5 cm, with marginal effect at 5-15 cm, and no significant impact
 on soils below 15 cm. Fine root density explained greater variability of
 SOC in the upper 15 cm, while a combination of fine root density and soil
 clay content accounted for more of the variation in SOC in soils below 15
 cm across this landscape. 5. Synthesis: Substantial SOC sequestration can
 occur in deeper portions of the soil profile following woody encroachment.
 Furthermore, vegetation patterns and soil properties influenced the
 spatial heterogeneity and uncertainty of SOC in this landscape,
 highlighting the need for spatially specific sampling that can
 characterize this variability and enable scaling and modeling. Given the
 geographic extent of woody encroachment on a global scale, this
 undocumented deep soil C sequestration suggests this vegetation change may
 play a more significant role in regional and global C sequestration than
 previously thought.
description: Soil carbon response to
 woody plant encroachmentPlease see the metadata
 tab in the excel file for data description.Zhou et al. 2017. Journal of
 Ecology..xlsx
DOI: 10.5061/dryad.g6m44
title: Data from: Shrub encroachment is linked to extirpation of an apex predator

description: The abundance of shrubs has increased throughout Earth's arid lands.
 This ‘shrub encroachment’ has been linked to livestock grazing,
 fire-suppression and elevated atmospheric CO2 concentrations facilitating
 shrub recruitment. Apex predators initiate trophic cascades which can
 influence the abundance of many species across multiple trophic levels
 within ecosystems. Extirpation of apex predators is linked inextricably to
 pastoralism, but has not been considered as a factor contributing to shrub
 encroachment. Here, we ask if trophic cascades triggered by the
 extirpation of Australia's largest terrestrial predator, the dingo
 (Canis dingo), could be a driver of shrub encroachment in the Strzelecki
 Desert, Australia. We use aerial photographs spanning a 51-year period to
 compare shrub cover between areas where dingoes are historically rare and
 common. We then quantify contemporary patterns of shrub, shrub seedling
 and mammal abundances, and use structural equation modelling to compare
 competing trophic cascade hypotheses to explain how dingoes could
 influence shrub recruitment. Finally, we track the fate of seedlings of an
 encroaching shrub, hopbush (Dodonaea viscosa angustissima), during a
 period optimal for seedling recruitment, and quantify removal rates of
 hopbush seeds by rodents from enriched seed patches. Shrub cover was
 26–48% greater in areas where dingoes were rare than common. Our
 structural equation modelling supported the hypothesis that dingo removal
 facilitates shrub encroachment by triggering a four level trophic cascade.
 According to this model, increased mesopredator abundance in the absence
 of dingoes results in suppressed abundance of consumers of shrub seeds and
 seedlings, rodents and rabbits respectively. In turn, suppressed
 abundances of rodents and rabbits in the absence of dingoes relaxed a
 recruitment bottleneck for shrubs. The results of our SEM were supported
 by results showing that rates of hopbush seedling survival and seed
 removal were 1·7 times greater and 2·1 times lower in areas where dingoes
 were rare than common. Our study provides evidence linking the suppression
 of an apex predator to the historic encroachment of shrubs. We contend
 that trophic cascades induced by apex predator extirpation may be an
 overlooked driver of shrub encroachment.
description: Gordonetal_2016_JAE_DataDryadData relating to the publication: "Shrub encroachment is linked to extirpation of an apex predator"