cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vd127
title: Data from: Three molecular markers show no evidence of population genetic structure in the Gouldian finch (Erythrura gouldiae)

description: Assessment of genetic diversity and connectivity between regions can
 inform conservation managers about risk of inbreeding, potential for
 adaptation and where population boundaries lie. The Gouldian finch
 (Erythrura gouldiae) is a threatened species in northern Australia,
 occupying the savannah woodlands of the biogeographically complex monsoon
 tropics. We present the most comprehensive population genetic analysis of
 diversity and structure the Gouldian finch using 16 microsatellite
 markers, mitochondrial control region and 3,389 SNPs from
 genotyping-by-sequencing. Mitochondrial diversity is compared across three
 related, co-distributed finches with different conservation
 threat-statuses. There was no evidence of genetic differentiation across
 the western part of the range in any of the molecular markers, and
 haplotype diversity but not richness was lower than a common
 co-distributed species. Individuals within the panmictic population in the
 west may be highly dispersive within this wide area, and we urge caution
 when interpreting anecdotal observations of changes to the distribution
 and/or flock sizes of Gouldian finch populations as evidence of overall
 changes to the population size of this species.
description: Microsatellite
 DataMicrosatellite
 data.csvGBS Final Filtered
 VCFFinalFiltered.vcfmtDNA Arlequin Input FileStandard Arlequin including the haplotype numbers and their associated genbank accessions. Also includes the pairwise geographic distances between sampling localities for use in the mantel test.mtDNA_Arlequin.arp
DOI: 10.15468/dl.2sydtm
title: Occurrence Download

description: A dataset containing 209 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Duttaphrynus scaber"
 ]
}

 The dataset includes 209 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001477-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.q74p1
title: Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

description: Understanding the demography of species over recent history (e.g.,
 &lt; 100 years) is critical in studies of ecology and evolution, but
 records of population history are rarely available. Surveying genetic
 variation is a potential alternative to census-based estimates of
 population size, and can yield insight into the demography of a
 population. However, to assess the performance of genetic methods it is
 important to compare their estimates of population history to known
 demography. Here, we leveraged the exceptional resources from a wetland
 with 37 years of amphibian mark-recapture data to study the utility of
 genetically-based demographic inference on salamander species with
 documented population declines (Ambystoma talpoideum) and expansions (A.
 opacum); patterns that have been shown to be correlated with changes in
 wetland hydroperiod. We generated ddRAD data from two temporally sampled
 populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and
 used coalescent-based demographic inference to compare alternate
 evolutionary models. For both species, demographic model inference
 supported population size changes that corroborated mark-recapture data.
 Parameter estimation in A. talpoideum was robust to our variations in
 analytical approach, while estimates for A. opacum were highly
 inconsistent, tempering our confidence in detecting a demographic trend in
 this species. Overall, our robust results in A. talpoideum suggest that
 genome-based demographic inference has utility on an ecological scale, but
 researchers should also be cognizant that these methods may not work in
 all systems and evolutionary scenarios. Demographic inference may be an
 important tool for population monitoring and conservation management
 planning.
description: fsc2_runfilesInput files for fastsimcoal2SNP_genotypesFilter 1 SNP genotypes in vcf format
DOI: 10.5061/dryad.gf1bq
title: Data from: Regulation of HBEGF by micro-RNA for survival of developing human trophoblast cells

description: Introduction: The growth factor HBEGF is upregulated
 post-transcriptionally in the low O2 environment of the human placenta
 during the first 10 weeks of pregnancy. We have examined the possible
 roles of HBEGF turnover and micro-RNA (miRNA) in its regulation by O2 in
 human first trimester trophoblast. Methods: HTR-8/SVneo trophoblast cells
 were cultured at 2% or 20% O2. The cells were transfected with a dual
 luciferase reporter construct (psiCHECK-2) containing no insert (control),
 the HBEGF 3’ untranslated region (3’UTR), or sub-regions of the 3’UTR, as
 well as with siRNA for DGCR8. RNA was extracted from trophoblast cells
 cultured at 2% O2 for 0–4 h for next-generation sequencing. HBEGF was
 quantified by ELISA. HBEGF, DGCR8, and β–actin were examined by western
 blotting. Results: Protein turnover studies, using 10 μg/ml cyclohexamide,
 1 μg/ml lactocystin, or 100 μg/ml MG132, demonstrated faster HBEGF
 degradation at 20% O2 than 2% O2, mediated by the proteasome. However,
 proteasome inhibition failed to initiate HBEGF accumulation at 20% O2.
 Reporter assays, comparing to empty vector, demonstrated that the intact
 HBEGF 3’ UTR inhibited expression (0.26), while fragments containing only
 its flanking regions increased reporter activity (3.15; 3.43). No
 differential expression of miRNAs was found in trophoblast cells cultured
 at 2% and 20% O2. Nevertheless, HBEGF upregulation at 2% O2 was blocked
 when the miRNA-processing protein DGCR8 was silenced, suggesting a role
 for miRNA. Conclusion: Our findings suggest involvement of flanking
 regions of the 3’UTR in activating HBEGF protein synthesis in response to
 2% O2, possibly through a miRNA-mediated mechanism.
description: Log_scale_MicroRNA_Data_Compiled-2016
DOI: 10.34810/data2228
title: Partitura i enregistrament de la Sonata en Re Major / D Major, de Carles Baguer (1768-1808)

description: &lt;br&gt;[CAT] Sota el marc del projecte Estudi i Recuperació de Patrimoni Musical que estan desenvolupant la UB i el CSIC, juntament amb el CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, el Grup per a l’Estudi del Patrimoni Musical (GEPAM), el Grup de Recerca Patrimoni Musical Històric de la Institució Milà i Fontanals d’Investigació en Humanitats del CSIC, l’Arquebisbat de Barcelona, la Catedral de Barcelona, l’Arxiu de l’Església de Santa Maria del Pi i l'Oratori de Sant Felip Neri de Barcelona, s'ha recuperat una peça musical de Carles Baguer (1768-1808) que es troba al manuscrit MS. 1378 del fons musical del CRAI Biblioteca de Fons Antic de la Universitat de Barcelona. 
Aquest dataset conté dos arxius:
&lt;br&gt;- Transcripció de la Sonata en Re Major de Carles Baguer del manuscrit Ms. 1378.
&lt;br&gt;- Enregistrament sonor de la peça interpretada per: Roger Illa, amb un piano A. Walter de 1803 (còpia moderna de Paul Poletti). 
&lt;br&gt;
description: &lt;br&gt;[ENG]The Study and Recovery of Musical Heritage project being developed by the UB and the CSIC, together with the CRAI Biblioteca de Fons Antic de la Universitat de Barcelona, ​​the Grupo de Investigación Patrimonio Musical Histórico de la Institución Milá y Fontanals de Investigación en Humanidades of the CSIC, the Archdiocese of Barcelona, ​​the Barcelona Cathedral, the Arxiu de l’Església de Santa Maria del Pi, and the Oratory of Sant Felip Neri in Barcelona, has recovered musical heritage: a musical piece by Carles Baguer (1768-1808) which is found in the manuscript Ms.1378 of the music collection of theCRAI Biblioteca de Fons Antic de la Universitat de Barcelona. 
This dataset contains two files:
&lt;br&gt;- Transcription of the Sonata in D Major by Carles Baguer from the manuscript Ms. 1378.
&lt;br&gt;- Sound recording of the piece performed by: Roger Illa, with a piano A. Walter from 1803 (modern copy by Paul Poletti).
DOI: 10.5061/dryad.6q4g6
title: Data from: Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys

description: Background: New World monkeys (NWMs) are unique in that they exhibit
 remarkable interspecific variation in color vision and feeding behavior,
 making them an excellent model for studying sensory ecology. However, it
 is largely unknown whether non-visual senses co-vary with feeding ecology,
 especially gustation, which is expected to be indispensable in food
 selection. Bitter taste, which is mediated by bitter taste receptors
 (TAS2Rs) in the tongue, helps organisms avoid ingesting potentially toxic
 substances in food. In this study, we compared the ligand sensitivities of
 the TAS2Rs of five species of NWMs by heterologous expression in HEK293T
 cells and calcium imaging. Results: We found that TAS2R1 and TAS2R4
 orthologs differ in sensitivity among the NWM species for colchicine and
 camphor, respectively. We then reconstructed the ancestral receptors of
 NWM TAS2R1 and TAS2R4, measured the evolutionary shift in ligand
 sensitivity, and identified the amino acid replacement at residue 62 as
 responsible for the high sensitivity of marmoset TAS2R4 to colchicine.
 Conclusions: Our results provide a basis for understanding the differences
 in feeding ecology among NWMs with respect to bitter taste.
description: Fluorescent data
 (wild-type)Fluorescence measurement
 data140815IPS(140226-27Flex).pxpFluorescent data (mutants)Fluorescence measurement data131218_19Flex (mutants).pxp
DOI: 10.5061/dryad.r7825
title: Data from: Climate forcing of an emerging pathogenic fungus across a montane multi-host community

description: Changes in the timings of seasonality as a result of anthropogenic climate
 change are predicted to occur over the coming decades. While this is
 expected to have widespread impacts on the dynamics of infectious disease
 through environmental forcing, empirical data are lacking. Here, we
 investigated whether seasonality, specifically the timing of spring
 ice-thaw, affected susceptibility to infection by the emerging pathogenic
 fungus Batrachochytrium dendrobatidis (Bd) across a montane community of
 amphibians that are suffering declines and extirpations as a consequence
 of this infection. We found a robust temporal association between the
 timing of the spring thaw and Bd infection in two host species, where we
 show that an early onset of spring forced high prevalences of infection. A
 third highly susceptible species (the midwife toad, Alytes obstetricans)
 maintained a high prevalence of infection independent of time of spring
 thaw. Our data show that perennially overwintering midwife toad larvae may
 act as a year-round reservoir of infection with variation in time of
 spring thaw determining the extent to which infection spills over into
 sympatric species. We used future temperature projections based on global
 climate models to demonstrate that the timing of spring thaw in this
 region will advance markedly by the 2050s, indicating that climate change
 will further force the severity of infection. Our findings on the effect
 of annual variability on multi-host infection dynamics show that the
 community-level impact of fungal infectious disease on biodiversity will
 need to be re-evaluated in the face of climate change. This article is
 part of the themed issue ‘Tackling emerging fungal threats to animal
 health, food security and ecosystem resilience’.
description: Water temperature from
 datalogger 2007 to 2015 in Lac ArletWater temperature at Lac
 Arlet (Longitude: 0°36'54.12"W, Latitude:
 42°50'24.20"N) was monitored in the field with the use of a data
 logger (HOBO Water Temperature Pro v2 Data Logger - U22-001). The logger
 was positioned approximately half a meter below the water surface. The
 logger was configured to take a reading of the water temperature every
 half an hour throughout the year and was manually uploaded once a
 year.ARL-datalogger-07-15.csv
DOI: 10.5061/dryad.dp4kb
title: Data from: Waiting time to infectious disease emergence

description: Emerging diseases must make a transition from stuttering chains of
 transmission to sustained chains of transmission, but this critical
 transition need not coincide with the system becoming supercritical. That
 is, the introduction of infection to a supercritical system results in a
 significant fraction of the population becoming infected only with a
 certain probability. Understanding the waiting time to the first major
 outbreak of an emerging disease is then more complicated than determining
 when the system becomes supercritical. We treat emergence as a dynamic
 bifurcation, and use the concept of bifurcation delay to understand the
 time to emergence after a system becomes supercritical. Specifically, we
 consider an SIR model with a time-varying transmission term and random
 infections originating from outside the population. We derive an analytic
 density function for the delay times and find it to be, in general, in
 agreement with stochastic simulations. We find the key parameters to be
 the rate of introduction of infection and the rate of change of the basic
 reproductive ratio. These findings aid our understanding of real emergence
 events, and can be incorporated into early-warning systems aimed at
 forecasting disease risk.
description: obs_delay_summarySummary statistics of raw simulation data. Stochastic simulations created via Gillespe's direct method using SIR model with time-varying transmission. Raw data is 7.2 million rows, 1.2 gb. Please email Chris to arrange ftp of raw data. Column heading meanings in tab 1 (metadata)kl_divergenceKullback-Leibler divergence for difference (in bits) between observed and expected values of bifurcation delay. Observed values come from stochastic simulations, expected values come from analytic derivations. Metadata located on first tab ('metadata').
DOI: 10.5061/dryad.3mc1v
title: Data from: Strategic use of affiliative vocalizations by wild female baboons

description: Although vocal production in non-human primates is highly constrained,
 individuals appear to have some control over whether to call or remain
 silent. We investigated how contextual factors affect the production of
 grunts given by wild female chacma baboons, Papio ursinus, during social
 interactions. Females grunted as they approached other adult females 28%
 of the time. Supporting previous research, females were much more likely
 to grunt to mothers with young infants than to females without infants.
 Grunts also significantly increased the likelihood of affiliative
 interactions among all partners. Notably, however, grunts did not simply
 mirror existing social bonds. Instead, they appeared to perform a very
 different function: namely, to serve as signals of benign intent between
 partners whose relationship is not necessarily close or predictable.
 Females were less likely to grunt to their mothers or adult daughters—the
 individuals with whom they shared the closest and least aggressive
 bonds—than to other females. In contrast, patterns of grunting between
 sisters were similar to those between nonkin, perhaps reflecting sisters’
 more ambivalent relationships. Females grunted at higher rates to
 lower-ranking, than to higher-ranking, females, supporting the hypothesis
 that grunts do not simply signal the signaler’s level of arousal or
 anxiety about receiving aggression, but instead function as signals of
 benign intent. Taken together, results suggest that the grunts given by
 female baboons serve to reduce uncertainty about the likely outcome of an
 interaction between partners whose relationship is not predictably
 affiliative. Despite their limited vocal repertoire, baboons appear to be
 skilled at modifying call production in different social contexts and for
 different audiences.
description: Dryad
 dataSource data for analyses
 of the context and consequences of grunts
DOI: 10.5061/dryad.2b7d5
title: Data from: Uncovering higher-taxon diversification dynamics from clade age and species-richness data

description: The relationship between clade age and species richness has been
 increasingly used in macroevolutionary studies as evidence for
 ecologically versus time-dependent diversification processes. However,
 theory suggests that phylogenetic structure, age type (crown or stem age),
 and taxonomic delimitation can affect estimates of the age-richness
 correlation (ARC) considerably. We currently lack an integrative
 understanding of how these different factors affect ARCs, which in turn,
 obscures further interpretations. To assess its informative breadth, we
 characterize ARC behavior with simulated and empirical phylogenies,
 considering phylogenetic structure and both crown and stem ages. First, we
 develop a two-state birth-death model to simulate phylogenies including
 the origin of higher taxa and a hierarchical taxonomy to determine ARC
 expectations under ecologically and time-dependent diversification
 processes. Then, we estimate ARCs across various taxonomic ranks of extant
 amphibians, squamate reptiles, mammals, birds, and flowering plants. We
 find that our model reproduces the general ARC trends of a wide range of
 biological systems despite the particularities of taxonomic practice
 within each, suggesting that the model is adequate to establish a
 framework of ARC null expectations for different diversification processes
 when taxa are defined with a hierarchical taxonomy. ARCs estimated with
 crown ages were positive in all the scenarios we studied, including
 ecologically dependent processes. Negative ARCs were only found at less
 inclusive taxonomic ranks, when considering stem age, and when rates
 varied among clades. This was the case both in ecologically and
 time-dependent processes. Together, our results warn against direct
 interpretations of single ARC estimates and advocate for a more
 integrative use of ARCs across age types and taxonomic ranks in
 diversification studies.
description: Online_Figures_Sanchez_Reyes_etalSupplementary figures S1 to S7 referenced in the text.Tables_Suppl_Sanchez_Reyes_etalSupplementary tables S1-S4, mentioned in the text.
DOI: 10.5281/zenodo.18387568
title: Design Patterns to Support the Usability and User Experience Evaluation of Dashboards for Decision Support Systems
DOI: 10.5281/zenodo.18387567
title: Design Patterns to Support the Usability and User Experience Evaluation of Dashboards for Decision Support Systems
DOI: 10.5061/dryad.n4cv3
title: Data from: ITS all right mama: Investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities

description: The formation of chimeric sequences can create significant methodological
 bias in PCR-based DNA metabarcoding analyses. During mixed-template
 amplification of barcoding regions, chimera formation is frequent and well
 documented. However, profiling of fungal communities typically uses the
 more variable rDNA region ITS. Due to a larger research community, tools
 for chimera detection have been developed mainly for the 16S/18S markers.
 However, these tools are widely applied to the ITS region without
 verification of their performance. We examined the rate of chimera
 formation during amplification and 454 sequencing of the ITS2 region from
 fungal mock communities of different complexities. We evaluated the
 chimera detecting ability of two common chimera-checking algorithms:
 Perseus and UCHIME. Large proportions of the chimeras reported were false
 positives. No false negatives were found in the dataset. Verified chimeras
 accounted for only 0.2% of the total ITS2 reads, which is considerably
 less than what is typically reported in 16S and 18S metabarcoding
 analyses. Verified chimeric "parent sequences" had significantly
 higher percent identity to one another than to random members of the mock
 communities. Community complexity increased the rate of chimera formation.
 GC content was higher around the verified chimeric break points,
 potentially facilitating chimera formation through base pair mismatching
 in the neighboring regions of high similarity in the chimeric region. We
 conclude that the hypervariable nature of the ITS region seem to buffer
 the rate of chimera formation in comparison to other, less variable
 barcoding regions, due to shorter regions of high sequence similarity.
description: Reads and verified
 chimeric sequences (ITS2)This contains 1) Raw
 reads (.fna) 2) Qual files (.qual) 3) mapping file 4) all 52 verified
 chimeric sequences (.fasta) 5) All fungi used in the mock communites
 (fasta)Aas
 et al 2016.zip
DOI: 10.5061/dryad.s5s7r
title: Data from: How does epistasis influence the response to selection?

description: Much of quantitative genetics is based on the "infinitesimal
 model", under which selection has a negligible effect on the genetic
 variance.  This is typically justified by assuming a very large
 number of loci with additive effects.  However, it applies even
 when genes interact, provided that the number of loci is large enough that
 selection on each of them is weak relative to random drift.  In
 the long term, directional selection will change allele frequencies, but
 even then, the effects of epistasis on the ultimate change in trait mean
 due to selection may be modest.  Stabilising selection can
 maintain many traits close to their optima, even when the underlying
 alleles are weakly selected. However, the number of traits that can be
 optimised is apparently limited to ~4Ne by the "drift load",
 which is hard to reconcile with the apparent complexity of many organisms,
 which arguably implies that selection maintains a very large number of
 traits. Just as for the mutation load, this limit can be evaded by a
 particular form of negative epistasis. A more robust limit is set by the
 variance in reproductive success. This suggests that selection accumulates
 information most efficiently in the infinitesimal regime, when selection
 on individual alleles is weak, and comparable with random drift. A review
 of evidence on selection strength suggests that while most variance in
 fitness may be due to alleles with large Subscript[N, e]s, substantial
 amounts of adaptation may be due to alleles in the infinitesimal regime,
 in which epistasis has modest effects.
description: Epistasis and selection
 response code 19.9.16This Mathematica
 notebook contains the code used to generate figures in the MS. It can be
 read using a free reader from Wolfram.com, but to execute the code
 requires running the Mathematica package.