cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m2271pf1
title: Data from: Genome-wide association genetics of an adaptive trait in lodgepole pine

description: Pine cones that remain closed and retain seeds until fire causes the cones
 to open (cone serotiny) represent a key adaptive trait in a variety of
 pine species. In lodgepole pine, there is substantial geographic variation
 in serotiny across the Rocky Mountain region. This variation in serotiny
 has evolved as a result of geographically divergent selection, with
 consequences that extend to forest communities and ecosystems. An
 understanding of the genetic architecture of this trait is of interest due
 to the wide-reaching ecological consequences of serotiny, and also because
 of the repeated evolution of the trait across the genus. Here we present
 and utilize an inexpensive and time effective method for generating
 population genomic data. The method uses restriction enzymes and PCR
 amplification to generate a library of fragments that can be sequenced
 with a high level of multiplexing. We obtained data for more than 95,000
 single nucleotide polymorphisms across 98 serotinous and non serotinous
 lodgepole pines from three populations. We used a Bayesian generalized
 linear model to test for an association between genotypic variation at
 these loci and serotiny. The probability of serotiny varied by genotype at
 11 loci and the association between genotype and serotiny at these loci
 was consistent in each of the three populations of pines. Genetic
 variation across these 11 loci explained 50% of the phenotypic variation
 in serotiny. Our results provide a first genome-wide association map of
 serotiny in pines and demonstrate an inexpensive and efficient method for
 generating population genomic data.
description: rfseq_protocolThis is a protocol for enzymatically guided genomic reduction and highly multiplexed Illumina library preparation.c_code_bassC code for bayesian association mappingcode_bass.tgzP_contorta_assembly.bamAssembly in BAM format. This assembly was created by using an artificial reference created through a denovo assembly. This artificial reference was then used a template onto which we assembled the remaining Illumina reads.REFpine27apr11-0.bampine_refThis artificial reference consists of contig consensus sequences created with a de novo assembly of a subset of reads, joined by stretches of 30 Ns. This was then used in a template guided assembly, where all Illumina reads were assembled onto the reference.
DOI: 10.5061/dryad.83s7k
title: Data from: The global distribution of tetrapods reveals a need for targeted reptile conservation

description: The distributions of amphibians, birds and mammals have underpinned global
 and local conservation priorities, and have been fundamental to our
 understanding of the determinants of global biodiversity. In contrast, the
 global distributions of reptiles, representing a third of terrestrial
 vertebrate diversity, have been unavailable. This prevented the
 incorporation of reptiles into conservation planning and biased our
 understanding of the underlying processes governing global vertebrate
 biodiversity. Here, we present and analyse the global distribution of
 10,064 reptile species (99% of extant terrestrial species). We show that
 richness patterns of the other three tetrapod classes are good spatial
 surrogates for species richness of all reptiles combined and of snakes,
 but characterize diversity patterns of lizards and turtles poorly.
 Hotspots of total and endemic lizard richness overlap very little with
 those of other taxa. Moreover, existing protected areas, sites of
 biodiversity significance and global conservation schemes represent birds
 and mammals better than reptiles. We show that additional conservation
 actions are needed to effectively protect reptiles, particularly lizards
 and turtles. Adding reptile knowledge to a global complementarity
 conservation priority scheme identifies many locations that consequently
 become important. Notably, investing resources in some of the world’s
 arid, grassland and savannah habitats might be necessary to represent all
 terrestrial vertebrates efficiently.
description: the distributions of all
 reptile speciesthe polygonal and points
 (buffered or modeled to produce MCPs and alpha hulls as described in the
 methods) for all reptile speciesGARD1.1_dissolved_ranges.zipSourcesThe sources for the geographic data (per species and place)
DOI: 10.5061/dryad.34s86
title: Data from: Singing whales generate high levels of particle motion: implications for acoustic communication and hearing?

description: Acoustic signals are fundamental to animal communication, and cetaceans
 are often considered bioacoustic specialists. Nearly all studies of their
 acoustic communication focus on sound pressure measurements, overlooking
 the particle motion components of their communication signals. Here we
 characterized the levels of acoustic particle velocity (and pressure) of
 song produced by humpback whales. We demonstrate that whales generate
 acoustic fields that include significant particle velocity components that
 are detectable over relatively long distances sufficient to play a role in
 acoustic communication. We show that these signals attenuate predictably
 in a manner similar to pressure and that direct particle velocity
 measurements can provide bearings to singing whales. Whales could
 potentially use such information to determine the distance of signalling
 animals. Additionally, the vibratory nature of particle velocity may
 stimulate bone conduction, a hearing modality found in other low-frequency
 specialized mammals, offering a parsimonious mechanism of acoustic energy
 transduction into the massive ossicles of whale ears. With substantial
 concerns regarding the effects of increasing anthropogenic ocean noise and
 major uncertainties surrounding mysticete hearing, these results highlight
 both an unexplored pathway that may be available for whale acoustic
 communication and the need to better understand the biological role of
 acoustic particle motion.
description: 150309_whale1_recordThis is a compass output from the M20 digital compass/accelerometer chip. It contains timing information and the outputs from those sensors.150309_whale2_record150309_whale3_recordM20_acoustic_data
DOI: 10.5061/dryad.g58k0
title: Data from: State-and-transition simulation models: a framework for forecasting landscape change

description: A wide range of spatially explicit simulation models have been developed
 to forecast landscape dynamics, including models for projecting changes in
 both vegetation and land use. While these models have generally been
 developed as separate applications, each with a separate purpose and
 audience, they share many common features. We present a general framework,
 called a state-and-transition simulation model (STSM), which captures a
 number of these common features, accompanied by a software product, called
 ST-Sim, to build and run such models. The STSM method divides a landscape
 into a set of discrete spatial units and simulates the discrete state of
 each cell forward as a discrete-time-inhomogeneous stochastic process. The
 method differs from a spatially interacting Markov chain in several
 important ways, including the ability to add discrete counters such as age
 and time-since-transition as state variables, to specify one-step
 transition rates as either probabilities or target areas, and to represent
 multiple types of transitions between pairs of states. We demonstrate the
 STSM method using a model of land-use/land-cover (LULC) change for the
 state of Hawai'i, USA. Processes represented in this example include
 expansion/contraction of agricultural lands, urbanization, wildfire, shrub
 encroachment into grassland and harvest of tree plantations; the model
 also projects shifts in moisture zones due to climate change. Key model
 output includes projections of the future spatial and temporal
 distribution of LULC classes and moisture zones across the landscape over
 the next 50 years. State-and-transition simulation models can be applied
 to a wide range of landscapes, including questions of both land-use change
 and vegetation dynamics. Because the method is inherently stochastic, it
 is well suited for characterizing uncertainty in model projections. When
 combined with the ST-Sim software, STSMs offer a simple yet powerful means
 for developing a wide range of models of landscape dynamics.
description: Case study files for
 ST-Sim softwareAs outlined in Appendix
 S2, this file contains all of the files required to run and view the
 results of the paper's simulations using the ST-Sim
 softwarecase-study-files-2015-12-02.zip
DOI: 10.5061/dryad.p236p
title: Data from: Unique features of germline variation in five Egyptian familial breast cancer families revealed by exome sequencing

description: Genetic predisposition increases the risk of familial breast cancer.
 Recent studies indicate that genetic predisposition for familial breast
 cancer can be ethnic-specific. However, current knowledge of genetic
 predisposition for the disease is predominantly derived from Western
 populations. Using this existing information as the sole reference to
 judge the predisposition in non-Western populations is not adequate and
 can potentially lead to misdiagnosis. Efforts are required to collect
 genetic predisposition from non-Western populations. The Egyptian
 population has high genetic variations in reflecting its divergent ethnic
 origins, and incident rate of familial breast cancer in Egypt is also
 higher than the rate in many other populations. Using whole exome
 sequencing, we investigated genetic predisposition in five Egyptian
 familial breast cancer families. No pathogenic variants in BRCA1, BRCA2
 and other classical breast cancer-predisposition genes were present in
 these five families. Comparison of the genetic variants with those in
 Caucasian familial breast cancer showed that variants in the Egyptian
 families were more variable and heterogeneous than the variants in
 Caucasian families. Multiple damaging variants in genes of different
 functional categories were identified either in a single family or shared
 between families. Our study demonstrates that genetic predisposition in
 Egyptian breast cancer families may differ from those in other disease
 populations, and supports a comprehensive screening of local disease
 families to determine the genetic predisposition in Egyptian familial
 breast cancer.
description: Egyptian_familial_breast_cancer_exome_variantsExome variants from five breast cancer families collected in Gharbiah disctrict, Egypt. DNA was extracted from blood cells using a FlexiGene DNA kit. Exome sequencing was done with TrueSeq Exome Enrichment Kit and on HiSeq2500, paired-end 2x150 at 100X coverage. Exome sequences were mapped to hg19 using Burrows-Wheeler Aligner and pre-processed with Picard Toolkit. Variants were called using Freebayes and annotated with ANNOVAR.EgyptianFBCExomeVariants.zip
DOI: 10.15468/dl.utxaru
title: Occurrence Download

description: A dataset containing 519611 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence)",
 "CoordinateUncertaintyInMeters 0.0-350.0",
 "Geometry POLYGON((-0.14651 42.02361,5.13442 42.02361,5.13442 45.25074,-0.14651 45.25074,-0.14651 42.02361))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Botaurus stellaris, Oenanthe hispanica, Sylvia conspicillata, Calandrella brachydactyla, Lanius meridionalis, Melanocorypha calandra, Galerida theklae, Lanius excubitor, Ixobrychus minutus, Ciconia ciconia, Ficedula hypoleuca, Ichthyaetus melanocephalus, Mareca strepera, Pyrrhula pyrrhula, Recurvirostra avosetta, Oenanthe oenanthe, Phylloscopus sibillatrix, Sylvia hortensis, Apus pallidus, Aythya ferina, Charadrius dubius, Emberiza citrinella, Falco peregrinus, Merops apiaster, Netta rufina, Tachymarptis melba, Athene noctua, Burhinus oedicnemus, Carduelis cannabina, Carduelis citrinella, Jynx torquilla, Prunella collaris, Pyrrhocorax graculus, Cisticola juncidis, Riparia riparia, Saxicola rubicola, Acrocephalus scirpaceus, Bubo bubo, Carduelis spinus, Himantopus himantopus, Otus scops, Locustella naevia, Galerida cristata, Lanius collurio, Passer montanus, Tyto alba, Alcedo atthis, Muscicapa striata, Rallus aquaticus, Dendrocopos medius, Petronia petronia, Sylvia melanocephala, Tachybaptus ruficollis, Anthus spinoletta, Bubulcus ibis, Carduelis chloris, Haematopus ostralegus, Hirundo rustica, Regulus regulus, Tadorna tadorna, Upupa epops, Scolopax rusticola, Streptopelia turtur, Sylvia cantillans, Dendrocopos minor, Lophophanes cristatus, Podiceps cristatus, Serinus serinus, Sturnus unicolor)"
 ]
}

 The dataset includes 519611 records from 428 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000325-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kg52rj5
title: Data from: Haltere removal alters responses to gravity in standing flies

description: Animals detect the force of gravity with multiple sensory organs, from
 subcutaneous receptors at body joints to specialized sensors like the
 vertebrate inner ear. The halteres of flies, specialized mechanoreceptive
 organs derived from hindwings, are known to detect body rotations during
 flight, and some groups of flies also oscillate their halteres while
 walking. The dynamics of halteres are such that they could act as gravity
 detectors for flies standing on substrates, but their utility during
 non-flight behaviors is not known. We observed the behaviors of intact and
 haltere-ablated flies during walking and during perturbations in which the
 acceleration due to gravity suddenly changed. We found that intact
 halteres are necessary for flies to maintain normal walking speeds on
 vertical surfaces and to respond to sudden changes in gravity. Our results
 suggest that halteres can serve multiple sensory purposes during different
 behaviors, expanding their role beyond their canonical use in flight.
description: DropNotes_updatedSpreadsheet scoring results of free falls in intact and haltere-ablated flies.Jess code
DOI: 10.5061/dryad.hn40n
title: Data from: Prolific observer bias in the life sciences: why we need blind data recording

description: Observer bias and other “experimenter effects” occur when researchers’
 expectations influence study outcome. These biases are strongest when
 researchers expect a particular result, are measuring subjective
 variables, and have an incentive to produce data that confirm predictions.
 To minimize bias, it is good practice to work “blind,” meaning that
 experimenters are unaware of the identity or treatment group of their
 subjects while conducting research. Here, using text mining and a
 literature review, we find evidence that blind protocols are uncommon in
 the life sciences and that nonblind studies tend to report higher effect
 sizes and more significant p-values. We discuss methods to minimize bias
 and urge researchers, editors, and peer reviewers to keep blind protocols
 in mind.
description: Evolution literature
 review dataExact p value
 datasetjournal_categoriesp values data 24 SeptProportion of significant p values per paperR script to filter and classify the p value dataQuiz answers - guessing effect size from abstractsThe answers provided by the 9 evolutionary biologists to quiz we designed, which aimed to test whether trained specialists are able to infer the relative size/direction of effect size from a paper's title and abstract.readmeDescription of the contents of all the other files in this Dryad submission.R script to statistically analyse the p value dataR script detailing the statistical analyses we performed on the p value datasets.
DOI: 10.5061/dryad.9tg56
title: Data from: DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade

description: In eastern Mediterranean countries orchids continue to be collected from
 the wild for the production of salep, a beverage made of dried orchid
 tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to
 identify orchid and other plant species present in 55 commercial salep
 products purchased in Iran, Turkey, Greece and Germany. Thirty samples
 yielded a total of 161 plant taxa, and 13 products (43%) contained orchid
 species and these belonged to 10 terrestrial species with tuberous roots.
 Another 70% contained the substitute ingredient Cyamopsis tetraganoloba
 (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2
 shows the potential of these markers and approach for identification of
 species used in salep products. The analysis of interspecific genetic
 distances between sequences of these markers for the most common salep
 orchid genera shows that species level identifications can be made with a
 high level of confidence. Understanding the species diversity and
 provenance of salep orchid tubers will enable the chain of
 commercialization of endangered species to be traced back to the
 harvesters and their natural habitats, and thus allow for targeted efforts
 to protect or sustainably use wild populations of these orchids.
description: Dryad Salep PGM
 dataSalep samples 1-55 (chip
 1 and chip 2). Per chip raw demultiplexed data. Per chip demultiplexed and
 split on primer data processed. Primer sequences. The number of reads per
 MOTU as well as the top BLAST hits per MOTU were compiled using custom
 scripts available online as part of the HTS-barcode-checker pipeline
 http://145.136.240.164:8080/ [56].
DOI: 10.5061/dryad.bq64j
title: Data from: Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli

description: Background: In 2011 northern Germany experienced a large outbreak of
 Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent
 to microbiology laboratories for epidemiological assessment highlighted
 the importance of fast and inexpensive typing procedures. We have
 therefore evaluated the applicability of a MALDI-TOF mass spectrometry
 based strategy for outbreak strain identification. Methods: Specific peaks
 in the outbreak strain’s spectrum were identified by comparative analysis
 of archived pre-outbreak spectra that had been acquired for routine
 species-level identification. Proteins underlying these discriminatory
 peaks were identified by liquid chromatography tandem mass spectrometry
 and validated against publicly available databases. The resulting typing
 scheme was evaluated against PCR genotyping with 294 E. coli isolates from
 clinical samples collected during the outbreak. Results: Comparative
 spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z
 10883. The underlying proteins were found to be of low prevalence among
 genome sequenced E. coli strains. Marker peak detection correctly
 classified 292 of 293 study isolates, including all 104 outbreak isolates.
 Conclusions: MALDI-TOF mass spectrometry allowed for reliable outbreak
 strain identification during a large outbreak of Shiga-Toxigenic E. coli.
 The applied typing strategy could probably be adapted to other typing
 tasks and might facilitate epidemiological surveys as part of the routine
 pathogen identification workflow.
description: Whoel cell MALDI-TOF
 mass spectra of Escherichia coli isolatesspecs.zip
DOI: 10.5281/zenodo.15694219
title: Aggression profiling dataset using eye-tracking (youth and college)

description: This dataset allows for aggression profiling research using eye-tracking data in youth and college populations. It contains two preprocessed, standardized tabular datasets (CSV) and their corresponding BIDS version based on the Brain Imaging Data Structure (BIDS) specification.

Each dataset contains eye-tracking features at the subject level and aggression labels according to tasks with emotional and attentional stimuli. Variables are cleaned, normalized, and labeled consistently. The tabular format is ready for direct use in machine learning pipelines. The BIDS format assures long-term interoperability and reproducibility.

The data were collected and curated by Omar Alvarado Cando and colleagues.

Please reference this dataset using the DOI provided. Contact the corresponding author for inquiries regarding access or reuse.
DOI: 10.5281/zenodo.15694220
title: Aggression profiling dataset using eye-tracking (youth and college)

description: This dataset allows for aggression profiling research using eye-tracking data in youth and college populations. It contains two preprocessed, standardized tabular datasets (CSV) and their corresponding BIDS version based on the Brain Imaging Data Structure (BIDS) specification.

Each dataset contains eye-tracking features at the subject level and aggression labels according to tasks with emotional and attentional stimuli. Variables are cleaned, normalized, and labeled consistently. The tabular format is ready for direct use in machine learning pipelines. The BIDS format assures long-term interoperability and reproducibility.

The data were collected and curated by Omar Alvarado Cando and colleagues.

Please reference this dataset using the DOI provided. Contact the corresponding author for inquiries regarding access or reuse.
DOI: 10.5061/dryad.ph104
title: Data from: Human visual exploration reduces uncertainty about the sensed world

description: In previous papers, we introduced a normative scheme for scene
 construction and epistemic (visual) searches based upon active inference.
 This scheme provides a principled account of how people decide where to
 look, when categorising a visual scene based on its contents. In this
 paper, we use active inference to explain the visual searches of normal
 human subjects; enabling us to answer some key questions about visual
 foraging and salience attribution. First, we asked whether there is any
 evidence for 'epistemic foraging'; i.e. exploration that
 resolves uncertainty about a scene. In brief, we used Bayesian model
 comparison to compare Markov decision process (MDP) models of scan-paths
 that did - and did not - contain the epistemic, uncertainty-resolving
 imperatives for action selection. In the course of this model comparison,
 we discovered that it was necessary to include non-epistemic (heuristic)
 policies to explain observed behaviour (e.g., a reading-like strategy that
 involved scanning from left to right). Despite this use of heuristic
 policies, model comparison showed that there is substantial evidence for
 epistemic foraging in the visual exploration of even simple scenes.
 Second, we compared MDP models that did - and did not - allow for changes
 in prior expectations over successive blocks of the visual search
 paradigm. We found that implicit prior beliefs about the speed and
 accuracy of visual searches changed systematically with experience.
 Finally, we characterised intersubject variability in terms of
 subject-specific prior beliefs. Specifically, we used canonical
 correlation analysis to see if there were any mixtures of prior
 expectations that could predict between-subject differences in
 performance; thereby establishing a quantitative link between different
 behavioural phenotypes and Bayesian belief updating. We demonstrated that
 better scene categorisation performance is consistently associated with
 lower reliance on heuristics; i.e., a greater use of a generative model of
 the scene to direct its exploration.
description: Scan-path
 dataThis file contains the
 scan-paths of the subjects that performed the "Scene construction
 task" described in the paper "Human visual exploration reduces
 uncertainty about the sensed world". There are some additional files
 that can be used to regenerate the figures and results in this
 paper.