cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.19sq4
title: Data from: Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments

description: The depth distribution of reef-building corals exposes their
 photosynthetic symbionts of the genus Symbiodinium to extreme gradients in
 the intensity and spectral quality of the ambient light environment.
 Characterizing the mechanisms used by the coral holobiont to respond to
 the low intensity and reduced spectral composition of the light
 environment in deeper reefs (greater than 20 m) is fundamental to our
 understanding of the functioning and structure of reefs across depth
 gradients. Here, we demonstrate that host pigments, specifically
 photoconvertible red fluorescent proteins (pcRFPs), can promote coral
 adaptation/acclimatization to deeper-water light environments by
 transforming the prevalent blue light into orange-red light, which can
 penetrate deeper within zooxanthellae-containing tissues; this facilitates
 a more homogeneous distribution of photons across symbiont communities.
 The ecological importance of pcRFPs in deeper reefs is supported by the
 increasing proportion of red fluorescent corals with depth (measured down
 to 45 m) and increased survival of colour morphs with strong expression of
 pcRFPs in long-term light manipulation experiments. In addition to
 screening by host pigments from high light intensities in shallow water,
 the spectral transformation observed in deeper-water corals highlights the
 importance of GFP-like protein expression as an ecological mechanism to
 support the functioning of the coral–Symbiodinium association across steep
 environmental gradients.
description: Discosoma
 ImagesUnprocessed chlorophyll
 emission images at different excitation wavelengths in
 Discosoma.Suspension
 ImagesUnprocessed chlorophyll
 emission images at different excitation wavelengths in zooxanthellae
 suspension.ILM for
 DryadRaw data used to produce
 figures in the manuscript.
DOI: 10.5061/dryad.s353f
title: Data from: New information on Brindabellaspis stensioi Young, 1980, highlights morphological disparity in Early Devonian placoderms

description: Acid prepared specimens of the placoderm Brindabellaspis stensioi (Early
 Devonian of New South Wales, Australia) revealed placoderm endocranial
 anatomy in unprecedented detail. Brindabellaspis has become a key taxon in
 discussions of early gnathostome phylogeny, and the question of placoderm
 monophyly versus paraphyly. The anterior orientation of the facial nerve
 and related hyoid arch structures in this taxon resemble fossil
 osteostracans (jawless vertebrates) rather than other early gnathostomes.
 New specimens of Brindabellaspis now reveal the previously unknown
 anterior region of the skull, including an exceptionally elongate
 premedian bone forming a long rostrum, supported by a thin extension of
 the postethmo-occipital unit of the braincase. Lateral bone overlap
 surfaces indicate an unusual anterior position for the jaws. Digital
 rendering of a synchrotron radiation scan reveals a uniquely specialised
 ethmoid commissure sensory canal, doubled back and fused into a midline
 canal. The visceral surface of the premedian bone has a plexus of
 perichondral bone canals. An updated skull roof reconstruction of
 Brindabellaspis adds to the highly variable dermal skull patterns of the
 probably non-monophyletic ‘acanthothoracids’. The unusual morphology
 revealed by the new specimens suggests that the earliest known reef fish
 fauna contained a diverse range of fishes with specialised ecological
 roles.
description: ply file of
 Brindabellaspis ethmoid commissureBrindabellaspis_ethmoid_commissure.plyply file of Brindabellaspis ethmoid commissure with nervesBrindabellaspis_ethmoid_commissure_with_nerves.ply3D pdf of ethmoid commissure and nervesBRINDABELLASPIS_ethmoid_commisure_3D.pdf
DOI: 10.5061/dryad.40f6v
title: Data from: Decisions reduce sensitivity to subsequent information

description: Behavioural studies over half a century indicate that making categorical
 choices alters beliefs about the state of the world. People seem biased to
 confirm previous choices, and to suppress contradicting information. These
 choice-dependent biases imply a fundamental bound of human rationality.
 However, it remains unclear whether these effects extend to lower level
 decisions, and only little is known about the computational mechanisms
 underlying them. Building on the framework of sequential-sampling models
 of decision-making, we developed novel psychophysical protocols that
 enable us to dissect quantitatively how choices affect the way
 decision-makers accumulate additional noisy evidence. We find robust
 choice-induced biases in the accumulation of abstract numerical
 (experiment 1) and low-level perceptual (experiment 2) evidence. These
 biases deteriorate estimations of the mean value of the numerical sequence
 (experiment 1) and reduce the likelihood to revise decisions (experiment
 2). Computational modelling reveals that choices trigger a reduction of
 sensitivity to subsequent evidence via multiplicative gain modulation,
 rather than shifting the decision variable towards the chosen alternative
 in an additive fashion. Our results thus show that categorical choices
 alter the evidence accumulation mechanism itself, rather than just its
 outcome, rendering the decision-maker less sensitive to new information.
description: Experimental
 Data
DOI: 10.5061/dryad.g487s21
title: Data from: Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.

description: Interactions between environmental factors and complex life-history
 characteristics of marine organisms produce the genetic diversity and
 structure observed within species. Our main goal was to test for genetic
 differentiation among eastern oyster populations from the coastal region
 of Canadian Maritimes against expected genetic homogeneity caused by
 historical events, taking into account spatial and environmental
 (temperature, salinity, turbidity) variation. This was achieved by
 genotyping 486 individuals originating from 13 locations using RADSeq. A
 total of 11 321 filtered SNPs were used in a combination of population
 genomics and environmental association analyses. We revealed significant
 neutral genetic differentiation (mean FST= 0.009) between sampling
 locations, and the occurrence of six major genetic clusters within the
 studied system. Redundancy analyses (RDA) revealed that spatial and
 environmental variables explained 3.1% and 4.9% of the neutral genetic
 variation and 38.6% and 12.2% of the putatively adaptive genetic
 variation, respectively. These results indicate that these environmental
 factors play a role in the distribution of both neutral and putatively
 adaptive genetic diversity in the system. Moreover, polygenic selection
 was suggested by genotype–environment association analysis and significant
 correlations between additive polygenic scores and temperature and
 salinity. We discuss our results in the context of their conservation and
 management implications for the eastern oyster.
description: genepop_6SNPs_divergent_notimputedGenotypes data (not imputed) for potentially selected SNPs in Genepop formatgenepop_6SNPs_divergent_IMPUTEDImputed genotypes data for potentially selected SNPs in Genepop formatgenepop_8246SNPs_NEUTRAL_notimputedGenotypes data for putatively neutral SNPs in Genepop formatgenepop_8246SNPs_NEUTRAL_IMPUTEDImputed genotypes data for putatively neutral SNPs in Genepop formatgenepop_11321SNPs_IMPUTEDImputed genotypes data for all filtered SNPs in Genepop formatgenepop_11321SNPs_notimputedGenotypes data for all filtered SNPs in Genepop formatgenepop_11321SNP_6clusters_IMPUTED_33indvImputed genotypes data for putatively all filtered SNPs with individuals in 6 cluters (equal sample size, n=33) in Genepop formatgenepop_11321SNP_6clusters_IMPUTEDImputed genotypes data for putatively all filtered SNPs with individuals in 6 clutersin Genepop formatenvironmental_data_polygenicRDAEnvironmental data for the polygenic RDA analysis11321SNPs_matrix012Matrix (genotypes coded as 012) data for all filtered SNPs in Genepop formathaplotypes_4307Haplotypes data for genetic diversity in tsv formatenvironmental_data_pcnmRDAEnvironmental data for the PCNM+RDA analysismatrix012_6SNPs_divergent_IMPUTEDMatrix (genotypes coded as 012) data for potentially selected SNPsmatrix012_8246SNPs_NEUTRAL_IMPUTEDMatrix (genotypes coded as 012) data for putatively neutral SNPspopulation_mapIndividual's population membershipread_meDescription of all files.
DOI: 10.15468/dl.yxjt6j
title: Occurrence Download

description: A dataset containing 967442 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Living Specimen, Occurrence evidence, Specimen)",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Caudata"
 ]
}

 The dataset includes 967442 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000356-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5jv56
title: Data from: Alterations of gray and white matter networks in patients with obsessive-compulsive disorder: a multimodal fusion analysis of structural MRI and DTI using mCCA+jICA

description: Many of previous neuroimaging studies on neuronal structures in patients
 with obsessive-compulsive disorder (OCD) used univariate statistical tests
 on unimodal imaging measurements. Although the univariate methods revealed
 important aberrance of local morphometry in OCD patients, the covariance
 structure of the anatomical alterations remains unclear. Motivated by
 recent developments of multivariate techniques in the neuroimaging field,
 we applied a fusion method called “mCCA+jICA” on multimodal structural
 data of T1-weighted magnetic resonance imaging (MRI) and diffusion tensor
 imaging (DTI) of 30 unmedicated patients with OCD and 34 healthy controls.
 Amongst six highly correlated multimodal networks (p &lt; 0.0001), we
 found significant alterations of the interrelated gray and white matter
 networks over occipital and parietal cortices, frontal interhemispheric
 connections and cerebella (False Discovery Rate q ≤ 0.05). In addition, we
 found white matter networks around basal ganglia that correlated with a
 subdimension of OC symptoms, namely ‘harm/checking’ (q ≤ 0.05). The
 present study not only agrees with the previous unimodal findings of OCD,
 but also quantifies the association of the altered networks across imaging
 modalities.
description: Preprocessed MR images,
 demographics and clinical assessmentsYou can find
 preprocessed magnetic resonance (MR) images, demographics of 30 patients
 with obsessive-compulsive disorder (OCD) and 34 age-/sex-matched healthy
 controls that were analyzed in the original article. Clinical assessments
 of Y-BOCS (Yale-Brown obsessive-compulsive scale) for the patients are
 included in the file.Kim.2015.PLOS1.OCD-mm.data.zip
DOI: 10.5061/dryad.97tt75g
title: Data from: Differential impacts of vaccination on wildlife disease spread during epizootic and enzootic phases

description: 1. Dissemination of oral vaccine baits is a cost-effective method to
 contain and control infectious wildlife diseases. The effectiveness of
 vaccine barriers in slowing or halting the disease spread depends on host
 ecology and landscape variability. It is not clear, however, how the
 success of vaccine barriers to manage disease may change from an epizootic
 to an enzootic phase of a disease invasion, and if this depends on the
 quality and configuration of host habitat. 2. We explore these questions
 using the raccoon variant rabies virus (RRV) as a model system. This
 zoonotic disease of high concern has been enzootic in eastern North
 America for decades, pushing into new areas and re-emerging in previously
 controlled zones. 3. We use a spatially-explicit individual-based model to
 assess how levels of oral vaccination and habitat fragmentation affect RRV
 spread across vaccine barriers during epizootic and enzootic phases.
 Simulated outcomes are compared using space-time characteristics of
 infection chains (individual-to-individual transmission of RRV). 4.
 Results indicate that the impact of vaccine barriers on control of RRV is
 strongest during the epizootic phase. Counterproductively, mid-levels of
 immunisation during an enzootic phase lead to more rabies-induced
 mortalities than lower or higher vaccination levels. Infection chains
 spread faster during the epizootic phase. Landscape effects on chain
 characteristics were more subtle than effects of invasion phase and
 vaccination. 5. Synthesis and applications. Space-time patterns of
 infection chains provide insight into mechanisms of wildlife disease
 spread. Our results demonstrate the importance of detecting and
 controlling outbreaks before they become enzootic. We discuss the
 implications for moving vaccine barriers to push back and decrease the
 size of enzootic areas.
description: MortalitiesA summary of all rabies-related mortalities that occurred across time and space for all simulations. Used to create Figure 2.PopulationDescribes how many animals are alive in each cell of the study area across time and space for each simulation.Chain Level ResultsThis file contains part of the information required to create Figure 3; mean velocity northwards, mean step length, and number of cases caused by each chain member.Host Level ResultsThis file contains information required to create Figure 4; quality of habitat (k) used by each chain member.Number dead summaryThis file is used to create part of Figure 3; it contains summary information about how many animals died in each phase, epizootic and enzootic.
DOI: 10.5061/dryad.9kd74
title: Data from: Alternative mating tactics in male chameleons (Chamaeleo chamaeleon) are evident in both long-term body color and short-term courtship pattern

description: Alternative mating tactics in males of various taxa are associated with
 body color, body size, and social status. Chameleons are known for their
 ability to change body color following immediate environmental or social
 stimuli. In this study, we examined whether the differential appearance of
 male common chameleon during the breeding season is indeed an expression
 of alternative mating tactics. We documented body color of males and used
 computer vision techniques to classify images of individuals into discrete
 color patterns associated with seasons, individual characteristics, and
 social contexts. Our findings revealed no differences in body color and
 color patterns among males during the non-breeding season. However, during
 the breeding season males appeared in several color displays, which
 reflected body size, social status, and behavioral patterns. Furthermore,
 smaller and younger males resembled the appearance of small females.
 Consequently, we suggest that long-term color change in males during the
 breeding season reflects male alternative mating tactics. Upon encounter
 with a receptive female, males rapidly alter their appearance to that of a
 specific brief courtship display, which reflects their social status. The
 females, however, copulated indiscriminately in respect to male color
 patterns. Thus, we suggest that the differential color patterns displayed
 by males during the breeding season are largely aimed at inter-male
 signaling.
description: Raw pattern
 photos
DOI: 10.5061/dryad.42qj362
title: Data from: Internal cranial anatomy of Early Triassic species of †Saurichthys (Actinopterygii: †Saurichthyiformes): implications for the phylogenetic placement of †saurichthyiforms

description: Background: †Saurichthyiformes was a successful group of latest
 Permian-Middle Jurassic predatory actinopterygian fishes and constituted
 important and widely-distributed components of Triassic marine and
 freshwater faunas. Their systematic affinities have long been debated,
 with †saurichthyiforms often being aligned with chondrosteans, a group
 today comprising sturgeons and paddlefishes. However, their character-rich
 endocranial anatomy has not been investigated in detail since the first
 half of the 20th century. Since that time, major advances have occurred in
 terms of our understanding of early actinopterygian anatomy, as well as
 techniques for extracting morphological data from fossils. Results: We
 used µCT to study the internal cranial anatomy of two of the
 stratigraphically oldest representatives of †Saurichthys, from the Early
 Triassic of East Greenland and Nepal. Our work revealed numerous
 previously unknown characters (e.g., cryptic oticooccipital fissure;
 intramural diverticula of braincase; nasobasal canals; lateral cranial
 canal; fused dermohyal), and permitted the reevalution of features
 relating to the structure of cranial fossae, basicranial circulation and
 opercular anatomy of the genus. Critically, we reinterpret the former
 †saurichthyiform opercle as an expanded subopercle. For comparison, we
 also produced the first digital models of a braincase and endocast of a
 sturgeon (A. brevirostrum). New information from these taxa was included
 in a broad phylogenetic analysis of Actinopterygii. †Saurichthyiforms are
 resolved as close relatives of †Birgeria, forming a clade that constitutes
 the immediate sister group of crown actinopterygians. However, these and
 other divergences near the actinopterygian crown node are weakly
 supported. Conclusions: Our phylogeny disagrees with the historically
 prevalent hypothesis favoring the chondrostean affinities of
 †saurichthyiforms. Previously-proposed synapomorphies uniting the two
 clades, such as the closure of the oticooccipital fissure, the posterior
 extension of the parasphenoid, and the absence of an opercular process are
 widespread amongst actinopterygians. Others, like those relating to
 basicranial circulation, are found to be based on erroneous
 interpretations. Our work renders the †saurichthyiform character complex
 adequately understood, and permits detailed comparisons with other early
 crown actinopterygians. Our phylogenetic scheme highlights outstanding
 questions concerning the affinity of many crown actinopterygians, such as
 the Paleozoic-early Mesozoic deep-bodied forms, which are largely caused
 by lack of endoskeletal data.
description: Saurichthys sp.
 (Greenland)PLY of all segmented
 structures in .zip folderGreenland
 Saurichthys.zipSaurichthys
 nepalensisPLY of braincase and
 rostral endocast in .zip folderAcipenser
 brevirostrumPLY of braincase and
 endocast in .zip folder
DOI: 10.5061/dryad.bp683
title: Data from: Ecological niche modelling for conservation planning of an endemic snail in the verge of becoming a pest in cardamom plantations in the Western Ghats biodiversity hotspot

description: Conservation managers and policy makers are often confronted with a
 challenging dilemma of devising suitable strategies to maintain
 agricultural productivity while conserving endemic species that at the
 early stages of becoming pests of agricultural crops. Identification of
 environmental factors conducive to species range expansion for forecasting
 species distribution patterns will play a central role in devising
 management strategies to minimize the conflict between the agricultural
 productivity and biodiversity conservation. Here, we present results of a
 study that predicts the distribution of Indrella ampulla, a snail endemic
 to the Western Ghats biodiversity hotspot, which is becoming a pest in
 cardamom (Ellettaria cardamomum) plantations. We determined the
 distribution patterns and niche overlap between I. ampulla and Ellettaria
 cardamomum using maximum entropy (MaxEnt) niche modeling techniques under
 current and future (2020–2080) climatic scenarios. The results showed that
 climatic (precipitation of coldest quarter and isothermality) and soil
 (cation exchange capacity of soil [CEC]) parameters are major factors that
 determine the distribution of I. ampulla in Western Ghats. The model
 predicted cardamom cultivation areas in southern Western Ghats are highly
 sensitive to invasion of I. ampulla under both present and future climatic
 conditions. While the land area in the central Western Ghats is predicted
 to become unsuitable for I. ampulla and Ellettaria cardamomum in future,
 we found 71% of the Western Ghats land area is suitable for Ellettaria
 cardamomum cultivation and 45% suitable for I. ampulla, with an overlap of
 35% between two species. The resulting distribution maps are invaluable
 for policy makers and conservation managers to design and implement
 management strategies minimizing the conflicts to sustain agricultural
 productivity while maintaining biodiversity in the region.
description: Bias file for cultivated
 location of E. cardamomumecardcultibias.ascBias file for wild location of E. cardamomumecardwildbias.ascBias file created using all records of E. cardamomumecradallbias.ascBias file for Indrella ampullaiampbiasnew.ascDistribution records of Indrella ampullaIampNew.csvWild records of E. cardamomumWildEcard.csvCultivation records of E. cardamomumCultiEcard.csv
DOI: 10.34740/kaggle/dsv/14630597
title: KANPM-DTA Pretrained Models
DOI: 10.5061/dryad.9fm28
title: Data from: The dawn of open access to phylogenetic data

description: The scientific enterprise depends critically on the preservation of and
 open access to published data. This basic tenet applies acutely to
 phylogenies (estimates of evolutionary relationships among species).
 Increasingly, phylogenies are estimated from increasingly large,
 genome-scale datasets using increasingly complex statistical methods that
 require increasing levels of expertise and computational investment.
 Moreover, the resulting phylogenetic data provide an explicit historical
 perspective that critically informs research in a vast and growing number
 of scientific disciplines. One such use is the study of changes in rates
 of lineage diversification (speciation – extinction) through time. As part
 of a meta-analysis in this area, we sought to collect phylogenetic data
 (comprising nucleotide sequence alignment and tree files) from 217 studies
 published in 46 journals over a 13-year period. We document our attempts
 to procure those data (from online archives and by direct request to
 corresponding authors), and report results of analyses (using Bayesian
 logistic regression) to assess the impact of various factors on the
 success of our efforts. Overall, complete phylogenetic data for ~ 60% of
 these studies are effectively lost to science. Our study indicates that
 phylogenetic data are more likely to be deposited in online archives
 and/or shared upon request when: (1) the publishing journal has a strong
 data-sharing policy; (2) the publishing journal has a higher impact
 factor, and; (3) the data are requested from faculty rather than students.
 Importantly, our survey spans recent policy initiatives and
 infrastructural changes; our analyses indicate that the positive impact of
 these community initiatives has been both dramatic and immediate. Although
 the results of our study indicate that the situation is dire, our findings
 also reveal tremendous recent progress in the sharing and preservation of
 phylogenetic data.
description: Dawn_of_Open_Access_Data_filesData table analyzed in the paper and data files gathered. Includes ReadMe.