cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1r634nj
title: Data from: Evolution of vertebrate postcranial complexity: axial skeleton regionalization and paired appendages in a Devonian jawless fish

description: One of the major events in vertebrate evolution involves the transition
 from jawless (agnathan) to jawed (gnathostome) vertebrates, including a
 variety of cranial and postcranial innovations. It has long been assumed
 that characters such as the pelvic girdles and fins, male intromittent
 organs independent from the pelvic girdles, as well as a regionalized
 axial skeleton first appeared in various basal gnathostome groups if not
 at the origin of gnathostomes. Here we describe the first occurrence of
 pelvic girdles and intromittent organs in the Late Devonian jawless
 anaspid‐like fish Euphanerops longaevus Woodward (Miguasha Lagerstätte,
 eastern Canada), associated with a morphologically differentiated region
 of the axial skeleton. Morphological differentiation of the axial skeleton
 is also described for the first time in an extant jawless fish, the sea
 lamprey Petromyzon marinus Linnaeus. Our data indicate that
 regionalization of the axial skeleton occurred earlier in vertebrate
 evolutionary history than previously appreciated. This regionalization is
 coupled with modifications of the appendicular skeleton in Euphanerops.
 These new observations combined with a new phylogenetic analysis of early
 vertebrates provide a more precise understanding of how the appendicular
 and axial skeletons developed and evolved within vertebrate evolutionary
 history.
description: Chevrinais_SupplementaryInformation_review13 figures, one table, one list of phylogenetic charactersPhylogenetic matrix of charactersCoding matrixChevrinais_Matrix_review
DOI: 10.5061/dryad.m4g1601
title: Data from: A latitudinal gradient in dimensionality of biodiversity

description: Biodiversity is multifaceted and represents numerous dimensions expressing
 variation in richness and abundances of species, ecosystem functions,
 phylogenetic relationships, morphology, traits and interactions. Such
 dimensions are correlated to varying degrees and recent research has
 attempted to better understand behavior of such correlations. We define
 dimensionality of biodiversity as degree of redundancy in variation among
 multiple dimensions of biodiversity. One fundamental question regarding
 biodiversity is whether its dimensionality is spatially structured, also
 exhibiting geographic gradients. We examine if redundancy among dimensions
 of biodiversity changes latitudinally thereby contributing to increased
 tropical complexity. Geographic range maps of bats were overlaid on a 100
 × 100 km grid of the New World to determine species composition of each
 cell. Species richness and three measures each of phylogenetic, functional
 and phenetic diversity were calculated. Dimensionality was estimated as
 evenness of eigenvalues generated from a principal components analysis
 (PCA) of multiple measures of biodiversity. High dimensionality is
 characterized by low correlations among biodiversity measures and high
 evenness of eigenvalues from PCA, whereas low dimensionality is
 characterized by high correlations and low evenness of eigenvalues.
 Latitudinal gradients of dimensionality were determined by regression
 analysis. Slope of the empirical relationship was compared to slopes
 generated from two null models that randomized the distribution of
 species. Dimensionality of biodiversity does indeed exhibit a latitudinal
 gradient, decreasing with increasing latitude. This empirical gradient was
 stronger than expected by the random distribution of species.
 Additionally, spatial variation in dimensionality of biodiversity could
 not be explained by a similar underlying pattern in variation of
 environmental conditions. Correlations among different dimensions of
 biodiversity vary spatially, and interpretations of such correlations
 should be geographically explicit. Mechanisms proposed to explain
 latitudinal gradients need not only account for gradients of biodiversity,
 but gradients in dimensionality as well. A gradient in dimensionality
 suggests that conservation strategies that rely on maximization of a
 single metric, such as species richness, might be of varying utility in
 different geographic contexts.
description: EmpiricalSppCompositionEmpiricalDivGradientsEmpirical diversity gradients across grid cells calculated from species composition data
DOI: 10.5061/dryad.jk127ng
title: Data from: Movement ecology of brown bears (Ursus arctos) in the Romanian Eastern Carpathians

description: Brown bear movement patterns are driven by their opportunistic feeding
 behaviour, with their complex life history and seasonality playing an
 important role in habitat selection. Within a large unfragmented forest
 habitats persisting over decades in the Romanian Carpathians and a
 prohibitive hunting management during 40 years of communist centralised
 game management, information about brown bear movements and spatial
 ecology is lacking. Using data obtained from 13 brown bears fitted with
 GPS telemetry collars, we estimated home ranges and core activity areas
 and we investigated the daily, seasonal and altitudinal movements of brown
 bears in the Eastern Romanian Carpathians and surrounding high hills. The
 median MCP95% home ranges of brown bears was 629.92 km2 and the median
 size of core activity areas (estimated as 50% kernel density) was 36.37
 km2, with no significant differences between males and females. The mean
 daily distance travelled, measured as daily displacement length, was 1818
 m and an analysis of seasonal movements indicated significant differences
 between seasons (greatest movements during the Hyperphagia season). The
 GPS-collared brown bears travelled between a minimum altitude measured at
 ~234 m and a maximum at ~1634 m. Analysing the spatial overlap between the
 estimated home range and the game management units (GMU) limits, we
 obtained a median number of 8 GMUs overlapping totally or partially with
 estimated home range polygons. Our study, using GPS telemetry, highlights
 the complex spatial ecology of the brown bear in the Romanian Carpathians,
 with larger home range size than those estimated in other European brown
 bear populations and with daily movements that vary by season and within a
 large altitude range. Our study supports the implementation of brown bear
 monitoring at a regional scale, rather than focusing on county level GMUs
 as the monitoring unit.
description: R script and
 dataR
 script and data to reproduce analyses and figures in the paper Movement
 ecology of brown bears (Ursus arctos) in the Romanian Eastern Carpathians.
 The script was tested on R 3.4.3. R packages used: adehabitatHR 0.4.15,
 maptools 0.9-2, ggpubr 0.1.6. Some files are generated outside of R script
 (using Microsoft Excel, ArcGIS 10.3.1, ArcMET 10.3.1.
 v1).DataS1.zip
DOI: 10.5061/dryad.c6f7453
title: Data from: Evolutionary history of the flora of Mexico: dry forests cradles and museums of endemism

description: Mexico is considered an exceptional biogeographic area with a varied and
 unique endemic vascular flora that is estimated at half of the global
 total of approximately 24,500 species. However, spatial phylogenetic
 measures of biodiversity for this flora have not yet been estimated to
 understand how the Mexican flora assembled to form current vegetation.
 Patterns of species richness, weighted endemism, phylogenetic diversity
 and weighted phylogenetic endemism, as well as centers of neo- and
 paleo-endemism were determined to examine differences and congruence among
 these measures, and the implications of these results for conservation.
 Out from 24,445 vascular plant species 10,271 (42%) are endemic to Mexico.
 Areas of endemism and phylogenetic endemism were associated with zones of
 topographic complexity in the main mountain systems, in the deserts, and
 in isolated dry zones. Every single locality that seasonal tropical dry
 forests have been reported in Mexico was identified as an area of
 endemism. Areas of significant phylogenetic diversity were the most
 restricted and occurred in dry forests of the Trans-Mexican Volcanic Belt
 and of the Sierra de Chiapas. The highest phylogenetic clustering
 comprising neo- paleo- and super endemism was identified in the southern
 extreme of Mexico. The flora of Mexico bears a signature of mixed neo- and
 paleo-endemism, and areas of endemism occurred in dry forests. The
 majority of vascular plant ineages diverged in the Miocene (5-20 million
 of years ago) when arid environments expanded across the world. The
 position of Mexico in the middle of two landmasses and the presence of
 more than fifty percent of arid surface favored the establishment and
 diversification of tropical lineages adapted to extreme seasonality and to
 aridity that migrated from North America and from South America. Our
 results identified areas of elevated species richness and phylogenetic
 diversity and provide a foundation on which to propose conservation
 efforts in Mexico.
description: MexicanEndemicVascularPlantsDryadThe checklist of Mexican endemic vascular plantGeoreferencesMexicanVascularPlantsDryadIt includes the georeferences of Mexican vascular plants used in analyses.NonendemicMexicanVascularPlantsDryadChecklist of the non-endemic Mexican vascular plantsPhylogenyThe tree file from PhyloMaker including all Mexican vascular plant species.
DOI: 10.5061/dryad.9s85m06
title: Data from: Measuring visual search and distraction in immersive virtual reality

description: An important issue of psychological research is how experiments conducted
 in the laboratory or theories based on such experiments relate to human
 performance in daily life. Immersive virtual reality (VR) allows control
 over stimuli and conditions at increased ecological validity. The goal of
 the present study was to accomplish a transfer of traditional paradigms
 that assess attention and distraction to immersive VR. To further increase
 ecological validity we explored attentional effects with daily objects as
 stimuli instead of simple letters. Participants searched for a target
 among distractors on the countertop of a virtual kitchen.
 Target-distractor discriminability was varied and the displays were
 accompanied by a peripheral flanker that was congruent or incongruent to
 the target. RT was slower when target-distractor discriminability was low
 and when flankers were incongruent. The results were replicated in a
 second experiment in which stimuli were presented on a computer screen in
 2D. The study demonstrates the successful translation of traditional
 paradigms and manipulations into immersive VR and lays a foundation for
 future research on attention and distraction in VR. Further, we provide an
 outline for future studies that should utilize features of VR that are not
 available in traditional laboratory research.
description: raw_data_Experiment_1raw_data_Experiment_2Location of Experiment Implementations
DOI: 10.5061/dryad.g047010
title: Data from: Geometric morphometrics reveal altered corpus callosum shape in pyridoxine-dependent epilepsy

description: Objective: To evaluate the features and maturational changes in overall
 callosal shape in patients with pyridoxine-dependent epilepsy (PDE).
 Methods: Measurements were conducted through landmark based geometric
 morphometrics applied on cerebral MRIs of PDE patients and age-matched
 control subjects. The outline of the corpus callosum was manually traced
 in the midsagittal plane. 300 semi-landmarks along the outline were
 collected and underwent statistical generalized Procrustes analysis. An
 allometric regression was applied to evaluate the callosal shape due to
 growth over time. Results: 38 patients with PDE and 38 age- and
 sex-matched control subjects were included. Mean age at the time of the
 MRI in the patient group was 9.3 years (median 6.3 years, range 0.01- 48
 years). Significant differences (p&lt;0.01) in the mean callosal shape
 between patients and controls were found. The allometric regression model
 revealed significant shape variations (p&lt;0.01) between the two
 study groups across the developmental course after controlling for the
 effect of callosal size on shape. This latter effect turned out to be
 significant as well (p&lt;0.001). Conclusions: Patients with PDE show
 an altered callosal shape and variations in callosal ontogeny which are
 likely secondary to the underlying genetic defect with abnormal function
 of antiquitin, the product of the ALDH7A1 gene.
description: Supplemental Figure
 6Supplemental Figure 6.
 Midsagittal cerebral MRI slices of all PDE patients. Included are T1-, T2-
 weighted as well as FLAIR- images. The re-oriented MRI slice was loaded
 into Osirix software where the callosal outline was traced (red) and the
 CC was colored (black or white). The light green point corresponds to the
 rectangular projection of the interface between CC and fornix. All
 annotations with identifying data on the image were cropped. The yellow
 numbers correspond to the patient numbers 1-38.Fig6_labelled.pdfSupplemental Figure 7Fig7_labelledSupplemental Figure 7. Midsagittal cerebral MRI slices of all control subjects. For image preparation we refer to suppl. Figure 6. The light green point corresponds to the rectangular projection of the interface between CC and fornix. The yellow numbers relate to the control numbers 1-38 matching to the same corresponding patient numbers.Fig7_labelled.pdf
DOI: 10.5061/dryad.2bs5231
title: Data from: Ecophenotypy, temporal and spatial fidelity, functional morphology, and physiological trade-offs among intertidal bivalves

description: Ecophenotypic variation in populations is driven by differences in
 environmental variables. In marine environments, ecophenotypic variation
 may be caused by differences in hydrodynamic conditions, substrate type,
 water depth, temperature, salinity, oxygen concentration, and habitat
 heterogeneity, among others. Instances of ecophenotypic variation in
 modern and fossil settings are common, but little is known about the
 influences of time-averaging and spatial-averaging on their preservation.
 Here we examine the shell morphology of two adjacent populations, both
 live-collected and death assemblages, of the infaunal, suspension-feeding,
 intertidal bivalve Leukoma staminea from the well-studied Argyle Creek and
 Argyle Lagoon locations on San Juan Island, Washington, USA. Individuals
 in the low energy lagoon are free to burrow in the fine-grained substrate
 while clams in the high energy creek are precluded from burrowing in the
 rocky channel. Our results demonstrate variation in size and shape between
 the adjacent habitats. Lagoon clams are larger, more disc-shaped, and have
 relatively larger siphons than their creek counterparts, which are
 smaller, more spherical in shape, and have a relatively shallower pallial
 sinus. This ecophenotypy is preserved among death assemblages, although
 with generally greater variation due to time averaging and shell
 transport. Our interpretation is that ecophenotypic variation, in this
 case, is induced by differing hydrodynamic regimes and substrate types,
 cumulatively resulting in physiological tradeoffs diverting resources from
 feeding and respiration to stability and shell strength, all of which has
 the potential to be preserved in the fossil record.
description: Supplemental Figure
 1Supplemental Figure 1.
 Scree and loadings plots for Principal components analysis of
 Procrustes-transformed landmark data of Leukoma staminea from Argyle Creek
 and Argyle Lagoon (PC1 v. PC2).Supplement Figure 1 Huntley et
 al r2.tifSupplemental Figure
 2Supplemental Figure 2.
 Principal components analysis of Procrustes-transformed landmark data of
 Leukoma staminea from Argyle Creek and Argyle Lagoon (A-D: PC2 v. PC3;
 E-H: PC3 v. PC4).Supplement Figure 2 Huntley et
 al r2.tif
DOI: 10.5061/dryad.k48mr0c
title: Data from: The ecological roots of human susceptibility to social influence: a pre-registered study investigating the impact of early life adversity

description: There is considerable variability in the degree to which individuals rely
 on their peers to make decisions. Although theoretical models predict that
 environmental risks shift the cost-benefit trade-off associated with
 social information use, this idea has received little empirical support.
 Here we aim to test the effect of childhood environmental adversity on
 humans’ susceptibility to follow others’ opinion in the context of a
 standard face evaluation task. Results collected in a pilot study
 involving 121 adult participants tested online showed that susceptibility
 to social influence and childhood environmental adversity are positively
 associated. Computational analyses further confirmed that this effect is
 not explained by the fact that participants exposed to early adversity
 produce noisier decisions overall but that they are indeed more likely to
 follow the group’s opinion. To test the robustness of these findings, a
 pre-registered direct replication using an optimal sample size was run.
 The results obtained from 262 participants in the pre-registered study did
 not reveal a significant association between childhood adversity and task
 performance but the meta-analysis ran on both the pilot and the
 pre-registered study replicated the initial finding. The present work
 provides experimental evidence for an association between individuals’
 past ecology and their susceptibility to social influence.
description: PilotStudyPilot Study: raw and preprocessed data, preprocessing matlab scripts, statistical analyses R scriptsReplicationStudyReplication Study: raw and preprocessed data, preprocessing matlab scripts, statistical analyses R scripts
DOI: 10.5061/dryad.j0nf1sn
title: Data from: Employing hypothesis testing and data from multiple genomic compartments to resolve recalcitrant backbone nodes in Goodenia s.l. (Goodeniaceae)

description: Goodeniaceae is a primarily Australian flowering plant family with a
 complex taxonomy and evolutionary history. Previous phylogenetic analyses
 have successfully resolved the backbone topology of the largest clade in
 the family, Goodenia s.l., but have failed to clarify relationships within
 the species-rich and enigmatic Goodenia clade C, a prerequisite for
 taxonomic revision of the group. We used genome skimming to retrieve
 sequences for chloroplast, mitochondrial, and nuclear markers for 24 taxa
 representing Goodenia s.l., with a particular focus on Goodenia clade C.
 We performed extensive hypothesis tests to explore incongruence in clade C
 and evaluate statistical support for clades within this group, using
 datasets from all three genomic compartments. The mitochondrial dataset is
 comparable to the chloroplast dataset in providing resolution within
 Goodenia clade C, though backbone support values within this clade remain
 low. The hypothesis tests provided an additional, complementary means of
 evaluating support for clades. We propose that the major subclades of
 Goodenia clade C (C1–C3 + Verreauxia) are the result of a rapid radiation,
 and each represents a distinct lineage.
description: Jabailyetal_cpDNAGenetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Helianthus annuus chloroplast genome. Post g-blocks dataset.Jabailyetal_mtDNAGenetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Helianthus annuus mitochondrial genome.Post g-blocks dataset.Jabailyetal_G3PDHGenetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Verreauxia sequence.Jabailyetal_NRRGenetic samples taken in the field and vouchered at PERTH. Genomic skimming accomplished on Illumina Hiseq 2500 rapid run with 150 bp paired-end chemistry. Filtered and reference-guided assembled against Verreauxia sequence.Jabailyetal_COS alignmentsGenetic samples taken in the field and vouchered at PERTH.Zip file of alignments of 85 Conserved ortholog sets. Illumina library with paired-end reads. HybPiper pipeline with default settings (Johnson et al., 2016) to assemble reads corresponding to COS loci based on the probe set published by Mandel et al. (2014)COS alignments.zip
DOI: 10.5061/dryad.567mc91
title: Data from: Improving the signal subtle feature extraction performance based on dual improved fractal box dimension eigenvectors

description: Aiming at the limitation of traditional fractal box-counting dimension
 algorithm in subtle feature extraction of radiation source signals, a dual
 improved generalized fractal box-counting dimension eigenvector algorithm
 was proposed in the paper. Firstly, the radiation source signal was
 preprocessed, and Hilbert transform was performed to obtain the
 instantaneous amplitude of the signal. Then, the improved fractal
 box-counting dimension of signal instantaneous amplitude was extracted as
 the first eigenvector. At the same time, the improved fractal box-counting
 dimension of the signal without Hilbert transform was extracted as the
 second eigenvector. Finally, the dual improved fractal box-counting
 dimension eigenvectors form the multi-dimensional eigenvectors as signal
 subtle features, used for radiation source signal recognition by the gray
 relation algoritm. The experimental results show that compared with the
 traditional fractal box-counting dimension algorithm and the single
 improved fractal box-counting dimension algorithm, the proposed dual
 improved fractal box-counting dimension algorithm can better extract the
 signal subtle distribution characteristics under different reconstruction
 phase space, and has a better recognition effect with good real-time
 performance.
description: the radiation source
 signals for testingIn the paper, the
 radiation source signals for testing are from Case Western Reserve
 University Bearing Data Center. The database has been a standard dataset
 for testing the effectiveness of feature extraction algorithm and pattern
 recognition algorithm. Besides, the sampled signals of the database are
 full of random mechanical noise, which makes the test closer to the real
 situation. The motor drive end rotor is supported by a test bearing, where
 a single point of failure is set through discharge machining. The
 radiation source signals of bearing vibration data used for analysis are
 obtained under the motor speed of 1797 r/min and load of 0 horsepower. An
 accelerometer is installed on the motor drive end housing with a bandwidth
 of up to 5000 Hz, and the vibration data for the test bearing under
 different fault patterns is collected by a recorder as the radiation
 source signals, in which the sampling frequency is 12 kHz. The fault types
 contain outer race fault, the inner race fault, and the ball fault, and
 the fault diameters, i.e., fault severities, contain 28 mils, 21 mils, 14
 mils and 7 mils. Totally 11 types of radiation source signals of bearing
 vibration data considering different fault categories and fault severities
 are analyzed, as seen in Table 1. Each data sample is made up of 2048 time
 series points. For those 550 data samples, each of those 550 data sample
 are different with different random mechanical noise. Among them, 110 data
 samples are chosen randomly for the establishment of the knowledge base,
 with the rest 440 data samples taken as testing data
 samples.Data.zip