cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5hg71mj
title: Data from: Mechanics of composite hydrogels approaching phase separation

description: For polymer-particle composites, limited thermodynamic compatibility of
 polymers and particles often leads to poor dispersal and agglomeration of
 the particles in the matrix, which negatively impacts the mechanics of
 composites. To study the impact of particle compatibility in polymer
 matrices on the mechanical properties of composites, we here study
 composite silica- protein based hydrogels. The polymer used is a
 previously studied telechelic protein-based polymer with end groups that
 form triple helices, and the particles are silica nanoparticles that only
 weakly associate with the polymer matrix. At 1mM protein polymer, up to 7%
 of silica nanoparticles can be embedded in the hydrogel. At higher
 concentrations the system phase separates. Oscillatory rheology shows that
 at high frequencies the particles strengthen the gels by acting as
 short-lived multivalent cross-links, while at low frequencies, the
 particles reduce the gel strength, presumably by sequestering part of the
 protein polymers in such a way that they can no longer contribute to the
 network strength. As is generally observed for polymer/particle
 composites, shear-induced polymer desorption from the particles leads to a
 viscous dissipation that strongly increases with increasing particle
 concentration. While linear rheological properties as function of particle
 concentration provide no signals for an approaching phase separation, this
 is very different for the non-linear rheology, especially fracture.
 Strain-at-break decreases rapidly with increasing particle concentration
 and vanishes as the phase boundary is approached, suggesting that the
 interfaces between regions of high and low particle densities in
 composites close to phase separation provide easy fracture planes.
description: Complete data set
 accompanying manuscriptComplete data set
 including cryo-SEM, turbidity, rheology and dynamic light scattering data
 and scripts in open standard data formats.Dryad-repo.zip
DOI: 10.5061/dryad.s0b80
title: Data from: Integrating multiple technologies to understand the foraging behaviour of Hawaiian monk seals

description: The objective of this research was to investigate and describe the
 foraging behaviour of monk seals in the main Hawaiian Islands.
 Specifically, our goal was to identify a metric to classify foraging
 behaviour from telemetry instruments. We deployed accelerometers,
 seal-mounted cameras and GPS tags on six monk seals during 2012–2014 on
 the islands of Molokai, Kauai and Oahu. We used pitch, calculated from the
 accelerometer, to identify search events and thus classify foraging dives.
 A search event and consequent ‘foraging dive’ occurred when the pitch was
 greater than or equal to 70° at a depth less than or equal to −3 m. By
 integrating data from the accelerometers with video and GPS, we were able
 to ground-truth this classification method and identify environmental
 variables associated with each foraging dive. We used Bayesian logistic
 regression to identify the variables that influenced search events. Dive
 depth, body motion (mean overall dynamic body acceleration during the
 dive) and proximity to the sea floor were the best predictors of search
 events for these seals. Search events typically occurred on long, deep
 dives, with more time spent at the bottom (more than 50% bottom time). We
 can now identify where monk seals are foraging in the main Hawaiian
 Islands (MHI) and what covariates influence foraging behaviour in this
 region. This increased understanding will inform management strategies and
 supplement outreach and recovery efforts.
description: Open Tag data for
 Hawaiian monk sealsAccelerometer data
 collected from Open Tags (Loggerhead Instruments) in the main Hawaiian
 Islands. Seals were instrumented on the islands of Molokai, Kauai, and
 Oahu.HMS_openTag.csvMovement and Corresponding Environmental Data for monk seal divesAccelerometer data, per dive, collected for Hawaiian monk seals in the main Hawaiian Islands. A GPS location for each dive was used to extract environmental data.HMS_openTag&EnvVars.csvAnimation of the pitch metric to identify search events for Hawaiian monk seals in the main Hawaiian IslandsThis is an animation of the Pitch Metric that was used to identify search events for Hawaiian monk seals. The animation shows pitch (bottom figure) for one complete dive with concurrent dive depth (middle) and video footage (top). Video footage shows seal RW02 foraging off the coast of Kauai. The orange line across the pitch figure is our threshold for identifying search events (70 degrees). Time is along the X axis in both figures with depth and pitch on the Y axes, respectively.PitchAnimation.pptx
DOI: 10.5061/dryad.j2718
title: Data from: Positive selection drives faster-Z evolution in silkmoths

description: Genes linked to X or Z chromosomes, which are hemizygous in the
 heterogametic sex, are predicted to evolve at different rates than those
 on autosomes. This “faster-X effect” can arise either as a consequence of
 hemizygosity, which leads to more efficient selection for recessive
 beneficial mutations in the heterogametic sex, or as a consequence of
 reduced effective population size of the hemizygous chromosome, which
 leads to increased fixation of weakly deleterious mutations due to genetic
 drift. Empirical results to date suggest that, while the overall pattern
 across taxa is complicated, systems with male-heterogamy show a faster-X
 effect attributable to more efficient selection, while the faster-Z effect
 in female-heterogametic taxa is attributable to increased drift. To test
 the generality of the faster-Z pattern seen in birds and snakes, we
 sequenced the genome of the Lepidopteran silkmoth Bombyx huttoni. We show
 that silkmoths experience faster-Z evolution, but unlike in birds and
 snakes, the faster-Z effect appears to be attributable to more efficient
 positive selection. These results suggest that female-heterogamy alone is
 unlikely to explain the reduced efficacy of selection on the bird Z
 chromosome. It is likely that many factors, including differences in
 overall effective population size, influence Z chromosome evolution.
description: Bombyx huttoni
 assemblyFinal Bombyx huttoni
 assembly. Fasta format.bhut_final.fasta.gzUnfiltered B. mori alignmentsCompressed tarball containing alignments between each B. mori gene (1st sequence) and the B. huttoni sequence (2nd sequence), the B. mandarina major allele (3rd sequence), and the B. mandarina minor allele (4th sequence). These alignments include all B. mandarina polymorphic sites detected at Q30 or above. Note that these are consensus chromosomes that do not capture phase information among B. mandarina alleles; rather, they simply represent the major and minor allele at each polymorphic site.all.sites.tar.gzMales only B. mori alignmentsCompressed tarball containing alignments between each B. mori gene (1st sequence) and the B. huttoni sequence (2nd sequence), the B. mandarina major allele (3rd sequence), and the B. mandarina minor allele (4th sequence). These alignments include all B. mandarina polymorphic sites detected at Q30 or above after excluding females. B. mori and B. huttoni sequence are identical to the unfiltered alignments.males.only.tar.gzSingletons removed B. mori alignments.Compressed tarball containing alignments between each B. mori gene (1st sequence) and the B. huttoni sequence (2nd sequence), the B. mandarina major allele (3rd sequence), and the B. mandarina minor allele (4th sequence). These alignments include all B. mandarina polymorphic sites detected at Q30 or above after excluding singletons. The B. huttoni and B. mori sequences are identical to the unfiltered alignments.singletons.excluded.tar.gzRaw data for analysisRaw data used for analysis. See readme for column descriptions.gene_statistics.tsv
DOI: 10.5061/dryad.cv270
title: Data from: Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

description: Phylogenetic analyses of trait evolution can provide insight into the
 evolutionary processes that initiate and drive phenotypic diversification.
 However, recent phylogenomic studies have revealed extensive gene
 tree-species tree discordance, which can lead to incorrect inferences of
 trait evolution if only a single species tree is used for analysis. This
 phenomenon—dubbed “hemiplasy”—is particularly important to consider during
 analyses of character evolution in rapidly radiating groups, where
 discordance is widespread. Here we generate whole-transcriptome data for a
 phylogenetic analysis of 14 species in the plant genus Jaltomata (the
 sister clade to Solanum), which has experienced rapid, recent trait
 evolution, including in fruit and nectar color, and flower size and shape.
 Consistent with other radiations, we find evidence for rampant gene tree
 discordance due to incomplete lineage sorting (ILS) and to introgression
 events among the well-supported subclades. Since both ILS and
 introgression increase the probability of hemiplasy, we perform several
 analyses that take discordance into account while identifying genes that
 might contribute to phenotypic evolution. Despite discordance, the history
 of fruit color evolution in Jaltomata can be inferred with high
 confidence, and we find evidence of de novo adaptive evolution at
 individual genes associated with fruit color variation. In contrast,
 hemiplasy appears to strongly affect inferences about floral character
 transitions in Jaltomata, and we identify candidate loci that could arise
 either from multiple lineage-specific substitutions or standing ancestral
 polymorphisms. Our analysis provides a generalizable example of how to
 manage discordance when identifying loci associated with trait evolution
 in a radiating lineage.
description: Jalt_noSolyc_codon.tarThe mvf file used for PhyloGWAS analysis on Jaltomata lineages. Tomato (the outgroup) sequences were not included in this dataset.phylogeny_aln.tarThe gene sequence alignments (codon-forced; FASTA format) used for phylogeny reconstruction, introgression and genetic distance analyses.paml_aln_noCap.tarThe gene sequence alignments (codon-forced; FASTA format) used for PAML branch-site and clade analyses within Jaltomata lineages.paml_aln_wtCap.tarThe gene sequence alignments (codon-forced; FASTA format) used for PAML branch-site on the ancestral branch of Jaltomata lineages with Capsicum as outgroup.variants_v2.mvf.tarThe mvf file used for estimating heterozygous and shared polymorphism sites among Jaltomata lineages. To generate this dataset, reads from each RNA-seq library were mapped to the tomato reference genome and then variants were called.
DOI: 10.5061/dryad.2v462
title: Data from: Extinction as a driver of avian latitudinal diversity gradients

description: The role of historical factors in driving latitudinal diversity gradients
 is poorly understood. Here we used an updated global phylogeny of
 terrestrial birds to test the role of three key historical factors –
 speciation, extinction and dispersal rates – in generating latitudinal
 diversity gradients for eight major clades. We fit a model that allows
 speciation, extinction and dispersal rates to differ, both with latitude
 and between the New and Old World. Our results consistently support
 extinction (all clades had lowest extinction where species richness was
 highest) as a key driver of species richness gradients across each of
 eight major clades. In contrast, speciation and dispersal rates showed no
 consistent latitudinal patterns across replicate bird clades, and thus are
 unlikely to represent general underlying drivers of latitudinal diversity
 gradients.
description: All_birds_MaxCladeCredTreeMaximum Clade Credibility tree (MCC) from 1000 time-calibrated Bayesian posterior phylogenies of all birds evenly sampled from the Bayesian posterior distribution of trees provided by Jetz et al. (2012). Including the large Neotropical family Furnariidae (Derryberry et al. 2011). MCC tree was calculated in TreeAnnotator v 2.1.3 (implemented in BEAST; Heled and Bouckaert 2013) using median node ages.Bayesian_sample_1000_posterior_treesBayesian sample of 1000 posterior phylogenies of all birds evenly sampled from the Bayesian posterior distribution of trees provided by Jetz et al. (2012). Including the large Neotropical family Furnariidae (Derryberry et al. 2011).
DOI: 10.5061/dryad.609g597
title: Data from: Adaptive multi-degree of freedom Brain Computer Interface using online feedback: Towards novel methods and metrics of mutual adaptation between humans and machines for BCI.

description: This paper proposes a novel adaptive online-feedback methodology for Brain
 Computer Interfaces (BCI). The method uses ElectroEncephaloGraphic (EEG)
 signals and combines motor with speech imagery to allow for tasks that
 involve multiple degrees of freedom (DoF). The main approach utilizes the
 covariance matrix descriptor as feature, and the Relevance Vector Machines
 (RVM) classifier. The novel contributions include, (1) a new method to
 select representative data to update the RVM model, and (2) an online
 classifier which is an adaptively-weighted mixture of RVM models to
 account for the users' exploration and exploitation processes during
 the learning phase. Instead of evaluating the subjects' performance
 solely based on the conventional metric of accuracy, we analyze their
 skill's improvement based on 3 other criteria, namely the confusion
 matrix's quality, the separability of the data, and their
 instability. After collecting calibration data for 8 minutes in the first
 run, 8 participants were able to control the system while receiving visual
 feedback in the subsequent runs. We observed significant improvement in
 all subjects, including two of them who fell into the BCI illiteracy
 category. Our proposed BCI system complements the existing approaches in
 several aspects. First, the co-adaptation paradigm not only adapts the
 classifiers, but also allows the users to actively discover their own way
 to use the BCI through their exploration and exploitation processes.
 Furthermore, the auto-calibrating system can be used immediately with a
 minimal calibration time. Finally, this is the first work to combine motor
 and speech imagery in an online feedback experiment to provide multiple
 DoF for BCI control applications.
description: PONE-D-18-20002-dataEEG data from subjects during the speech imagery tasks described in PONE-D-18-20002
DOI: 10.15468/dl.wptaub
title: Occurrence Download

description: A dataset containing 760871 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Canada",
 "Country is Canada"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Tracheophyta [GBIF Backbone Taxonomy])",
 "Country is one of (Canada)",
 "GadmGid is one of (CAN.11_1)"
 ]
 }
 ]
}

 The dataset includes 760871 records from 245 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000350-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.98n8c
title: Data from: Encounter complexes and dimensionality reduction in protein-protein association

description: An outstanding challenge has been to understand the mechanism whereby
 proteins associate. We report here the results of exhaustively sampling
 the conformational space in protein–protein association using a
 physics-based energy function. The agreement between experimental
 intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE
 profiles calculated from the docked structures shows that the method
 captures both specific and non-specific encounter complexes. To explore
 the energy landscape in the vicinity of the native structure, the
 nonlinear manifold describing the relative orientation of two solid bodies
 is projected onto a Euclidean space in which the shape of low energy
 regions is studied by principal component analysis. Results show that the
 energy surface is canyon-like, with a smooth funnel within a two
 dimensional subspace capturing over 75% of the total motion. Thus,
 proteins tend to associate along preferred pathways, similar to sliding of
 a protein along DNA in the process of protein-DNA recognition.
description: Visualisation of
 Encounter LandscapesWe provide videos that
 show the motion of the ligand protein along the PCA directions for all the
 protein complexes mentioned in Table 1. We also provide distributions of
 IRMSD and energy values for these complexesEncounter_Landscape.zip
DOI: 10.5061/dryad.k9h76
title: Data from: Transcriptome sequencing and marker development for four underutilized legumes

description: Premise of the study: Combating threats to food and nutrition security in
 the context of climate change and global population increase is one of the
 highest priorities of major international organizations. Hundreds of
 species are grown on a small scale in some of the most drought/flood-prone
 regions of the world and as such may harbor some of the most
 environmentally tolerant crops (and alleles). Methods and Results: In this
 study, transcriptomes were sequenced, assembled, and annotated for four
 underutilized legume crops. Microsatellite markers were identified in each
 species, as well as a conserved orthologous set of markers for
 cross-family phylogenetics and comparative mapping, which were
 ground-truthed on a panel of diverse legume germplasm. Conclusions: An
 understanding of these underutilized legumes will inform crop selection
 and breeding by allowing the investigation of genetic variation and the
 genetic basis of adaptive traits to be established.
description: Lablab purpureus
 transcriptome assemblyLablab purpureus
 transcriptome assemblyLapuTrinityEd.fastaLathyrus sativus transcriptome assemblyLathyrus sativus transcriptome assemblyLasaTrinityEd.fastaPsophocarpus tetragonolobus transcriptome assemblyPsophocarpus tetragonolobus transcriptome assemblyPsteTrinityEd.fastaVigna subterranea transcriptome assemblyVigna subterranea transcriptome assemblyVisuTrinityEd.fasta
DOI: 10.5061/dryad.760sc
title: Data from: Evidence for a mid-Jurassic adaptive radiation in mammals

description: A series of spectacular discoveries have transformed our understanding of
 Mesozoic mammals in recent years. These finds reveal hitherto-unsuspected
 ecomorphological diversity that suggests that mammals experienced a major
 adaptive radiation during the Middle to Late Jurassic. Patterns of
 mammalian macroevolution must be reinterpreted in light of these new
 discoveries, but only taxonomic diversity and limited aspects of
 morphological disparity have been quantified. We assess rates of
 morphological evolution and temporal patterns of disparity using large
 datasets of discrete characters. Rates of morphological evolution were
 significantly elevated prior to the Late Jurassic, with a pronounced peak
 occurring during the Early to Middle Jurassic. This intense burst of
 phenotypic innovation coincided with a stepwise increase in apparent
 long-term standing diversity and the attainment of maximum disparity,
 supporting a “short-fuse” model of early mammalian diversification. Rates
 then declined sharply, and remained significantly low until the end of the
 Mesozoic, even among therians. This supports the “long-fuse” model of
 diversification in Mesozoic therians. Our findings demonstrate that
 sustained morphological innovation in Triassic stem-group mammals
 culminated in a global adaptive radiation of crown-group members during
 the Early to Middle Jurassic.
description: Analysis R Code and Full
 ResultsR scripts and input data
 for all analyses performed in study, including full output
 files.Dryad Supplementary
 Figures for Close et al. Elevated morphological rates and high disparity
 support a mid-Jurassic adaptive radiation in mammalsDryad supplementary
 figures, including captions.Close_et_al_Current_Biology_Mesozoic_Mammals_BEAST2BEAST 2 XML file for the morphological-clock/tip-dating analysis conducted using the Zhou et al. (2013) Mesozoic mammal matrix.
DOI: 10.15468/dl.edf8u9
title: Occurrence Download

description: A dataset containing 402 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ilyodon furcidens"
 ]
}

 The dataset includes 402 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000396-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7b2s3
title: Data from: No substitute for real data: a cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses

description: The statistical estimation of phylogenies is always associated with
 uncertainty, and accommodating this uncertainty is an important component
 of modern phylogenetic comparative analysis. The birth-death polytomy
 resolver is a method of accounting for phylogenetic uncertainty that
 places missing (unsampled) taxa onto phylogenetic trees, using taxonomic
 information alone. Recent studies of birds and mammals have used this
 approach to generate pseudo-posterior distributions of phylogenetic trees
 that are complete at the species level, even in the absence of genetic
 data for many species. Many researchers have used these distributions of
 phylogenies for downstream evolutionary analyses that involve inferences
 on phenotypic evolution, geography, and community assembly. I demonstrate
 that the use of phylogenies constructed in this fashion is inappropriate
 for many questions involving traits. Because species are placed on trees
 at random with respect to trait values, the birth-death polytomy resolver
 breaks down natural patterns of trait phylogenetic structure. Inferences
 based on these trees are predictably and often drastically biased in a
 direction that depends on the underlying (true) pattern of phylogenetic
 structure in traits. I illustrate the severity of the phenomenon for both
 continuous and discrete traits using examples from a global bird
 phylogeny.
description: rabosky_evolution