cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r720b
title: Data from: The effects of temporal and spatial predictions on stretch reflexes of ankle flexor and extensor muscles while standing

description: The purpose of the present study was to investigate how stretch reflex
 (SR) responses in the ankle extensor (soleus: SOL) and flexor (tibialis
 anterior: TA) muscles would be modulated with temporal and/or spatial
 predictions of external perturbations and whether their effects are
 specific to the standing posture. SR responses in the SOL/TA were elicited
 by imposing quick ankle toes-up/toes-down rotations while standing upright
 and in the supine position. We designed four experimental conditions based
 on pre-information about perturbations: no information (No Cue), the
 timing of the perturbation onset (TIM), the direction of the perturbation
 (DIR), and both the timing and direction of the perturbation (TIM/DIR).
 Each condition was separated and its order was counterbalanced. In the SR
 of TA evoked by toes-down rotation, integrated electromyography activities
 of the late component were significantly reduced in the TIM and TIM/DIR
 conditions as compared with those in the No Cue and DIR conditions. The
 occurrence rate of late SR components that reflects how often the reflex
 response was observed was also lower in the TIM and TIM/DIR conditions as
 compared with that in the No Cue and DIR conditions. On the other hand, no
 significant changes were seen among the four conditions in the early SR
 component in the TA and both SR components in the SOL. The same results in
 the occurrence rate were found in the supine position. The present results
 suggest (1) only temporal predictions have a remarkable effect on the SR
 excitability of the TA, and (2) this effect is independent of posture.
description: Exp1_Kinematics_DataJoint angles of lower limb for 7 subjects in Experiment 1Exp1_Kinematics.zipExp1_Angle_Torque_EMG_DataFootplate angle, foolplate torque and EMG dataExp2_Angle_Torque_EMG_DataFootplate angle, footplate torque and EMG data
DOI: 10.5061/dryad.69fc0
title: Data from: Including fossils in phylogenetic climate reconstructions: a deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)

description: Fossils and other paleontological information can improve phylogenetic
 comparative method estimates of phenotypic evolution and generate
 hypotheses related to species diversification. Here, we use fossil
 information to calibrate ancestral reconstructions of suitable climate for
 Sceloporus lizards in North America. Integrating data from the fossil
 record, general circulation models of paleoclimate during the Miocene,
 climate envelope modeling, and phylogenetic comparative methods provides a
 geographically and temporally explicit species distribution model of
 Sceloporus-suitable habitat through time. We provide evidence to support
 the historic biogeographic hypothesis of Sceloporus diversification in
 warm North American deserts and suggest a relatively recent Sceloporus
 invasion into Mexico around 6 Ma. We use a physiological model to map
 extinction risk. We suggest that the number of hours of restriction to a
 thermal refuge limited Sceloporus from inhabiting Mexico until the climate
 cooled enough to provide suitable habitat at approximately 6 Ma. If the
 future climate returns to the hotter climates of the past, Mexico, the
 place of highest modern Sceloporus richness, will no longer provide
 suitable habitats for Sceloporus to survive and reproduce.
description: ppgmThis is a snapshot of
 the ppgm repository that is available on github. It contains code and data
 to run the analyses in the linked paper. Please see
 https://github.com/michellelawing/ppgm for the most up to date version of
 ppgm.DESCRIPTION
DOI: 10.5061/dryad.nf578
title: Data from: Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA

description: Preserving biodiversity is a global challenge requiring data on species’
 distribution and abundance over large geographic and temporal scales.
 However, traditional methods to survey mobile species’ distribution and
 abundance in marine environments are often inefficient, environmentally
 destructive, or resource-intensive. Metabarcoding of environmental DNA
 (eDNA) offers a new means to assess biodiversity and on much larger
 scales, but adoption of this approach for surveying whole animal
 communities in large, dynamic aquatic systems has been slowed by
 significant unknowns surrounding error rates of detection and relevant
 spatial resolution of eDNA surveys. Here, we report the results of a 2.5
 km eDNA transect surveying the vertebrate fauna present along a gradation
 of diverse marine habitats associated with a kelp forest ecosystem. Using
 PCR primers that target the mitochondrial 12S rRNA gene of marine fishes
 and mammals, we generated eDNA sequence data and compared it to
 simultaneous visual dive surveys. We find spatial concordance between
 individual species’ eDNA and visual survey trends, and that eDNA is able
 to distinguish vertebrate community assemblages from habitats separated by
 as little as ~60 m. eDNA reliably detected vertebrates with low
 false-negative error rates (1/12 taxa) when compared to the surveys and
 revealed cryptic species known to occupy the habitats, but overlooked by
 visual methods. This study also presents an explicit accounting of false
 negatives and positives in metabarcoding data, which illustrate the
 influence of gene marker selection, replication, contamination, biases
 impacting eDNA count data, and ecology of target species on eDNA detection
 rates in an open ecosystem.
description: Vert-12S BLAST database
 (nhr file)This is one of three
 data files composing the marine vertebrate 12S mitochondrial BLAST
 database used in this study. This is the header (nhr)
 file.Vert_12S.nhrVert-12S BLAST database (nin file)This is one of three data files composing the marine vertebrate 12S mitochondrial BLAST database used in this study. This is the index (nin) file.Vert_12S.ninVert-12S BLAST database (nsq file)This is one of three data files composing the marine vertebrate 12S mitochondrial BLAST database used in this study. This is the sequence (nsq) file.Vert_12S.nsqTable of taxon counts by sampleThis table lists the number of sequence reads assigned to each taxon by sampling location. The table represents raw output from our bioinformatic pipeline. Secondary data processing steps were performed to generate the final table used for data analysis (see manuscript). The primer tag sequence refers to the unique 6 bp sample identifier at the 5' of the forward and reverse primers.Taxon_count_table_Raw_Hopkins_eDNA2.csv
DOI: 10.15468/dl.gvuk3v
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Doedicurus"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000403-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.31q7p
title: Data from: Recruitment of Pontin/Reptin by E2f1 amplifies E2f transcriptional response during cancer progression

description: Changes in gene expression during tumorigenesis are often considered the
 consequence of de novo mutations occurring in the tumor. An alternative
 possibility is that the transcriptional response of oncogenic
 transcription factors evolves during tumorigenesis. Here, we show that
 aberrant E2f activity, following inactivation of the Rb gene family in a
 mouse model of liver cancer, initially activates a robust gene expression
 program associated with the cell cycle. Slowly accumulating E2f1
 progressively recruits a Pontin/Reptin complex to open the chromatin
 conformation at E2f target genes and amplifies the E2f transcriptional
 response. This mechanism enhances the E2f-mediated transactivation of cell
 cycle genes and initiates the activation of low binding affinity E2f
 target genes that regulate non-cell cycle functions, such as the Warburg
 effect. These data indicate that both the physiological and the oncogenic
 activities of E2f result in distinct transcriptional responses, which
 could be exploited to target E2f oncogenic activity for therapy.
description: Interactome of E2f1 and
 E2f3 in Rb family deficient liver cancerEndogenous E2f1 and E2f3
 were pulled-down from Rb family deficient liver cancer derived cell lines
 (in parallel, an anti HA pull-down was performed as a negative control).
 The resulting fractions were loaded on a polyacrylamide gel and different
 bands were excised to be run on a Mass Spectrometer. The experiment was
 performed independently three times and the associated file is one of the
 three replicates.PV885_Frozen.sf3
DOI: 10.5061/dryad.rb334
title: Data from: Restructuring higher taxonomy using broad-scale phylogenomics: the living Ophiuroidea

description: The power and throughput of next-generation sequencing is instigating a
 major transformation in our understanding of evolution and classification
 of life on our planet. The new trees of life are robust and comprehensive.
 Here we provide a landmark phylogeny of the living ophiuroids and use it
 as the basis for a major revision of the higher classification of this
 class of marine invertebrates. We used an exon-capture system to generate
 a 1484 exon (273 kbp) data-matrix from DNA extracted from
 ethanol-preserved museum samples. We successfully obtained an average of
 90% of our target sequence from 576 species spread across the known
 taxonomic diversity. The topology of the major lineages was robust to
 taxon sampling, exon-sampling, models and methods. However, estimates of
 node age were much less precise, varying by about a quarter of mean age.
 We used a combination of phylogenetic distinctiveness and temporal-banding
 to guide our revision of the family-level classification. Empirically, we
 determined that limiting family crown age to 110 ± 10 Ma (mid Cretaceous)
 selected phylogenetically distinct nodes while minimising disruption to
 the existing taxonomy. The resulting scheme of 32 families and six orders
 considerably expands the number of higher taxa. The families are generally
 longitudinally widespread across the world’s oceans, although 17 are
 largely confined to temperate and equatorial latitudes and six to
 relatively shallow water (less than 1000 m depth).
description: OphiuroidHC_TableS1S1. Table of information on samples, exons and genes.OphiuroidHC_Table S2S2. Calibrations and fossil evidence used to date the molecular phylogeny.OphiuroidHC_576taxa_treesNexus format RAxML tree with bootstrap values, and PLRS version.OphiuroidHC_185taxa_RAxMLtreesOphiuroidHC_185taxa_BEASTtreesOphiuroidHC_576taxa_1484exonNexus format 416 gene, 1484 exon, 272,952 site, 576 taxa data-matrix.OphiuroidHC_S7_revised_classificationSupplementary material S7, Revised classification of the recent Ophiuroidea.OphiuroidHC_FigS3S3. 576 taxa all-sites RAxML phylogeny with bootstrap (BS) support.OphiuroidHC_FigS4S4. 185 taxa all-sites nucleotide RAxML with BS support.OphiuroidHC_FigS5S5. 185 taxa all-sites amino acid RAxML tree with BS support.OphiuroidHC_FigS6S6. 185 taxa ASTRAL species tree, with local posterior probability support.OphiuroidHC_DRYAD_readme_fileWord document with information on constituents of this Dryad packageOphiuroidHC_distribution_summaryExcel file of family latitude, longitude and depth distribution summary histogram values, with ggplot script, used to generate Figure 4.
DOI: 10.5061/dryad.8338565
title: Data from: Sex-biased transcriptomic response of the reproductive axis to stress

description: Stress is a well-known cause of reproductive dysfunction in many species,
 including birds, rodents, and humans, though males and females may respond
 differently. A powerful way to investigate how stress affects re-
 production is by examining its effects on a biological system essential
 for regulating reproduction, the hy- pothalamic-pituitary-gonadal (HPG)
 axis. Often this is done by observing how a stressor affects the amount of
 glucocorticoids, such as cortisol or corticosterone, circulating in the
 blood and their relationship with a handful of known HPG-producing
 reproductive hormones, like testosterone and estradiol. Until now, we have
 lacked a full understanding of how stress affects all genomic activity of
 the HPG axis and how this might differ between the sexes. We leveraged a
 highly replicated and sex-balanced experimental approach to test how male
 and female rock doves (Columba livia) respond to stress at the level of
 their transcriptome. Females exhibit increased genomic responsiveness to
 stress at all levels of their HPG axis as compared to males, and these
 responsive genes are mostly unique to females. Reasons for this may be due
 to fluctuations in the female endocrine environment over the reproductive
 cycle and/or their evolutionary history, including parental investment and
 the potential for maternal effects. Direct links between genome to phenome
 cause and effect cannot be ascertained at this stage; however, the data we
 report provide a vital genomic foundation on which sex-specific
 reproductive dysfunction and adaptation in the face of stress can be
 further experimentally studied, as well as novel gene targets for genetic
 intervention and therapy investigations.
description: RockDove.HPG.v1.1.0Transcriptome Assembly
DOI: 10.5061/dryad.7h853
title: Data from: Ontogeny of the middle-ear air-sinus system in Alligator mississippiensis (Archosauria: Crocodylia)

description: Modern crocodylians, including Alligator mississippiensis, have a greatly
 elaborated system of pneumatic sinuses invading the cranium. These sinuses
 invade nearly all the bones of the chondrocranium and several bony
 elements of the splanchnocranium, but patterns of postnatal paratympanic
 sinus development are poorly understood and documented. Much of
 crocodylomorph—indeed archosaurian—evolution is characterized by the
 evolution of various paratympanic air sinuses, the homologies of which are
 poorly understood due in large part to the fact that individual sinuses
 tend to become confluent in adults, obscuring underlying patterns. This
 study seeks to explore the ontogeny of these sinuses primarily to clarify
 the anatomical relations of the individual sinuses before they become
 confluent and thus to provide the foundation for later studies testing
 hypotheses of homology across extant and extinct Archosauria. Ontogeny was
 assessed using computed tomography in a sample of 13 specimens covering an
 almost 19-fold increase in head size. The paratympanic sinus system
 comprises two major inflations of evaginated pharyngeal epithelium: the
 pharyngotympanic sinus, which communicates with the pharynx via the
 lateral (true) Eustachian tubes and forms the cavum tympanicum proprium,
 and the median pharyngeal sinus, which communicates with the pharynx via
 the median pharyngeal tube. Each of these primary inflations gives rise to
 a number of secondary inflations that further invade the bones of the
 skull. The primary sinuses and secondary diverticula are well developed in
 perinatal individuals of Alligator, but during ontogeny the number and
 relative volumes of the secondary diverticula are reduced. In addition to
 describing the morphological ontogeny of this sinus system, we provide
 some preliminary exploratory analyses of sinus function and allometry,
 rejecting the hypothesis that changes in the volume of the paratympanic
 sinuses are simply an allometric function of braincase volume, but instead
 support the hypothesis that these changes may be a function of the
 acoustic properties of the middle ear.
description: Dufeau-and-Witmer-2015_Alligator_OUVC10606_head_DICOM (1)DICOM formatted CT data of a perinatal alligator head scanned at 45 μm slice thickness.Dufeau-and-Witmer_2015-allometryDataMeasurement data from an ontogenetic series of Alligator used to perform allometric analyses
DOI: 10.5061/dryad.6b183
title: Data from: The diet of Myotis lucifugus across Canada: assessing foraging quality and diet variability

description: Variation in prey resources influences the diet and behaviour of
 predators. When prey become limiting, predators may travel farther to find
 preferred food or adjust to existing local resources. When predators are
 habitat limited, local resource abundance impacts foraging success. We
 analysed the diet of Myotis lucifugus (little brown bats) from Nova Scotia
 (eastern Canada) to the Northwest Territories (north-western Canada). This
 distribution includes extremes of season length and temperature and
 encompasses colonies on rural monoculture farms, and in urban and
 unmodified areas. We recognized nearly 600 distinct species of prey, of
 which ≈30% could be identified using reference sequence libraries. We
 found a higher than expected use of lepidopterans, which comprised a range
 of dietary richness from ≈35% early in the summer to ≈55% by late summer.
 Diptera were the second largest prey group consumed, representing ≈45% of
 dietary diversity early in the summer. We observed extreme local dietary
 variability and variation among seasons and years. Based on the species of
 insects that were consumed, we observed that two locations support prey
 species with extremely low pollution and acidification tolerances,
 suggesting that these are areas without environmental contamination. We
 conclude that there is significant local population variability in little
 brown bat diet that is likely driven by seasonal and geographical changes
 in insect diversity, and that this prey may be a good indicator of
 environment quality.
description: Main Sequence
 DataMOTU_BLASTSupplement - Montmorency ForestSupplement - Aiguebelle_National_ParkDryad Read Me File
DOI: 10.15468/dl.6jprth
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-106.30325 -20.20937,-35.56228 -20.20937,-35.56228 8.07490,-106.30325 8.07490,-106.30325 -20.20937))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hsunycteris pattoni"
 ]
}

 The dataset includes 18 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000401-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h6gfpp
title: Occurrence Download

description: A dataset containing 47859 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-89.1295 14.1828,-88.85029 14.1828,-88.85029 14.5844,-89.1295 14.5844,-89.1295 14.1828))",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 47859 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000402-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d7d71
title: Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

description: The use of whole-genome phylogenetic analysis has revolutionized our
 understanding of the evolution and spread of many important bacterial
 pathogens due to the high resolution view it provides. However, the
 majority of such analyses do not consider the potential role of accessory
 genes when inferring evolutionary trajectories. Moreover, the recently
 discovered importance of the switching of gene regulatory elements
 suggests that an exhaustive analysis, combining information from core and
 accessory genes with regulatory elements could provide unparalleled detail
 of the evolution of a bacterial population. Here we demonstrate this
 principle by applying it to a worldwide multi-host sample of the important
 pathogenic E. coli lineage ST131. Our approach reveals the existence of
 multiple circulating subtypes of the major drug–resistant clade of ST131
 and provides the first ever population level evidence of core genome
 substitutions in gene regulatory regions associated with the acquisition
 and maintenance of different accessory genome elements.
description: ST131GBKCollection of annotated genomes used in the analysis of this study
DOI: 10.5061/dryad.4874jt7
title: Data from: Evolutionary and biogeographical shifts in response to the Late Ordovician mass extinction

description: The Late Ordovician mass extinction was an interval of high extinction
 with inferred low ecological selectivity, resulting in little change in
 community structure after the event. In contrast, the mass extinction may
 have fundamentally changed evolutionary dynamics in the surviving groups.
 We investigated the phylogenetic relationships among strophomenoid
 brachiopods, a diverse brachiopod superfamily that was a primary component
 of Ordovician ecosystems. Four Ordovician families/subfamilies sampled in
 the analysis (Rafinesquinidae, Strophomeninae, Glyptomenidae and
 Furcitellinae) were reconstructed as monophyletic groups, and the base of
 the strophomenoid clade that dominated the Silurian recovery was
 reconstructed as diversifying alongside these families during the Middle
 Ordovician. We time‐calibrated the phylogeny and used geographical
 occurrences to investigate biogeographical changes in the strophomenoids
 through time with the R package BiogeoBEARS. Our results indicate that
 extinction was higher in taxa whose ranges were constrained to tropical or
 subtropical regions. Furthermore, our results suggest important shifts in
 the diversification patterns of these brachiopods after the mass
 extinction. While most of the strophomenoid families survived the Late
 Ordovician event, ecologically abundant taxonomic groups during the
 Ordovician were either driven to extinction, reduced in diversity, or
 slowly died off during the Silurian. The new abundant strophomenoid taxa
 derived from one clade (consisting of Silurian–Devonian groups such as
 Douvillinidae, Strophodontidae and Amphistrophiidae) that diversified
 during the post‐extinction radiation. Our results suggest the selective
 diversification during the Silurian radiation, rather than selective
 extinction in the Late Ordovician, had a greater impact on the
 evolutionary history of strophomenoid brachiopods.
description: Supplemental Info
 2Output for all 10
 replicates from the BiogeoBEARS analyses.Supplemental Info
 1Character matrix,
 character descriptions, and ancestral node reconstructions for the
 analysis.