cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.58j041n
title: Data from: Rautangaroa, a new genus of feather star (Echinodermata: Crinoidea) from the Oligocene of New Zealand

description: We describe a nearly complete, and thus extremely rare, featherstar
 (Crinoidea, Comatulida) from Oligocene strata of North Otago/South
 Canterbury, New Zealand. A detailed analysis of this specimen, as well as
 newly recovered material and previously described fragmentary remains from
 nearby contemporaneous sedimentary units, in addition to relevant
 historical specimens, lead us to conclude that it cannot be placed in any
 currently established genus. A new genus, Rautangaroa, is proposed to
 accommodate it. This intact specimen of Rautangaroa aotearoa (Eagle,
 2007), new combination, provides rare data on the morphology of arms and
 cirri. It represents the first example of arm autotomy and regeneration in
 a fossil featherstar, and thus has bearing on the importance of predation
 to the evolutionary history of this group.
description: Supplemental Data
 1Methods used in
 generating 3D rendering and μCT scansSupplemental Data
 2Micro-CT slices of
 Rautangaroa aotearoa n. gen. and comb. novSupplemental Data
 33 D
 rendering of Rautangaroa aotearoa n. gen. and comb. nov
DOI: 10.5061/dryad.23vp5
title: Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome

description: We assembled a de novo transcriptome of short-read Illumina RNA-Seq data
 generated from telencephalon and diencephalon tissue samples from the
 Kentish plover, Charadrius alexandrinus. This is a species of considerable
 interest in behavioural ecology for its highly variable mating system and
 parental behaviour, but it lacks genomic resources and is evolutionarily
 distant from the few available avian draft genome sequences. We assembled
 and identified over 21 000 transcript contigs with significant expression
 in our samples, showing high homology to exonic sequences in avian draft
 genomes. From these, we identified &gt;31 000 high-quality SNPs and
 &gt; 2500 simple sequence repeats (SSRs). We also analysed expression
 patterns in our data to identify potential candidate genes related to
 differences in male and female behaviour, identifying over 200
 nonoverlapping putative autosomal transcripts that show significant
 expression differences between males and females. Gene ontology analysis
 revealed that female-biased transcripts were significantly enriched for
 cerebral functions related to learning, cognition and memory, and
 male-biased transcripts were mostly enriched for terms related to neural
 function such as neuron projection and synapses. This data set provides
 one of the first de novo transcriptome assemblies from non-normalized
 short-read next-generation data and outlines an effective strategy for
 measuring sequence and expression variability simultaneously without the
 aid of a reference genome.
description: READMEShorebird_Full_cDNA_Assembly.fastaThis file holds all transcript assemblies generated through the trinity package (version 2012-01-25) (Grabherr et al. 2011) in fasta format.Shorebird_Count_Data_DESeq.txtThis file holds the count data for all the transcripts with putative "avian origins" i.e., those contigs that have a 1:1 ortholog within the genomes of chicken and/or zebra finch. Differential gene expression was conducted using the R Bioconductor package, DESeq (version 10.1.1) (Anders & Huber 2010).Putative_Autosomal_SNPContains the VCF files for all the putative autosomal SNPs.Putative_Z_SNPContains the VCF files for all the putative Z-linked SNPs.Putative_Autosoma_SSRContains the SSR information for all the putative autosomal transcripts.Putative_Z_SSRContains the SSR information for all the putative Z-linked transcripts.
DOI: 10.5061/dryad.n77k3
title: Data from: First direct measurements of behavioural responses by Cuvier’s beaked whales to mid-frequency active sonar

description: Most marine mammal strandings coincident with naval sonar exercises have
 involved Cuvier’s beaked whales (Ziphius cavirostris). We recorded
 acoustic and animal movement data on two tagged Ziphius and obtained the
 first direct measurements of behavioural responses of this species to
 mid-frequency active (MFA) sonar signals. Each recording included a
 30-minute playback (one 1.6-s simulated MFA sonar signal repeated every 25
 s); one whale was also incidentally exposed to MFA sonar from distant
 naval exercises. Whales responded strongly to playbacks at low received
 levels (89-127 dB re1µPa): after ceasing normal fluking and echolocation,
 they swam rapidly, silently away, extending both dive duration and
 subsequent non-foraging interval. Distant sonar exercises (78-106 dB re 1
 µPa) did not elicit such responses, suggesting that context may moderate
 reactions. The observed responses to playback occurred at received levels
 well below current regulatory thresholds; equivalent responses to
 operational sonars could elevate stranding risk and reduce foraging
 efficiency.
description: Dive parameter data used
 in statistical analysisDive parameters for
 Ziphius cavirostris, calculated from DTAG data collected in the field.
 Further details of the experimental methods and data processing are
 included in the manuscript and electronic supplemental material.
 Abbreviations: max, maximum; m, meters; sec, seconds; h, hours; Hz, Hertz;
 id, identification code.ZcDiveData_noNaN.txtDTAG non-acoustic sensor data from 2010 (whale ID zc10_272a)zc10_272a.txtDTAG non-acoustic sensor data from 2011 (whale ID zc11_267a)zc11_267a.txtMFA sonar received levelsReceived levels (RLs) of mid-frequency active sonar sounds from controlled exposure experiments and incidental exposure to U.S. Naval exercises. Levels were measured using recordings obtained by tagging Cuvier's beaked whales (Ziphius cavirostris) with DTAGs, digital archival tags that record acoustic data and animal movement data. RLs are reported in dB re 1 uPa rms, measured in a 1/3 octave band centered on the signal frequency; reported levels are the highest in any one 200 msec window over the duration of the recorded signal.ZcRLs.txt
DOI: 10.5061/dryad.4kn05
title: Data from: Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

description: We assessed spatio-temporal patterns of diversity in deep-sea sediment
 communities using metabarcoding. We chose a recently developed eukaryotic
 marker based on the v7 region of the 18S rRNA gene. Our study was
 performed in a submarine canyon and its adjacent slope in the Northwestern
 Mediterranean Sea, sampled along a depth gradient at two different
 seasons. We found a total of 5,569 molecular operational taxonomic units
 (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans,
 Nematoda, Arthropoda and Annelida were the most diverse. We found a marked
 heterogeneity at all scales, with important differences between layers of
 sediment and significant changes in community composition with zone
 (canyon vs slope), depth, and season. We compared the information obtained
 from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs
 per sample with DNA (ca. 20% and 40% increase, respectively). Both
 datasets showed overall similar spatial trends, but most groups had higher
 MOTU richness with the DNA template, while others, such as nematodes, were
 more diverse in the RNA dataset. We provide metabarcoding protocols and
 guidelines for biomonitoring of these key communities in order to generate
 information applicable to management efforts.
description: MOTUdatasetThis excel file presents filtered data found in the samples with the 18S_allshorts primers. It contains the number of occurrences of each MOTU in the different samples, as well as different columns related to the taxonomic identification of the MOTUs and the representative sequences of themassembled sequencesFasta file containing the raw assembled sequences (singletons eliminated). For each sequence the codes of the samples where the sequence has been found are indicated, as well as the number of reads in each, the total counts of the sequence, and the sequence lengthassembled seqs.fastacode equivalencesThis excel file provides the equivalences of sample codes between the file MOTUdataset.xlsx and the file assembled seqs.fastacodes.xlsx
DOI: 10.5061/dryad.45sg0
title: Data from: Locking of correlated neural activity to ongoing oscillations

description: Population-wide oscillations are ubiquitously observed in mesoscopic
 signals of cortical activity. In these network states a global oscillatory
 cycle modulates the propensity of neurons to fire. Synchronous activation
 of neurons has been hypothesized to be a separate channel of signal
 processing information in the brain. A salient question is therefore if
 and how oscillations interact with spike synchrony and in how far these
 channels can be considered separate. Experiments indeed showed that
 correlated spiking co-modulates with the static firing rate and is also
 tightly locked to the phase of beta-oscillations. While the dependence of
 correlations on the mean rate is well understood in feed-forward networks,
 it remains unclear why and by which mechanisms correlations tightly lock
 to an oscillatory cycle. We here demonstrate that such correlated
 activation of pairs of neurons is qualitatively explained by
 periodically-driven random networks. We identify the mechanisms by which
 covariances depend on a driving periodic stimulus. Mean-field theory
 combined with linear response theory yields closed-form expressions for
 the cyclostationary mean activities and pairwise zero-time-lag covariances
 of binary recurrent random networks. Two distinct mechanisms cause
 time-dependent covariances: the modulation of the susceptibility of single
 neurons (via the external input and network feedback) and the time-varying
 variances of single unit activities. For some parameters, the effectively
 inhibitory recurrent feedback leads to resonant covariances even if mean
 activities show non-resonant behavior. Our analytical results open the
 question of time-modulated synchronous activity to a quantitative
 analysis.
description: data_manuscript.tarpy_manuscript_dryad_version.tarContains the python files that produce all figures in the manuscript and the python files on which these files depend.
DOI: 10.5061/dryad.8h646s0
title: Data from: Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

description: The earliest developmental origins of dysmorphologies are poorly
 understood in many congenital diseases. They often remain elusive because
 the first signs of genetic misregulation may initiate as subtle changes in
 gene expression, which are hard to detect and can be obscured later in
 development by secondary effects. Here, we develop a method to trace the
 origins of phenotypic abnormalities by accurately quantifying the 3D
 spatial distribution of gene expression domains in developing organs. By
 applying geometric morphometrics to 3D gene expression data obtained by
 Optical Projection Tomography, we determined that our approach is
 sensitive enough to find regulatory abnormalities that have never been
 detected previously. We identified subtle but significant differences in
 the gene expression of a downstream target of the Fgfr2 mutation that were
 associated with Apert syndrome, demonstrating that these mouse models can
 further our understanding of limb defects in the human condition. Our
 method can be applied to different organ systems and models to investigate
 the etiology of malformations.
description: Reconstructions of
 embryonic limbs and Dusp6 gene expression domains from OPT scans of Apert
 syndrome mouse models.This zip folder contains
 the surface files (.stl) of the limbs and the Dusp6 gene expression
 domains obtained from OPT scanning mouse embryos of Apert syndrome mouse
 models at E10.5 and E11.5. Surface files are grouped into forelimbs and
 hindlimbs of Early, Mid and Late developmental periods as specified in
 Table 2.Source data_Martínez-Abadías et
 al 2018.zip
DOI: 10.5061/dryad.gk1qk
title: Data from: Transcriptome dynamics over a lunar month in a broadcast spawning Acroporid coral

description: On one night per year, at a specific point in the lunar cycle, one of the
 most extraordinary reproductive events on the planet unfolds as hundreds
 of millions of broadcast spawning corals release their trillions of
 gametes into the waters of the tropical seas. Each species spawns on a
 specific night within the lunar cycle, typically from full moon to third
 quarter moon, and in a specific time window after sunset. This accuracy is
 essential to achieve efficient fertilization in the vastness of the
 oceans. In this report we use transcriptome sequencing at noon and
 midnight across an entire lunar cycle to explore how Acroporid corals
 interpret lunar signals. The data were interrogated by both time of day
 dependent and independent methods to identify different types of lunar
 cycles. Time of day methods found that genes associated with biological
 clocks and circadian processes change their diurnal cycles over the course
 of a synodic lunar cycle. Some genes have large differences between day
 and night at some lunar phases, but little or no diurnal differences at
 other phases. Many clock genes display an oscillation pattern indicative
 of phase shifts linked to the lunar cycle. Time independent methods found
 that signal transduction, protein secretion and modification, cell cycle
 and ion transport change over the lunar time scale, and peak at various
 phases of the moon. Together these data provide unique insights into how
 the moon impinges on coral transcription cycles how lunar light may
 regulate circalunar timing systems and coral biology.
description: Table mapping
 transcriptome sequence to isogroup IDThis file maps the A.
 millepora sequence name to the isogroup number and also includes the
 sequence. Generated by Matz lab.transcriptome_seq2iso.tabamil.fastaThe A. millepora transcriptome used for alignments in this study. This is based on the transcriptome of Moya et al. (PMID 22490231) modified by the Matz lab.NormalizedCount-lab-labelsNormalized read counts generated by DESeq2 LRT analysisLRT_Updated GO annotationsUpdated GO annotations for the 55 genes identified via LRTLRT_B2G.txtGLM new GO annotationsBlast2GO updates of annotations for DE genes detected by GLMGLM new annotations.txtsalmon_count_tableRead count table from Salmon light-weight alignment
DOI: 10.5061/dryad.29gb5
title: Data from: Why pair? Evidence of aggregative mating in a socially monogamous marine fish (Siganus doliatus, Siganidae)

description: Many species live in stable pairs, usually to breed and raise offspring
 together, but this cannot be assumed. Establishing whether pairing is
 based on mating, or an alternative cooperative advantage, can be
 difficult, especially where species show no obvious sexual dimorphism and
 where the act of reproduction itself is difficult to observe. In the
 tropical marine fishes known as rabbitfish (Siganidae), half of extant
 species live in socially monogamous, territorial pairs. It has been
 assumed that partnerships are for mating, but the reproductive mode of
 pairing rabbitfish is currently unconfirmed. Using passive acoustic
 telemetry to track movements of fishes belonging to one such species
 (Siganus doliatus), we provide the first evidence that paired adult fish
 undertake highly synchronized migrations with multiple conspecifics on a
 monthly cycle. All tagged individuals migrated along the same route in
 three consecutive months and were absent from home territories for 2–3
 days just after the new moon. The timing and directionality of migrations
 suggest that S. doliatus may form spawning aggregations, offering the
 potential for exposure to multiple reproductive partners. The finding
 raises fundamental questions about the basis of pairing, mate choice and
 partnership longevity in this family.
description: Fox et al_Evidence of
 aggregative mating in a socially monogamous marine fish Siganus
 doliatusDetection sequences
 recorded on acoustic receivers for 8 individuals of the species Siganus
 doliatus at Pioneer Bay, Orpheus Island, Australia
DOI: 10.5061/dryad.553t5
title: Data from: Does 1,8-Diiodooctane affect the aggregation state of PC71BM in solution?

description: 1,8-Diiodooctane (DIO) is an additive used in the processing of organic
 photovoltaics and has previously been reported, on the basis of
 small-angle X-ray scattering (SAXS) measurements, to deflocculate
 nano-aggregates of [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) in
 chlorobenzene. We have critically re-examined this finding in a series of
 scattering measurements using both X-rays and neutrons. With SAXS, we find
 that the form of the background solvent scattering is influenced by the
 presence of DIO, that there is substantial attenuation of the X-rays by
 the background solvent and that there appears to be beam-induced
 aggregation. All three factors call into question the suitability of SAXS
 for measurements on these samples. By contrast, SANS measurements,
 performed at concentrations of 15 mg ml21 up to and including 40 mg ml21,
 show no difference in the aggregation state for PC71BM in chlorobenzene
 with and without 3% DIO; we find PC71BM to be molecularly dissolved in all
 solvent cases. In situ film thinning measurements of spin- coated PC71BM
 solution with the DIO additive dry much slower. Optical imaging shows that
 the fullerene films possess enhanced molecular mobility in the presence of
 DIO and it is this which, we conclude, improves the nanomorphology and
 consequently solar cell performance. We propose that any compatible high
 boiling solvent would be expected to show the same behaviour.
description: Spin coated ellipsometry
 thickness measurementsThese are ellipsometry
 thickness measurements for the spin coated films after they were spin
 coated for the PC71BM fullerene thin films after spin
 coatingSpin
 coated PC71BM fullerene ellipsometry
 data.xlsxOptical microscopy
 dewetted imagesOptical images of the
 PC71BM fullerene films processed with 3 % (v/v) DIO. The folder contains
 an image of the graticule used where 1 teil is 0.01 mm.SAXS
 dataSaxs data scaled by
 transmission but not thickness. The optical images of the capillaries are
 included for each capillary. The log book detailing which run is which
 capillarySANS_2Log book with file
 designations and descriptions. Mask file, empty cell, empty beam and
 sample measurementsIn situ spin
 coatingIn situ spin coating
 measurements, intensity change as a function of time along with the
 thickness change as a function of timrHigh q (0.8 m SAXS data
 and SasView Guinier fits)This contains the high q
 SAXS taken at at 0.8 m along with the sample designation. The extracted
 data from the Lou et al paper is also included. Fits to all four of the
 SAXS data using SasView 4.1high q SAXS data and
 fitting.zipSANS measurement of
 PC71BM in carbon disulfideSANS measurements taken
 on the instrument Loq, with the same concentration of 15 mg/ml in the
 solvent carbon disulfide.SANS PC71BM
 cd.zip
DOI: 10.5061/dryad.30374
title: Data from: Rapid postglacial diversification and long-term stasis within the songbird genus Junco: phylogeographic and phylogenomic evidence

description: Natural systems composed of closely-related taxa that vary in the degree
 of phenotypic divergence and geographic isolation, provide an opportunity
 to investigate the rate of phenotypic diversification and the relative
 roles of selection and drift in driving lineage formation. The genus Junco
 (Aves: Emberizidae) of North America includes parapatric northern forms
 that are markedly divergent in plumage pattern and color, in contrast to
 geographically isolated southern populations in remote areas that show
 moderate phenotypic divergence. Here, we quantify patterns of phenotypic
 divergence in morphology and plumage color, and use mitochondrial DNA
 genes, a nuclear intron, and genome-wide SNPs to reconstruct the
 demographic and evolutionary history of the genus to infer relative rates
 of evolutionary divergence among lineages. We found that geographically
 isolated populations have evolved independently for hundreds of thousands
 of years despite little differentiation in phenotype, in sharp contrast to
 phenotypically diverse northern forms, which have diversified within the
 last few thousand years as a result of the rapid postglacial
 recolonization of North America. SNP data resolved young northern lineages
 into reciprocally monophyletic lineages, indicating low rates of gene flow
 even among closely related parapatric forms, and suggesting a role for
 strong genetic drift or multifarious selection acting on multiple loci in
 driving lineage divergence. Juncos represent a compelling example of
 speciation-in-action, where the combined effects of historical and
 selective factors have produced one of the fastest cases of speciation
 known in vertebrates.
description: 2016_06_27
 MalesSpecMorph_museumColorimetric Spectra and
 Morphological variable measures per museum skin, males.SNP calls output from
 the GBS Bioinformatics pipelineSNP calls in HapMap
 format with basic filtering on missingness and allele frequency for 95
 Junco samples, generated by the Cornell University’s Institute for Genomic
 Diversity (IGD).c1.snpmerged.filtered.hmp
DOI: 10.5061/dryad.4950k
title: Data from: Cavin-3 dictates the balance between ERK and Akt signaling

description: Cavin-3 is a tumor suppressor protein of unknown function. Using a
 combination of in vivo knockout and in vitro gain/loss of function
 approaches, we show that cavin-3 dictates the balance between ERK and Akt
 signaling. Loss of cavin-3 increases Akt signaling at the expense of ERK,
 while gain of cavin-3 increases ERK signaling at the expense Akt. Cavin-3
 facilitates signal transduction to ERK by anchoring caveolae, a lipid-raft
 specialization that contains an ERK activation module, to the membrane
 skeleton of the plasma membrane. Loss of cavin-3 reduces the number of
 caveolae, thereby separating this ERK activation module from signaling
 receptors. Loss of cavin-3 promotes Akt signaling through suppression of
 EGR1 and PTEN. The in vitro consequences of the loss of cavin-3 include
 induction of Warburg metabolism (aerobic glycolysis), accelerated cell
 proliferation and resistance to apoptosis. The in vivo consequences of
 cavin-3 loss are increased lactate production and cachexia.
description: Table
 S1Tabulated microarray
 data in means +/- standard deviation, n = 3.TableS1.xlsxTable S2Ratios of experimental vs control microarray data in means +/- standard deviations, n = 3.TableS2.xlsx