cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.32b88
title: Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

description: Rapid and inexpensive methods for genomewide single nucleotide
 polymorphism (SNP) discovery and genotyping are urgently needed for
 population management and conservation. In hybridized populations, genomic
 techniques that can identify and genotype thousands of species-diagnostic
 markers would allow precise estimates of population- and individual-level
 admixture as well as identification of ‘super invasive’ alleles, which
 show elevated rates of introgression above the genomewide background
 (likely due to natural selection). Techniques like
 restriction-site-associated DNA (RAD) sequencing can discover and genotype
 large numbers of SNPs, but they have been limited by the length of
 continuous sequence data they produce with Illumina short-read sequencing.
 We present a novel approach, overlapping paired-end RAD sequencing, to
 generate RAD contigs of &gt;300–400 bp. These contigs provide
 sufficient flanking sequence for design of high-throughput SNP genotyping
 arrays and strict filtering to identify duplicate paralogous loci. We
 applied this approach in five populations of native westslope cutthroat
 trout that previously showed varying (low) levels of admixture from
 introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used
 these data to filter and genotype 3180 previously identified
 species-diagnostic SNP loci. Our population-level and individual-level
 estimates of admixture were generally consistent with previous
 microsatellite-based estimates from the same individuals. However, we
 observed slightly lower admixture estimates from genomewide markers, which
 might result from natural selection against certain genome regions,
 different genomic locations for microsatellites vs. RAD-derived SNPs
 and/or sampling error from the small number of microsatellite loci (n =
 7). We also identified candidate adaptive super invasive alleles from RBT
 that had excessively high admixture proportions in hybridized cutthroat
 trout populations.
description: README.txtMetadata describing the contents of all data files.dutch.tar.gzRaw RAD sequencing data in fastq format for Dutch population.lowhay.tar.gzRaw RAD sequencing data in fastq format for Lower Hay population.meadow.tar.gzRaw RAD sequencing data in fastq format for Meadow population.nicola.tar.gzRaw RAD sequencing data in fastq format for Nicola population.tepee.tar.gzRaw RAD sequencing data in fastq format for Tepee population.genotyped_121009.txtGenotyped diagnostic SNPs across 5 westslope cutthroat trout populations.FinalContigs120611.fafasta file of RAD contigs
DOI: 10.5061/dryad.st3gt
title: Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

description: • Studies of the macroevolutionary legacy of polyploidy are limited by an
 incomplete sampling of these events across the tree of life. To better
 locate and understand these events, we need comprehensive taxonomic
 sampling as well as homology inference methods that accurately reconstruct
 the frequency and location of gene duplications. • We assembled a dataset
 of transcriptomes and genomes from 169 species in Caryophyllales, of which
 43 were newly generated for this study, representing one of the densest
 sampled genomic-scale datasets available. We carried out phylogenomic
 analyses using a modified phylome strategy to reconstruct the species
 tree. We mapped phylogenetic distribution of polyploidy events by both
 tree-based and distance-based methods, and explicitly tested scenarios for
 allopolyploidy. • We identified twenty-six ancient and more recent
 polyploidy events distributed throughout Caryophyllales. Two of these
 events were inferred to be allopolyploidy. • Through dense phylogenomic
 sampling, we show the propensity of polyploidy throughout the evolutionary
 history of Caryophyllales. We also provide a framework for utilizing
 transcriptome data to detect allopolyploidy, which is important as it may
 have different macro-evolutionary implications compared to autopolyploidy.
description: 1_cds_genomesCDS from 43 genomes2_pep_genomesPeptides from 43 genomes3_cds_transcriptomeCDS from 87 of the 175 transcriptomes3_cds_transcriptome_continuedCDS from 84 of the 175 transcriptomes4_pep_transcriptomePeptides from 171 of the 175 transcriptomes5_modified_phylomeAnalysis of peptides for the overall Caryophyllales species tree6_subcladesAnalysis of CDS in each of the five subclades
DOI: 10.5061/dryad.t894r
title: Data from: Genetic hitchhiking and the dynamic buildup of genomic divergence during speciation with gene flow

description: A major issue in evolutionary biology is explaining patterns of
 differentiation observed in population genomic data, as divergence can be
 due to both direct selection on a locus and genetic hitchhiking.
 “Divergence hitchhiking” (DH) theory postulates that divergent selection
 on a locus reduces gene flow at physically linked sites, facilitating the
 formation of localized clusters of tightly linked, diverged loci. “Genome
 hitchhiking” (GH) theory emphasizes genome-wide effects of divergent
 selection. Past theoretical investigations of DH and GH focused on static
 snapshots of divergence. Here, we used simulations assessing a variety of
 strengths of selection, migration rates, population sizes, and mutation
 rates to investigate the relative importance of direct selection, GH, and
 DH in facilitating the dynamic buildup of genomic divergence as speciation
 proceeds through time. When divergently selected mutations were limiting,
 GH promoted divergence, but DH had little measurable effect. When
 populations were small and divergently selected mutations were common, DH
 enhanced the accumulation of weakly selected mutations, but this
 contributed little to reproductive isolation. In general, GH promoted
 reproductive isolation by reducing effective migration rates below that
 due to direct selection alone, and was important for genome-wide
 “congealing” or “coupling” of differentiation (FST) across loci as
 speciation progressed.
description: Flaxman_Feder_Nosil_data
DOI: 10.5061/dryad.84c1m
title: Data from: The distribution of cool spots as microrefugia in a mountainous area

description: It has recently been proposed that microrefugia played an important role
 in species survival during past climate change events. However, the
 current distributions of microrefugia remain largely unknown. Wind-hole
 sites are areas affected by preferential flows of cool air generated in
 interstitial spaces created by rock fragments or colluvia. Alpine plant
 species occurring in lowland wind-hole sites isolated from alpine zones
 may be relicts of the last glacial period. Hokkaido, northern Japan, is
 known to contain many wind-hole sites in which alpine plant species can
 occur. Here we surveyed 55 wind-hole sites in the Kitami region, eastern
 Hokkaido, and observed two alpine plant species (lingonberry, Vaccinium
 vitis-idaea, and Labrador tea, Rhododendron groenlandicum ssp.
 diversipilosum var. diversipilosum) in 14 wind-hole sites. Statistical
 modeling showed that wind-hole sites are likely to occur in areas with
 high maximum slope angles and volcanic rock cover, and concave surfaces.
 Our predictions of wind-hole site distributions suggest that such
 topographic conditions are common in our study area, and that many
 undiscovered wind-hole sites exist. Ignoring microhabitats may greatly
 underestimate species distributions in topographically complex regions,
 and dispersed cool spots may also function as stepping stones and temporal
 habitats for cold-adapted species. Because these localized unique habitats
 usually occur in economically unproductive sites, identifying and
 protecting potential microrefugia (cool spots) would be a robust and
 cost-effective mitigation of climate change impacts.
description: Description of uploaded
 data filesfile
 description.docxcsvcurvature
 0-100curvature_0-100.zipcurvature 200-500curvature_200-500.zipgeological variablegeological_variable.zipmaximum slope 0-100maximum_slope_0-100.zipmaximum slope 200-500maximum_slope_200-500.zipmean slope 25-200mean_slope_25-200.zipmean slope 300-500mean_slope_300-500.zip
DOI: 10.15468/dl.2u2puz
title: Occurrence Download

description: A dataset containing 114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Mexico",
 "TaxonKey is Quercus crassifolia",
 "Year 2015-2026"
 ]
}

 The dataset includes 114 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000449-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.202m6h0
title: Data from: Non-rhythmic head-direction cells in the parahippocampal region are not constrained by attractor network dynamics

description: Computational models postulate that HD cells are part of an attractor
 network integrating angular head turns. This network requires inputs from
 visual landmarks to anchor the HD signal to the external world. We
 investigated whether information about HD and visual landmarks is
 integrated in the medial entorhinal cortex and parasubiculum, resulting in
 neurons expressing a conjunctive code for HD and visual landmarks. We
 found that parahippocampal HD cells could be divided into two classes
 based on their theta-rhythmic activity: non-rhythmic and theta-rhythmic HD
 cells. Manipulations of the visual landmarks caused tuning curve
 alterations in most HD cells, with the largest visually driven changes
 observed in non-rhythmic HD cells. Importantly, the tuning modifications
 of non-rhythmic HD cells were often non-coherent across cells, refuting
 the notion that attractor-like dynamics control non-rhythmic HD cells.
 These findings reveal a new population of non-rhythmic HD cells whose
 malleable organization is controlled by visual landmarks.
description: Electrophysiological
 data from Kornienko et al., 2018Data from: Non-rhythmic
 head-direction cells in the parahippocampal region are not constrained by
 attractor network dynamicsdata_kornienko_2018.tar.gz
DOI: 10.5067/asdc/suborbital/staqs/data001/gv/aircraftremotesensing/hsrl2_1
title: STAQS High Spectral Resolution Lidar-2 (HSRL-2) Data
DOI: 10.5067/asdc/suborbital/staqs/data001/gv/aircraftremotesensing/gcas_1
title: STAQS JSC GV GEOstationary Coastal and Air Pollution Events (GEO-CAPE) Airborne Simulator Data
DOI: 10.5061/dryad.t8v2gg7
title: Data from: Endogenous opioids in the nucleus accumbens promote approach to high-fat food in the absence of caloric need

description: When relatively sated, people (and rodents) are still easily tempted to
 consume calorie-dense foods, particularly those containing fat and sugar.
 Consumption of such foods while calorically replete likely contributes to
 obesity. The nucleus accumbens (NAc) opioid system has long been viewed as
 a critical substrate for this behavior, mainly via contributions to the
 neural control of consumption and palatability. Here, we test the
 hypothesis that endogenous NAc opioids also promote appetitive approach to
 calorie-dense food in states of relatively high satiety. We simultaneously
 recorded NAc neuronal firing and infused a μ-opioid receptor antagonist
 into the NAc while rats performed a cued approach task in which appetitive
 and consummatory phases were well separated. The results reveal elements
 of a neural mechanism by which NAc opioids promote approach to high-fat
 food despite the lack of caloric need, demonstrating a potential means by
 which the brain is biased towards overconsumption of palatable food.
description: READMErestricted
 ctaprestricted
 recordingssalinesated
 ctapsated
 recordingsunilateral
 ctap
DOI: 10.5067/suborbital/staqs/data001
title: Synergistic TEMPO Air Quality Science
DOI: 10.5061/dryad.s2743
title: Data from: Sympatric, temporally isolated populations of the pine white butterfly Neophasia menapia, are morphologically and genetically differentiated

description: Temporal isolation remains an understudied, and potentially
 under-appreciated, mechanism of reproductive isolation. Phenological
 differences have been discovered in populations of the pine white
 butterfly (Neophasia menapia), a typically univoltine species found
 throughout western North America. At two locations in the Coast Range of
 California there are two periods of adult emergence per year, one in early
 summer (July) and one in late summer/autumn (September/October).
 Differences in flight time are accompanied by differences in wing shape
 and pigmentation. Here we use a combination of population genomics and
 morphological analyses to assess the extent to which temporal isolation is
 able to limit gene flow between sympatric early and late flights. Not only
 did we detect both genetic and morphological differences between early and
 late flights at the two sites, we also found that the patterns of
 differentiation between the two flights were different at each location,
 suggesting an independent origin for the two sympatric flights.
 Additionally, we found no evidence that these sympatric flights originated
 via colonization from any of the other sampled localities. We discuss
 several potential hypotheses about the origin of these temporally isolated
 sympatric flights.
description: N. menapia DP Fastq
 filesIndividual fastq files
 for Donner Pass sample of N. menapia.ndd_fastq.tar.gzN. terlootii Fastq FilesIndividual fastq files for N. terlootii sampled from Arizonanaz_fastq.tar.gzN. menapia GL Fastq FilesIndividual fastq files for Goat Mountain Late sample of N. menapia.ngf_fastq.tar.gzN. menapia GE Fastq FilesIndividual fastq files for Goat Mountain Early sample of N. menapia.ngj_fastq.tar.gzN. menapia LA Fastq FilesIndividual fastq files for Lang sample of N. menapia.nll_fastq.tar.gzN. menapia ML Fastq filesIndividual fastq files for Mendocino Pass late sample of N. menapia.nmf_fastq.tar.gzN. menapia ME Fastq filesIndividual fastq files for Mendocino Pass early sample of N. menapia.nmj_fastq.tar.gzN. menapia OR fastq filesIndividual fastq files for Oregon sample of N. menapia.noo_fastq.tar.gzN. menapia WO Fastq filesIndividual fastq files for Woodfords sample of N. menapia.nww_fastq.tar.gz
DOI: 10.5061/dryad.7qk36
title: Data from: TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells

description: Change in the identity of the components of the transcription
 pre-initiation complex is proposed to control cell type-specific gene
 expression. Replacement of the canonical TFIID-TBP complex with TRF3/TBP2
 was reported to be required for activation of muscle-gene expression. The
 lack of a developmental phenotype in TBP2 null mice prompted further
 analysis to determine whether TBP2 deficiency can compromise adult
 myogenesis. We show here that TBP2 null mice have an intact regeneration
 potential upon injury and that TBP2 is not expressed in established C2C12
 muscle cell or in primary mouse MuSCs. While TFIID subunits and TBP are
 downregulated during myoblast differentiation, reduced amounts of these
 proteins form a complex that is detectable on promoters of muscle genes
 and is essential for their expression. This evidence demonstrates that
 TBP2 does not replace TBP during muscle differentiation, as previously
 proposed, with limiting amounts of TFIID-TBP being required to promote
 muscle-specific gene expression.
description: IMR90 overexpressing
 MyoD in growth mediumHuman fibroblasts IMR90
 transfected with doxycycline inducible mouse MYOD were cultured in growth
 media (DMEM high glucose, 10% FBS). MYOD was induced with doxycycline
 treatment 24 hrs prior collection.YD18.fastq.bz2IMR90 overexpressing MyoD in growth medium, replicateHuman fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs prior collection.YD21.fastq.bz2IMR90 overexpressing MyoD in differentiation mediumHuman fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (GM, DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs in GM and 72-96 hrs in differentiation media (DM, DMEM high glucose, 2% HS, ITS) prior collection.YD5.fastq.bz2IMR90 overexpressing MyoD in differentiation medium, replicateHuman fibroblasts IMR90 transfected with doxycycline inducible mouse MYOD were cultured in growth media (GM, DMEM high glucose, 10% FBS). MYOD was induced with doxycycline treatment 24 hrs in GM and 72-96 hrs in differentiation media (DM, DMEM high glucose, 2% HS, ITS) prior collection.YD22.fastq.bz2
DOI: 10.5067/asdc/suborbital/staqs/data001/g3/aircraftremotesensing/gcas_1
title: STAQS NASA G-III GEOstationary Coastal and Air Pollution Events (GEO-CAPE) Airborne Simulator Data
DOI: 10.5061/dryad.46cg87c
title: Data from: State-aware detection of sensory stimuli in the cortex of the awake mouse

description: Cortical responses to sensory inputs vary across repeated presentations of
 identical stimuli, but how this trial-to-trial variability impacts
 detection of sensory inputs is not fully understood. Using multi-channel
 local field potential (LFP) recordings in primary somatosensory cortex
 (S1) of the awake mouse, we optimized a data-driven cortical state
 classifier to predict single-trial sensory-evoked responses, based on
 features of the spontaneous, ongoing LFP recorded across cortical layers.
 Our findings show that, by utilizing an ongoing prediction of the sensory
 response generated by this state classifier, an ideal observer improves
 overall detection accuracy and generates robust detection of sensory
 inputs across various states of ongoing cortical activity in the awake
 brain, which could have implications for variability in the performance of
 detection tasks across brain states.
description: analysis_scripts_and_functionsProcessing scripts for state-dependent detection analysis of cortical LFP in awake mouse.code_files.zipcsd_allchannelsevoked responses and pre-stimulus activity across all channels (CSD)csd_dimReduce.ziplfp_dimReduceevoked responses and pre-stimulus activity across all channels (LFP)lfp_cont_l4channels
DOI: 10.5061/dryad.9bc43
title: Data from: Data for evaluation of fast kurtosis imaging, b-value optimization and exploration of diffusion MRI contrast

description: Here we describe and provide diffusion magnetic resonance imaging (dMRI)
 data that was acquired in neural tissue and a physical phantom. Data
 acquired in biological tissue includes: fixed rat brain (acquired at 9.4T)
 and spinal cord (acquired at 16.4T) and in normal human brain (acquired at
 3T). This data was recently used for evaluation of diffusion kurtosis
 imaging (DKI) contrasts and for comparison to diffusion tensor imaging
 (DTI) parameter contrast. The data has also been used to optimize b-values
 for ex vivo and in vivo fast kurtosis imaging. The remaining data was
 obtained in a physical phantom with three orthogonal fiber orientations
 (fresh asparagus stems) for exploration of the kurtosis fractional
 anisotropy. However, the data may have broader interest and, collectively,
 may form the basis for image contrast exploration and simulations based on
 a wide range of dMRI analysis strategies.
description: Diffusion MRI data from
 a physical phantom with three orthogonal fiber directions. Data was
 acquired at 9.4T.This zip file contains
 raw dMRI data in a matlab (.mat) file (phantom_data), corresponding
 b-values (effective_b), gradient table (DWI_encoding_directions), and
 structural scan (structural_data). The data is also included as dicom and
 nifti.Phantom_data.zipDiffusion MRI data from fixed rat brain acquired at 9.4T.The data is provided as nifti files. The data is also provided as a matlab file which contains raw dMRI data (rat_brain_data), corresponding b-values (nominal_bvalues and effective_b, the latter includes b-value contributions from imaging gradients) and gradient table (DWI_encoding_directions_pr_b_value).Rat_brain.zipHigh resolution diffusion MRI data from fixed rat spinal cord acquired at 16.4T.This matlab file contains raw dMRI data (ratSC_DWI_data), corresponding effective b-values (effective_b) and gradient table (DWI_encoding_directions), and masks for all slices (masks). The data is also provided as nifti.Rat_spinal_cord.zipHuman_brainThis matlab file contains raw dMRI data (human_brain_data), corresponding b-values (effective_b), and gradient table (DWI_encoding_directions), and an anatomical scan (T1_anat). The DWI data is also included as dicom and nifti. The anatomical scans are provided as nifti only and were defaced using SPM12.
DOI: 10.5281/zenodo.18370260
title: Source code and input files used in Miller et al, Proceedings of the Royal Society A, 2026

description: Source code and input files used in Miller et al, Proceedings of the Royal Society A, 2026

Article DOI: TBD

Contained within this repository are the MATLAB scripts relating to the calibration of the depth-dependent collagen fibril dispersion parameters and the implementation of the angular integration convergence analysis. Additionally, the executable and input files corresponding to the performed finite element simulations are provided. All other relevant data and source code are available upon request.
DOI: 10.5281/zenodo.18370261
title: Source code and input files used in Miller et al, Proceedings of the Royal Society A, 2026

description: Source code and input files used in Miller et al, Proceedings of the Royal Society A, 2026

Article DOI: TBD

Contained within this repository are the MATLAB scripts relating to the calibration of the depth-dependent collagen fibril dispersion parameters and the implementation of the angular integration convergence analysis. Additionally, the executable and input files corresponding to the performed finite element simulations are provided. All other relevant data and source code are available upon request.
DOI: 10.5067/asdc/suborbital/staqs/data001/g3/aircraftremotesensing/halo_1
title: STAQS NASA G-III High Altitude Lidar Observatory (HALO) Data
DOI: 10.5067/asdc/suborbital/staqs/data001/sondes_1
title: STAQS Balloonsondes and Ozonesondes Data
DOI: 10.5067/asdc/suborbital/staqs/data001/searey_1
title: STAQS SeaRey Data
DOI: 10.5061/dryad.3mt523q
title: Data from: A reciprocal translocation radically reshapes sex-linked inheritance in the common frog

description: X and Y chromosomes can diverge when rearrangements block recombination
 between them. Here we present the first genomic view of a reciprocal
 translocation that causes two physically unconnected pairs of chromosomes
 to be coinherited as sex chromosomes. In a population of the common frog
 (Rana temporaria), both pairs of X and Y chromosomes show extensive
 sequence differentiation, but not degeneration of the Ys. A new method
 based on gene trees shows both chromosomes are sex-linked. Further, the
 gene trees from the two Y chromosomes have identical topologies, showing
 they have been coinherited since the reciprocal translocation occurred.
 Reciprocal translocations can thus reshape sex linkage on a much grander
 scale than do inversions, the type of rearrangement that is much better
 known in sex chromosome evolution, and they can greatly amplify the power
 of sexually antagonistic selection to drive genomic rearrangement. Two
 other populations show evidence of yet other rearrangements, suggesting
 that this species has unprecedented structural polymorphism in its sex
 chromosomes.
description: Rana.RSEM.counts.gonads.matrixUnfiltered.Site.Calls.vcf.gzAmmarnas.Sites.vcfKilpisjarvi.Sites.vcfTvedora.Sites.vcfReadMe.Dryad