cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4p9j3
title: Data from: The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

description: We investigated the genetic architecture of courtship song and cuticular
 hydrocarbon traits in two phygenetically distinct populations of
 Drosophila montana. In order to study natural variation in these two
 important traits, we analysed within-population crosses among individuals
 sampled from the wild. Hence, the genetic variation analysed should
 represent that available for natural and sexual selection to act upon. In
 contrast to previous between-population crosses in this species, no major
 QTLs were detected, perhaps because the between-population QTL were due to
 fixed differences between the populations. Partitioning the trait
 variation to chromosomes suggested a broadly polygenic genetic
 architecture of within population variation, although some chromosomes
 explained more variation in one population compared to the other. Studies
 of natural variation provide an important contrast to crosses between
 species or divergent lines, but our analysis highlights recent concerns
 that segregating variation within populations for important quantitative
 ecological traits may largely consist of small effect alleles, difficult
 to detect with studies of moderate power.
description: Raw 454 reads of
 transcriptomesedinburgh.sff - Oulanka
 reads produced in Genepool in Edinburgh. liverpool.sff &
 RocheLiverpool.sff - Vancouver reads produced by the CGR in Liverpool, the
 former contained less reads than quoted so the library was run again to
 produce the latter file. All files were used for the
 assembly.rawdMontanaReads.zipScripts used to identify and filter the best SNPs.File_S1_SNPdesign.zipQTL analysis dataGenotyping data separated by chromosome, pedigree data and phenotypic (song and CHC) data. 'v' in the filenames stands for Vancouver, 'k' stands for Kuusamo, Oulanka.File_S2_QTLdata.zipassembled TranscriptomeFasta file with first blast hit of the assembled transcriptome, and blast2GO project with the same information.assembledTranscriptome.zip
DOI: 10.5061/dryad.9k9n0
title: Data from: Dye-enhanced visualization of rat whiskers for behavioral studies

description: Visualization and tracking of the facial whiskers is required in an
 increasing number of rodent studies. Though many approaches have been
 employed, only high-speed videography has proven adequate for measuring
 whisker motion and deformation during interaction with an object. However,
 whisker visualization and tracking is challenging for multiple reasons,
 primary among them the low contrast of the whisker against its background.
 Here we demonstrate a fluorescent dye method suitable for visualization of
 one or more rat whiskers. The process makes the dyed whisker(s) easily
 visible against a dark background. The coloring does not influence the
 behavioral performance of rats trained on a vibrissal vibrotactile
 discrimination task, nor does it affect the whiskers’ mechanical
 properties.
description: READMEinstructionselab_video.zipthe whole pre-elaborated dataset (i.e., whisker shape has been extracted from videos through time). to unzip please note that it is needed the whole file list in the same folder of unzipData.sh, where the file list is {elab_video.zip elab_video.z01 elab_video.z03 elab_video.z05 elab_video.z07 elab_video.z02 elab_video.z04 elab_video.z06}elab_video.z01elab_video.z02elab_video.z03elab_video.z04elab_video.z05elab_video.z06elab_video.z07ratto1.zipone video trial shared for a whisker tracking demo, which can produce the data which is shared in elab_video folder. to unzip please note that it is needed the whole file list in the same folder of unzipData.sh, where the file list is {ratto1.zip ratto1.z01}ratto1.z01whisker-dynamic-response.zipsource code to elaborate videos and produce figures. it was cloned from github by "git clone -b shared4paper https://github.com/pgallir/whisker-dynamic-response".camrec450_verFunc.ziplabview project for data acquisition. the folder camrec450_verFunc/stim/ contains the stimulus library that was used as input to the shaker, and the code to generate it.compressData.shcode used to compress and split data to produce this shared dataset.unzipData.shcode to merge data parts and decompress from this shared dataset back to folders.supplementaryimages to produce supplementary figures are in folders: colorationprocess; photobleaching. updated code: updated-whisker-dynamic-response
DOI: 10.5061/dryad.vb654
title: Data from: How social network structure affects decision-making in Drosophila melanogaster

description: Animals use a number of different mechanisms to acquire crucial
 information. During social encounters animals can pass information from
 one to another but, ideally, they would only use information that benefits
 survival and reproduction. Therefore, individuals need to be able to
 determine the value of the information they receive. One cue can come from
 the behaviour of other individuals that are already using the information.
 Here we study how individual decision-making is influenced by the
 behaviour of conspecifics in Drosophila melanogaster. We analysed how
 uninformed flies acquire and later use information about oviposition site
 choice they learn from informed flies. Interestingly, after social
 interaction, uninformed flies tended either to collectively follow the
 choice of the informed flies or to avoid it. Using social network
 analysis, we show that this discriminating decision-making process seems
 to be based on the level of homogeneity of the social network. Uninformed
 flies were not influenced by how frequently they observed a behaviour in
 informed peers; rather, they chose to follow the information they acquired
 from informed flies that exhibited the behaviour consistently. More
 generally, further examination of a previous extended dataset confirmed
 the evidence that the information informed individuals transmit through
 their behaviour can either encourage or discourage specific oviposition
 site preference in uninformed peers, and we demonstrate the main role of
 social network structure on the learning process.
description: Flies'
 positionsThis .zip file contains
 10 positions per second for each fly collected during 62 experiments
 lasting 4 hours each one.Pasquaretta_PRSB_2016.zip
DOI: 10.5061/dryad.5p0c3
title: Data from: A first look at the Oxford Nanopore MinION sequencer

description: Oxford Nanopore's third-generation, single-molecule sequencing
 platform promises to decrease costs for reagents and instrumentation.
 After a two-year hiatus following the initial announcement, the first
 devices have been released as part of an early access program. We explore
 the performance of this platform by re-sequencing the lambda phage genome,
 and amplicons from a snake venom gland transcriptome. Although the
 handheld MinION sequencer can generate more than 150 megabases of raw data
 in one run, at most a quarter of the resulting reads map to the reference,
 with less than average 10% identity. Much of the sequence consists of
 insertion/deletion errors, or is seemingly without similarity to the
 template. Using the lambda phage data as an example, although the reads
 are long, averaging 5kb, at best 890±1,932 bases per mapped read could be
 matched to the reference without soft clipping. In the course of a 36 hour
 run on the MinION it was possible to re-sequence the 48kb lambda phage
 reference at 16x coverage. Currently substantially larger projects would
 not be feasible using the MinION. Without increases in accuracy, which
 would be required for applications such as genome scaffolding and phasing,
 the current utility of the MinION appears limited. Library preparation
 requires access to a molecular lab, and is of similar complexity and cost
 to that of other next-generation sequencing platforms. The MinION is an
 exciting step in a new direction for single-molecule sequencing, though it
 will require dramatic decreases in error rates before it lives up to its
 promise.
description: Raw
 readsLambda phage reads
 processed with the 1D and 2D workflows.reads.tar.gzReads for snake transcriptome dataReads for venom gland transcriptome of Protobothrops flavoviridis.snake.tar.gzprocessed_data.tar.gzThis file contains all the analysis files except raw Illumina data (available as a separate file) and raw Oxford Nanopore read in FAST5 format. As FAST5 files require Oxford Nanopore's proprietary software to analyze and are large (~30G compressed), they are probably not useful to most readers, but are available from the authors upon request.Illumina forward reads for the Protobothrops flavoviridis transcriptomeFrom: Aird, S.D. et al., 2013. Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis). BMC Genomics, 14(1), p.790.GGCTAC_pe1.fq.gzIllumina reverse reads for the Protobothrops flavoviridis transcriptomeFrom: Aird, S.D. et al., 2013. Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis). BMC Genomics, 14(1), p.790.GGCTAC_pe2.fq.gz
DOI: 10.15468/dl.zrsbw3
title: Occurrence Download

description: A dataset containing 1104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Coccus viridis)"
 ]
}

 The dataset includes 1104 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000705-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kv920
title: Data from: No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions

description: Mechanisms that suppress recombination are known to help maintain species
 barriers by preventing the breakup of coadapted gene combinations. The
 sympatric butterfly species Heliconius melpomene and Heliconius cydno are
 separated by many strong barriers, but the species still hybridize
 infrequently in the wild, and around 40% of the genome is influenced by
 introgression. We tested the hypothesis that genetic barriers between the
 species are maintained by inversions or other mechanisms that reduce
 between-species recombination rate. We constructed fine-scale
 recombination maps for Panamanian populations of both species and their
 hybrids to directly measure recombination rate within and between species,
 and generated long sequence reads to detect inversions. We find no
 evidence for a systematic reduction in recombination rates in F1 hybrids,
 and also no evidence for inversions longer than 50 kb that might be
 involved in generating or maintaining species barriers. This suggests that
 mechanisms leading to global or local reduction in recombination do not
 play a significant role in the maintenance of species barriers between H.
 melpomene and H. cydno.
description: heliconius_speciation_inversions_dryad_repository.tarThis archive contains all code and data files required to replicate the analyses in this manuscript.
DOI: 10.5061/dryad.nq4fs
title: Data from: Contributions of subsurface cortical modulations to discrimination of executed and imagined grasp forces through stereoelectroencephalography

description: Stereoelectroencephalographic (SEEG) depth electrodes have the potential
 to record neural activity from deep brain structures not easily reached
 with other intracranial recording technologies. SEEG electrodes were
 placed through deep cortical structures including central sulcus and
 insular cortex. In order to observe changes in frequency band modulation,
 participants performed force matching trials at three distinct force
 levels using two different grasp configurations: a power grasp and a
 lateral pinch. Signals from these deeper structures were found to contain
 information useful for distinguishing force from rest trials as well as
 different force levels in some participants. High frequency components
 along with alpha and beta bands recorded from electrodes located near the
 primary motor cortex wall of central sulcus and electrodes passing through
 sensory cortex were found to be the most useful for classification of
 force versus rest although one participant did have significant modulation
 in the insular cortex. This study electrophysiologically corroborates with
 previous imaging studies that show force-related modulation occurs inside
 of central sulcus and insular cortex. The results of this work suggest
 that depth electrodes could be useful tools for investigating the
 functions of deeper brain structures as well as showing that central
 sulcus and insular cortex may contain neural signals that could be used
 for control of a grasp force BMI.
description: Participant B Data
 FilesAll experimental data
 files for Participant B.ParticipantB.zipParticipant C Data FilesExperimental data for Participant CParticipantC.zipParticipant D Data FilesAll experimental data files for Participant D.ParticipantD.zipParticipantAPowerExecutedAll experimental data for Participant A Executed Power Grasp force trials. Participant A's data is segmented into multiple files due to the larger size.ParticipantAPowerImaginedAll experimental data for Participant A Imagined Power Grasp force trials. Participant A's data is segmented into multiple files due to the larger size.ParticipantAPinchExecutedAll experimental data for Participant A Executed Pinch Grasp force trials. Participant A's data is segmented into multiple files due to the larger size.ParticipantAPinchImaginedAll experimental data for Participant A Imagined PinchGrasp force trials. Participant A's data is segmented into multiple files due to the larger size.
DOI: 10.5061/dryad.cj32g
title: Data from: Constrained body shape among highly genetically divergent allopatric lineages of the supralittoral isopod Ligia occidentalis (Oniscidea)

description: Multiple highly divergent lineages have been identified within Ligia
 occidentalis sensu lato, a rocky supralittoral isopod distributed along a
 ~3000 km latitudinal gradient that encompasses several proposed marine
 biogeographic provinces and ecoregions in the eastern Pacific. Highly
 divergent lineages have nonoverlapping geographic distributions, with
 distributional limits that generally correspond with sharp environmental
 changes. Crossbreeding experiments suggest postmating reproductive
 barriers exist among some of them, and surveys of mitochondrial and
 nuclear gene markers do not show evidence of hybridization. Populations
 are highly isolated, some of which appear to be very small; thus, the
 effects of drift are expected to reduce the efficiency of selection. Large
 genetic divergences among lineages, marked environmental differences in
 their ranges, reproductive isolation, and/or high isolation of populations
 may have resulted in morphological differences in L. occidentalis, not
 detected yet by traditional taxonomy. We used landmark-based geometric
 morphometric analyses to test for differences in body shape among highly
 divergent lineages of L. occidentalis, and among populations within these
 lineages. We analyzed a total of 492 individuals from 53 coastal
 localities from the southern California Bight to Central Mexico, including
 the Gulf of California. We conducted discriminant function analyses (DFAs)
 on body shape morphometrics to assess morphological variation among
 genetically differentiated lineages and their populations. We also tested
 for associations between phylogeny and morphological variation, and
 whether genetic divergence is correlated to multivariate morphological
 divergence. We detected significant differences in body shape among highly
 divergent lineages, and among populations within these lineages.
 Nonetheless, neither lineages nor populations can be discriminated on the
 basis of body shape, because correct classification rates of
 cross-validated DFAs were low. Genetic distance and phylogeny had weak to
 no effect on body shape variation. The supralittoral environment appears
 to exert strong stabilizing selection and/or strong functional constraints
 on body shape in L. occidentalis, thereby leading to morphological stasis
 in this isopod.
description: Santamaria_etal_2016_Part1Thanks for your interest in our research on Ligia isopods from the region between Central California and Central Mexico, including the Gulf of California. Herein you will find all picture files used for the morphometrics analyses. Due to the large size of our pictures, we have uploaded them as four separate zip files. You may download each and extract to the same folder.Santamaria_etal_2016_Part2Santamaria_etal_2016_Part3Santamaria_etal_2016_Part4Symmetrical_MexicoMorphometric dataset for all Ligia individuals used in the study.
DOI: 10.5061/dryad.g5jj6
title: Data from: Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards

description: Humans have had a significant impact on the distribution and abundance of
 Saccharomyces cerevisiae through its widespread use in beer, bread and
 wine production. Yet, similar to other Saccharomyces species, S.
 cerevisiae has also been isolated from habitats unrelated to
 fermentations. Strains of S. cerevisiae isolated from grapes, wine must
 and vineyards worldwide are genetically differentiated from strains
 isolated from oak-tree bark, exudate and associated soil in North America.
 However, the causes and consequences of this differentiation have not yet
 been resolved. Historical differentiation of these two groups may have
 been influenced by geographic, ecological or human-associated barriers to
 gene flow. Here, we make use of the relatively recent establishment of
 vineyards across North America to identify and characterize any active
 barriers to gene flow between these two groups. We examined S. cerevisiae
 strains isolated from grapes and oak-trees within three North American
 vineyards and compared them to those isolated from oak-trees outside of
 vineyards. Within vineyards we found evidence of migration between grapes
 and oak-trees and potential gene flow between the divergent oak-tree and
 vineyard groups. Yet, we found no vineyard genotypes on oak-trees outside
 of vineyards. In contrast, S. paradoxus isolated from the same sources
 showed population structure characterized by isolation by distance. The
 apparent absence of ecological or genetic barriers between sympatric
 vineyard and oak-tree populations of S. cerevisiae implies that vineyards
 play an important role in the mixing between these two groups.
description: cerevisiae_fastqfastq files split by barcode for S. cerevisiae isolatescerevisiae.zipparadoxus_fastqfastq files split by barcode for S. paradoxus isolatesparadoxus.zipcerevisiae_alignmentSequence alignment (concatenated) and corresponding genomic positions for S. cerevisiaeparadoxus_alignmentSequence alignment (concatenated) and genomic coordinates for S. paradoxus isolatespara_assembly_d500S. paradoxus assemblyscriptsscripts
DOI: 10.5061/dryad.d449r
title: Data from: A Turing Test for Collective Motion

description: A widespread problem in biological research is assessing whether a model
 adequately describes some real-world data. But even if a model captures
 the large-scale statistical properties of the data, should we be satisfied
 with it? We developed a method, inspired by Alan Turing, to assess the
 effectiveness of model fitting. We first built a self-propelled particle
 model whose properties (order and cohesion) statistically matched those of
 real fish schools. We then asked members of the public to play an online
 game (a modified Turing test) in which they attempted to distinguish
 between the movements of real fish schools or those generated by the
 model. Even though the statistical properties of the real data and the
 model were consistent with each other, the public could still distinguish
 between the two, highlighting the need for model refinement. Our results
 demonstrate that we can use ‘citizen science’ to cross-validate and
 improve model fitting not only in the field of collective behaviour, but
 also across a broad range of biological systems.
description: Results of the online
 Turing testThe data files contain
 players' scores for experts and general public. See filenames for
 description.test_results.zipPositional data 1Data files containing coordinates of fish in experimentspositional_data_1.zipPositional data 2Data files containing coordinates of fishpositional_data_2.zipPositional data 3Data files containing coordinates of fishpositional_data_3.zip
DOI: 10.5061/dryad.0fg55
title: Data from: A fish that uses its hydrodynamic tongue to feed on land

description: To capture and swallow food on land, a sticky tongue supported by the
 hyoid and gill arch skeleton has evolved in land vertebrates from aquatic
 ancestors that used mouth-cavity-expanding actions of the hyoid to suck
 food into the mouth. However, the evolutionary pathway bridging this
 drastic shift in feeding mechanism and associated hyoid motions remains
 unknown. Modern fish that feed on land may help to unravel the physical
 constraints and biomechanical solutions that led to terrestrialization of
 fish-feeding systems. Here, we show that the mudskipper emerges onto land
 with its mouth cavity filled with water, which it uses as a protruding and
 retracting ‘hydrodynamic tongue’ during the initial capture and subsequent
 intra-oral transport of food. Our analyses link this hydrodynamic action
 of the intra-oral water to a sequence of compressive and expansive cranial
 motions that diverge from the general pattern known for suction feeding in
 fishes. However, the hyoid motion pattern showed a remarkable resemblance
 to newts during tongue prehension. Consequently, although alternative
 scenarios cannot be excluded, hydrodynamic tongue usage may be a
 transitional step onto which the evolution of adhesive mucosa and
 intrinsic lingual muscles can be added to gain further independence from
 water for terrestrial foraging.
description: Mud_Per1Individual 1 Lateral and Ventral external 500 HzMud_Per2Individual 2 Lateral and Ventral external 500 HzMud_Per4Individual 3 Lateral and Ventral external 500 HzMud_Per5Individual 4 Lateral and Ventral external 500 HzWaterAbsorbPeriophthalmus absorptionxrayvidsComparison Highspeed X-ray Video of Lepomis gibbosus and Triturus carnifex Hyoid movementsHyoidXRHighspeed X-ray videos of Hyoid movement in PeriophthalmusCT_Buccal_VolumeCT-Scan internal buccal cavity volume WRL fileReadmeRead this file for information on the files presented here