cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00715
title: Data from: Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex

description: High throughput sequencing technologies have revolutionized the potential
 to reconcile incongruence between gene and species trees, and numerous
 approaches have been developed to take advantage of these advances.
 Genotyping-by-sequencing is becoming a regular tool for gathering
 phylogenetic data, yet comprehensive evaluations of phylogenetic methods
 using these data are sparse. Here we use multiple phylogenetic and
 population genetic methods for genotyping-by-sequencing data to assess
 species relationships in a group of forest insect pests, the spruce
 budworm (Choristoneura fumiferana) species complex. With few exceptions,
 all methods agree on the same relationships, most notably placing C. pinus
 as basal to the remainder of the group, rather than C. fumiferana as
 previously suggested. We found strong support for the monophyly of C.
 pinus, C. fumiferana, and C. retinana, but more ambiguous relationships
 and signatures of introgression in a clade of western lineages, including
 C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis
 biennis, and C. orae. This represents the most taxonomically comprehensive
 genomic treatment of the spruce budworm species group, which is further
 supported by the broad agreement among multiple methodologies.
description: SBW_noOG_0.9missingPopulation genetic analyses input file (5,048 SNPs).SBW_26438SNPsPhylogenetic data alignment of 26,438 SNPs (no flanking sequence)SBW_448500lociPhylogenetic data alignment of SNPs plus flanking sequence after removing loci with &gt;50% missing data (448,500 bp).SBW_noOG_0.9missingPhylogenetic data alignment of SNPs plus flanking sequence after removing loci with &gt;90% missing data (944,564 bp).SBW_944564loci.phy
DOI: 10.5061/dryad.f2n6f
title: Data from: Surface energies of elemental crystals

description: The surface energy is a fundamental property of the different facets of a
 crystal that is crucial to the understanding of various phenomena like
 surface segregation, roughening, catalytic activity, and the crystal’s
 equilibrium shape. Such surface phenomena are especially important at the
 nanoscale, where the large surface area to volume ratios leads to
 properties that are significantly different from the bulk. In this work,
 we present the largest database of the calculated surface energies of
 elemental crystals to date. This database contains the surface energies of
 more than 100 polymorphs of about 70 elements, up to a maximum Miller
 index of two and three for non-cubic and cubic crystals, respectively.
 Well-known reconstruction schemes are also accounted for. The database is
 systematically improvable and has been rigorously validated against
 previous experimental and computational data where available. We will
 describe the methodology used in constructing the database, and how it can
 be accessed for further studies and design of materials.
description: Surface Energies of
 Elemental CrystalsThis file contains the
 surface energies and related properties of elemental crystals computed
 using density functional theory calculations. DFT calculations were
 performed using Vienna Ab initio Simulation Package (VASP) and analysis
 performed using Python Materials Genomics (pymatgen)
 package.surfaces.jsonInputs/Outputs of each Surface Calculation run in VASPFor the convenience of the readers, we have included the relevant inputs of each surface calculation run using the Vienna Ab intio Simulation Package (VASP). The relevant outputs generated from these calculations have also been included in this file.surfaces_vasp_details.json
DOI: 10.5061/dryad.r1j3051
title: Data from: A multi-target brain-computer based on code modulated visual evoked potentials

description: The number of selectable targets is one of the main factors that affect
 the performance of a brain-computer interface (BCI). Most existing code
 modulated visual evoked potential (c-VEP) based BCIs use a single
 pseudorandom binary sequence and its circularly shifting sequences to
 modulate different stimulus targets, making the number of selectable
 targets limited by the length of modulation codes. This paper proposes a
 novel paradigm for c-VEP BCIs, which divides the stimulus targets into
 four target groups and each group of targets are modulated by a unique
 pseudorandom binary code and its circularly shifting codes. Based on the
 paradigm, a four-group c-VEP BCI with a total of 64 stimulus targets was
 developed and eight subjects were recruited to participate in the BCI
 experiment. Based on the experimental data, the characteristics of the
 c-VEP BCI were explored by the analyses of auto- and cross-correlation,
 frequency spectrum, signal to noise ratio and correlation coefficient. On
 the basis, single-trial data with the length of one stimulus cycle were
 classified and the attended target was recognized. The averaged
 classification accuracy across subjects was 88.36% and the corresponding
 information transfer rate was as high as 184.6 bit/min. These results
 suggested that the c-VEP BCI paradigm is both feasible and effective, and
 provides a new solution for BCI study to substantially increase the number
 of available targets.
description: A multi-target BCI based
 on c-VEPThe EEG data set was
 recorded during a c-VEP BCI experiment. The experimental system consists
 of a personal computer (Lenovo China) and an EEG amplifier (a Synamps2
 system, Neuroscan Inc.) with 64 EEG channels. The computer has a 24-in.
 liquid crystal display (LCD) monitor and a parallel port linked to the
 amplifier. The LCD monitor has a refresh rate of 60 Hz and a resolution
 of1920 1080 pixels. Stimulus presentation was operated in the computer
 and controlled by the stimulus program developed under Visual C++ 9.0
 platform. DirectX (Microsoft Inc.) was employed to ensure the stability of
 frame-based rendering of stimuli. Event trigger signals yielded by the
 stimulus programwere sent from the parallel port of the computer to the
 EEG amplifier and recorded on an event channel for synchronizingstimulus
 presentation and EEG data recordings.
DOI: 10.5061/dryad.cb448
title: Data from: Structural biomechanics determine spectral purity of bush-cricket calls

description: Bush-crickets (Orthoptera: Tettigoniidae) generate sound using tegminal
 stridulation. Signalling effectiveness is affected by the widely varying
 acoustic parameters of temporal pattern, frequency and spectral purity
 (tonality). During stridulation, frequency multiplication occurs as a
 scraper on one wing scrapes across a file of sclerotized teeth on the
 other. The frequency with which these tooth–scraper interactions occur,
 along with radiating wing cell resonant properties, dictates both
 frequency and tonality in the call. Bush-cricket species produce calls
 ranging from resonant, tonal calls through to non-resonant, broadband
 signals. The differences are believed to result from differences in file
 tooth arrangement and wing radiators, but a systematic test of the
 structural causes of broadband or tonal calls is lacking. Using
 phylogenetically controlled structural equation models, we show that
 parameters of file tooth density and file length are the best-fitting
 predictors of tonality across 40 bush-cricket species. Features of file
 morphology constrain the production of spectrally pure signals, but
 systematic distribution of teeth alone does not explain pure-tone sound
 production in this family.
description: Buschcricket_file_and_entropy_data_Chiversetal_after_revisionData file of species, acoustic, and morphological information for 40 species of bush-cricket.Data_file_images_ChiversetalFolder contains SEM images of the stridulatory file of 40 species of bush-cricket.Data_sound_text_files_ChiversetalFolder contains acoustic recordings of 40 species of bush-cricket presented ascii files. Each file contains time and signal data.
DOI: 10.5061/dryad.r1j0s
title: Data from: Physiological tremor reveals how thixotropy adapts skeletal muscle for posture and movement

description: People and animals can move freely, but they must also be able to stay
 still. How do skeletal muscles economically produce both movement and
 posture? Humans are well known to have motor units with relatively
 homogeneous mechanical properties. Thixotropic muscle properties can
 provide a solution by providing a temporary stiffening of all skeletal
 muscles in postural conditions. This stiffening is alleviated almost
 instantly when muscles start to move. In this paper, we probe this
 behaviour. We monitor both the neural input to a muscle, measured here as
 extensor muscle electromyography (EMG), and its output, measured as tremor
 (finger acceleration). Both signals were analysed continuously as the
 subject made smooth transitions between posture and movement. The results
 showed that there were marked changes in tremor which systematically
 increased in size and decreased in frequency as the subject moved faster.
 By contrast, the EMG changed little and reflected muscle force requirement
 rather than movement speed. The altered tremor reflects naturally
 occurring thixotropic changes in muscle behaviour. Our results suggest
 that physiological tremor provides useful and hitherto unrecognized
 insights into skeletal muscle's role in posture and movement.
description: DataDryadDirectoryZip-file with raw data-files for all 10 trials of each of 15 subjects. Each data-file is a .mat file including recorded signals as well as the target-signal. A variable explaining the columns of the recorded data is also included
DOI: 10.5061/dryad.60b9p56
title: Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

description: Selective breeding and genetic improvement have left detectable signatures
 on the genomes of domestic species. The elucidation of such signatures is
 fundamental for detecting genomic regions of biological relevance to
 domestication and improving management practices. In aquaculture,
 domestication was carried out independently in different locations
 worldwide, which provides opportunities to study the parallel effects of
 domestication on the genome of individuals that have been selected for
 similar traits. In the present study, we aimed to detect potential genomic
 signatures of domestication in two independent pairs of wild/domesticated
 Atlantic salmon populations of Canadian and Scottish origins respectively.
 Putative genomic regions under divergent selection were investigated using
 a 200K SNP array by combining three different statistical methods based
 either on allele frequencies (LFMM, Bayescan) or haplotype differentiation
 (Rsb). We identified 337 and 270 SNPs potentially under divergent
 selection in wild and hatchery populations of Canadian and Scottish
 origins respectively. We observed little overlap between results obtained
 from different statistical methods, highlighting the need to test
 complementary approaches for detecting a broad range of genomic footprints
 of selection. The vast majority of the outliers detected were
 population-specific but we found four candidate genes that were shared
 between the populations. We propose that these candidate genes may play a
 role in the parallel process of domestication. Overall, our results
 suggest that genetic drift may have override the effect of artificial
 selection and/or point towards a different genetic basis underlying the
 expression of similar traits in different domesticated strains. Finally,
 it is likely that domestication may predominantly target polygenic traits
 (e.g., growth) such that its genomic impact might be more difficult to
 detect with methods assuming selective sweeps.
description: Genotypes_CAN-W-D_SCT-W-DThis VCF file includes the genotypes of four populations used in this study.CAN_SCT_151509.recode.vcf
DOI: 10.5061/dryad.tv055
title: Data from: Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

description: Two common approaches for estimating phylogenies in species-rich groups
 are to: (i) sample many loci for few species (e.g. phylogenomic approach),
 or (ii) sample many species for fewer loci (e.g. supermatrix approach). In
 theory, these approaches can be combined to simultaneously resolve both
 higher-level relationships (with many genes) and species-level
 relationships (with many taxa). However, fundamental questions remain
 unanswered about this combined approach. First, will higher-level
 relationships more closely resemble those estimated from many genes or
 those from many taxa? Second, will branch support increase for
 higher-level relationships (relative to the estimate from many taxa)?
 Here, we address these questions in squamate reptiles. We combined two
 recently published datasets, one based on 44 genes for 161 species, and
 one based on 12 genes for 4161 species. The likelihood-based tree from the
 combined matrix (52 genes, 4162 species) shared more higher-level clades
 with the 44-gene tree (90% vs. 77% shared). Branch support for higher
 level-relationships was marginally higher than in the 12-gene tree, but
 lower than in the 44-gene tree. Relationships were apparently not obscured
 by the abundant missing data (92% overall). We provide a time-calibrated
 phylogeny based on extensive sampling of genes and taxa as a resource for
 comparative studies.
description: zheng_wiens_RAXML_datamatrixData matrix of 4162 squamate reptile species and 10 outgroup species with 52 genes, for maximum likelihood analysis in RAxML.
DOI: 10.5061/dryad.5q91d
title: Data from: Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

description: PREMISE OF THE STUDY: Hybridization between diploids and tetraploids can
 lead to new allopolyploid species, often via a triploid intermediate.
 Viable triploids are often produced asymmetrically, with greater success
 observed for “maternal-excess” crosses where the mother has a higher
 ploidy than the father. Here we investigated the evolutionary origins of
 Mimulus peregrinus, an allohexaploid recently derived from the triploid M.
 ×robertsii, to determine whether reproductive asymmetry has shaped the
 formation of this new species. METHODS: We used reciprocal crosses between
 the diploid (M. guttatus) and tetraploid (M. luteus) progenitors to
 determine the viability of triploid M. ×robertsii hybrids resulting from
 paternal- vs. maternal-excess crosses. To investigate whether experimental
 results predict patterns seen in the field, we performed parentage
 analyses comparing natural populations of M. peregrinus to its diploid,
 tetraploid, and triploid progenitors. Organellar sequences obtained from
 pre-existing genomic data, supplemented with additional genotyping was
 used to establish the maternal ancestry of multiple M. peregrinus and M.
 ×robertsii populations. KEY RESULTS: We found strong evidence for
 asymmetric origins of M. peregrinus, but opposite to the common pattern,
 with paternal-excess crosses significantly more successful than
 maternal-excess crosses. These results successfully predicted hybrid
 formation in nature: 111 of 114 M. ×robertsii individuals, and 27 of 27 M.
 peregrinus, had an M. guttatus maternal haplotype. CONCLUSION: This study,
 which includes the first Mimulus chloroplast genome assembly, demonstrates
 the utility of parentage analysis through genome skimming. We highlight
 the benefits of complementing genomic analyses with experimental
 approaches to understand asymmetry in allopolyploid speciation.
description: Phylogenetic Analyses
 (trees, alignments, filtered regions)This zipped directory
 contains the phylogenetic trees, sequence alignments, and filtered
 regions.PhylogeneticAnalayses.tar
DOI: 10.5061/dryad.kn087
title: Data from: A genomic approach for distinguishing between recent and ancient admixture as applied to cattle

description: Genomic data facilitate opportunities to track complex population
 histories of divergence and gene flow. We developed a metric, scaled block
 size (SBS), that uses the unrecombined block size of introgressed regions
 of chromosomes to differentiate between recent and ancient admixture, and
 applied it to reconstructing admixture in cattle. Cattle are descendants
 of two independently domesticated lineages, taurine and indicine, that
 diverged 200,000 or more years ago. Several breeds have hybrid ancestry
 between these divergent lineages. Using 47,506 SNPs, we analyzed the
 genomic architecture of ancestry of 1369 indivduals. We focussed on four
 groups with admixed ancestry, including two anciently admixed African
 breeds (n=58; n=43), New World cattle of Spanish origin (n=51), and known
 recent hybrids (n=46). We estimated ancestry of chromosomal regions for
 each individual and used the SBS metric to differentiate timing of
 admixture among groups and among individuals within groups. By comparing
 SBS values of test individuals to standards with known recent hybrid
 ancestry, we were able to differentiate individuals of recent hybrid
 origin from other admixed cattle. We also estimated ancestry at the
 chromosomal scale. The X chromosome exhibits reduced indicine ancestry in
 recent hybrid, New World, and western African cattle, with virtually no
 evidence of indicine ancestry in New World cattle.
description: 50K cattle SNP
 dataThis folder contains 50k
 cattle SNP data in the format:[SNPNUMBER, INDIVDUAL ID, GENOTYPE], where:
 SNPnumber is described in ibmc_markers041709.csv; InidvdualID is described
 in the file all_ind_info.csv; Genotype is in form 1= homozygous for A,
 2=homozygous for B, 3= heterozygous, 10 missing data; Indivduals are
 separated into files by their Breed Code, as described in breedcodes.csv,
 and in all_ind_info.csv. Xheterozygosity.csv lists number of heterozygotes
 at X loci, used to differentiate males and females. The 1369 indivduals
 listed in Xheterozygosity.csv are the indivduals retained in anayses after
 filtering. autosomal_snp.csv lists all automsal snp loci retained after
 filtering. X_snp.csv lists all snps retained on the X chromosome after
 removing pseudo-autosomal region and filtering. For further information
 please contact Emily Jane McTavish
 ejmctavish@utexas.eduRawData_JHered.zip
DOI: 10.5061/dryad.ft928
title: Data from: Restriction site associated DNA (RAD) for de novo sequencing and marker discovery in sugarcane borer, Diatraea saccharalis Fab. (Lepidoptera: Crambidae)

description: We present the development of a genomic library using RADseq (restriction
 site associated DNA sequencing) protocol for marker discovery that can be
 applied on evolutionary studies of the sugarcane borer Diatraea
 saccharalis, an important South American insect pest. A RADtag protocol
 combined with Illumina paired-end sequencing allowed de novo discovery of
 12 811 SNPs and a high-quality assembly of 122.8M paired-end reads from
 six individuals, representing 40 Gb of sequencing data. Approximately 1.7
 Mb of the sugarcane borer genome distributed over 5289 minicontigs were
 obtained upon assembly of second reads from first reads RADtag loci where
 at least one SNP was discovered and genotyped. Minicontig lengths ranged
 from 200 to 611 bp and were used for functional annotation and
 microsatellite discovery. These markers will be used in future studies to
 understand gene flow and adaptation to host plants and control tactics.
description: Final SNP
 set.This file contains the
 final SNP set (after several filtering steps detailed at manuscript) in
 .vcf and .fasta format. Fasta file contains ~80bp sequences of each RADtag
 loci. After alignment of each sequences from same loci, SNP of each sample
 can be accessed.final_SNP_set.zipMinicontigs associated with RADtag loci.Minicontigs associated with RADseq loci in .fasta format.minicontigs_RADtag_loci.faMicrosatellites found in minicontigs.This file contains a table of identified microsatellite with contig ID, motif and coordinates of each motif, and a file with parameters used in MiSA for SSR search.microsatellites.zipRepetitive elements identified with RepeatMasker.This file contains a table of the identified repetitive elements (.tbl), a file with masked contigs and repetitive elements (.fasta format) and a file with contig ID, repetitive element ID and coordinates.RepeatMasker_minicontigs_RADtag_loci.zipBlast2GO annotation file.This .gff file contain the final annotation of minicontigs obtained using Blast2GO pipeline.minicontigs_final_annotation_Blast2go.gffScripts and command line of each program used in this pipeline.This file contains all necessary commands and scripts to reproduce the outputs uploaded here (SNP, minicontigs, microsatellites, repetitive element discovery and functional annotation.All kmer=27 minicontigsThis file contains minicontigs assembled with all second reads we generated. Second reads correspond to reads generated from random sheared ends of a genomic fragment. Since reads with different start and endings position were generated from the same genomic regions it allows the assemble of minicontigs bigger than read size usually sequenced (bigger than ~80bp reads)all_minicontigs_random_sheared_ends_kmer27.fa
DOI: 10.5061/dryad.266k4
title: Data from: Complex disease and phenotype mapping in the domestic dog

description: The domestic dog is becoming an increasingly valuable model species in
 medical genetics, showing particular promise to advance our understanding
 of cancer and orthopaedic disease. Here we undertake the largest canine
 genome-wide association study to date, with a panel of over 4,200 dogs
 genotyped at 180,000 markers, to accelerate mapping efforts. For complex
 diseases, we identify loci significantly associated with hip dysplasia,
 elbow dysplasia, idiopathic epilepsy, lymphoma, mast cell tumour and
 granulomatous colitis; for morphological traits, we report three novel
 quantitative trait loci that influence body size and one that influences
 fur length and shedding. Using simulation studies, we show that modestly
 larger sample sizes and denser marker sets will be sufficient to identify
 most moderate- to large-effect complex disease loci. This proposed design
 will enable efficient mapping of canine complex diseases, most of which
 have human homologues, using far fewer samples than required in human
 studies.
description: plink files for cornell
 canine datasetID and sex information
 for each dogcornell_canine.famplink files for cornell canine datasetchromosome, name, location, alleles for each SNPcornell_canine.bimplink files for cornell canine datasetgenotypes for each dog at each SNPcornell_canine.bedphenotypesphenotypes for each dog