cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8vj84
title: Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

description: Intense artificial selection over the last 100 years has produced elite
 maize (Zea mays) inbred lines that combine to produce high-yielding
 hybrids. To further our understanding of how genome and transcriptome
 variation contribute to the production of high-yielding hybrids, we
 generated a draft genome assembly of the inbred line PH207 to complement
 and compare with the existing B73 reference sequence. B73 is a founder of
 the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent
 germplasm, both of which have contributed substantially to the production
 of temperate commercial maize and are combined to make heterotic hybrids.
 Comparison of these two assemblies revealed over 2,500 genes present in
 only one of the two genotypes and 136 gene families that have undergone
 extensive expansion or contraction. Transcriptome profiling revealed
 extensive expression variation, with as many as 10,564 differentially
 expressed transcripts and 7,128 transcripts expressed in only one of the
 two genotypes in a single tissue. Genotype-specific genes were more likely
 to have tissue/condition-specific expression and lower transcript
 abundance. The availability of a high-quality genome assembly for the
 elite maize inbred PH207 expands our knowledge of the breadth of natural
 genome and transcriptome variation in elite maize inbred lines across
 heterotic pools.
description: Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0_proteinProtein multifasta file for the PH207 version 1.0 draft genome assemblyZm-PH207-REFERENCE_NS-UIUC_UMN-1.0_transcriptTranscript multifasta file for the PH207 version 1.0 draft genome assemblyZm-PH207-REFERENCE_NS-UIUC_UMN-1.0Annotation GFF file for the PH207 version 1.0 draft genome assemblyZm-PH207-REFERENCE_NS-UIUC_UMN-1.0Chromosome multifasta file for the PH207 version 1.0 draft genome assembly
DOI: 10.5061/dryad.1b52s
title: Data from: Are cranial biomechanical simulation data linked to known diets in extant taxa? A method for applying diet-biomechanics linkage models to infer feeding capability of extinct species

description: Performance of the masticatory system directly influences feeding and
 survival, so adaptive hypotheses often are proposed to explain
 craniodental evolution via functional morphology changes. However, the
 prevalence of “many-to-one” association of cranial forms and functions in
 vertebrates suggests a complex interplay of ecological and evolutionary
 histories, resulting in redundant morphology-diet linkages. Here we
 examine the link between cranial biomechanical properties for taxa with
 different dietary preferences in crown clade Carnivora, the most diverse
 clade of carnivorous mammals. We test whether hypercarnivores and
 generalists can be distinguished based on cranial mechanical simulation
 models, and how such diet-biomechanics linkages relate to morphology.
 Comparative finite element and geometric morphometrics analyses document
 that predicted bite force is positively allometric relative to skull
 strain energy; this is achieved in part by increased stiffness in larger
 skull models and shape changes that resist deformation and displacement.
 Size-standardized strain energy levels do not reflect feeding preferences;
 instead, caniform models have higher strain energy than feliform models.
 This caniform-feliform split is reinforced by a sensitivity analysis using
 published models for six additional taxa. Nevertheless, combined bite
 force-strain energy curves distinguish hypercarnivorous versus generalist
 feeders. These findings indicate that the link between cranial
 biomechanical properties and carnivoran feeding preference can be clearly
 defined and characterized, despite phylogenetic and allometric effects.
 Application of this diet-biomechanics linkage model to an analysis of an
 extinct stem carnivoramorphan and an outgroup creodont species provides
 biomechanical evidence for the evolution of taxa into distinct
 hypercarnivorous and generalist feeding styles prior to the appearance of
 crown carnivoran clades with similar feeding preferences.
description: Canis_lupus_FE_modelsCanis_mesomelas_FE_modelsCrocuta_crocuta_FE_modelsHerpestes_javanicus_FE_modelsLycaon_pictus_FE_modelsMephitis_mephitis_FE_modelsOodectes_herpestoides_FE_modelsPanthera_pardus_FE_modelsParahyaena_brunnea_FE_modelsProcyon_lotor_FE_modelsThinocyon_lotor_FE_modelsUrsus_arctos_FE_modelsUrsus_maritimus_FE_models
DOI: 10.5061/dryad.3kh7820
title: Data from: Understanding the transition from water to land: insights from multi-omic analyses of the perivitelline fluid of apple snail eggs

description: Most gastropods deposit their eggs either on land or underwater, but the
 family Ampullariidae includes members that exhibit both underwater and
 aerial oviposition, making it an ideal model for understanding mechanisms
 underlying the evolutionary transition from water to land. We applied
 SDS-PAGE and LC-MS/MS to analyse the proteome of the egg perivitelline
 fluid (PVF) of Marisa cornuarietis – an aquatic ovipositing ampullariid.
 Comparison with the reported PVF proteomes of two aerial ovipositing
 ampullariids (Pomacea canaliculata and P. maculata) showed that the three
 species all contain several major perivitellins that nourish the embryos.
 However, M. cornuarietis invests more heavily on immune-related proteins,
 which might be due to exposure to aquatic pathogens. Interestingly, only
 the PVF of out-of-water egg laying species have PV2 – a neurotoxin lethal
 to mice, and a calcium-binding protein which might be involved in the
 formation of calcareous eggshell. Integrated phylogenetic, evolutionary
 and gene expressional analyses detected the involvement of gene
 duplication, positive selection and neofunctionalisation in the formation
 of several major PVF proteins. Overall, our study provides multiple lines
 of evidence of adaptive evolution in the PVF proteins, and contributes to
 a better understanding of how aquatic gastropod ancestors invaded
 terrestrial habitats.
description: MS data (mgf files) of
 the egg perivitelline fluid of Marisa cornuarietisRAW MS files were
 converted to mgf files as input for Mascot v2.3.2 (Matrix Sciences,
 London, UK)Mc_PVF_mgf.7zGenome data of three ampullariidsGenome data used for PVF protein identification and evolutionary analysisAmp_genomeV1.zip
DOI: 10.5061/dryad.2459s12
title: Data from: Intercomparison of photogrammetry software for three-dimensional vegetation modelling

description: Photogrammetry-based 3D reconstruction of objects is becoming increasingly
 appealing in research areas unrelated to computer vision. It has the
 potential to facilitate the assessment of forest inventory-related
 parameters by enabling or expediting resource measurements in the field.
 We hereby compare several implementations of photogrammetric algorithms
 (CMVS/PMVS, CMPMVS, MVE, OpenMVS, SURE, and Agisoft PhotoScan) with
 respect to their performance in vegetation assessment. The evaluation is
 based on (a) a virtual scene where the precise location and dimensionality
 of objects is known a priori and is thus conducive to a quantitative
 comparison, and (b) using series of in-situ acquired photographs of
 vegetation with overlapping field of view where the photogrammetric
 outcomes are compared quantitatively. Performance is quantified by
 computing ROC curves that summarize the type-I and type-II errors between
 the reference and reconstructed tree models. Similar artifacts are
 observed in synthetic- and in-situ- based reconstructions.
description: Supplementary
 MaterialsOriginal aerial
 UAS-based and synthetics imagery data used for the comparison of
 photogrammetric algorithmsSupplementary_Materials.zip
DOI: 10.5061/dryad.r503m
title: Data from: How body torque and Strouhal number change with swimming speed and developmental stage in larval zebrafish

description: Small undulatory swimmers such as larval zebrafish experience both
 inertial and viscous forces, the relative importance of which is indicated
 by the Reynolds number (Re). Re is proportional to swimming speed (vswim)
 and body length; faster swimming reduces the relative effect of viscous
 forces. Compared with adults, larval fish experience relatively high
 (mainly viscous) drag during cyclic swimming. To enhance thrust to an
 equally high level, they must employ a high product of tail-beat frequency
 and (peak-to-peak) amplitude fAtail, resulting in a relatively high
 fAtail/v̅swim ratio (Strouhal number, St), and implying relatively high
 lateral momentum shedding and low propulsive efficiency. Using kinematic
 and inverse-dynamics analyses, we studied cyclic swimming of larval
 zebrafish aged 2–5 days post-fertilization (dpf). Larvae at 4–5 dpf reach
 higher f (95 Hz) and Atail (2.4 mm) than at 2 dpf (80 Hz, 1.8 mm),
 increasing swimming speed and Re, indicating increasing muscle powers. As
 Re increases (60 → 1400), St (2.5 → 0.72) decreases nonlinearly towards
 values of large swimmers (0.2–0.6), indicating increased propulsive
 efficiency with vswim and age. Swimming at high St is associated with
 high-amplitude body torques and rotations. Low propulsive efficiencies and
 large yawing amplitudes are unavoidable physical constraints for small
 undulatory swimmers.
description: Data_J_R_Soc_Interface_rsfi20150479This zip file contains the raw data that have been used in Van Leeuwen JL, Voesenek CJ, Muller UK, J. R. Soc. Interface 12: 20150479 (http://dx.doi.org/10.1098/fsif.2015.0479). Three text files are provided on the data formatting (data_formats.txt), an overview of the swimming sequences (overview.txt), and the measured tail beat amplitudes for the swimming sequences (tail_amplitudes.txt). Raw video data (directory: Video), digitised longitudinal axis data (directory: Axes), and three-dimensional body models (directory: Body models) are arranged in three main directories.Data_Interface_rsfi20150479.zip
DOI: 10.5061/dryad.nc8qr
title: Data from: De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin

description: Camptotheca acuminata is 1 of a limited number of species that produce
 camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity
 due to its ability to inhibit DNA topoisomerase. While transcriptome
 studies have been performed previously with various camptothecin-producing
 species, no genome sequence for a camptothecin-producing species is
 available to date. We generated a high-quality de novo genome assembly for
 C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50
 scaffold size of 1752 kbp. Quality assessments of the assembly revealed
 robust representation of the genome sequence including genic regions.
 Using a novel genome annotation method, we annotated 31 825 genes encoding
 40 332 gene models. Based on sequence identity and orthology with
 validated genes from Catharanthus roseus as well as Pfam searches, we
 identified candidate orthologs for genes potentially involved in
 camptothecin biosynthesis. Extensive gene duplication including tandem
 duplication was widespread in the C. acuminata genome, with 2571 genes
 belonging to 997 tandem duplicated gene clusters. To our knowledge, this
 is the first genome sequence for a camptothecin-producing species, and
 access to the C. acuminata genome will permit not only discovery of genes
 encoding the camptothecin biosynthetic pathway but also reagents that can
 be used for heterologous expression of camptothecin and camptothecin
 analogs with novel pharmaceutical applications.
description: Readme.txtReadme.txtcac_genome_assembly_v2.4.faGenome assembly of C. acuminata, containing 1,394 scaffold sequencesfull_table_BUSCO.tsvfull_table_BUSCO.tsvshort_summary_BUSCO.txtshort_summary_BUSCO.txtmissing_busco_list_BUSCO.tsvcac_hc_gene_models.gff3Generic feature format file (gff3) of high-confidence genes in C. acuminatacac_hc_gene_models.cdna.faTranscript sequences (cDNA) of high-confidence genes in C. acuminatacac_hc_gene_models.cds.faCoding sequences (CDS) of high-confidence genes in C. acuminatacac_hc_gene_models.pep.faProtein sequences of high-confidence genes in C. acuminatacac_hc_gene_models.func_anno.txtFunctional annotation of high-confidence genes in C. acuminatacac_hc_gene_models.repr.gff3gff3 of representative models of high-confidence genes in C. acuminatacac_hc_gene_models.repr.pep.faProtein sequences of representative models of high-confidence genes in C. acuminataCamptotheca_gene_expression_matrix.xlsxExpression abundance of representative gene modelstopoisomerase_ML_tree.nwkTopoisomerase phylogenetic tree file in newick formatCac_scaffolds_v2.4.fa.repeatmasker.gffGFF file of the repeat-masked genome
DOI: 10.15468/dl.ywmzh4
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is one of (Venezuela (Bolivarian Republic of), Colombia, Ecuador)",
 "TaxonKey is Philydor rufum"
 ]
}

 The dataset includes 56 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000349-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pq93h
title: Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants

description: Detailed information about the geographic distribution of genetic and
 genomic variation is necessary to better understand the organization and
 structure of biological diversity. In particular, spatial isolation within
 species and hybridization between them can blur species boundaries and
 create evolutionary relationships that are inconsistent with a strictly
 bifurcating tree model. Here we analyze genome-wide DNA sequence and
 genetic ancestry variation in Lycaeides butterflies to quantify the
 effects of admixture and spatial isolation on how biological diversity is
 organized in this group. We document geographically widespread and
 pervasive historic admixture, with more restricted recent hybridization.
 This includes evidence supporting previously known and unknown instances
 of admixture. The genome composition of admixed individuals varies much
 more among than within populations, and tree- and genetic ancestry-based
 analyses indicate that multiple distinct admixed lineages or populations
 exist. We find that most genetic variants in Lycaeides are rare (minor
 allele frequency &lt; 0.5%). Because the spatial and taxonomic
 distributions of alleles reflect demographic and selective processes since
 mutation, rare alleles, which are presumably younger than common alleles,
 were spatially and taxonomically restricted compared to common variants.
 Thus, we show patterns of genetic variation in this group are
 multifaceted, and we argue that this complexity challenges simplistic
 notions concerning the organization of biological diversity into discrete,
 easily delineated, and hierarchically structured entities.
description: entropy.tarThis compressed directory contains the source code (C++), example files, and a README file for the admixture proportion and admixture class models described in the publication. Compile the pogram and type the program name for a list of command line options. Source code for a second program (estpost_h5_entropy.c) is incluced to summarize the MCMC output from the analysis.isolationByDistanceAndTaxonR code to test for isolation by distance and isolation by taxon. This is a Bayesian implementation of the mixed model described by Clarke et al. 2002 to model the lack of independence among pair-wise distances. This code requires JAGS and rjags.maf_0.05_0.5_lycaeides_gbs_admix_d80Variant call format (VCF) file for the full set of common variants identified in Lycaeides. Rare and low-frequency VCF files are too large to include on Dryad, but are available from the authors upon request.lycaeides_gbscontigs_referenceLycaeides reference sequence set generated from the GBS data. This was used for the reference based alignments with bwa.
DOI: 10.15468/dl.2g5dbh
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((31.71016 30.83985,32.35418 30.83985,32.35418 31.5142,31.71016 31.5142,31.71016 30.83985))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phalacrocorax carbo",
 {
 "or" : [
 "Year 1980-2017",
 "Year 2018-2021",
 "Year 2022-2026"
 ]
 }
 ]
}

 The dataset includes 84 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000355-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mbhbyk
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lipaphis alliariae"
 ]
}

 The dataset includes 156 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000351-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3447g
title: Data from: Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR

description: Objective: To validate the targeted next-generation sequencing (NGS)
 platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations
 detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer
 (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion
 real-time PCR. Setting: Beijing, China. Participants: 51 archived FFPE CRC
 samples (36 men, 15 women) were retrospectively randomly selected and then
 checked by an experienced pathologist for sequencing based on histological
 confirmation of CRC and availability of sufficient tissue. Methods: RAS
 mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger
 sequencing and the Therascreen KRAS assay, respectively. Agreement among
 the 3 methods was assessed. Assay sensitivity was further determined by
 sequencing serially diluted DNA from FFPE cell lines with known mutation
 statuses. Results: 13 of 51 (25.5%) cases had a mutation in KRAS exon 2,
 as determined by PGM analysis. PGM analysis showed 100% (51/51)
 concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04%
 (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1)
 for detecting KRAS exon 2 mutations, respectively. The only discrepant
 case harboured a KRAS exon 2 mutation (c.37G&gt;T) that was not
 covered by the Therascreen kit. The dilution series experiment results
 showed that PGM was able to detect KRAS mutations at a frequency of as low
 as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were
 also detected in 10 samples by PGM. Furthermore, mutations in other
 CRC-related genes could be simultaneously detected in a single test by
 PGM. Conclusions: The targeted NGS platform is specific and sensitive for
 KRAS exon 2 mutation detection and is appropriate for use in routine
 clinical testing. Moreover, it is sample saving and cost-efficient and
 time-efficient, and has great potential for clinical application to expand
 testing to include mutations in RAS and other CRC-related genes.
description: Sanger
 sequencingSanger sequencing for
 Assay sensitivitySanger sequecing
 2.zipPGM
 sequencingPGM sequencing for assay
 sensitivityKRAS ARMS
 resultsKRAS ARMS
 resultsKRAS
 ARMS2.zip
DOI: 10.5061/dryad.9tt2t
title: Data from: Ancient collagen reveals evolutionary history of the endemic South American ‘ungulates’

description: Since the late eighteenth century, fossils of bizarre extinct creatures
 have been described from the Americas, revealing a previously unimagined
 chapter in the history of mammals. The most bizarre of these are the
 ‘native’ South American ungulates thought to represent a group of mammals
 that evolved in relative isolation on South America, but with an uncertain
 affinity to any particular placental lineage. Many authors have considered
 them descended from Laurasian ‘condylarths’, which also includes the
 probable ancestors of perissodactyls and artiodactyls, whereas others have
 placed them either closer to the uniquely South American xenarthrans
 (anteaters, armadillos and sloths) or the basal afrotherians (e.g.
 elephants and hyraxes). These hypotheses have been debated owing to
 conflicting morphological characteristics and the hitherto inability to
 retrieve molecular information. Of the ‘native’ South American mammals,
 only the toxodonts and litopterns persisted until the Late
 Pleistocene–Early Holocene. Owing to known difficulties in retrieving
 ancient DNA (aDNA) from specimens from warm climates, this research
 presents a molecular phylogeny for both Macrauchenia patachonica
 (Litopterna) and Toxodon platensis (Notoungulata) recovered using
 proteomics-based (liquid chromatography–tandem mass spectrometry)
 sequencing analyses of bone collagen. The results place both taxa in a
 clade that is monophyletic with the perissodactyls, which today are
 represented by horses, rhinoceroses and tapirs.
description: Macrauchenia_MLP
 71-III-6-1Proteomics MGF
 file.Macrauchenia_Museo
 Olavarria (MO)Proteomics MGF
 file.Toxodon_MLP
 81-II-5-7Proteomics MGF
 file.Toxodon_MLP
 86-III-25-15BlankBayesian
 AnalysisBayes.treMaximum Likelihood treeMaximum Likelihood tree from sequences found in both specimens for each taxa above highest false positive match.ML.newickPMF treeMaximum Likelihood tree from sequences observed in PMFPMF.newickCropped ML treeMaximum Likelihood tree from sequences when cropped to match only sequences present in specimens analysed.Pseudoextinction.newickParsimony tree created in PhylipParsimony tree created in Phylip from sequences found in both specimens for each taxa.ParsimonyTree
DOI: 10.13140/rg.2.2.33177.48481
title: RHTest (0.95) User Manual
DOI: 10.5061/dryad.c7366
title: Data from: A serial multiplex immunogold labeling method for identifying peptidergic neurons in connectomes

description: Electron microscopy-based connectomics aims to comprehensively map
 synaptic connections in neural tissue. However, current approaches are
 limited in their capacity to directly assign molecular identities to
 neurons. Here, we use serial multiplex immunogold labeling (siGOLD) and
 serial-section transmission electron microscopy (ssTEM) to identify
 multiple peptidergic neurons in a connectome. The high immunogenicity of
 neuropeptides and their broad distribution along axons, allowed us to
 identify distinct neurons by immunolabeling small subsets of sections
 within larger series. We demonstrate the scalability of siGOLD by using 11
 neuropeptide antibodies on a full-body larval ssTEM dataset of the annelid
 Platynereis. We also reconstruct a peptidergic circuitry comprising the
 sensory nuchal organs, found by siGOLD to express pigment-dispersing
 factor, a circadian neuropeptide. Our approach enables the direct
 overlaying of chemical neuromodulatory maps onto synaptic connectomic maps
 in the study of nervous systems.
description: Figure2_Source_dataHigh-resolution immunogold layers. High-resolution images (2.22 nm/pixel) showing the area of the VNC. The archive contains one image file for each antibody.