cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m80d7
title: Data from: Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets

description: Human-mediated biological exchange has had global social and ecological
 impacts. In sub-Saharan Africa, several domestic and commensal animals
 were introduced from Asia in the pre-modern period; however, the timing
 and nature of these introductions remain contentious. One model supports
 introduction to the eastern African coast after the mid-first millennium
 CE, while another posits introduction dating back to 3000 BCE. These
 distinct scenarios have implications for understanding the emergence of
 long-distance maritime connectivity, and the ecological and economic
 impacts of introduced species. Resolution of this longstanding debate
 requires new efforts, given the lack of well-dated fauna from
 high-precision excavations, and ambiguous osteomorphological
 identifications. We analysed faunal remains from 22 eastern African sites
 spanning a wide geographic and chronological range, and applied
 biomolecular techniques to confirm identifications of two Asian taxa:
 domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our
 approach included ancient DNA (aDNA) analysis aided by BLAST-based
 bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen
 fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon
 dating. Our results support a late, mid-first millennium CE introduction
 of these species. We discuss the implications of our findings for models
 of biological exchange, and emphasize the applicability of our approach to
 tropical areas with poor bone preservation.
description: Shotgun sequences for
 bird remains from Swahili coast archaeological sitesShotgun sequences for
 bird remains from Swahili coast archaeological sites. Files that are
 labeled "JK" correspond to specific archaeological bone samples,
 each 4-digit number representing a single library: JK2992, JK3005, JK2999,
 JK2989, JK3002, JK2995, JK2993, JK3004, JK3003, JK2994, JK2988, JK3001,
 JK2990, JK3008, JK2998, JK3007, JK1996, JK3006, JK3000, JK2991, JK2997 .
 The other files represent extraction blanks (EBB1, EBB2) and library
 blanks (LBB2, LBB1). Please see supplementary data in the Prendergast et
 al. paper to link JK numbers to archaeological
 contexts.2017-06-19_Samples_Oxford.tar
DOI: 10.5061/dryad.v5n53
title: Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

description: The yeast Chd1 protein acts to position nucleosomes across genomes. Here,
 we model the structure of the Chd1 protein in solution and when bound to
 nucleosomes. In the apo state, the DNA-binding domain contacts the edge of
 the nucleosome while in the presence of the non-hydrolyzable ATP analog,
 ADP-beryllium fluoride, we observe additional interactions between the
 ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad
 axis of symmetry. Binding in this conformation involves unravelling the
 outer turn of nucleosomal DNA and requires substantial reorientation of
 the DNA-binding domain with respect to the ATPase domains. The orientation
 of the DNA-binding domain is mediated by sequences in the N-terminus and
 mutations to this part of the protein have positive and negative effects
 on Chd1 activity. These observations indicate that the unfavorable
 alignment of C-terminal DNA-binding region in solution contributes to an
 auto-inhibited state.
description: RAW PELDOR
 DATAThis is a Zipped folder
 containing raw data for PELDOR measurements reported in the associated
 publication. Within the folder are directories named with the pair of
 labeling sites (residues in the Chd1 protein) used for each PELDOR
 measurement. The data is in the format of a .DSC and .DAT files. These
 represent the echo signal from the paired spin interaction. The data can
 be opened with the DeerAnalysis software available at
 http://www.epr.ethz.ch/software.html .RAWPELDORDATA.zipPELDORMODEL1This file includes the co-ordinates for the solution structure of the Chd1 protein determined from PELDOR measurements as described in the associated publication. This is a pymol session file that can be opened with the program Pymol https://www.pymol.org/ .Chd1-apoThese are the picked particle stacks used to generate the structure of the apo complex (Figure 6). http://www.pdbe.org/emd-3517 . The file can be processed using RELION as described in the manuscript.Chd1-Native.tgzChd1-engagedThese are the motion corrected picked particle stacks used for processing the Chd1-nucleosome complex in the engaged conformation (Figure 7). http://www.pdbe.org/emd-3502. The file can be opened and processed as described in the manuscript using RELION.Chd1-NEG.tgz
DOI: 10.5061/dryad.9f33sq1
title: Data from: Stress and early experience underlie dominance status and division of labour in a clonal insect

description: Cooperation and division of labour are fundamental in the “major
 transitions” in evolution. While the factors regulating cell
 differentiation in multicellular organisms are quite well understood, we
 are just beginning to unveil the mechanisms underlying individual
 specialization in cooperative groups of animals. Clonal ants allow
 studying which factors influence task allocation without confounding
 variation in genotype and morphology. Here, we subjected larvae and
 freshly hatched workers of the clonal ant Platythyrea punctata to
 different rearing conditions and investigated how these manipulations
 affected division of labour among pairs of oppositely treated, same-aged
 clonemates. High rearing temperature, physical stress, injury, and
 malnutrition increased the propensity of individuals to become subordinate
 foragers rather than dominant reproductives. This is reflected in changed
 gene regulation: early stages of division of labour were associated with
 different expression of genes involved in nutrient signalling pathways,
 metabolism, and the phenotypic response to environmental stimuli. Many of
 these genes appear to be capable of responding to a broad range of
 stressors. They might link environmental stimuli to behavioural and
 phenotypic changes and could therefore be more broadly involved in caste
 differentiation in social insects. Our experiments also shed light on the
 causes of behavioural variation among genetically identical individuals.
description: HKPLAriuTAACRAAPEI-203see Supplementary MaterialHKPLAriuTAADRAAPEI-204see Supplementary MaterialHKPLAriuTAAIRAAPEI-209see Supplementary MaterialHKPLAriuTAAJRAAPEI-210see Supplementary MaterialHKPLAriuTAAORAAPEI-215see Supplementary MaterialHKPLAriuTAAPRAAPEI-216see Supplementary MaterialHKPLAriuTAAURAAPEI-222see Supplementary MaterialHKPLAriuTAAVRAAPEI-223see Supplementary MaterialHKPLAriuTABARAAPEI-203see Supplementary MaterialHKPLAriuTABBRAAPEI-204see Supplementary MaterialBehavioural_dataData: Hierarchy formation and division of labour among control clonemates, Division of labour and experimental manipulations, Effect of treatment on social status and Effect of experimental treatment on body size and fat content.
DOI: 10.5061/dryad.t2q53
title: Data from: Inferring pathobiology from structural MRI in schizophrenia and bipolar disorder: modeling head motion and neuroanatomical specificity

description: Despite over 400 peer-reviewed structural MRI publications documenting
 neuroanatomic abnormalities in bipolar disorder and schizophrenia, the
 confounding effects of head motion and the regional specificity of these
 defects are unclear. Using a large cohort of individuals scanned on the
 same research dedicated MRI with broadly similar protocols, we observe
 reduced cortical thickness indices in both illnesses, though less
 pronounced in bipolar disorder. While schizophrenia (n = 226) was
 associated with wide-spread surface area reductions, bipolar disorder
 (n = 227) and healthy comparison subjects (n = 370) did not differ. We
 replicate earlier reports that head motion (estimated from time-series
 data) influences surface area and cortical thickness measurements and
 demonstrate that motion influences a portion, but not all, of the observed
 between-group structural differences. Although the effect sizes for these
 differences were small to medium, when global indices were covaried during
 vertex-level analyses, between-group effects became nonsignificant. This
 analysis raises doubts about the regional specificity of structural brain
 changes, possible in contrast to functional changes, in affective and
 psychotic illnesses as measured with current imaging technology. Given
 that both schizophrenia and bipolar disorder showed cortical thickness
 reductions, but only schizophrenia showed surface area changes, and
 assuming these measures are influenced by at least partially unique sets
 of biological factors, then our results could indicate some degree of
 specificity between bipolar disorder and schizophrenia.
description: Supplementary
 MaterialThis Supplementary
 Material contains a large set of figures that depict the results of all
 analyses described in the paper. There are three sets of results: one
 using data from all subjects (N=823), and one for each of the two MRI
 sequence protocols with the largest number of subjects (N=196 and N=460).
 See the paper for the complete details. After opening the .tar file,
 locate and open the "index.html" in a web browser to navigate
 the figures.Yao_etal_2017.tar
DOI: 10.5061/dryad.25f502n
title: Data from: The genetic legacy of 50 years of desert bighorn sheep translocations

description: Conservation biologists have increasingly used translocations to mitigate
 population declines and restore locally extirpated populations. Genetic
 data can guide the selection of source populations for translocations and
 help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a
 managed big game species that suffered widespread population extirpations
 across western North America throughout the early 1900’s. Subsequent
 translocation programs have successfully re-established many formally
 extirpated bighorn herds, but most of these programs pre-date
 genetically-informed management practices. The state of Nevada presents a
 particularly well-documented case of decline followed by restoration of
 extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations
 declined to less than 3,000 individuals restricted to remnant herds in the
 Mojave Desert and a few locations in the Great Basin Desert. Beginning in
 1968, the Nevada Department of Wildlife translocated ~2,000 individuals
 from remnant populations to restore previously extirpated areas, possibly
 establishing herds with mixed ancestries. Here we examined genetic
 diversity and structure among remnant herds and the genetic consequences
 of translocation from these herds using a genotyping-by-sequencing
 approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a
 signal of population genetic structure among remnant Mojave Desert
 populations, even across geographically proximate mountain ranges.
 Further, we found evidence of a genetically distinct, potential relict
 herd from a previously hypothesized Great Basin lineage of desert bighorn
 sheep. The genetic structure of source herds was clearly reflected in
 translocated populations. In most cases, herds retained genetic evidence
 of multiple translocation events and subsequent admixture when founded
 from multiple remnant source herds. Our results add to a growing
 literature on how population genomic data can be used to guide and monitor
 restoration programs.
description: desert_bighorn_gprobsMatrix of genotype probabilities for all individuals included in the paper. File compressed with gzip.genotype_probs.txt.gzgbs_protocolThis file describes the full genotyping-by-sequencing library preparation protocol.desert_bighorn_fastqsDirectory containing .fastq files for all individuals analyzed in the paper. This includes 337 Ovis canadensis nelsoni individuals from across Nevada. This directory has been compressed as a tar archive. To uncompress from the command line:$ tar -zxvf desert_bighorn_fastqs.tar.gz
DOI: 10.5061/dryad.14ks803
title: Data from: Genetic differentiation between endemic Eriogonum soredium and its common relative E. shockleyi (Polygonaceae)

description: Discovering the extent of genetic differentiation between closely related
 taxa facilitates decisions regarding species protection under the
 Endangered Species Act. Here, we analyze genotype data to explore the
 relatedness of two buckwheat species: Eriogonum soredium, a narrow endemic
 under consideration for protection, and a widespread close relative,
 Eriogonum shockleyi. Eriogonum soredium grows only on Ordovician limestone
 outcroppings in west central Utah, whereas the range of E. shockleyi is
 broad, spanning the western United States from Colorado to California, and
 Idaho to Arizona. Eriogonum shockleyi is suspected of hybridizing with
 other buckwheats throughout this range. We detected higher levels of
 genetic diversity in E. shockleyi than in E. soredium, supporting the
 hypothesis that E. soredium is a derivative of E. shockleyi. We found
 moderate levels of admixture between the two taxa, implying the presence
 of incomplete reproductive barriers. Analysis of population structure
 revealed a genetic distinction between the two species. We found that
 genetic distance between samples is influenced more by taxon designation
 than geographic distance. Genetic evidence supports continued treatment of
 E. soredium as a distinct evolutionary entity.
description: erisor_codeERISOR_S2_L002_R1_001.fastq.gz_replaceERISOR_S2_L002_R1_001.fastq.gzERISOR_NoIndex_L006_R1_001.fasta.gz_replaceERISOR_NoIndex_L006_R1_001.fastq.gz
DOI: 10.5061/dryad.5bf77
title: Data from: Phosphorylated Groucho delays differentiation in the follicle stem cell lineage by providing a molecular memory of EGFR signaling in the niche

description: In the epithelial follicle stem cells (FSCs) of the Drosophila ovary,
 Epidermal Growth Factor Receptor (EGFR) signaling promotes self-renewal,
 whereas Notch signaling promotes differentiation of the prefollicle cell
 (pFC) daughters. We have identified two proteins, Six4 and Groucho (Gro),
 that link the activity of these two pathways to regulate the earliest cell
 fate decision in the FSC lineage. Our data indicate that Six4 and Gro
 promote differentiation towards the polar cell fate by promoting Notch
 pathway activity. This activity of Gro is antagonized by EGFR signaling,
 which inhibits Gro-dependent repression via p-ERK mediated
 phosphorylation. We have found that the phosphorylated form of Gro
 persists in newly formed pFCs, which may delay differentiation and provide
 these cells with a temporary memory of the EGFR signal. Collectively,
 these findings demonstrate that phosphorylated Gro labels a transition
 state in the FSC lineage and describe the interplay between Notch and EGFR
 signaling that governs the differentiation processes during this period.
description: RNA-Seq of early
 follicle cells – Ctrl Rep1 Read1Paired-end
 RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4,
 UAS-mCD8::GFP Replicate #1, Read 1Ctrl_Rep1_R1.fq.gzRNA-Seq of early follicle cells – Ctrl Rep1 Read2Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP Replicate #1, Read 2Ctrl_Rep1_R2.fq.gzRNA-Seq of early follicle cells – Ctrl Rep2 Read1Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP Replicate #2, Read 1Ctrl_Rep2_R1.fq.gzRNA-Seq of early follicle cells – Ctrl Rep2 Read2Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP Replicate #2, Read 2Ctrl_Rep2_R2.fq.gzRNA-Seq of early follicle cells – EGFRact Rep1 Read1Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP, UAS-EGFR[lambda]top Replicate #1, Read 1EGFRact_Rep1_R1.fq.gzRNA-Seq of early follicle cells – EGFRact Rep1 Read2Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP, UAS-EGFR[lambda]top Replicate #1, Read 2EGFRact_Rep1_R2.fq.gzRNA-Seq of early follicle cells – EGFRact Rep2 Read1Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP, UAS-EGFR[lambda]top Replicate #2, Read 1EGFRact_Rep2_R1.fq.gzRNA-Seq of early follicle cells – EGFRact Rep2 Read2Paired-end RNA-Sequencing data from early follicle cells Genotype 109-30-Gal4, UAS-mCD8::GFP, UAS-EGFR[lambda]top Replicate #2, Read 2EGFRact_Rep2_R2.fq.gz
DOI: 10.5061/dryad.db339
title: Data from: An exon-capture system for the entire class Ophiuroidea

description: Exon-capture studies have typically been restricted to relatively shallow
 phylogenetic scales due primarily to hybridisation constraints. Here, we
 present an exon-capture system for an entire class of marine
 invertebrates, the Ophiuroidea, built upon a phylogenetically diverse
 transcriptome foundation. The system captures ~90% of the 1552 exon
 target, across all major lineages of the quarter-billion year old extant
 crown group. Key features of our system are: 1) basing the target on an
 alignment of orthologous genes determined from 52 transcriptomes spanning
 the phylogenetic diversity and trimmed to remove anything difficult to
 capture, map or align, 2) use of multiple artificial representatives based
 on ancestral state reconstructions rather than exemplars to improve
 capture and mapping of the target, 3) mapping reads to a multi-reference
 alignment, and 4) using patterns of site polymorphism to distinguish among
 paralogy, polyploidy, allelic differences and sample contamination. The
 resulting data gives a well-resolved tree (currently standing at 417
 samples, 275,352 sites, 91% data-complete) that will transform our
 understanding of ophiuroid evolution and biogeography.
description: Phylogenetic data
 matrixZipped fasta format
 datamatrix of 417 samples for 1494 exons used to infer associated RAxML
 phylogenetic tree. See main ReadMe file for details.set417_TASSMAP_ExT4.zipPhylogenetic tree figurePDF figure of the RAxML bootstrap phylogenetic tree generated from the 417 sample 1494 exon phylogenetic data matrix. See main ReadMe file for details.set417_TASSMAP_ExT4_RAxML.pdfPhylogenetic treeNewick format RAxML tree of 417 samples using 1494 exons. See main ReadMe file for details.set417_TASSMAP_ExT4_RAxML.phyInformation TablesExcel format tables S1-3 providing information on samples, exons and genes. See main ReadMe for details.Supp_Tables_v3.xlsxDryad_submission_ReadMe_v1Word format main readme file, with information on contents of this DRYAD package.Reference filesNucleotide and amino acid fasta format reference files, and associated mapping text files; zipped.reference_files.zipmapping pipeline scriptsBiolinux shell script files for contig and read mapping and COI candidate contig collation. See main ReadMe file for details.shell_scripts.zipOPH01OPH01 trimmed fastq.gz reads - 175 files, 83 samplesOPH02OPH02 trimmed fastq.gz read files - 190 files, 95 samplesOPH03OPH03 trimmed fastq.gz read files - 192 files, 96 samplesOPH04OPH04 trimmed fastq.gz read files - 192 files, 96 samples
DOI: 10.5061/dryad.10tn7qb
title: Data from: The developmental transcriptomes of two sea biscuit species with differing larval types

description: Background: Larval developmental patterns are extremely varied both
 between and within phyla, however the genetic mechanisms leading to this
 diversification are poorly understood. We assembled and compared the
 developmental transcriptomes for two sea biscuit species (Echinodermata:
 Echinoidea) with differing patterns of larval development, to provide a
 resource for investigating the evolution of alternate life cycles. One
 species (Clypeaster subdepressus) develops via an obligately feeding larva
 which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster
 rosaceus) develops via a facultatively feeding larva that can develop
 through metamorphosis entirely based on egg provisioning in under one
 week. Results: Overall, the two transcriptomes are highly similar,
 containing largely orthologous contigs with similar functional annotation.
 However, we found distinct differences in gene expression patterns between
 larvae of the two species. Larvae from C. rosaceus, the facultative
 planktotroph, turned genes on at earlier stages and had less
 differentiation in gene expression between larval stages, whereas, C.
 subdepressus showed a higher degree of stage-specific gene expression.
 Conclusion: This study is the first genetic analysis of a species with
 facultatively feeding larvae. Our results are consistent with known
 developmental differences between the larval types and raise the question
 of whether earlier onset of developmental genes is a key step in the
 evolution of a reduced larval period. By publishing a transcriptome for
 this rare, intermediate, larval type, this study adds developmental
 breadth to the current genetic resources, which will provide a valuable
 tool for future research on echinoderm development as well as studies on
 the evolution of development in general.
description: Clypeaster rosaceus
 TranscriptomeDevelopmental
 transcriptome of Clypeaster rosaceus. Fasta file.Crosaceus_DevTranscriptome.fastaCsubdepressus_DevTranscriptomeClypeaster rosaceus annotationsAnnotations from Blast2Go for C, rosacues, including transcript IDs, GO terms, Enzyme codes, and BLAST hits.CrDev.annotClypeaster subdepressus annotationsAnnotations from Blast2GO for C. subdepressus.CsDev.annotCrEgg1a.fastqCrEgg2a.fastqCrEgg2b.fastqCrEgg3a.fastqCrEgg3b.fastqCrGastrula1b.fastqCrGastrula2a.fastqCrGastrula2b.fastqCrGastrula3a.fastqCrGastrula3b.fastqCr4arm1a.fastqCr4arm3a.fastqCr4arm3b.fastqCr4arm2a.fastqCr4arm2b.fastqCr8arm1b.fastqCr8arm2a.fastqCr8arm2b.fastqCsEgg2a.fastqCsEgg2b.fastqCsEgg1a.fastqCsEgg3a.fastqCsEgg3b.fastqCsGastrula1a.fastqCsGastrula1b.fastqCsGastrula2b.fastqCsGastrula3a.fastqCsGastrula3b.fastqCs4arm1a.fastqCs4arm2a.fastqCs4arm1b.fastqCs4arm2b.fastqCs4arm3a.fastqCs4arm3b.fastqCs8arm2a.fastqCs8arm2b.fastqCs8arm3a.fastqCs8arm3b.fastqCr8arm3a.fastqCr8arm3b.fastq
DOI: 10.5061/dryad.c697436
title: Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

description: Metabarcoding allows the genetic analysis of pooled samples of various
 sources. It is becoming popular in the study of animal diet, especially
 because it allows the analysis of the composition of feces without the
 need of handling animals. In this work, we studied the diet of the
 Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic
 to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes
 from feces using next-generation sequencing techniques. For the
 identification of assembled sequences, we employed a tree-based
 identification method that used a reference tree of sequences of
 freshwater organisms. The comparison of freshly collected fecal samples
 and older samples showed that fresh samples produced significantly more
 sequencing reads. They also rendered more operational taxonomical units
 (OTUs), but not significantly. Our analyses of 41 samples identified 224
 OTUs corresponding to species of the reference tree. Ephemeroptera,
 Diptera excl. Chironomidae, and Chironomidae were the most highly
 represented groups in terms of reads as well as samples. Other groups of
 freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida,
 Coleoptera, Crustacea, and Annelida. Our results are largely in line with
 previous morphological and genetic studies on the diet of the Pyrenean
 desman, but allowed the identification of a higher diversity of OTUs in
 each sample. Additionally, the bioinformatic pipeline we developed for
 deep sequencing of fecal samples will enable the quantitative analysis of
 the diet of this and other species, which can be highly useful to
 determine their ecological requirements.
description: ddRAD
 dataOriginal reads for each
 sample in FASTQ format.ddRAD_data.zip