cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gk117
title: Data from: Loss of mTORC2 signaling in oligodendrocyte precursor cells delays myelination

description: Myelin abnormalities are increasingly being recognized as an important
 component of a number of neurologic developmental disorders. The
 integration of many signaling pathways and cell types are critical for
 correct myelinogenesis. The PI3-K and mechanistic target of rapamycin
 (mTOR) pathways have been found to play key roles. mTOR is found within
 two distinct complexes, mTORC1 and mTORC2. mTORC1 activity has been shown
 to play a major role during myelination, while the role of mTORC2 is not
 yet well understood. To determine the role of mTORC2 signaling in
 myelinogenesis, we generated a mouse lacking the critical mTORC2 component
 Rictor in oligodendrocyte precursors (OPCs). Targeted deletion of Rictor
 in these cells decreases and delays the expression of myelin related
 proteins and reduces the size of cerebral white matter tracts. This is
 developmentally manifest as a transient reduction in myelinated axon
 density and g-ratio. OPC cell number is reduced at birth without
 detectable change in proliferation with proportional reductions in mature
 oligodendrocyte number at P15. The total number of oligodendrocytes as
 well as extent of myelination, does improve over time. Adult conditional
 knock-out (CKO) animals do not demonstrate a behavioral phenotype likely
 due in part to preserved axonal conduction velocities. These data support
 and extend prior studies demonstrating an important but transient
 contribution of mTORC2 signaling to myelin development.
description: Western
 BlotsBarnes
 MazeBuried
 MarblesBuried
 MarblesCell
 CountsConduction
 VelocityEZMMRI
 measurementsMRI
 MWFRictor CKO
 WesternRictor Olig2 Open
 FieldRotarodMRI ImagesT1 MRI images for measurementsP15 APC P5 PDGFRa imagesImages for APC and PDGFRa cell countsP60 APC imagesAPC images used for P60 cell countsP60 APC APC images.zip
DOI: 10.5061/dryad.2qs35
title: Data from: Forensic genomics as a novel tool for identifying the causes of mass mortality events

description: Toxic spills, hypoxia, disease outbreaks and toxin-producing algal blooms
 are all possible causes of mass mortality events, but in many cases it can
 be difficult to pinpoint the cause of death. Here we present a new
 approach that we name ‘forensic genomics’, combining field surveys, toxin
 testing and genomic scans. Forensic genomics queries allele frequencies of
 surviving animals for signatures of agents causing mass mortality and,
 where genetic diversity is high, is uniquely suited to identify natural
 selection in action. As a proof of concept, we use this approach to
 investigate the causes of an invertebrate mass mortality event, and its
 genetic effects on an abalone population. Our results support that a
 harmful algal bloom producing a yessotoxin was a major causative agent to
 the event.
description: SNPs and genotypes
 identified in H. rufescens, Fort Ross 2011.tab-delimited text file
 containing all SNPs passing the GATK VQSR algorithm found in Fort Ross
 abalone in 2011, and genotypes in all individuals assigned with Q20 as
 cutoff. The standard GATK best practise protocol v2 was followed, using an
 initial call set with Q30 as cutoff to train the VQSR. Raw data files are
 accessible at the NCBI Short Read Archive (SRA), project accession #
 SRP037568.Genotypes.txt
DOI: 10.5061/dryad.1k450
title: Data from: Retrotransposon proliferation coincident with the evolution of dioecy in asparagus

description: Current phylogenetic sampling reveals that dioecy and an XY sex chromosome
 pair evolved once or possibly twice in the genus Asparagus. Although there
 appear to be some lineage-specific polyploidization events, the base
 chromosome number of 2n=2x=20 is relatively conserved across the Asparagus
 genus. Regardless, dioecious species tend to have larger genomes than
 hermaphroditic species. Here we test whether this genome size expansion in
 dioecious species is related to a polyploidization and subsequent
 chromosome fusion or retrotransposon proliferation in dioecious species.
 We first estimate genome sizes or use published values for four
 hermaphrodites and four dioecious species distributed across the phylogeny
 and show that dioecious species typically have larger genomes than
 hermaphroditic species. Utilizing a phylogenomic approach we find no
 evidence for ancient polyploidization contributing to increased genome
 sizes of sampled dioecious species. We do find support for an ancient
 whole genome duplication event predating the diversification of the
 Asparagus genus. Repetitive DNA content of the four hermaphroditic and
 four dioecious species was characterized based on randomly sampled whole
 genome shotgun sequencing and common elements were annotated. Across our
 broad phylogenetic sampling, Ty-1 Copia retroelements in particular have
 undergone a marked proliferation in dioecious species. In the absence of a
 detectable whole genome duplication event, retrotransposon proliferation
 is the most likely explanation for the precipitous increase in genome size
 in dioecious Asparagus species.
description: Asparagus officinalis
 RepeatMasker databaseThis fasta file contains
 a custom garden asparagus RepeatMasker database. A total of 893,623 454
 FLX Titanium reads were generated from leaf tissue of a doubled haploid
 (YY) garden asparagus individual. Reads were stringently filtered to a
 150nt minimum length. RepeatExplorer was then run, and the resulting cap3
 consensus assemblies for each cluster were annotated using
 RepeatClassifier, part of the RepeatModeler (v1.0.8) suite, with default
 settings. A total of 22,361 sequences greater than 150nt in length and
 with annotations.Asparagus.repeatexplorer.annotatedRepeats.faAsparagus genus 454 readsThis tar.bz2 file contains 454 sequencing fasta files for A. aphyllus, A. asparagoides, A. densiflorus, A. falcatus, A. maritimus, A. officinalis, A. pyrimidalis, A. stipularis, and A. virgatus. There is an additional A. officinalis 454 dataset that is significantly higher coverage, named "A_officinalis_WGS_in.454.AdditionalHighCoverage.fasta".Asparagus_454_wgs.tar.bz2
DOI: 10.5061/dryad.qs113
title: Data from: Selection on a genetic polymorphism counteracts ecological speciation in a stick insect

description: The interplay between selection and aspects of the genetic architecture of
 traits (such as linkage, dominance, and epistasis) can either drive or
 constrain speciation. Despite accumulating evidence that speciation can
 progress to “intermediate” stages—with populations evolving only partial
 reproductive isolation—studies describing selective mechanisms that impose
 constraints on speciation are more rare than those describing drivers. The
 stick insect Timema cristinae provides an example of a system in which
 partial reproductive isolation has evolved between populations adapted to
 different host plant environments, in part due to divergent selection
 acting on a pattern polymorphism. Here, we demonstrate how selection on a
 green/melanistic color polymorphism counteracts speciation in this system.
 Specifically, divergent selection between hosts does not occur on color
 phenotypes because melanistic T. cristinae are cryptic on the stems of
 both host species, are resistant to a fungal pathogen, and have a mating
 advantage. Using genetic crosses and genome-wide association mapping, we
 quantify the genetic architecture of both the pattern and color
 polymorphism, illustrating their simple genetic control. We use these
 empirical results to develop an individual-based model that shows how the
 melanistic phenotype acts as a “genetic bridge” that increases gene flow
 between populations living on different hosts. Our results demonstrate how
 variation in the nature of selection acting on traits, and aspects of
 trait genetic architecture, can impose constraints on both local
 adaptation and speciation.
description: spec_data.tarContains all raw reflectance and irradiance spectra.mate_choice_dataData table of no-choice mating.fungal_infection_dataData table containing fungal infection information.Simulation scriptsSource code and wrapper scripts for running simulations.chc_dataData table containing CHC profiles for each individual. Individuals are given in the first column, their sex in the second, and their color phenotype in the third. The remaining columns represent different CHC compounds measured.fst_tablecontains population codes, geographical distance between them, whether they are found on the same host or different hosts, and estimates of Fst for the locus controlling color. Also included is the mean genome-wide Fst (from Nosil et al. 2012 Proc B.) and the difference between Fst at the color locus minus mean genomic Fst.
DOI: 10.5061/dryad.c0g33
title: Data from: Single molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

description: Highly-repetitive satellite DNA (satDNA) repeats are found in most
 eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome
 stability and chromosome segregation. Their repetitive nature poses a
 challenge for genome assembly and makes progress on the detailed study of
 satDNA structure difficult. Here we use single-molecule sequencing long
 reads from Pacific Biosciences (PacBio) to determine the detailed
 structure of all major autosomal complex satDNA loci in Drosophila
 melanogaster, with a particular focus on the 260-bp and Responder
 satellites. We determine the optimal de novo assembly methods and
 parameter combinations required to produce a high quality assembly of
 these previously unassembled satDNA loci and validate this assembly using
 molecular and computational approaches. We determined that the
 computationally intensive PBcR-BLASR assembly pipeline yielded better
 assemblies than the faster and more efficient pipelines based on the MHAP
 hashing algorithm, and that it is essential to validate assemblies of
 repetitive loci. The assemblies reveal that satDNA repeats are organized
 into large arrays interrupted by transposable elements. The repeats in the
 center of the array tend to be homogenized in sequence, suggesting that
 gene conversion and unequal crossovers lead to repeat homogenization
 through concerted evolution, though the degree of unequal crossing-over
 may differ among complex satellite loci. We find evidence for higher order
 structure within satDNA arrays that suggest recent structural
 rearrangements. These assemblies provide a platform for the evolutionary
 and functional genomics of satDNAs in pericentric heterochromatin.
description: PacBio assemblies from
 Khost et al 2017Five PacBio assemblies
 of D. melanogaster ISO1 strain used in Khost et al 2017 (doi:
 https://doi.org/10.1101/054155) This paper focuses on assembly and
 structure of satellite DNA loci in D. mel. Please see the README for
 addition details.Khost_et_al_Dryad.tar.gz
DOI: 10.5061/dryad.cp8sr
title: Data from: Sinonasal microbiome sampling: a comparison of techniques

description: Background: The role of the sino-nasal microbiome in CRS remains unclear.
 We hypothesized that the bacteria within mucosal-associated biofilms may
 be different from the more superficial-lying, free-floating bacteria in
 the sinuses and that this may impact on the microbiome results obtained.
 This study investigates whether there is a significant difference in the
 microbiota of a sinonasal mucosal tissue sample versus a swab sample.
 Methods: Cross-sectional study with paired design. Mucosal biopsy and swab
 samples were obtained intra-operatively from the ethmoid sinuses of 6
 patients with CRS. Extracted DNA was sequenced on a Roche-454 sequencer
 using 16S-rRNA gene targeted primers. Data were analyzed using QIIME 1.8
 software package. Results: At a maximum subsampling depth of 1,100 reads,
 the mean observed species richness was 33.3 species (30.6 for swab, versus
 36 for mucosa; p &gt; 0.05). There was no significant difference in
 phylogenetic and non-phylogenetic alpha diversity metrics (Faith’s
 PD_Whole_Tree and Shannon’s index) between the two sampling methods (p
 &gt; 0.05). The type of sample also had no significant effect on
 phylogenetic and non-phylogenetic beta diversity metrics (Unifrac and
 Bray-Curtis; p &gt; 0.05). Conclusion: We observed no significant
 difference between the microbiota of mucosal tissue and swab samples. This
 suggests that less invasive swab samples are representative of the
 sinonasal mucosa microbiome and can be used for future sinonasal
 microbiome studies.
description: SFF
 FileSFF File containing raw
 454 sequence data. PCR and pyrosequencing was performed by MR DNA Lab
 (Shallowater, TX) on a Roche 454 sequencer (F. Hoffmann-La Roche Ltd,
 Basel, Switzerland).51712Cleland16S_pr.sffMapping fileMapping File (in standard QIIME tab-separated format). Sample IDs are in the form of PatientNumber_SampleType. Included samples in the study are the paired samples of patients one to six. Other swab samples included in same run with no corresponding tissue samples were excluded from the study and are marked as such in the mapping file.51712Cleland16S_pr.map.txt
DOI: 10.5061/dryad.tb2p4
title: Data from: Using viromes to predict novel immune proteins in non-model organisms

description: Immunity is mostly studied in a few model organisms, leaving the majority
 of immune systems on the planet unexplored. To characterize the immune
 systems of non-model organisms alternative approaches are required.
 Viruses manipulate host cell biology through the expression of proteins
 that modulate the immune response. We hypothesized that metagenomic
 sequencing of viral communities would be useful to identify both known and
 unknown host immune proteins. To test this hypothesis, a mock human virome
 was generated and compared to the human proteome using tBLASTn, resulting
 in 36 proteins known to be involved in immunity. This same pipeline was
 then applied to reef-building coral, a non-model organism that currently
 lacks traditional molecular tools like transgenic animals, gene-editing
 capabilities, and in vitro cell cultures. Viromes isolated from corals and
 compared with the predicted coral proteome resulted in 2503 coral
 proteins, including many proteins involved with pathogen sensing and
 apoptosis. There were also 159 coral proteins predicted to be involved
 with coral immunity but currently lacking any functional annotation. The
 pipeline described here provides a novel method to rapidly predict host
 immune components that can be applied to virtually any system with the
 potential to discover novel immune proteins.
description: Coral
 ViromesCoral viromes extracted
 from Porites rus, Acropora sp., Acropora yongei, Pocillopora
 verrucosaFile S2- Coral
 Viromes.zip
DOI: 10.5061/dryad.q1t7v
title: Data from: Chlamydomonas genome resource for laboratory strains reveals a mosaic of sequence variation, identifies true strain histories, and enables strain-specific studies

description: Chlamydomonas reinhardtii is a widely used reference organism in studies
 of photosynthesis, cilia, and biofuels. Most research in this field uses a
 few dozen standard laboratory strains that are reported to share a common
 ancestry, but exhibit substantial phenotypic differences. In order to
 facilitate ongoing Chlamydomonas research and explain the phenotypic
 variation, we mapped the genetic diversity within these strains using
 whole-genome resequencing. We identified 524,640 single nucleotide
 variants and 4812 structural variants among 39 commonly used laboratory
 strains. Nearly all (98.2%) of the total observed genetic diversity was
 attributable to the presence of two, previously unrecognized, alternate
 haplotypes that are distributed in a mosaic pattern among the extant
 laboratory strains. We propose that these two haplotypes are the remnants
 of an ancestral cross between two strains with ∼2% relative divergence.
 These haplotype patterns create a fingerprint for each strain that
 facilitates the positive identification of that strain and reveals its
 relatedness to other strains. The presence of these alternate haplotype
 regions affects phenotype scoring and gene expression measurements. Here,
 we present a rich set of genetic differences as a community resource to
 allow researchers to more accurately conduct and interpret their
 experiments with Chlamydomonas.
description: tpc00508-SupplementalDS1Detailed Strain Historiestpc00508-SupplementalDS2SNV and Small InDel VCF Filetpc00508-SupplementalDS3Structural Variant VCF Filetpc00508-SupplementalDS4Pairwise SNVs for All Strainstpc00508-SupplementalDS6Allele-Specific PCR Primer Sequencestpc00508-SupplementalDS5Transposon Position BED File
DOI: 10.5061/dryad.dg32560
title: Data from: Urbanization as a facilitator of gene flow in a human health pest

description: Urban fragmentation can reduce gene flow that isolates populations,
 reduces genetic diversity and increases population differentiation, all of
 which have negative conservation implications. Alternatively, gene flow
 may actually be increased among urban areas consistent with an urban
 facilitation model. In fact, urban adapter pests are able to thrive in the
 urban environment and may be experiencing human-mediated transport. Here,
 we used social network theory with a population genetic approach to
 investigate the impact of urbanization on genetic connectivity in the
 Western black widow spider, as an urban pest model of human health
 concern. We collected genomewide SNP variation from mitochondrial and
 nuclear ddRAD sequence datasets from 210 individuals sampled from 11 urban
 and 10 non-urban locales across its distribution of the Western U.S. From
 urban and non-urban contrasts of population, phylogenetic, and network
 analyses, urban locales have higher within-population genetic diversity,
 lower between-population genetic differentiation, and higher estimates of
 genetic connectivity. Social network analyses show that urban locales not
 only have more connections, but can act as hubs that drive connectivity
 among non-urban locales, which show signatures of historical isolation.
 These results are consistent with an urban facilitation model of gene
 flow, and demonstrate the importance of sampling multiple cities and
 markers to identify the role that urbanization has had on larger spatial
 scales. As the urban landscape continues to grow, this approach will help
 determine what factors influence the spread and adaptation of pests, like
 the venomous black widow spider, in building policies for human and
 biodiversity health.
description: LhesUrbanGeneFlowR scripts used for analysesLhesmtDNAseqFASTA format for mitochondrial ND1 region 210 L. hesperus and 3 L. mactans samplesTotalRawSNPsddRADseq SNPs for 21 populations of Latrodectus hesperus and 3 L. mactans individuals
DOI: 10.5061/dryad.3264f
title: Data from: A theoretical foundation for multi-scale regular vegetation patterns

description: Self-organized regular vegetation patterns are widespread1 and thought to
 mediate ecosystem functions such as productivity and robustness, but the
 mechanisms underlying their origin and maintenance remain disputed.
 Particularly controversial are landscapes of overdispersed (evenly spaced)
 elements, such as North American Mima mounds, Brazilian murundus, South
 African heuweltjies, and, famously, Namibian fairy circles. Two competing
 hypotheses are currently debated. On the one hand, models of
 scale-dependent feedbacks, whereby plants facilitate neighbours while
 competing with distant individuals, can reproduce various regular patterns
 identified in satellite imagery. Owing to deep theoretical roots and
 apparent generality, scale-dependent feedbacks are widely viewed as a
 unifying and near-universal principle of regular-pattern formation,
 despite scant empirical evidence. On the other hand, many overdispersed
 vegetation patterns worldwide have been attributed to subterranean
 ecosystem engineers such as termites, ants, and rodents. Although
 potentially consistent with territorial competition, this interpretation
 has been challenged theoretically and empirically and (unlike
 scale-dependent feedbacks) lacks a unifying dynamical theory, fuelling
 scepticism about its plausibility and generality. Here we provide a
 general theoretical foundation for self-organization of social-insect
 colonies, validated using data from four continents, which demonstrates
 that intraspecific competition between territorial animals can generate
 the large-scale hexagonal regularity of these patterns. However, this
 mechanism is not mutually exclusive with scale-dependent feedbacks. Using
 Namib Desert fairy circles as a case study, we present field data showing
 that these landscapes exhibit multi-scale patterning—previously
 undocumented in this system—that cannot be explained by either mechanism
 in isolation. These multi-scale patterns and other emergent properties,
 such as enhanced resistance to and recovery from drought, instead arise
 from dynamic interactions in our theoretical framework, which couples both
 mechanisms. The potentially global extent of animal-induced regularity in
 vegetation—which can modulate other patterning processes in functionally
 important ways—emphasizes the need to integrate multiple mechanisms of
 ecological self-organization.
description: FC lifespan and
 snapshotssnapshots_and_FC_lifespan.zipMound coordinates - termite modeltermite_model_mound_locations.zipMound coordinates - field datatermite_mound_location_field_data.zipMatrix vegetation - FT analysis (model and data)vegetation_FT_spatial_analysis.zipVoronoi analysis of moundsVoronoi data.xlsx
DOI: 10.5061/dryad.qj925
title: Data from: Geographically widespread honeybee-gut symbiont subgroups show locally distinct antibiotic-resistant patterns

description: How long-term antibiotic treatment affects host bacterial associations is
 still largely unknown. The honeybee-gut microbiota has a simple
 composition, so we used this gut community to investigate how long-term
 antibiotic treatment affects host-associated microbiota. We investigated
 the phylogenetic relatedness, genomic content (GC percentage, genome size,
 number of genes, and CRISPR), and antibiotic-resistant genes for strains
 from two abundant members of the honeybee core gut microbiota (Gilliamella
 apicola and Snodgrassella alvi). Domesticated honeybees are subjected to
 geographically different management policies, so we used two research
 apiaries, representing different antibiotic treatment regimens in their
 apiculture: Low antibiotic usage (Norway) and high antibiotic usage
 (Arizona, USA). We applied whole-genome shotgun sequencing on 48 G.
 apicola and 22 S. alvi. We identified three predominating subgroups of G.
 apicola in honeybees from both Norway and Arizona. For G. apicola, genetic
 content substantially varied between subgroups and distance-similarity
 calculations showed similarity discrepancy between subgroups. Functional
 differences between subgroups, such as pectin-degrading enzymes (G.
 apicola), were also identified. In addition, we identified horizontal gene
 transfer (HGT) of transposon- (Tn10) associated tetracycline resistance
 (Tet B) across the G. apicola subgroups in the Arizonan honeybees, using
 interspace polymorphisms in the Tet B determinant. Our results support
 that honeybee-gut symbiont subgroups can resist long-term antibiotic
 treatment and maintain functionality through acquisition of geographically
 distinct antibiotic-resistant genes by HGT.
description: gbk_Gillia_Snodgrassella