cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.68864
title: Data from: Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo

description: Background: A complex network of gene interactions controls gene
 regulation throughout development and the life of the organisms. Insights
 can be made into these processes by studying the functional interactions
 (or “motifs”) which make up these networks. Results: We sought to
 understand the functionality of one of these network motifs, negative
 feedback, in a multi-cellular system. This was accomplished using a
 synthetic network expressed in the Drosophila melanogaster embryo using
 the yeast proteins Gal4 (a transcriptional activator) and Gal80 (an
 inhibitor of Gal4 activity). This network is able to produce an
 attenuation or shuttling phenotype depending on the Gal80/Gal4 ratio. This
 shuttling behavior was validated by expressing Gal3, which inhibits Gal80,
 to produce a localized increase in free Gal4 and therefore signaling.
 Mathematical modeling was used to demonstrate the capacity for negative
 feedback to produce these varying outputs. Conclusions: The capacity of a
 network motif to exhibit different phenotypes due to minor changes to the
 network in multi-cellular systems was shown. This work demonstrates the
 importance of studying network motifs in multi-cellular systems.
description: Gal4x4In this zip folder are
 the gal4x4 images used to generate the data in the paper, in Zeiss lsm
 format. They are sorted into folders and subfolders by genotype, and named
 according to the date taken. The Zeiss lsm format has other metadata
 (voxel size, image size, etc) associated with it. The files were analyzed
 using Matlab code available on the Reeveslab website.Gal4x2In this zip folder are
 the gal4x2 images used to generate the data in the paper, in Zeiss lsm
 format. They are sorted into folders and subfolders by genotype, and named
 according to the date taken. The Zeiss lsm format has other metadata
 (voxel size, image size, etc) associated with it. The files were analyzed
 using Matlab code available on the Reeveslab website.Gal3In this zip folder are
 the gal3 images used to generate the data in the paper, in Zeiss lsm
 format. They are sorted into folders and subfolders by genotype, and named
 according to the date taken. The Zeiss lsm format has other metadata
 (voxel size, image size, etc) associated with it. The files were analyzed
 using Matlab code available on the Reeveslab website.
DOI: 10.5061/dryad.6pv18k3
title: Data from: A novel method for using ecoacoustics to monitor post‐translocation behaviour in an endangered passerine

description: 1. Conservation translocations are an important tool in wildlife
 management, but have traditionally suffered from a low success rate.
 Increasing understanding of animal behaviour is vital in improving the
 success of translocations, but few methods exist to efficiently monitor
 highly mobile and cryptic species post-release. 2. We present a novel
 approach to using dynamic occupancy modelling in combination with data
 derived from autonomous acoustic recording units to monitor the
 post-release behaviour of hihi (Notiomystis cincta), a threatened endemic
 bird, at a translocation site in New Zealand. The process of analysing
 large quantities of acoustic data was facilitated by using automated
 classifiers and manual validation, an approach that was both accurate and
 efficient. 3. We find that this approach detects behavioural change
 consistent with the transition from exploration of a new site to territory
 formation. We identify that hihi territories at the study site were
 closely linked to watercourses, but were not related to distance from
 release site. 4. We find that this method is able to effectively monitor
 post-release dispersal, and could provide a cost-efficient and less
 invasive alternative to radio-tracking for monitoring of vocal species.
description: SongScope Model
 parametersInput parameters for
 SongScope modelCode_for_mapR code for Figure 5final_modelR data file of final DOM modelHihiDOM_ModelselectionandcreationR code for DOM model selectionR_code_Variables_originalModel variablesTable1.020517_150001Sound data used in Table 1 and a subset of entire datasetTable1.020517_151457Sound data used in Table 1 and a subset of entire datasetTable1.020517_152952Sound data used in Table 1 and a subset of entire datasetTable1.020517_154448Sound data used in Table 1 and a subset of entire datasetTable1.020517_155944Sound data used in Table 1 and a subset of entire datasetTable1.020517_162934Sound data used in Table 1 and a subset of entire datasetTable1.020517_161439Sound data used in Table 1 and a subset of entire datasetTable1.020517_164429Sound data used in Table 1 and a subset of entire datasetTable1resultsResults for Table 1Table2.15_min_summary_test_resultsResults for Table 2Table3_Presence_absenceResults for Table 3
DOI: 10.5061/dryad.75b406n
title: Data from: Long-lived rodents reveal signatures of positive selection in genes associated with lifespan

description: The genetics of lifespan determination is poorly understood. Most research
 has been done on short-lived animals and it is unclear if these insights
 can be transferred to long-lived mammals like humans. Some African
 mole-rats (Bathyergidae) have life expectancies that are multiple times
 higher than similar sized and phylogenetically closely related rodents. To
 gain new insights into genetic mechanisms determining mammalian lifespans,
 we obtained genomic and transcriptomic data from 17 rodent species and
 scanned eleven evolutionary branches associated with the evolution of
 enhanced longevity for positively selected genes (PSGs). Indicating
 relevance for aging, the set of 250 identified PSGs showed in liver of
 long-lived naked mole-rats and short-lived rats an expression pattern that
 fits the antagonistic pleiotropy theory of aging. Moreover, we found the
 PSGs to be enriched for genes known to be related to aging. Among these
 enrichments were “cellular respiration” and “metal ion homeostasis”, as
 well as functional terms associated with processes regulated by the mTOR
 pathway: translation, autophagy and inflammation. Remarkably, among PSGs
 are RHEB, a regulator of mTOR, and IGF1, both central components of
 aging-relevant pathways, as well as genes yet unknown to be
 aging-associated but representing convincing functional candidates, e.g.
 RHEBL1, AMHR2, PSMG1 and AGER. Exemplary protein homology modeling
 suggests functional consequences for amino acid changes under positive
 selection. Therefore, we conclude that our results provide a meaningful
 resource for follow-up studies to mechanistically link identified genes
 and amino acids under positive selection to aging and lifespan
 determination.
description: Alignments and
 positively selected sitesThe package contains
 visualizations of alignments and positively selected sites for all genes
 and branches that were analyzed in the corresponding
 article.supplement_data.tar.gz
DOI: 10.5061/dryad.h752n4q
title: Data from: Impaired spatial memory codes in a mouse model of Rett syndrome

description: The Mecp2+/-mouse model recapitulates many phenotypes of patients with
 Rett syndrome (RTT), including learning and memory deficits. It is
 unknown, however, how the disease state alters memory circuit functions in
 vivoin RTT mice. Here we recorded from hippocampal place cells, which are
 thought to encode spatial memories, in freely moving RTT mice and
 littermate controls. We found that place cells in RTT mice are impaired in
 their experience-dependent increase of spatial information. This
 impairment is accompanied by an enhanced baseline firing synchrony of
 place cells within ripple oscillations during rest, which consequently
 occludes the increase in synchrony after a novel experience. Behaviorally,
 contextual memory is normal at short but not long time scale in RTT mice.
 Our results suggest that hypersynchrony interferes with memory
 consolidation and leads to impaired spatial memory codes in RTT mice,
 providing a possible circuit mechanism for memory deficits in Rett
 Syndrome.
description: SpikeSourceDataThis is the newer version of the source spike data used in the analysis, which should replace the old SpikeSourceData. The file can be opened using the Matlab "load" function. A small modification is made during the the 2nd revision of the manuscript.BehavioralSourceData_finalThis is the newer version of the source behavioral data used in the analysis, which should replace the old Behavioral Data. The file can be opened using the Matlab "load" function. A minor modification is made during the the 2nd revision of the manuscript.
DOI: 10.5061/dryad.8v528
title: Data from: Sorting things out: assessing effects of unequal specimen biomass on DNA metabarcoding

description: Environmental bulk samples often contain many different taxa that vary
 several orders of magnitude in biomass. This can be problematic in DNA
 metabarcoding and metagenomic high-throughput sequencing approaches, as
 large specimens contribute disproportionately high amounts of DNA
 template. Thus, a few specimens of high biomass will dominate the dataset,
 potentially leading to smaller specimens remaining undetected. Sorting of
 samples by specimen size (as a proxy for biomass) and balancing the
 amounts of tissue used per size fraction should improve detection rates,
 but this approach has not been systematically tested. Here, we explored
 the effects of size sorting on taxa detection using two freshwater
 macroinvertebrate bulk samples, collected from a low-mountain stream in
 Germany. Specimens were morphologically identified and sorted into three
 size classes (body size &lt; 2.5 × 5, 5 × 10, and up to 10 × 20 mm).
 Tissue powder from each size category was extracted individually and
 pooled based on tissue weight to simulate samples that were not sorted by
 biomass (“Unsorted”). Additionally, size fractions were pooled so that
 each specimen contributed approximately equal amounts of biomass
 (“Sorted”). Mock samples were amplified using four different DNA
 metabarcoding primer sets targeting the Cytochrome c oxidase I (COI) gene.
 Sorting taxa by size and pooling them proportionately according to their
 abundance lead to a more equal amplification of taxa compared to the
 processing of complete samples without sorting. The sorted samples
 recovered 30% more taxa than the unsorted samples at the same sequencing
 depth. Our results imply that sequencing depth can be decreased
 approximately fivefold when sorting the samples into three size classes
 and pooling by specimen abundance. Even coarse size sorting can
 substantially improve taxa detection using DNA metabarcoding. While
 high-throughput sequencing will become more accessible and cheaper within
 the next years, sorting bulk samples by specimen biomass or size is a
 simple yet efficient method to reduce current sequencing costs.
description: Metabarcoding pipeline
 and scriptsFull metabarcoding
 pipeline and R scripts to produce figures and statistical analysis in the
 paper. Includes intermediate scripts, always use the script with the
 latest version number.2 HiSeq biomass
 160707.zipDereplicated and
 preprocessed metabarcoding dataThese are the processed
 reads that were used for OTU clustering. Files are 10 samples (5 for each
 stream) amplified with 4 primer pairs (=40). The two sequencing lanes are
 differentiated with L001 and L002 but were merged into one file for each
 of the 40 sample in the analysis (only sequencing replicates). NOTE: If
 you want to access the raw sequencing data without any processing, please
 refer to the NCBI SRA accession numbers in the
 manuscript.6
 dereplicate.zipFastQC and run
 informationFastQC check and
 metadata for all 3 lanes run on the Illumina HiSeq (1,5 rapid runs v2, 250
 bp PE).FastQC.zip
DOI: 10.5061/dryad.f51f5
title: Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?

description: Flounder change colour and pattern for camouflage. We used a spectrometer
 to measure reflectance spectra and a digital camera to capture body
 patterns of two flounder species camouflaged on four natural backgrounds
 of different spatial scale (sand, small gravel, large gravel and rocks).
 We quantified the degree of spectral match between flounder and background
 relative to the situation of perfect camouflage in which flounder and
 background were assumed to have identical spectral distribution.
 Computations were carried out for three biologically relevant observers:
 monochromatic squid, dichromatic crab and trichromatic guitarfish. Our
 computations present a new approach to analysing datasets with multiple
 spectra that have large variance. Furthermore, to investigate the spatial
 match between flounder and background, images of flounder patterns were
 analysed using a custom program originally developed to study cuttlefish
 camouflage. Our results show that all flounder and background spectra fall
 within the same colour gamut and that, in terms of different observer
 visual systems, flounder matched most substrates in luminance and colour
 contrast. Flounder matched the spatial scales of all substrates except for
 rocks. We discuss findings in terms of flounder biology; furthermore, we
 discuss our methodology in light of hyperspectral technologies that
 combine high-resolution spectral and spatial imaging.
description: Spectra and
 photographsThis .zip file contains
 the spectral measurements taken from the flounders' skin, as well as
 photographs of the animal against backgrounds of sand, rocks, small
 gravel, and large gravel. You may find the details of data acquisition and
 processing in our paper titled:"Changeable camouflage: how well can
 flounder resemble the colour and spatial scale of substrates in their
 natural habitats?" Please email the corresponding author for any
 questions. Code we have used to process these data is also available upon
 request.Akkaynak_et_al_data_file.zip
DOI: 10.5061/dryad.9mb54
title: Data from: Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

description: The advent of a new generation of electron microscopes and direct electron
 detectors has realized the potential of single particle cryo-electron
 microscopy (cryo-EM) as a technique to generate high-resolution
 structures. Calculating these structures requires high performance
 computing clusters, a resource that may be limiting to many likely cryo-EM
 users. To address this limitation and facilitate the spread of cryo-EM, we
 developed a publicly available 'off-the-shelf' computing
 environment on Amazon's elastic cloud computing infrastructure. This
 environment provides users with single particle cryo-EM software packages
 and the ability to create computing clusters with 16 to 480+ CPUs. We
 tested our computing environment using a publicly available 80S yeast
 ribosome dataset and estimate that laboratories could determine
 high-resolution cryo-EM structures for $50 to $1,500 per structure within
 a timeframe comparable to local clusters. Our analysis shows that
 Amazon's cloud computing environment may offer a viable computing
 environment for cryo-EM.
description: Compressed folder:
 Cianfrocco_Leschziner_Dryad_UploadThis folder contains the
 necessary data files to extract particles, classify 3D data, and determine
 a 4.6 Angstrom cryo-EM structure of the 80S yeast ribosome. For a
 step-by-step guide, please read more here:
 http://git.io/8LrCqg.Cianfrocco_Leschziner_Dryad_Upload.zip
DOI: 10.5061/dryad.mc270
title: Data from: Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae)

description: Background: Flower size varies dramatically across angiosperms,
 representing innovations over the course of &gt;130 million years of
 evolution and contributing substantially to relationships with
 pollinators. However, the genetic underpinning of flower size is not well
 understood. Saltugilia (Polemoniaceae) provides an excellent non-model
 system for extending the genetic study of flower size to interspecific
 differences that coincide with variation in pollinators. Results: Using
 targeted gene capture methods, we infer phylogenetic relationships among
 all members of Saltugilia to provide a framework for investigating the
 genetic control of flower size differences via RNA-Seq de novo assembly.
 Nuclear concatenation and species tree inference methods provide congruent
 topologies. The inferred evolutionary trajectory of flower size is from
 small flowers to larger flowers. We identified 4 to 10,368 transcripts
 that are differentially expressed during flower development, with many
 unigenes associated with cell wall modification and components of the
 auxin and gibberellin pathways. Conclusions: Saltugilia is an excellent
 model for investigating covarying floral and pollinator evolution. Four
 candidate genes from model systems (BIG BROTHER, BIG PETAL, GASA, and
 LONGIFOLIA) show differential expression during development of flowers in
 Saltugilia, and four other genes (FLOWERING-PROMOTING FACTOR 1,
 PECTINESTERASE, POLYGALACTURONASE, and SUCROSE SYNTHASE) fit into
 hypothesized organ size pathways. Together, these gene sets provide a
 strong foundation for future functional studies to determine their roles
 in specifying interspecific differences in flower size.
description: de novo assemblies for
 each taxa and a master reference for the genusThis includes de novo
 assembly of a "master reference" using all reads in the study,
 then filtered assemblies for each taxa using a 1 TPM
 threshold.denovo_assemblies.tarNuclear_gene_alignmentsMAFFT gene alignments for 89 putatively single copy nuclear genes, with a concatenated file in both .phy and .nex formats. Genes were sequenced using MYbaits exon capture kit, sequenced on Illumina platform, and then analyzed using HybPiper.Plastid_gene_alignmentsMAFFT gene alignments for 80 plastid protein coding genes, as well as a concatenated alignment in both .phy and .nex formats. Genes were sequenced using MYbaits targeted exon capture baits, sequenced on Illumina platform, and analyzed using HybPiper.Assembly annotation reportGO annotation report of the Saltugilia assembly using Annotate as part of the Trinity pipeline.Dryad_annotation_report.xlsx
DOI: 10.5061/dryad.8pg7963
title: Data from: Differential responses to ocean acidification between populations of Balanophyllia elegans corals from high and low upwelling environments

description: Ocean acidification (OA), the global decrease in surface water pH from
 absorption of anthropogenic CO2, may put many marine taxa at risk.
 However, populations that experience extreme localized conditions, and are
 adapted to these conditions predicted in the global ocean in 2100, may be
 more tolerant to future OA. By identifying locally adapted populations,
 researchers can examine the mechanisms used to cope with decreasing pH.
 One oceanographic process that influences pH, is wind driven upwelling.
 Here we compare two Californian populations of the coral Balanophyllia
 elegans from distinct upwelling regimes, and test their physiological and
 transcriptomic responses to experimental seawater acidification. We
 measured respiration rates, protein and lipid content, and gene expression
 in corals from both populations exposed to pH levels of 7.8 and 7.4 for 29
 days. Corals from the population that experiences lower pH due to high
 upwelling, maintained the same respiration rate throughout the exposure.
 In contrast, corals from the low upwelling site had reduced respiration
 rates, protein content, and lipid-class content at low pH exposure,
 suggesting they have depleted their energy reserves. Using RNA-Seq, we
 found that corals from the high upwelling site upregulated genes involved
 in calcium ion binding and ion transport, most likely related to pH
 homeostasis and calcification. In contrast, corals from the low upwelling
 site downregulated stress response genes at low pH exposure. Divergent
 population responses to low pH observed in B. elegans highlight the
 importance of multi-population studies for predicting a species’ response
 to future OA.
description: Orthogroup
 TranscriptomeTranscriptome in fasta
 file format containing all contigs for the PAC and GOL population that
 were assigned an Orthogroup.all_transcriptome_orthogroups_blastorphansPAC TranscriptomeTranscriptome in fasta file format containing all contigs for the PAC populationPAC_transcriptome.txtGOL TranscriptomeTranscriptome in fasta file format containing all contigs for the GOL populationGOL_transcriptome.txtOrthogroup RSEM merged matrixRSEM matrix file containing total expression counts for all contigs in each Orthogroup category; header explanantion: P or G referes to population origin (PAC or GOL), 1 2 or 3 refers to treatment replicate, H or L refers to high or low pH exposure, 1 or 2 referes to time point 1 (day 9) or time point 2 (day 29).Orthoblast_RSEM_merged_matrixOrthogroupText file containing all Orthogroup names and their corresponding contig names from the PAC and GOL population
DOI: 10.5061/dryad.fp1k7
title: Data from: History matters more when explaining genetic diversity within the context of the core-periphery hypothesis

description: The core–periphery hypothesis (CPH) predicts that populations located at
 the periphery of a species' range should have lower levels of genetic
 variation than those at the centre of the range. However, most of the
 research on the CPH focuses on geographic distance and not on ecological
 distance, or uses categorical definitions of core and periphery to explain
 the distribution of genetic diversity. We use current climate data and
 historical climate data from the last glacial maxima to develop
 quantitative estimates of contemporary and historical ecological
 suitability using ecological niche models. We analysed genetic diversity
 using 12 polymorphic microsatellites to estimate changes in
 heterozygosity, allelic richness and population differentiation in 31
 populations of the wood frog (Lithobates sylvaticus) spanning the species’
 entire eastern clade (33o to 45o latitude) from Alabama, USA, to Nova
 Scotia, Canada. Our data support predictions based on the CPH. Populations
 showed significant differences in genetic diversity across the range, with
 lower levels of genetic variation at the geographic range edge and in
 areas with lower levels of historical and contemporary ecological
 suitability. However, history and geography (not current ecological
 suitability) best explain the patterns. This study highlights the
 importance of examining more than just geography when assessing the CPH,
 and the importance of historical ecological suitability in the maintenance
 of genetic diversity and population differentiation.
description: BioClim 30s
 clippedBioClim 19 climate
 variables plus altitude clipped to United States and
 Canada.BioClim 2.5
 clippedBioclim 2.5 arc minute
 WorlClim layers clipped to the United States and
 Canada.Paleo 2.5
 clippedPaleo-climate layers
 from WorldClim clipped to the United States and Canada.Genotype_dataMicrosatellite genotypeseastclade_locality484 occurrence points downloaded from public databases, HerpNet and GBIFLocality_East&West CladeOccurrence data for wood frogs downloaded from public databases, HerpNet and GBIF.cGD_matrixLinearized FST matrixLog_Euclidean Distanceresistance matrix