cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kp1hk40
title: Data from: High-performance single-walled carbon nanotube transparent conducting film fabricated by using low feeding rate of ethanol solution

description: We report floating catalyst chemical vapor deposition synthesis of
 single-walled carbon nanotubes (SWCNTs) for high performance transparent
 conducting films (TCFs) using low feeding rate of precursor solution.
 Herein, ethanol acts as carbon source, ferrocene and thiophene as catalyst
 precursor and growth promoter, respectively. By adopting a low feeding
 rate of 4 μl/min, the fabricated TCFs present one of the lowest sheet
 resistances of ca. 78 ohm/sq. at 90% transmittance. Optical
 characterizations demonstrate that the mean diameter of high quality
 SWCNTs is up to 2 nm. Additionally, electron microcopy observations
 provide the evidences that the mean length of SWCNT bundles is as long as
 28.4 μm while the mean bundle diameter is only 5.3 nm. Moreover, very few
 CNT loops can be found in the film. Remarkably, the fraction of individual
 SWCNTs climbs up to 24.6%. All those morphology data account for the
 superior optoelectronic performance of our SWCNT TCFs.
description: Data in Supporting
 informationData
DOI: 10.5061/dryad.4jd39
title: Data from: Estimation of self-motion duration and distance in rodents

description: Spatial orientation and navigation rely on information about landmarks and
 self-motion cues gained from multi-sensory sources. In this study, we
 focused on self-motion and examined the capability of rodents to extract
 and make use of information about own movement, i.e. path integration.
 Path integration has been investigated in depth in insects and humans.
 Demonstrations in rodents, however, mostly stem from experiments on
 heading direction; less is known about distance estimation. We introduce a
 novel behavioural paradigm that allows for probing temporal and spatial
 contributions to path integration. The paradigm is a bisection task
 comprising movement in a virtual reality environment in combination with
 either timing the duration ran or estimating the distance covered. We
 performed experiments with Mongolian gerbils and could show that the
 animals can keep track of time and distance during spatial navigation.
description: bisection_dataBehavioral response data was aquired with custom made Python software and written into text files. For details see ReadMe file.data_dryad.zip
DOI: 10.5061/dryad.5242j
title: Data from: Nitrogen cycling and export in California chaparral: the role of climate in shaping ecosystem responses to fire

description: Climate change models predict that interannual rainfall variability will
 increase in California over the next several decades; these changes will
 likely influence how frequently California ecosystems burn and how they
 respond to fire. Fires uncouple N mobilization from uptake by destroying
 plant biomass and increasing nitrification. Following fire, autumn and
 winter rains can leach N into streams from slopes that have been denuded.
 The amount of N exported depends on how rapidly soil microbes metabolize
 it into mobile forms such as NO3-, and the rate that recovering plants
 take up available N. However, the long-term effects of a changing climate
 on postfire N dynamics remain unknown. We used the ecohydrologic model
 RHESSys (regional hydro-ecologic simulation system) to evaluate how
 interannual climate variability may affect the magnitude of N
 mineralization, nitrification, N export, and plant recovery following
 fire. N export was highest when fire was followed by drought; even though
 there was less water moving through the system, dry conditions prolonged
 the period during which N mobilization was decoupled from plant uptake. We
 also found that the effects of drought on N export were magnified in
 stands dominated by obligate seeders, which initially recovered more
 slowly than resprouters. These findings suggest that climate may regulate
 N balance most powerfully by influencing how quickly plants “turn on” and
 begin to immobilize N.
description: Model version and
 URLModelSettings.rtfInputs, settings, and state variables for RHESSys simulationsThis includes all files necessary to run RHESSys simulations with the file structure already set up.hanan2016.tar
DOI: 10.5061/dryad.b35td
title: Data from: Design of a 9K SNP chip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing

description: Single-nucleotide polymorphisms (SNPs) offer numerous advantages over
 anonymous markers such as microsatellites, including improved estimation
 of population parameters, finer-scale resolution of population structure
 and more precise genomic dissection of quantitative traits. However, many
 SNPs are needed to equal the resolution of a single microsatellite, and
 reliable large-scale genotyping of SNPs remains a challenge in nonmodel
 species. Here, we document the creation of a 9K Illumina Infinium BeadChip
 for polar bears (Ursus maritimus), which will be used to investigate: (i)
 the fine-scale population structure among Canadian polar bears and (ii)
 the genomic architecture of phenotypic traits in the Western Hudson Bay
 subpopulation. To this end, we used restriction-site associated DNA (RAD)
 sequencing from 38 bears across their circumpolar range, as well as
 blood/fat transcriptome sequencing of 10 individuals from Western Hudson
 Bay. Six-thousand RAD SNPs and 3000 transcriptomic SNPs were selected for
 the chip, based primarily on genomic spacing and gene function
 respectively. Of the 9000 SNPs ordered from Illumina, 8042 were
 successfully printed, and – after genotyping 1450 polar bears – 5441 of
 these SNPs were found to be well clustered and polymorphic. Using this
 array, we show rapid linkage disequilibrium decay among polar bears, we
 demonstrate that in a subsample of 78 individuals, our SNPs detect known
 genetic structure more clearly than 24 microsatellites genotyped for the
 same individuals and that these results are not driven by the SNP
 ascertainment scheme. Here, we present one of the first large-scale
 genotyping resources designed for a threatened species.
description: SNP and microsatellite
 dataRAD, transcriptomic, and
 microsatellite data used in the manuscript, as well as inputs/outputs of
 analyses. This archive contains the complete RAD .vcf file. For the
 complete transcriptomic .vcf file, see doi:10.5061/dryad.606j6, which is
 described in doi:10.1111/1755-0998.12190.DRYAD.zip
DOI: 10.5061/dryad.13t00
title: Data from: Genomic response to selection for predatory behavior in a mammalian model of adaptive radiation

description: If genetic architectures of various quantitative traits are similar, as
 studies on model organisms suggest, comparable selection pressures should
 produce similar molecular patterns for various traits. To test this
 prediction, we used a laboratory model of vertebrate adaptive radiation to
 investigate the genetic basis of the response to selection for predatory
 behavior and compare it with evolution of aerobic capacity reported in an
 earlier work. After 13 generations of selection, the proportion of bank
 voles (Myodes [=Clethrionomys] glareolus) showing predatory behavior was
 five times higher in selected lines than in controls. We analyzed the
 hippocampus and liver transcriptomes and found repeatable changes in
 allele frequencies and gene expression. Genes with the largest differences
 between predatory and control lines are associated with hunger,
 aggression, biological rhythms and functioning of the nervous system.
 Evolution of predatory behavior could be meaningfully compared with
 evolution of high aerobic capacity, because the experiments and analyses
 were performed in the same methodological framework. The number of genes
 that changed expression was much smaller in predatory lines and allele
 frequencies changed repeatably in predatory but not in aerobic lines. This
 suggests that more variants of smaller effects underlie variation in
 aerobic performance, whereas fewer variants of larger effects underlie
 variation in predatory behavior. Our results thus contradict the view that
 comparable selection pressures for different quantitative traits produce
 similar molecular patterns. Therefore, to gain knowledge about
 molecular-level response to selection for complex traits, we need to
 investigate not only multiple replicate populations, but also multiple
 quantitative traits.
description: transcriptome_and_annotationThe bank vole hippocampus transcriptome and its annotation. The transcriptome was assembled from 10 individuals derived form the laboratory model of adaptive radiation.expressionThe directory contains expression estimates (FPKM) for all studied transcripts in liver and hippocampus tissues. It contains also results for differentiation expression analyses between predatory and control lines.allele_frequenciesAllele frequencies for identified SNPs. Data are separated into noncoding, UTR-located, synonymous and nonsynonymous SNPs.Fst_tabels500 SNPs with largest overall Fst for predatory-control and aerobic-control comparison. The directory contains also Fst estimates between each pair of lines, calculated for mentioned above set of SNPs.scriptsThe set of scripts used for SNPs calling, expression analyses, Fst calculation and pedigree-based simulations.
DOI: 10.5061/dryad.7r5m6
title: Data from: Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

description: Anadromous Chinook salmon populations vary in the period of river entry at
 the initiation of adult freshwater migration, facilitating optimal arrival
 at natal spawning. Run timing is a polygenic trait that shows evidence of
 rapid parallel evolution in some lineages, signifying a key role for this
 phenotype in the ecological divergence between populations. Studying the
 genetic basis of local adaptation in quantitative traits is often
 impractical in wild populations. Therefore, we used a novel approach,
 Random Forest, to detect markers linked to run timing across 14
 populations from contrasting environments in the Columbia River and Puget
 Sound, USA. The approach permits detection of loci of small effect on the
 phenotype. Divergence between populations at these loci was then examined
 using both principle component analysis and FST outlier analyses, to
 determine whether shared genetic changes resulted in similar phenotypes
 across different lineages. Sequencing of 9107 RAD markers in 414
 individuals identified 33 predictor loci explaining 79.2% of trait
 variance. Discriminant analysis of principal components of the predictors
 revealed both shared and unique evolutionary pathways in the trait across
 different lineages, characterized by minor allele frequency changes.
 However, genome mapping of predictor loci also identified positional
 overlap with two genomic outlier regions, consistent with selection on
 loci of large effect. Therefore, the results suggest selective sweeps on
 few loci and minor changes in loci that were detected by this study. Use
 of a polygenic framework has provided initial insight into how divergence
 in a trait has occurred in the wild.
description: genotypes_input_filesGenotypes before and after flitering for missing values and minor allele frequencies; Description of the polymorphisms; Input files for BAPS, PowerMarker; Distance tree fileRandomForest_code_input_filesCode and input files for the random forest analysisRandom_forest.zipKernel_smoothing_code_input fileCode and input files for the kernel smoothing analysisKernel_smoothing.zipsamples_barcodes_coordinatesSamples description, barcodes for demultiplexing and GPS coordinates of sampling locations.samples_barcodes.xlsx
DOI: 10.5061/dryad.q2n78
title: Data from: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

description: For centuries ecologists have studied how the diversity and functional
 traits of plant and animal communities vary across biomes. In contrast, we
 have only just begun exploring similar questions for soil microbial
 communities despite soil microbes being the dominant engines of
 biogeochemical cycles and a major pool of living biomass in terrestrial
 ecosystems. We used metagenomic sequencing to compare the composition and
 functional attributes of 16 soil microbial communities collected from cold
 deserts, hot deserts, forests, grasslands, and tundra. Those communities
 found in plant-free cold desert soils typically had the lowest levels of
 functional diversity (diversity of protein-coding gene categories) and the
 lowest levels of phylogenetic and taxonomic diversity. Across all soils,
 functional beta diversity was strongly correlated with taxonomic and
 phylogenetic beta diversity; the desert microbial communities were clearly
 distinct from the nondesert communities regardless of the metric used. The
 desert communities had higher relative abundances of genes associated with
 osmoregulation and dormancy, but lower relative abundances of genes
 associated with nutrient cycling and the catabolism of plant-derived
 organic compounds. Antibiotic resistance genes were consistently threefold
 less abundant in the desert soils than in the nondesert soils, suggesting
 that abiotic conditions, not competitive interactions, are more important
 in shaping the desert microbial communities. As the most comprehensive
 survey of soil taxonomic, phylogenetic, and functional diversity to date,
 this study demonstrates that metagenomic approaches can be used to build a
 predictive understanding of how microbial diversity and function vary
 across terrestrial biomes.
description: 16S_rRNA_sequences_for_16_soilsThese sequences were demultiplexed using the 'split_libraries_fastq.py' command in QIIME v1.6.0 with default settings.seqs_16_soils.fna.gz16_soils_metadataSoil and site characteristics for the 16 soils
DOI: 10.5061/dryad.m691k
title: Data from: Low-canopy seagrass beds still provide important coastal protection services

description: One of the most frequently quoted ecosystem services of seagrass meadows
 is their value for coastal protection. Many studies emphasize the role of
 above-ground shoots in attenuating waves, enhancing sedimentation and
 preventing erosion. This raises the question if short-leaved, low density
 (grazed) seagrass meadows with most of their biomass in belowground
 tissues can also stabilize sediments. We examined this by combining
 manipulative field experiments and wave measurements along a typical
 tropical reef flat where green turtles intensively graze upon the seagrass
 canopy. We experimentally manipulated wave energy and grazing intensity
 along a transect perpendicular to the beach, and compared sediment bed
 level change between vegetated and experimentally created bare plots at
 three distances from the beach. Our experiments showed that i) even the
 short-leaved, low-biomass and heavily-grazed seagrass vegetation reduced
 wave-induced sediment erosion up to threefold, and ii) that erosion was a
 function of location along the vegetated reef flat. Where other studies
 stress the importance of the seagrass canopy for shoreline protection, our
 study on open, low-biomass and heavily grazed seagrass beds strongly
 suggests that belowground biomass also has a major effect on the
 immobilization of sediment. These results imply that, compared to shallow
 unvegetated nearshore reef flats, the presence of a short, low-biomass
 seagrass meadow maintains a higher bed level, attenuating waves before
 reaching the beach and hence lowering beach erosion rates. We propose that
 the sole use of aboveground biomass as a proxy for valuing coastal
 protection services should be reconsidered.
description: Data_Christianen_Plosone_2013_
DOI: 10.5061/dryad.q2102
title: Data from: Reconstruction of velocity fields in electromagnetic flow tomography

description: Electromagnetic flow meters (EMFMs) are the gold standard in measuring
 flow velocity in process industry. The flow meters can measure the mean
 flow velocity of conductive liquids and slurries. A drawback of this
 approach is that the velocity field cannot be determined. Asymmetric axial
 flows, often encountered in multiphase flows, pipe elbows and T-junctions,
 are problematic and can lead to serious systematic errors. Recently,
 electromagnetic flow tomography (EMFT) has been proposed for measuring
 velocity fields using several coils and a set of electrodes attached to
 the surface of the pipe. In this work, a velocity field reconstruction
 method for EMFT is proposed. The method uses a previously developed
 finite-element-based computational forward model for computing boundary
 voltages and a Bayesian framework for inverse problems. In the approach,
 the vz-component of the velocity field along the longitudinal axis of the
 pipe is estimated on the pipe cross section. Different asymmetric velocity
 fields encountered near pipe elbows, solids-in-water flows in inclined
 pipes and in stratified or multiphase flows are tested. The results
 suggest that the proposed reconstruction method could be used to estimate
 velocity fields in complicated pipe flows in which the conventional EMFMs
 have limited accuracy.
description: Data of the
 articleCode and data to
 reproduce all figures of the article.EMFT_inverse_figures_package.zip
DOI: 10.5061/dryad.56jt85j
title: Data from: Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

description: Understanding the genetic basis of local adaptation has long been the
 focus of evolutionary biology. Recently there has been increased interest
 in deciphering the evolutionary role of Daphnia’s plasticity and the
 molecular mechanisms of local adaptation. Using transcriptome data, we
 assessed the differences in gene expression profiles and sequences within
 and between four European Daphnia galeata populations. To distinguish
 neutral from adaptive differentiation, we corrected for phylogenetic
 differentiation of Daphnia populations. We also applied a “transcriptome
 scan” approach to investigate the role of natural selection in shaping
 divergent expression profiles among populations. Furthermore, a SNP
 analysis allowed inferring population structure and the distribution of
 genetic variation. Using sequence information, the transcripts were
 annotated using a comparative genomics approach. In total, ~33% of 32903
 transcripts were differentially expressed between populations. Among 10280
 differentially expressed transcripts, 5209 transcripts deviated from
 neutral expectations and were likely involved in local adaptation. The
 population divergence at the sequence level was higher than at the gene
 expression level by several orders of magnitude and revealed very distinct
 clusters according to population origin. Our analysis revealed the
 respective roles of genetic drift and selection in the four Daphnia
 populations. This study is a first attempt to understand the genetic
 background of adaptation to environmental changes in a key species of
 aquatic ecosystems in absence of any laboratory induced stressor.
description: Supporting information
 File 1Supplementary file 1:
 Tables S1-S7 accompanying the publication "Contrasting patterns of
 divergence at the regulatory and sequence level in European Daphnia
 galeata natural populations", Suda Parimala Ravindran, Maike Herrmann
 and Mathilde Cordellier. For the Table of Contents please refer to the
 README file.SI_1_Ravindran.xlsxSNP Data RavindranVCF file containing SNPs identified for Daphnia galeataSNPData_Ravindran.zip
DOI: 10.5061/dryad.83fr7
title: Data from: The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit trees

description: Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a
 popular fruit tree species with immense economic and nutritional value.
 Here, we report a draft genome of the dry jujube cultivar
 'Junzao' and the genome resequencing of 31 geographically
 diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var.
 spinosa). Comparative analysis revealed that the genome of
 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the
 'Junzao', partially due to the recent insertions of transposable
 elements in the 'Dongzao' genome. We constructed eight
 proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two
 sister families in the order Rosales, and elucidated the evolutionary
 processes that have shaped the genome structures of modern jujubes.
 Population structure analysis revealed the complex genetic background of
 jujubes resulting from extensive hybridizations between jujube and its
 wild relatives. Notably, several key genes that control fruit organic acid
 metabolism and sugar content were identified in the selective sweep
 regions. We also identified S-locus genes controlling gametophytic
 self-incompatibility and investigated haplotype patterns of the S locus in
 the jujube genomes. This study provides valuable genomic resources for
 jujube improvement, and offers insights into jujube genome evolution and
 its population structure and domestication.
description: Zjujuba.junzao.genome.chr.annotationZjujuba.junzao.annotation.gff3 file Generic Feature Format Version 3 (GFF3) format of RNA products annotated on the genome. Zjujuba.junzao.pep.fa file FASTA format of the accessioned protein products annotated on the genome assembly. Zjujuba.junzao.cds.fa file FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly. Zj.jz.final.annotation.txt file Tab-delimited text file reporting values for different aspects of the annotation data.
DOI: 10.5061/dryad.d689j
title: Data from: Vesicular monoamine transporter 2 (VMAT2) level regulates MPTP vulnerability and clearance of excess dopamine in mouse striatal terminals

description: The vesicular monoamine transporter 2 (VMAT2) packages neurotransmitters
 for release during neurotransmission and sequesters toxicants into
 vesicles to prevent neuronal damage. In mice, low VMAT2 levels causes
 catecholaminergic cell loss and behaviors resembling Parkinson’s disease,
 while high levels of VMAT2 increase dopamine release and protect against
 dopaminergic toxicants. However, comparisons across these VMAT2 mouse
 genotypes were impossible due to the differing genetic background strains
 of the animals. Following back-crossing to a C57BL/6 line, we confirmed
 that mice with approximately 95% lower VMAT2 levels compared with
 wild-type (VMAT2-LO) display significantly reduced vesicular uptake,
 progressive dopaminergic terminal loss with aging, and exacerbated
 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) toxicity. Conversely,
 VMAT2-overexpressing mice (VMAT2-HI) are protected from the loss of
 striatal terminals following MPTP treatment. We also provide evidence that
 enhanced vesicular filling in the VMAT2-HI mice modifies the handling of
 newly synthesized dopamine, indicated by changes in indirect measures of
 extracellular dopamine clearance. These results confirm the role of VMAT2
 in the protection of vulnerable nigrostriatal dopamine neurons and may
 also provide new insight into the side effects of L-DOPA treatments in
 Parkinson’s disease.
description: Dryad-Lohr-etal-westernsThese are all of the original images of the western blots in this manuscript. They are in a powerpoint file.Dryad-Lohr-etal-excelFSCVThis is an excel spreadsheet that shows all of the raw data collected for the fast scan cyclic voltammetry experiments. Tabs are used to delineate the various experiments.