cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kv028/1
title: Tree Rings and knots measurements

description: Tree, Ring and knot data used in the article 10.7717/peerj.873.
DOI: 10.5061/dryad.p1r02/8
title: Mapping file

description: Mapping file including metadata
DOI: 10.5061/dryad.rd234/52
title: Fig. 57

description: High-resolution Fig. 57
DOI: 10.5061/dryad.rd234/53
title: Fig. 58

description: High-resolution Fig. 58
DOI: 10.5061/dryad.rd234/54
title: Fig. 59

description: High-resolution Fig. 59
DOI: 10.5061/dryad.rd234/55
title: Fig. 60

description: High-resolution Fig. 60
DOI: 10.5061/dryad.rd234/56
title: Fig. 61

description: High-resolution Fig. 61
DOI: 10.5061/dryad.rd234/57
title: Fig. 62

description: High-resolution Fig. 62
DOI: 10.5061/dryad.rd234/58
title: Fig. 63

description: High-resolution Fig. 63
DOI: 10.5061/dryad.sf654.2
title: Data from: A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)
DOI: 10.5061/dryad.sf654.2/1.2
title: Trimmed_Kidney_Reads

description: These are the trimmed fasta and qual files for each of the individual kidney libraries and all of the individual libraries together in a whole tissue file
DOI: 10.5061/dryad.v7c54/1
title: Cytb_alignment

description: Alignment of cytochrome b gene haplotypes used in phylogenetic analysis
DOI: 10.5061/dryad.v7c54/2
title: Dloop_alignment

description: Alignment of Dloop haplotypes used in the phylogenetic analysis
DOI: 10.5061/dryad.v7c54/3
title: Czech red deer_microsatellites

description: Microsatellite data set used in the study
DOI: 10.5061/dryad.3k0d8/1
title: MicrosatGenotypes_Asterionella_formosa

description: Excel spreadsheet of genotypic data of 224 individuals of Asterionella formosa (freshwater diatom), from seven lakes in Switzerland and four lakes in The Netherlands, scored for nine microsatellite markers.
DOI: 10.5061/dryad.3s7r7/1
title: data_experiment1: intraspecific conflict and cooperation

description: Worksheet 1 ("copepods") contains information on each copepod used in the study including dead or incorrectly infected copepods. Worksheet 2 ("behavior") contains the behavior of only those copepods that survived until their infection status could be determined and that were infected by all parasites they had been exposed to. No behavior was recorded for any of the other copepods. The behavior consists of the position of each copepod every two seconds during one minute after a simulated predation attack and after a recovery period and, resulting from this whether or how far they moved during this time interval. This data was obtained from video recordings of copepod behavior using the manual tracking tool in imageJ and was done blindly as to the infection status of each copepod.
DOI: 10.5061/dryad.3s7r7/2
title: data_experiment2_effect_of_parasite_number_on_intraspecific_conflict

description: Worksheet 1 ("copepods") contains information on each copepod used in the study including dead or incorrectly infected copepods. Worksheet 2 ("behavior") contains the behavior of only those copepods that survived until their infection status could be determined and that were infected by all parasites they had been exposed to. No behavior was recorded for any of the other copepods. The behavior consists of the position of each copepod every two seconds during one minute after a simulated predation attack and after a recovery period and, resulting from this whether or how far they moved during this time interval. This data was obtained from video recordings of copepod behavior using the manual tracking tool in imageJ and was done blindly as to the infection status of each copepod.
DOI: 10.5061/dryad.3s7r7/3
title: data_preliminary_experiment: Parasite size and effect of parasite number on an intraspecific conflict

description: Data for supplementary results 2. Worksheet 1 ("copepods") contains information on each copepod used in the study including dead or incorrectly infected copepods. Worksheet 2 ("behavior") contains the behavior of only those copepods that survived until their infection status could be determined and that were infected by all parasites they had been exposed to. No behavior was recorded for any of the other copepods. The behavior consists of the position of each copepod every two seconds during one minute after a simulated predation attack and after a recovery period and, resulting from this whether or how far they moved during this time interval. This data was obtained from video recordings of copepod behavior using the manual tracking tool in imageJ and was done blindly as to the infection status of each copepod.
DOI: 10.5061/dryad.48vb7/1
title: GundersonLeal15_AmNat_Anole_Data

description: Activity data for Anolis cristatellus
DOI: 10.5061/dryad.48vb7/2
title: Christian varanid spp activity

description: Data on activity for Varanids from Christian and Weavers 1996
DOI: 10.5061/dryad.5pr61/1
title: Dryad microsat data Edelaar et al. 2015 monk parakeets Mol Ecol

description: Individual genotypic data for 6 microsatellite markers, including information on population, geographic area and country of sampling.
DOI: 10.5061/dryad.5pr61/2
title: monk parakeet mtdna aligned trimmed

description: Alignment of all analysed mtDNA control region haplotypes, trimmed to include only overlapping parts, FASTA file format.
DOI: 10.5061/dryad.659n8/1
title: Preference scores, katydid call measurements, and echolocation measurments

description: The excel file contains three parts. First, all bat interest-level scores are provided, with the reaction of each bat to each katydid call. Details on scoring are provided in the manuscript. Second, we provide the measurements for the individual katydid calls used in the experiment (number of pulses, duration, peak frequency, and bandwidth). Third, we we provide the measurements for the individual bat echolocation calls used in our analysis (duration, peak frequency, minimum frequency, maximum frequency, and bandwidth).
DOI: 10.5061/dryad.6km3j/1
title: EGGS
DOI: 10.5061/dryad.6km3j/2
title: FEMALES
DOI: 10.5061/dryad.6km3j/3
title: NESTLINGS
DOI: 10.5061/dryad.d0h71/10
title: analysis_scripts.txt

description: Commands used for conducting non-assembly based analysis.
DOI: 10.5061/dryad.d0h71/6
title: CN7_1.fasta.gz

description: Trinity generated assembly of CN7_1 individual in a gzipped fasta format.
DOI: 10.5061/dryad.d0h71/7
title: blacklight_script.txt

description: List of commands used to conduct assembly of pooled transcriptome on Blacklight cluster.
DOI: 10.5061/dryad.d0h71/8
title: silene_transcriptomes.vcf.gz

description: Compressed vcf file containing snps identified in all four transcriptomes against Trinity derived pooled assembly as reference. PF01 = CN7_1, PF02 = ZAG2_1, PF03 = ZAG5_1, PF04 =CN9_1.
DOI: 10.5061/dryad.d0h71/9
title: Annotation_report.xls

description: Contains full description of assembly component annotation generated by Trinotate.
DOI: 10.5061/dryad.f5c60/6
title: Chloroplast DNA sequence polymorphisms detected in two intergenic spacer (IGS) regions of F. suspensa identifying thirteen chlorotypes (C1–C13)
DOI: 10.5061/dryad.hf876/1
title: Microsat allele calls for D. robustus

description: Microsat allele calls for the extinct South Island giant moa (Dinornis robustus), genotyped in six microsatellite loci.
DOI: 10.5061/dryad.rd234/59
title: Fig. 64

description: High-resolution Fig. 64
DOI: 10.5061/dryad.rd234/60
title: Fig. 65

description: High-resolution Fig. 65
DOI: 10.5061/dryad.rd234/61
title: Fig. 66

description: High-resolution Fig. 66
DOI: 10.5061/dryad.rd234/62
title: Fig. 67

description: High-resolution Fig. 67
DOI: 10.5061/dryad.rd234/63
title: Fig. 68

description: High-resolution Fig. 68
DOI: 10.5061/dryad.rd234/64
title: Fig. 69

description: High-resolution Fig. 69
DOI: 10.5061/dryad.rd234/65
title: Fig. 70

description: High-resolution Fig. 70
DOI: 10.5061/dryad.rd234/66
title: Fig. 71

description: High-resolution Fig. 71
DOI: 10.5061/dryad.sf654.1
title: Data from: A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: Osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)
DOI: 10.5061/dryad.sf654.2/2.2
title: Trimmed_Spleen_Reads

description: Trimmed .fasta and .qual files for each individual spleen library and for the total tissue library
DOI: 10.5061/dryad.sf654.2/3.2
title: Kidney_contigs

description: These are the .fasta and .ace files for all of the contigs from individual kidney assemblies as well as all of the kidney libraries assembled into one total 'kidney' assembly as described in the paper.
DOI: 10.5061/dryad.sf654.2/4.2
title: Spleen_contigs

description: This file contains all of the spleen .fasta and .ace files for the contigs of all assemblies of individual spleen libraries as well as a total tissue 'spleen' library
DOI: 10.5061/dryad.sf654.2/5.2
title: Individual_Kidney_libraries_raw_reads

description: Individual .sff files for each of four individuals, for kidney
DOI: 10.5061/dryad.sf654.2/6.2
title: Spleen_indiv_libraries_raw_reads

description: Individual .sff files for each of four individuals, for spleen
DOI: 10.5061/dryad.sf654.2/7.2
title: Total_kidney_raw_reads

description: Single .sff file with all reads from the four individual kidney libraries concatenated into one total tissue file
DOI: 10.5061/dryad.sf654.2/8.2
title: Spleen_total_raw_reads

description: Single .sff file with all reads from the four individual spleen libraries concatenated into one total tissue file
DOI: 10.5061/dryad.088qv/1
title: Pandalus borealis microsatellite data

description: Microsatellite data (10 loci) for northern shrimp, Pandalus borealis: 2053 individuals, representing 21 samples and 16 geographic localities throughout the species' range in the North Atlantic.
DOI: 10.5061/dryad.300fq/1
title: Toad field hopping behavoir for 4 samples

description: These are the locomotor behaviors (number of successive launches) observed in the 4 samples studied. Rhinella marinus, Anaxyrus fowleri (from Michigan and Ohio populations) and Anaxyrus americanus (from Ohio).
DOI: 10.5061/dryad.300fq/2
title: Cane toad raw data forces and 3D landmarks

description: These are the raw forces and 3d landmarks for the toad hops and bounding sequences used in this study
DOI: 10.5061/dryad.3k0d8/2
title: AFLP_data_Asterionella_formosa

description: AFLP fingerprint data of 91 isolates of Asterionella formosa (freshwater diatom) at 121 loci, from seven lakes in Switzerland and tree lakes in The Netherlands.
DOI: 10.5061/dryad.3k0d8/3
title: Microsatellite sequences Asterionella formosa

description: Microsatellite sequences of Asterionella formosa, containing the repeat units and forward and reverse primer sites.
DOI: 10.5061/dryad.3q6n0/1
title: Population Phenotype Data

description: This file contains data on the UV pattern of individuals from populations of M. guttatus, M. nasutus, and M. laciniatus.
DOI: 10.5061/dryad.3q6n0/2
title: Hybrid Reflectance Data

description: This file contains standardized reflectance spectra for flowers from F1 hybrids between populations of M. guttatus
DOI: 10.5061/dryad.3q6n0/3
title: Field Pollinator Trials

description: This file contains data from choice trials in wild populations of M. guttatus using the native pollinator community
DOI: 10.5061/dryad.3q6n0/4
title: Captive Pollinator Trials

description: This file contains data from choice trials with captive Bombus impatiens using outbred lines of M. guttatus
DOI: 10.5061/dryad.47nm0/1
title: MYLU_microsatellites_Genepop_infile.txt

description: This file contains the genotypes (at 9 loci) of M. lucifugus bats at 29 sites in New Brunswick and Nova Scotia, Canada.
DOI: 10.5061/dryad.47nm0/2
title: MYSE_microsatellites_Genepop_infile

description: This file contains the genotypes (at 9 loci) of M. septentrionalis bats at  15 sites in New Brunswick and Nova Scotia, Canada.
DOI: 10.5061/dryad.5dk4p/1
title: Dataset_reaction

description: dataset used to analyse great tits behavioural reaction to the displayed image. the reaction is split into binary outputs at the four nodes of the reaction tree
DOI: 10.5061/dryad.5dk4p/2
title: Dataset_escapewindow

description: dataset used to analyse the escape window, ie the time lapsed between the first attack (which coincide with the image display) and the catching of the bait prey
DOI: 10.5061/dryad.5dr5k/1
title: Tri-partite interactions

description: Spreadsheet where all interactions described using molecular method and morphological approach are displayed. This file has been used to calculate the network metrics.
DOI: 10.5061/dryad.5dr5k/2
title: COI Barcode

description: Sequence alignement for COI barcode (658bp). This alignement has been used to build ML tree
DOI: 10.5061/dryad.5dr5k/3
title: COI Minibarcode

description: Sequence alignement for COI Minibarcode (130 bp). This alignement has been used to build ML tree.
DOI: 10.5061/dryad.5pr61/3
title: Dryad haplotype frequencies per population Edelaar et al. 2015 monk parakeets mol Ecol

description: Excel file showing haplotype frequenties per population.
DOI: 10.5061/dryad.5pr61/4
title: Dryad haplotypes per individual Edelaar et al. 2015 monk parakeets Mol Ecol

description: Haplotype of each individual, together with population and location data.
DOI: 10.5061/dryad.9387c/1
title: Lopez-Uribe_etal_Colletes_inaqualis

description: This file contains the genotypes of 18 microsallite loci for 547 female individuals of Colletes inaequalis.
DOI: 10.5061/dryad.bd2s0/1
title: Genotype data

description: Genotype data
DOI: 10.5061/dryad.bd2s0/2
title: Release data

description: Release data
DOI: 10.5061/dryad.gt678/1
title: MetaPCA

description: Data file containing standard deviations of population means and latitudes from published common garden studies
DOI: 10.5061/dryad.h814j/1
title: MS_japan_all_data

description: This file contains the tabulations of insects sampled from native and non-native plants. The methods involved were as follows:

Phytophagous insects were collected on native and non-native plants in two areas: Haren, province of Groningen, the Netherlands (53º10’N 06º36’E) and Sendai, Miyagi prefecture, Japan (38º16’N 140º52’E). In total, 47 plant species were sampled, which could be divided into four groups: (1) plant species native to the Netherlands and non-native to Japan, or vice versa (14 spp.), (2) plant species non-native to both areas (5 spp.), (3) plant species studied only in the Netherlands; either native or non-native (9 spp.), and (4) plant species studied only in Japan; either native or non-native (19 spp.).

Most data were collected simultaneously in both areas between late April and early August, 2010. Only the data on the level of herbivory were not collected simultaneously. Insect collection took place in forests, parks, and gardens. In both the Netherlands and Japan the same two standardised methods were used to sample insects. Insects were collected by shaking the branches of the plant for 10 s above a beating sheet of 1 m2 or by sweeping an insect net with a diameter of 50 cm for 10 s through the branches of the plant. All individuals of the same plant species were sampled with the same method. The collecting methods were rehearsed and standardised (in the Netherlands) by all collectors beforehand.

Collected insects were stored in 70% ethanol. Insects from nine taxonomic groups (table 2) were collected. For four taxonomic groups experts were found to identify the species (table 2, indicated by *). For all collected insects the insect load was determined in two ways: by counting the number of insect individuals per sample, and by determining their dry weight. The levels of herbivory were estimated for 17 plant species in the Netherlands and 16 in Japan, using other plant individuals than the ones we sampled insects from. We did this as follows. We first randomly collected ten leaves from a plant and counted the leaves with insect damage. This was repeated for 5-27 individuals per plant species (mean: 11.9). Then, the mean leaf area was determined per plant species, by scanning on average 42 (range: 10-190) leaves per plant species using a flatbed scanner, and calculating the surface area using the software Lafore (Lehsten 2005). Finally, a herbivory index was devised, as [proportion leaves damaged / mean leaf area * 10,000].
DOI: 10.5061/dryad.j22j1/1
title: File including all data used in the article

description: PROG = line IDSPECIES = common species nameID = sample IDDATE = day of capture (day 1 = January 1)AGE = age of individual (0 = second year; 1 = older)SEX = sex of the individual (1 = male; 2 = female)FAT = fat score (0-8 scale)MUSCLE = muscle score (0-3 scale)WING = wing lenght (mm x 10)MASS = body mass (g x 10)CLK_SHORT = Clock short allele lenght (Q-units)CLK_LONG = Clock long allele length (Q-units)CLK_MEAN = Clock mean allele length (Q-units)ADC_SHORT = Adcyap1 short allele length (bp units)ADC_LONG = Adcyap1 long allele length (bp units)ADC_MEAN = Adcyap1 mean allele length (bp units)
DOI: 10.5061/dryad.j22j1/2
title: Clock and Adcyap1 genomic sequences

description: Partial genomic sequences of Clock and Adcyap1 genes of Anthus trivialis, Luscinia megarhynchos, Saxicola rubetra and Ficedula hypoleuca and Clustal multiple sequence alignement highlighting sequence differences among species.
DOI: 10.5061/dryad.kb175/1
title: Thymus pulegioides AFLP data

description: The file Thymus pulegioides AFLP data.csv includes the binary matrix of AFLP band presence (1) – absence (0) for 155 AFLP-markers and 287 individuals of Thymus pulegioides sampled in 19 populations in central-east Flanders (Northern Belgium). The matrix also include the spatial coordinates of each sampled population, given in the two last columns. The markers are numbered M1 to M155.
DOI: 10.5061/dryad.kq2r1/1
title: Supplemental Data

description: Column A: 1=Intervention patient; 2=Control patient.  Column B: Age on submission in years.  Column C: 1=Male; 2=Female.  Column D: LOS in days.  Column E: Total nursing time for IV treatment in minutes.  Column F: Total price of antibiotic therapy in Euros.  Column G: Total DDDs of antibiotic therapy.  Column H: 1=DRG Group 1; 2=DRG Group 2.
DOI: 10.5061/dryad.qv0sk/1
title: Data for Intertemporal Similarity: Discounting as a Last Resort

description: These data were collected in three experiments in which human participants were asked to make binary intertemporal choices, staircase intertemporal choices, and similarity judgments for reward amounts and time delays.  Experiment 1 used real rewards and delays and was conducted in Berlin, Germany. Experiments 2 and 3 used hypothetical rewards and delays and were conducted in Lincoln, Nebraska.
DOI: 10.5061/dryad.rd234/67
title: Fig. 72

description: High-resolution Fig. 72
DOI: 10.5061/dryad.rd234/68
title: Fig. 73

description: High-resolution Fig. 73
DOI: 10.5061/dryad.rd234/69
title: Fig. 74

description: High-resolution Fig. 74
DOI: 10.5061/dryad.rd234/70
title: Fig. 75

description: High-resolution Fig. 75
DOI: 10.5061/dryad.rd234/71
title: Fig. 76

description: High-resolution Fig. 76
DOI: 10.5061/dryad.rd234/72
title: Fig. 77

description: High-resolution Fig. 77
DOI: 10.5061/dryad.rd234/73
title: Fig. 78

description: High-resolution Fig. 78
DOI: 10.5061/dryad.rd234/74
title: Fig. 79

description: High-resolution Fig. 79
DOI: 10.5061/dryad.rd234/75
title: Fig. 80

description: High-resolution Fig. 80
DOI: 10.5061/dryad.t24gg/1
title: seed and plant characteristics in response to herbivore treatment

description: In the experiment Sinapis arvensis plants were exposed to one of four treatment: no herbivory (=ct), healthy Pieris brassicae caterpillars (=Pier), caterpillars parasitized by the gregarious Cotesia glomerata  (=Cot), and caterpillars parasitized by the solitary Hyposoter eneninus (=Hyp). Plants were initially grown in the greenhouse but at the onset of flowering, they were transferred to tents placed in a garden to which pollinators were added. At this time point, the plants were exposed to the treatments. The experimental unit was a tray with 6 plants (=replicate), There were 4 replicates per treatment. When insect development was completed, we counted 1) the number of undamaged seed pods and 2) the number of damaged seed pods. Plants were then transferred to a garden in which the control plants were already present. When the seedpods had matured and dried, they were collected. Seed pods that had grown additionally were collected one month later (=new seed pods). Seeds were separated from their pods and weighed (=total seed mass in g). Per plant, cohorts of 20 seeds were weighed and their mean was calculated (=mean individual seed mass in microgram). We calculated the number of seeds per plants by dividing the weight of all seeds produced by a plant by its individual seeds mass (=number of seeds). After 2 years of storage in the dark, germination success of the seeds was determined by randomly choosing 50 seeds from each plant and allow them to germinate on wet filter paper. Germination success was calculated as the fraction of seeds that germinated out of 50. Reproductive potential was then calculated as the product of seed number and germination success.The data on the seed characteristics are in the ‘seed data per tray’ sheet, individual seed mass are in the sheet ‘seed mass of individual seeds) and the data on the seed pods are in ‘seed pods’ sheet.
DOI: 10.5061/dryad.300fq/3
title: Cane toad bounding Hildebrand gait data

description: These are the foot fall data used to generate the hildebrand gait plot for marine toad bounding gaits.
DOI: 10.5061/dryad.85sh7/1
title: Scripts

description: scripts from FASTX-toolkit for clipping, trimming and quality filter, as well as scripts for the ref map.pl. pipeline of Stacks (ustacks and sstacks) are available at Dryad data repository (http://dx.doi.org/10.5061/dryad.85sh7)
DOI: 10.5061/dryad.85sh7/2
title: batch_1.catalog.tags
DOI: 10.5061/dryad.85sh7/3
title: batch_1.catalog.snps
DOI: 10.5061/dryad.85sh7/4
title: batch_1.catalog.alleles
DOI: 10.5061/dryad.85sh7/5
title: genotypes of test population
DOI: 10.5061/dryad.cd711/1
title: Ancestral mitogenome reconstruction

description: As interspecific comparisons featured heavily in our analyses, it was important to choose a reference sequence that would limit the introduction of a bias during the mapping of sequences (“mapping bias”). Mapping algorithms become less effective when the reference is very dissimilar (Prüfer et al. 2010; Schubert et al. 2012) impacting the number of sequences identified as ‘on-target’. As some of the species in this study currently do not have a reference sequence available from GenBank (Table 1), we reconstructed an ancestral mitogenome of all Felidae (Appendix S1; Supporting Table S2) to be used as reference. To reconstruct the ancestral sequence, the most appropriate model of substitution for the alignment of the felid mitogenomes was estimated using jModeltest 2.1.4 under the Bayesian Information Criterion (Posada 2008), which was then implemented in PhyML (Guindon et al. 2010) to infer the topology of the phylogeny (as shown in Fig. 1A). Reconstruction of the ancestral sequence was performed using the webserver of Ancestors v1.1 (Diallo et al. 2007, 2010). For additional information, please refer to the manuscript and its supplements.
DOI: 10.5061/dryad.cd711/2
title: Perl script 1

description: Perl script written by Kanchon Dasmahapatra (University of York; kanchon.dasmahapatra@york.ac.uk). This script uses a variant file (VCF) generated by GATK to call the individual bases per position for a haploid genome. After this script, run "convert_callsfile_to_one_line_fasta.pl" script to covert the base calls to a fasta file.
DOI: 10.5061/dryad.cd711/3
title: Perl script 2

description: Perl script written by Kanchon Dasmahapatra (University of York; kanchon.dasmahapatra@york.ac.uk). This script uses the output from "filter_multiple_sample_gatk1.5_vcf_mtDNA_indels.pl" and writes the base calls to a fasta file.