cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.60s10/6
title: Figure_S6

description: Undersampling affects spectral density profiles. The spectral densities of 3 (out of 100) trees (solid line) simulated under (a) constant birth-death, (b) increasing speciation-rate, and (c) recent mass-extinction models and their jackknifed trees (dashed lines) at 90%, 80%, 70%, 60%, 50%, and 40% are plotted. As the tree moves further from complete, the density plot shifts left, as a result of a declining principal λ, and the shape of the spectral density becomes increasingly different from the original, notably by decreasing skewness. The mean and standard deviation of the Jensen-Shannon distance between each tree and its 100 jackknifed trees are shown in a barplot. The distance between trees increases linearly with incompleteness.
DOI: 10.5061/dryad.6pr6c/1
title: Supplementary Data Table 1. Hole sizes and specimen information; Chuar Group, Grand Canyon, Arizona, USA

description: Supplementary Data Table 1. Hole sizes in specimens from the Chuar Group, Grand Canyon, Arizona, with reference to data shown in Figure 3.  See Porter and Riedman (in press) for more details on samples. (UCMP = University of California Museum of Paleontology.)
DOI: 10.5061/dryad.75876/1
title: Porcine APOA2 gene expression in liver

description: Data from Analysis of the porcine APOA2 gene expression in liver, polymorphisms identification and association with fatty acid composition traits. Contains SNP genotypes for GWAS and eGWAS studies, mRNA expression of APOA2 in liver, and fatty acid composition in backfat and muscle
DOI: 10.5061/dryad.7t5r1/3
title: Wing sizes for F1 offspring

description: Wing size data for F1 offspring of individual Drosophila melanogaster females subjected to dormancy inducing conditions, and F1 offspring of unexposed control individuals as described in lines 391-402 of manuscript.
DOI: 10.5061/dryad.7t5r1/4
title: Wolbachia titre for Drosophila melanogaster individuals

description: Wolbachia titre (density) for F1 offspring arising from individual Drosophila melanogaster females subjected to dormancy inducing conditions and from unexposed control individuals ("Data" worksheet), and description of column headers ("Key" worksheet) as described in lines 404-429 of manuscript.
DOI: 10.5061/dryad.8t475/1
title: Squirrel locations

description: Fox squirrel locations entered on website from public and professionals. File contains  x,y coordinates and associated covariates
DOI: 10.5061/dryad.cq7t1/2
title: GB Prevalence

description: Contains raw prevalence data and statistical code (R) for GB survey of DWV-A and DWV-B.
DOI: 10.5061/dryad.d4d5d/1
title: Teiidae Concatenated Sequence Alignment
DOI: 10.5061/dryad.d4d5d/2
title: Locus partitions for Teiidae multiple sequence alignment
DOI: 10.5061/dryad.d4d5d/3
title: Teiidae Probe Sequences
DOI: 10.5061/dryad.d4d5d/4
title: Pairwise Alignments for Probe Design
DOI: 10.5061/dryad.f66db/1
title: root biomass per pot half

description: Root foraging data for 37 plant species. The experiment was run in two years. Each row corresponds to a pot. In each pot, there was either no spatial gradient of nutrients, or shallow gradient or steep gradient (column "contrast").  Dry belowground biomass is reported for each half of the pot (root biomass content in the nutrients-poor half: column "lowconc_half_roots[g]"; root biomass content in the nutrients-rich half: column "highconc_half_roots[g]"); for pots with no gradient, identity of halves was chosen at random. Aboveground dry biomass and sum of the belowground halves are reported, too.
DOI: 10.5061/dryad.hg578/1
title: Trait and biomass data from plants grown in pots by themselves, monoculture, and mixture

description: The data file contains data on shoot biomass, root biomass, average leaf area, average root diameter, specific leaf area, specific root length, and root to shoot ratios for 15 species. Traits were collected on plants grown alone, in monoculture, and in mixture.
DOI: 10.5061/dryad.kk174/1
title: Baviaanskloof percent cover, trait, and environment dataset

description: A dataset combining trait measurements for species observed in releve plots in the Baviaankloof region of South Africa. Environmental conditions at those plots also included.
DOI: 10.5061/dryad.n1g46/1
title: Figure 1 - source data.xlsx

description: phloem geometrical parameters for a medium sized foliated morning glory plant
DOI: 10.5061/dryad.n1g46/2
title: Figure 3 - source data

description: phloem geometrical parameters for a large partially defoliated morning glory plant
DOI: 10.5061/dryad.n1g46/3
title: Figure 5 - source data

description: phloem geometrical parameters for a large foliated morning glory plant
DOI: 10.5061/dryad.nt65q/13
title: RAD14.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/2
title: RAD4.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/3
title: RAD5.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/4
title: RAD7.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/5
title: RAD9b.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/6
title: RAD15.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/7
title: RAD16.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/8
title: RAD18.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/9
title: RAD19.txt

description: Fastq data file
DOI: 10.5061/dryad.r5b51/1
title: kbs_aviris2009_CRspectra_FINAL

description: Tab delimited .txt file of continuum removed spectral data for the 300 50x50 m plots used in this study, with header row of column names. First column is plot id, second is whether the plot is in forest or agriculture (0 = forest, 1 = agriculture), followed by the continuum removed spectral data. More info and R code to process can be found in the associated manuscript. Original data is from AVIRIS flightline f090720t01p00r05 which was supported by funding from the NASA Terrestrial Ecology program (Grant # NNX11AB88G; PI S. Ollinger); contact S. Ollinger for total flightline reflectance data.
DOI: 10.5061/dryad.v9b30/1
title: Supplemental Data 1

description: 3-D model (in STL format) of the skull of the theropod dinosaur Allosaurus fragilis (MOR 693) generated using box modeling.
DOI: 10.5061/dryad.v9b30/2
title: Supplemental Data 2

description: 3-D model (in STL format) of the skull of the theropod dinosaur Allosaurus fragilis (MOR 693) based on computed tomography (CT).
DOI: 10.5061/dryad.v9b30/3
title: Supplemental Data 3

description: 3-D model (in STL format) of a dorsal vertebra of the ornithischian dinosaur Stegosaurus stenops (NHMUK R36730) generated using box modeling.
DOI: 10.5061/dryad.v9b30/4
title: Supplemental Data 4

description: 3-D model (in STL format) of a dorsal vertebra of the ornithischian dinosaur Stegosaurus stenops (NHMUK R36730) based on photogrammetry.
DOI: 10.5061/dryad.v9b30/5
title: Supplemental Data 5

description: 3-D model (in STL format) of a complete individual of the cinctan echinoderm Protocinctus mansillaensis (MPZ 2004/170) generated using box modeling.
DOI: 10.5061/dryad.v9b30/6
title: Supplemental Data 6

description: 3-D model (in STL format) of a complete individual of the cinctan echinoderm Protocinctus mansillaensis (MPZ 2004/170) based on computed tomography (CT).
DOI: 10.5061/dryad.1f5h4/1
title: Supporting documents and tables for Dececchi et al. 2016

description: This includes all 15 supporting tables, 2 supporting nexus files, the supporting calculation spreadsheet for Dececchi et al. 2016
DOI: 10.5061/dryad.1p3kn/1
title: Read me (data file explanations)
DOI: 10.5061/dryad.1p3kn/2
title: Household data

description: This data file contains information on the information recrutied from the household transmission study in Hong Kong, from 2008-2012.
DOI: 10.5061/dryad.1p3kn/3
title: Influenza proxy data

description: The influenza proxy used in the analysis. ( 1/1/2008 is set as Day 1)
DOI: 10.5061/dryad.2dj50/1
title: Figure 2 Neighbor-joining phylogenetic tree of odorant-binding proteins (OBPs)

description: The NJ phylogenetic analysis of OBPs of E. hippophaecolus (EhipOBP, red) was performed with reference OBPs of D. melanogaster (DmelOBP, Diptera, blue) and OBPs of Lepidoptera species (black)[79]. The red circles refer to PBP/GOBP lineage. Pale yellow sector refer to the Lepidoptera-specific lineages. The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥ 0.6 are shown at the corresponding nodes. The scale bar represents 05 substitutions per site.
DOI: 10.5061/dryad.2dj50/2
title: Figure 3 Neighbor-joining phylogenetic tree of chemosensory proteins (CSPs)

description: Figure 3 Neighbor-joining phylogenetic tree of chemosensory proteins (CSPs)The NJ phylogenetic analysis of CSPs of E. hippophaecolus (EhipCSP, red) was performed with reference CSPs of D. melanogaster (DmelCSP, Diptera, blue) and CSPs of Lepidoptera species (black). The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥0.6 are shown at the corresponding nodes. The scale bar represents 0.5 substitutions per site.
DOI: 10.5061/dryad.2dj50/3
title: Figure 4 Neighbor-joining phylogenetic tree of sensory neuron membrane proteins (SNMPs)

description: Figure 4 Neighbor-joining phylogenetic tree of sensory neuron membrane proteins (SNMPs)The NJ phylogenetic analysis of SNMPs of E. hippophaecolus (EhipSNMP, red) was performed with reference SNMPs of D. ponderosae (DponSNMP, purple), I. typographus (ItypSNMP, purple), T. molitor (TmolSNMP, purple), T. castaneum (TcasSNMP, purple), D. melanogaster (DmelSNMP, Diptera, blue),  B. mori (BmorSNMP, Lepidoptera, dark), H.armigera (HarmSNMP, dark),and A. mellifera (AmelSNMP, Hymenoptera, green). The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥0.6 are shown at the corresponding nodes. The scale bar represents 0.04 substitutions per site.
DOI: 10.5061/dryad.2dj50/4
title: Figure 5 Neighbor-joining phylogenetic tree of odorant receptors (ORs)

description: The NJ phylogenetic analysis of ORs of E. hippophaecolus (EhipOR, red) was performed with reference ORs of D. melanogaster (DmelOR, Diptera, blue) and ORs of Lepidoptera species (black). The red circles refer to Orco and PR lineage. The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥0.6 are shown at the corresponding nodes. The scale bar represents 0.5 substitutions per site.
DOI: 10.5061/dryad.2dj50/5
title: Figure 6 Neighbor-joining phylogenetic tree of ionotropic receptors (IRs)

description: The NJ phylogenetic analysis of IRs of E. hippophaecolus (EhipIR, red) was performed with reference IRs of H.armigera (HarmIR, black), D. melanogaster (DmelIR, Diptera, blue) and IRs of other Lepidoptera species (black). The IRs groups labelled with red circle were reference of Van Schooten[82]. The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥0.6 are shown at the corresponding nodes. The scale bar represents 0.5 substitutions per site.
DOI: 10.5061/dryad.2dj50/6
title: Figure 7 Neighbor-joining phylogenetic tree of gustatory receptors (GRs)

description: Figure 7 Neighbor-joining phylogenetic tree of gustatory receptors (GRs)The NJ phylogenetic analysis of GRs of E. hippophaecolus (EhipGR, red) was performed with reference GRs of B.mori (BmorGR, dark), H.armigera (HarmGR, dark)[85], A. mellifera (AmelGR, Hymenoptera, green), T. castaneum (TcasGR, Coleoptera, purple) and D. melanogaster (DmelGR, Diptera, blue). The GRs group labelled with red circle refers to detect CO2. sugar and bitter. The stability of the nodes was assessed by bootstrap analysis with 1,000 replications, and only bootstrap values ≥0.6 are shown at the corresponding nodes. The scale bar represents 0.25 substitutions per site.
DOI: 10.5061/dryad.326r8/108
title: Assembled unitigs for Thunnus albacares
DOI: 10.5061/dryad.326r8/109
title: Assembled scaffolds for Helostoma temminckii
DOI: 10.5061/dryad.326r8/110
title: Assembled unitigs for Helostoma temminckii
DOI: 10.5061/dryad.326r8/111
title: Assembled scaffolds for Anabas testudineus
DOI: 10.5061/dryad.326r8/112
title: Assembled unitigs for Anabas testudineus
DOI: 10.5061/dryad.326r8/113
title: Assembled scaffolds for Selene dorsalis
DOI: 10.5061/dryad.326r8/114
title: Assembled unitigs for Selene dorsalis
DOI: 10.5061/dryad.326r8/115
title: Assembled scaffolds for Chromis chromis
DOI: 10.5061/dryad.326r8/116
title: Assembled unitigs for Chromis chromis
DOI: 10.5061/dryad.327sh/1
title: ZIKV_1.1.tar.gz

description: R-package: ZIKV. R-package containing data and functions associated with this manuscript.
DOI: 10.5061/dryad.327sh/2
title: ZIKV manual

description: PDF manual for the R-package: ZIKV
DOI: 10.5061/dryad.4rd14/1
title: Inventory of data repository

description: Schmid et al. – Inventory of data repository
DOI: 10.5061/dryad.4rd14/2
title: 01 - Dermis steady state

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/3
title: 02 - Dermis 14h PBS

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/4
title: 03 - Dermis 14h SGE

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/5
title: 04 - Dermis 14h primary DENV

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/6
title: 05 - Dermis 14h primary DENV+SGE

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.60s10/7
title: Figure_S7

description: The reliability of the eigengap heuristic versus MEDUSA in recovering shifts in speciation rate and diversification pattern in simulated trees. The absolute deviation of shifts recovered by the eigengap (red) and MEDUSA (blue) from the known number of shifts for trees with 0–10 shifts in (a) speciation rate and (b) diversification pattern. In (a), only when five or ten shifts were simulated, MEDUSA performed significantly better (T &gt; 2, P &lt; 0.05) than the eigengap. (a, Inset) The average deviation across all trees is slightly lower for MEDUSA (2.89) than for the eigengap heuristic (3.10), although this is not significant (T = 1.88, P &gt; 0.05). In (b), the eigengap heuristic outperformed MEDUSA for all trees with &gt; 2 shifts and (b, inset) overall (T = 10.44, P &lt; 0.01). In (a) and (b), only eigengaps supported by BIC post-hoc analysis were computed in the means. Asterisks indicate a significantly lower deviation for MEDUSA (blue) or the eigengap heuristic (red).
DOI: 10.5061/dryad.60s10/8
title: Figure_S8

description: Spectral density profile summary statistics across viral strains and hosts. Boxplot of avian (red) and human (gold) strains calculated from standard (a) and normalized (b) MGLs. Grey bars indicate across-host means; asterisks denote significant differences at P &lt; 0.05. (c) Mean differences between hosts across all strains calculated from standard graph Laplacians.
DOI: 10.5061/dryad.60s10/9
title: Figure_S9

description: The cluster assignments for strains by country of origin. Six clusters were found based on k-medoid clustering on the standard spectral density profiles of all strains (P &lt; 0.05). The distribution across those clusters for strains sampled from 25 countries are shown for avian (a) and human (b) hosts. Four clusters were found using the normalized profiles (P &lt; 0.05) and the distributions are shown for each country for avian (c) and human (d) hosts. Only countries with all seven strains sampled are represented.
DOI: 10.5061/dryad.7745p/1
title: Data Egg recognition

description: Raw data of the olfactory choice test.This file contains the time individuals spent in each preference zone, the ID of the test subjects, weight and origin of the used eggs.
DOI: 10.5061/dryad.8d724/1
title: Annotation file of open reading frames from 5 butterfly species

description: This is an annotation file for open reading frames (ORFs) from five species of heliconiine butterflies. The file includes ORFs from all five species, top BLAST hits, and the ortholog group the ORF belongs to. Column headers are as follows: "Row#" (row number), "Seq_ID" (sequence ID, including: 3 letter species code [Eis = Eueides isabella, Hdo = Heliconius doris, Her = Heliconius erato, Hmel = Heliconius melpomene, Hsa = Heliconius sara], Trinity 'gene' contig ID [e.g., compXXXX_cX], and ORF coordinates within contig), "H-ID" (hit ID), "H-Eval" (hit e-value), "H-Desc" (hit description), "H-Species" (hit species), "H-Type" (hit type), "H-Tag" (hit database), "H-Len" (hit length), and "OM" (orthocluster membership). NOTE: The program TCW produces two BLAST hits: 1. Best e-value, 2. best e-value with best evidence. The ones presented here are number 2.
DOI: 10.5061/dryad.8sj5g/1
title: deer

description: GPS locations of four black-tailed deer tracked for approximately seven months. Four columns: id, date, x, y
DOI: 10.5061/dryad.8t475/2
title: Squirrel validation points

description: Fox squirrel occurrence data from camera trapping
DOI: 10.5061/dryad.8vs89/1
title: Supplementary Table 1

description: Data from all specimens used in this study.  Data include: species name, specimen number, tooth, tooth measurements (Primary and Secondary RoCs, Edge measurements, long axis length), and type of data used to generate 3D models
DOI: 10.5061/dryad.9850t/1
title: InterferenceExploitative_Experiment

description: Contains treatment metadata (resource availability in mg and initial Colpidium density in cells/mL) as well as final Colpidium density in cells/mL. Also indicates which samples were randomly selected for 16S rRNA gene sequencing ("y"=yes, sample was sequenced; "n"=no, sample was not sequenced).
DOI: 10.5061/dryad.b91d1/1
title: morph_performance_regression_data

description: Data associated with analysis of change in morphology between repeated measures of an individual, and with regression analysis of relationship between morphology and swimming speed (Ucrit) measured at two time points ~3 months apart.
DOI: 10.5061/dryad.b91d1/2
title: Growth_and_Performance_data

description: Dataset associated with regression analysis addressing the question of whether changes in body shape between repeated measures of individuals was statistically associated with changes in Ucrit between repeated measures
DOI: 10.5061/dryad.b91d1/3
title: Ucrit_repeatability

description: Data associated with analysis of repeatability of Ucrit swimming performance
DOI: 10.5061/dryad.cs3h1/1
title: Data_Scalon et al. Oikos

description: Values of specific leaf area (SLA), and leaf nitrogen, phosphorus, potassium, magnesium and calcium concentrations for mistletoes and host species. Green leaf nutrient concentration are shown for mistletoes ([Nut]_green) and hosts ([Nut]_host). Senescent leaf nutrient concentration are shown for mistletoes only ([Nut]_old).
DOI: 10.5061/dryad.g60r3/2
title: 16S rRNA gene copy number estimates

description: Estimates of 16S rRNA gene copy number for OTUs analyzed in the Wagner et al. 2016 study. Created by following Kembel et al. (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Computational Biology 8 (10), e1002743.
DOI: 10.5061/dryad.g60r3/3
title: Glucosinolate data

description: Collection of glucosinolate data is described in Supplementary Note 1 of the article. HPLC peaks were called and area under each curve was integrated automatically by Agilent ChemStation software. Columns beginning with "area_" include the area under chromatogram peaks corresponding to the internal standard (Sinigrin) or one of the glucosinolate compounds (2OH1ME, 1ME, 6MSOH, 1MP, or I3M). "Weight" is the mass of air-dried samples, in mg. "Batch" is the identifier for groups of samples measured in the same HPLC run. "HPLC_ID" is a unique identifier for a glucosinolate sample, and "Plant_ID" is a unique identifier for individual plants in the field experiment.
DOI: 10.5061/dryad.g60r3/4
title: OTU phylogeny

description: Phylogeny of all OTUs (based on 97% 16S rRNA gene sequence identity). Generated from representative sequences using the midpoint method in QIIME.
DOI: 10.5061/dryad.g60r3/5
title: Field site coordinates

description: Latitude and longitude of 5 sites where genotypes were collected from natural B. stricta populations / where experimental common gardens were located.
DOI: 10.5061/dryad.h5r18.2
title: Data from: On the comparison of the strength of morphological integration across morphometric datasets
DOI: 10.5061/dryad.h5r18.2/1.2
title: Error Rate Simulation Code

description: R script used to evaluate the statistical error rates of the z-score method
DOI: 10.5061/dryad.h5r18.2/2.2
title: Simulation Results

description: Raw Data from simulation used to evaluate method's statistical error rates
DOI: 10.5061/dryad.ht4t3/1
title: Potential enzyme activity - NSCs - env - all

description: Potentential enzyme activity, nonstructural carbohydrates, and environmental measurements.
DOI: 10.5061/dryad.ht4t3/2
title: Potential enzyme activity - exploration type

description: Potential enzyme activity of contact and distance exploration types.
DOI: 10.5061/dryad.nt65q/10
title: RAD20.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/11
title: RAD21.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/12
title: RAD71.txt

description: Fastq data file
DOI: 10.5061/dryad.nt65q/15
title: Clustering_SNAPP_BarcodeFiles.tar

description: Barcode files (Individual sample names and associated barcode/molecular identifier) associated with clustering and SNAPP runs.  Formatted for analysis with AftrRAD.
DOI: 10.5061/dryad.nt65q/16
title: fsc_BarcodeFiles.tar

description: Barcode files (Individual sample names and associated barcode/molecular identifier) associated with fastsimcoal runs.  Formatted for analysis with AftrRAD.
DOI: 10.5061/dryad.v75mj/1
title: All CSV files used for analyses (ZIP file)

description: Please see Read me for how each files links to each analysis in the article.
DOI: 10.5061/dryad.vr954/5
title: Camarasaurus mandible model

description: Model of the mandible of Camarasaurus produced for this study
DOI: 10.5061/dryad.326r8/117
title: Assembled scaffolds for Parablennius parvicornis
DOI: 10.5061/dryad.326r8/118
title: Assembled unitigs for Parablennius parvicornis
DOI: 10.5061/dryad.326r8/119
title: Assembled scaffolds for Symphodus melops
DOI: 10.5061/dryad.326r8/120
title: Assembled unitigs for Symphodus melops
DOI: 10.5061/dryad.326r8/121
title: Assembled scaffolds for Pseudochromis fuscus
DOI: 10.5061/dryad.326r8/122
title: Assembled unitigs for Pseudochromis fuscus
DOI: 10.5061/dryad.326r8/123
title: Assembled scaffolds for Myoxocephalus scorpius
DOI: 10.5061/dryad.326r8/124
title: Assembled unitigs for Myoxocephalus scorpius