cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8mr56/4
title: Variance stabilized gene expression data and p-values

description: Variance stabilized gene expression and p-values were generated using the R package DESeq2. Row names are gene names. Column names are either sample names (columns 1-24) or p-values (columns 25-30). The letters following the p-value (pval or padj, for unadjusted and FDR corrected p-values respectively) indicate the contrast used to generate the pvalue: AH = ahead of the lesion to healthy, DA = disease to ahead of the lesion, DH = disease to healthy.
DOI: 10.5061/dryad.8mr56/5
title: WGCNA script

description: Script for network analysis of gene expression using the R package WGCNA. The script will require variance stabilized gene expression data for all samples and a table of trait values for each sample.
DOI: 10.5061/dryad.8mr56/6
title: Variance stabilized gene expression data for WGCNA

description: Variance stabilized gene expression data for all samples from the top differentially expressed genes (unadjusted p-value &lt; 0.1) for network analysis with the R package WGCNA. Rows are genes. Columns are samples.
DOI: 10.5061/dryad.8mr56/7
title: Samples and traits for WGCNA

description: Table of traits for samples for network analysis with the R package WGCNA. Rows are samples. Columns are traits. Values are binary indicators of whether the sample is positive for that trait. Traits are AL, H, and D for the three disease states (ahead of the lesion, healthy, and diseased) and 1-16 for each genotype.
DOI: 10.5061/dryad.8mr56/8
title: Acropora hyacinthus transcriptome

description: The version of the transcriptome used for this analysis.
DOI: 10.5061/dryad.fk2nh/1
title: External validation data for leopard resource selection function, South Africa, 2002-2012

description: For each of the 10 external validation sets, a Spearman's rank correlation is run between the observed number of locations and the ordinal rank of the corresponding RSF bins, and a linear regression between observed and expected number of locations in each bin is run to assess the predictive ability of the RSF.
DOI: 10.5061/dryad.gg273/1
title: gut-1
DOI: 10.5061/dryad.ht79k/1
title: Transgenerational effect of infection in Plasmodium-infected mosquitoes

description: These data allowed to quantify both the benefits and the costs of having an infected mother. We have measured : Blood meal size, wing size, number of eggs lay, prevalence infection and  intensity of infection
DOI: 10.5061/dryad.n0qr5/21
title: Matrix 11

description: Supermatrix of 67 orthologs and 13,540 sites. Occupancy: 92.7%. Criterion: Intersection of Matrix 1 and BUSCO-Ar data set.
DOI: 10.5061/dryad.n0qr5/22
title: Partitions file for Matrix 11

description: Partitions file for Matrix 11.
DOI: 10.5061/dryad.n0qr5/23
title: Matrix 12

description: Supermatrix of 280 orthologs and 63,274 sites. Occupancy: 86.9%. Criterion: Intersection of Matrix 2 and BUSCO-Ar data set.
DOI: 10.5061/dryad.n0qr5/24
title: Partitions file for Matrix 12

description: Partitions file for Matrix 12.
DOI: 10.5061/dryad.n0qr5/25
title: Matrix 13

description: Supermatrix of 689 orthologs and 162,067 sites. Occupancy: 80.4%. Criterion: Intersection of Matrix 3 and BUSCO-Ar data set.
DOI: 10.5061/dryad.n6c78/1
title: Monitoring development of aquatic and arboreal frog eggs

description: Developmental stage of aquatic and arboreal Dendropsophus ebraccatus embryos at approximately 16, 30 and 48 hours post-oviposition, in two ponds near Gamboa, Panama
DOI: 10.5061/dryad.n6c78/2
title: Predator discrimination tests by Dendropsophus ebraccatus

description: Number of arboreal eggs laid by Dendropsophus ebraccatus in small tubs with and without fish.
DOI: 10.5061/dryad.n6c78/3
title: Predator Oviposition site choice trials by Dendropsophus ebraccatus

description: Number of aquatic and non-aquatic embryos and egg masses laid by Dendropsophus ebraccatus in the presence or absence of fish.
DOI: 10.5061/dryad.p66jt/1
title: Ekanayake et al._Grey Value Data

description: The data from the pixel analysis of head colours of male and female Red-capped Plovers.
DOI: 10.5061/dryad.p66jt/2
title: Ekanayake et al._Spectrometric Data

description: The data from the Spectrophotometer used on different body parts of male and female Red-capped Plovers.
DOI: 10.5061/dryad.p66jt/3
title: Ekanayake et al._Artificial Model Data

description: The data from the artificial model experiment to assess the egg depredation rate between male and female Red-capped Plovers during night and daytime.
DOI: 10.5061/dryad.p66jt/4
title: Ekanayake et al._Incubation Division Data

description: The data from the video monitoring of real Red-capped Plover nests to investigate the incubation division among sexes.
DOI: 10.5061/dryad.q5j65/2
title: Mock Data for Prey Mass Model Predictions

description: Mock data used with home range models incorporating prey mass to generate home range size predictions for Figure 2 of "Energy and the scaling of animal space use". Details in manuscript.
DOI: 10.5061/dryad.q5j65/3
title: Mock Data for Home Range Prediction from Global Model

description: Mock data used with the final global home range model to generate home range size predictions for Online Figure A2 of "Energy and the scaling of animal space use". Details in manuscript.
DOI: 10.5061/dryad.q5j65/4
title: R Code Used in Analysis and Plotting (R Markdown)

description: The R code used for data analysis and plotting in "Energy and the scaling of animal space use", provided as an annotated R Markdown file.
DOI: 10.5061/dryad.q5j65/5
title: R Code Used in Analysis and Plotting (PDF)

description: The R code used for data analysis and plotting in "Energy and the scaling of animal space use", provided as an annotated PDF.
DOI: 10.5061/dryad.ss08k/1
title: Landmark-Data-Perrard-Loope-2015

description: Specimen information (colony, patriline) and landmark data of the wing shape of workers of Vespula flavopilosa studied in Perrard & Loope, 2015.
DOI: 10.5061/dryad.ss08k/2
title: Script R from Perrard & Loope, 2015

description: Script R used for the analyses of Perrard & Loope, 2015. This file contains both the script and the function "regallom" to compute multigroup allometry and allometric residuals using the multivariate regression approach.
DOI: 10.5061/dryad.tg58v/1
title: GarterSnakeTranscriptome.ContigsOnly

description: This is the multi-organ garter snake transcriptome assembled from 454 data. This file contains only the contigs.
DOI: 10.5061/dryad.tg58v/2
title: GarterSnakeTranscriptome.Contigs.and.Singletons

description: This garter snake transcriptome contains all the contigs and singletons. Sequence IDs in this file corresponds to the SeqID column in the Annotation File
DOI: 10.5061/dryad.tg58v/3
title: Annotation File

description: This is the Annotation file that corresponds to the transcriptome contigs and singletons
DOI: 10.5061/dryad.tg58v/4
title: Add.file1_Table_Samples

description: Additional files that are also available from BMC Genomics website.  Additional file 1 – Table containing details of the samples used for the sex-specific RNA pools.Tissue samples of the same type were pooled across individuals (either laboratory or field born animals) for total RNA extraction. Extracted pools of RNA were quantified and the quality checked on the Bioanalyzer. Equal amounts of RNA from each tissue type were pooled by sex.
DOI: 10.5061/dryad.tg58v/5
title: Add.file2_Dist.Reads

description: Additional files that are also available from BMC Genomics website.    Additional file 2 – Graphs illustrating the size distribution of the reads for each sex. Length (bp) distribution of reads obtained with the 454 GS-FLX Titanium sequencing. Read number (N) and length (L) in base pairs. A) Female run. B) Male runs.
DOI: 10.5281/zenodo.16192
title: MD simulation trajectory and related files for DMPC bilayer, Högberg et al, J.Comp.Chem., 29, 2359 (2008)

description: MD simulation trajectory and related files for DMPC bilayer, Högberg et al, J.Comp.Chem., 29, 2359 (2008)

25ns( excluded) + 55 ns trajectory<br>
T=303K, 98 lipids + 2700 H2O<br>
software: MDynaMix v  5.0

Relevant files:

md.input        : main MD input file

dmpc_2008.mmol  :  lipid topology/force field file<br>
H2O.mmol        :  SPC water

order.in        : Input for the analysis utility to extract order parameters

Trajectory files:

dmpc_NewMod.250 - dmpc_NewMod.849
DOI: 10.5061/dryad.202f5/3
title: MC1R Alligment
DOI: 10.5061/dryad.3rg5m/1
title: ultrametric

description: Ultrametric phylogeny used for running phylogenetic correlation analyses
DOI: 10.5061/dryad.436h0/1
title: P8-loci alignment

description: Loci that were found in all 8 samples were assembled in the more conservative ‘P8’ dataset, which was used to calculate pairwise population genetic metrics (e.g. heterozygosity, private alleles, pairwise distances) and to verify and support P2 results.
DOI: 10.5061/dryad.436h0/2
title: P2-loci alignment

description: All loci that were recovered from at least two samples were compiled in the extensive ‘P2’ dataset, which was used for all analyses, unless stated otherwise.
DOI: 10.5061/dryad.436h0/3
title: PdamT1P_Pst1

description: Pocillopora damicornis - Type 1 - Panama - Digested with Pst1, single-end RADSeq.
DOI: 10.5061/dryad.436h0/4
title: PdamT3P1GC_Pst1

description: Pocillopora damicornis - Type 3 - Panama, Gulf of Chiriquí - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.436h0/5
title: PdamT3P2GP_Pst1.fq

description: Pocillopora damicornis - Type 3 - Panama, Gulf of Panama - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.436h0/6
title: PdamT5JA_Pst1.fq

description: Pocillopora damicornis - Type 5 - Japan - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.436h0/7
title: PdamT13P_Pst1.fq

description: Pocillopora damicornis - Type 1/3 Het - Panama - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.436h0/9
title: PeleT1P_Pst1.fq

description: Pocillopora elegans - Type 1 - Panama - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.4m7v7/1
title: Anderson&Patek2015_species_data

description: Using 196 museum specimens from 36 stomatopod species, we measured morphological and biomechanical data related to the 4-bar system in the raptorial appendage. These data are divided into two files: Anderson&Patek2015_species_data contains species averages for Kinematic Transmission (KT) as well as average link lengths (Link1, Link 2, Link 3, and Link 4) and PC scores for the species (PC1-PC8). Note that in the manuscript, we divided links 1, 2 and 3 by link 4 for analyses.
DOI: 10.5061/dryad.4m7v7/2
title: Anderson&Patek2015_individuals_data

description: Using 196 museum specimens from 36 stomatopod species, we measured morphological and biomechanical data related to the 4-bar system in the raptorial appendage. These data are divided into two files: Anderson&Patek2015_individuals_data contains the PC scores and KT values for the 196 specimens measured. This data was used to construct the specimen-based morphospace in the manuscript.
DOI: 10.5061/dryad.5vv6t/2
title: Final Data for 565 sites
DOI: 10.5061/dryad.5vv6t/3
title: High Albedo Baseline Results
DOI: 10.5061/dryad.6g6r6/1
title: Boston et al - Leisler's bat (Nyctalus leisleri) - microsatellite data

description: Microsatellite data (genepop format) used in the MS entitled "New insights on postglacial colonisation in Western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri)"
DOI: 10.5061/dryad.7tb72/10
title: Library8_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/11
title: Library9_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/2
title: Table_2

description: Table_2 contains all the locus sequences (sheet 1: ‘Locus sequences’) and SNP information (sheet 2: ‘Genotypes’) that were used for the inference of phylogenetic relationships of Arctic charr and European whitefish.
DOI: 10.5061/dryad.7tb72/3
title: Library1_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/4
title: Library2_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/5
title: Library3_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/6
title: Library4_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/7
title: Library5_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/8
title: Library6_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/9
title: Library7_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.918bg/1
title: datasets

description: This compressed folder contains all AFLP, SSAP, MSAP and MSTD datasets in .txt
DOI: 10.5061/dryad.gg273/10
title: per-3
DOI: 10.5061/dryad.gg273/2
title: gut-2
DOI: 10.5061/dryad.gg273/3
title: gut-4
DOI: 10.5061/dryad.gg273/4
title: lut-1
DOI: 10.5061/dryad.gg273/5
title: gut-3
DOI: 10.5061/dryad.gg273/6
title: lut-2
DOI: 10.5061/dryad.gg273/7
title: lut-4
DOI: 10.5061/dryad.gg273/8
title: lut-3
DOI: 10.5061/dryad.gg273/9
title: per-2
DOI: 10.5061/dryad.n0qr5/26
title: Partitions file for Matrix 13

description: Partitions file for Matrix 13.
DOI: 10.5061/dryad.n0qr5/27
title: Matrix 14

description: Supermatrix of 1,725 orthologs and 421,446 sites. Occupancy: 66.4%. Criterion: Intersection of Matrix 4 and BUSCO-Ar data set.
DOI: 10.5061/dryad.n0qr5/28
title: Partitions file for Matrix 14

description: Partitions file for Matrix 14.
DOI: 10.5061/dryad.tg58v/10
title: Add.file7_Variants

description: Additional files that are also available from BMC Genomics website.   Additional file 7 – Details of variants. A 2007 Excel file (.xlsx) providing details for the variants (SNPs and INDELs). See the ReadME tab for description of columns.
DOI: 10.5061/dryad.tg58v/11
title: Add.file8_ContigOfInterest

description: Additional files that are also available from BMC Genomics website.   Additional file 8 - Contigs of interest. A 2007 Excel file (.xlsx) containing the sequences of interest including those that are sex-specific, that have homology to the chicken Z chromosome, those in the 1st percentile of TS/TV ratios, those in the top 99th percentile of Ka/Ks ratios, and those in the top 99th percentile of variability (number of variants per bp). See the ReadME tab for description of columns.
DOI: 10.5061/dryad.tg58v/12
title: Add.file9_sex-specificGOgraph

description: Additional files that are also available from BMC Genomics website.  Additional file 9 – Sex-specific enrichment of GO terms (level 2, Biological Processes) assigned to the 190 sex-specific sequences. The * indicates the significant over-enrichment of sequences involved in biosynthetic processes in the female-specific sequences (Fisher’s Exact Test, FDR &lt;0.006, p-value &lt; 0.0002).
DOI: 10.5061/dryad.tg58v/6
title: Add.file3_Graph-cluster.description

description: Additional files that are also available from BMC Genomics website.  Additional file 3 – Description of NEWBLER assembly and graph-clustering procedure.
DOI: 10.5061/dryad.tg58v/7
title: Add.file4_GOgraphs

description: Additional files that are also available from BMC Genomics website.   Additional file 4 – Pie graphs of GO assignments. GO slim (level 1, Biological Processes) assignments for all the sequences with annotation, broken down by class of sequences: male singletons, male contigs, both contigs (containing male and female reads), female contigs, female singletons.
DOI: 10.5061/dryad.tg58v/8
title: Add.file5_mapAnoCar1

description: Additional files that are also available from BMC Genomics website.  Additional file 5 - Snake transcripts mapped to coding and non-coding regions of the Anolis lizard draft genome (AnoCar1.0). A 2007 Excel file (.xlsx) providing details where the snake transcripts mapped to the Anolis draft genome. See the ReadME tab for description of columns.
DOI: 10.5061/dryad.tg58v/9
title: Add.file6_Clustering

description: Additional files that are also available from BMC Genomics website.  Additional file 6 - Clustering based on homology and contig-graphs. A) Distribution of the number of contigs in a HomoloGene accession, and B) the number of HomoloGene accessions that a contig is assigned to, both at e-value =1e-20. C) Distribution of the number of contigs belonging to a graph-cluster.
DOI: 10.5061/dryad.1m54f/1
title: Data used for constructing the path model

description: This data set includes automatically tracked movement data from 45 recorded trials of woodlice in an experimental fragmented landscape at different temperatures. 'body size' is the body mass in milligrams of the animal; 'temperature' gives the recorded temperature in degrees Celsius of the climate chamber where the trials were conducted and 'humidity' is given as a percentage; 'corridor crossing' is the number of complete crossings into the adjacent patch by the woodlice during a trial and 'corridor encounter' gives the number of times the woodlice crossed one threshold but did not cross the other into the adjacent patch; 'mean velocity' is the average speed in mm/s, 'max velocity' is the maximum speed moved in mm/s, and 'prop time moving' is the proportion of time that the woodlice spent moving during the trial period.
DOI: 10.5061/dryad.1rk60/1
title: Datasets for Quantifying Crowd Size for Mobile Phone and Twitter Data
DOI: 10.5061/dryad.21mp3/1
title: Chen Yao, Wang Faming-N and P addition on woody debris decompositon datasheet

description: The Raw data of this paper
DOI: 10.5061/dryad.3rg5m/2
title: Supplementary Data 1

description: Pairwise species comparisons and relative density data
DOI: 10.5061/dryad.3rg5m/3
title: Supplementary Data 2

description: Natural variation in H. titia female wing lightness and heterospecific males' responses
DOI: 10.5061/dryad.3rg5m/4
title: Supplementary Data 3

description: Results from the female wing-darkening experiment
DOI: 10.5061/dryad.3rg5m/5
title: Supplementary Data 4

description: Males' responses to tethered heterospecific and conspecific females
DOI: 10.5061/dryad.3rg5m/6
title: Supplementary Data 5

description: Males' responses to tethered heterospecific and conspecific males
DOI: 10.5061/dryad.436h0/10
title: PeydT1P_Pst1.fq

description: Pocillopora eydouxi - Type 1 - Panama - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.436h0/8
title: PdamT5TU_Pst1.fq

description: Pocillopora damicornis - Type 5 - French Polynesia, Tuamotus - Digested with Pst1, single-end RADSeq
DOI: 10.5061/dryad.51n8n/1
title: FE-2014-00400-RawData

description: Worksheets providing the raw data of Amax, gs, water potential, and morphofunctional traits measured in the field for individuals of the 20 species of Velloziaceae studied in the companion paper.
DOI: 10.5061/dryad.5vv6t/10
title: Sensitivity Gamma plus 10 percent
DOI: 10.5061/dryad.5vv6t/11
title: Sensitivity Stumpage minus 10 percent
DOI: 10.5061/dryad.5vv6t/4
title: Low Albedo Baseline Results
DOI: 10.5061/dryad.5vv6t/5
title: Sensitivity All minus 10 percent
DOI: 10.5061/dryad.5vv6t/6
title: Sensitivity All plus 10 percent
DOI: 10.5061/dryad.5vv6t/7
title: Sensitivity Alpha minus 10 percent
DOI: 10.5061/dryad.5vv6t/8
title: Sensitivity Alpha plus 10 percent
DOI: 10.5061/dryad.5vv6t/9
title: Sensitivity Gamma minus 10 percent
DOI: 10.5061/dryad.689v4/1
title: Pedigree and genotypes  from Mandarte Island song sparrows

description: Dam and sire for each individual (id) used in the publication in Molecular Ecology Resources together with their genotypes at 209 microsatellite loci (the two alleles of each marker are denoted by "a" and "b" appended to the marker name).
DOI: 10.5061/dryad.6v4h5/1
title: Alignment

description: Alignment of 166 partial and complete DNA barcode (mitochondrial COI gene) sequences derived during testing of the PCR primers and amplification strategy described in this study. All sequences except one (ww01176, which is less than 200 nt in length, too short) have been deposited in GenBank, accession numbers KP688405 - KP688569.
DOI: 10.5061/dryad.7nv0h/1
title: Adult nematode data

description: File includes species-specific counts of adult Trichostrongyle nematode specimens, strongyle fecal egg count (eggs/gram feces), capture date, and the GPS coordinates where each buffalo host was captured. These data were used to generate results reported in Figure 1a and Figure 2. An explanation of how these data were generated is included in the publication.
DOI: 10.5061/dryad.7tb72/12
title: Library10_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/13
title: Library11_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/14
title: Library12_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/15
title: Library13_SNPs

description: Sequences of all loci containing SNPs within the genomic library are listed in the first sheet ('Sequence'). Each SNP, its position on the respective locus and the genotype of each individual for that SNP is stored in the second sheet ('SNPs').
DOI: 10.5061/dryad.7tb72/16
title: RAxML_treefile

description: The tree file contains three Arctic charr and three European whitefish individuals from different localities in Europe
DOI: 10.5061/dryad.7tb72/17
title: Replicate_1_genotypes_8x

description: Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).
DOI: 10.5061/dryad.7tb72/19
title: Replicate_2_genotypes_8x

description: Input file for estimation of the SNP error rate. The R script to analyse this file is provided by Mastretta-Yanes et al. (2014).