cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2kp7vr8/2
title: SI File - Reduced Molecular-Morphological Matrix

description: A reduced exemplar dataset with which the methods can be replicated. This dataset produces the same topology of molecular-only taxa, but be aware that because this is not the full data set, the absolute values of the rates and ratios will not be identical to the values reported.
DOI: 10.5061/dryad.2kp7vr8/3
title: SI File - Genes

description: Descriptions of the original source of the genetic material used in the alignment
DOI: 10.5061/dryad.2kp7vr8/4
title: SI Morphological Matrix

description: The morphological matrix used in the analysis
DOI: 10.5061/dryad.2kp7vr8/7
title: SI File 2 constraint

description: Topological constraint file as used in the analysis.
DOI: 10.5061/dryad.357vn6p/1
title: Supplementary File
DOI: 10.5061/dryad.4bb5849/1
title: Probe sequences

description: Sequences of the 54,870 probes used in the exome capture. The probe name consists of the sequence number (subseq, alt1 and al2 refer to the second (alternative) approach used for probe design), contig name, the probes base region (start and stop position within the contig, 150bp), and the number of the tiled probe of the probe base.
DOI: 10.5061/dryad.4bb5849/2
title: Allele frequencies of the seven populations

description: Alternative allele frequencies of the 13,228 SNPs in the seven population pools.
DOI: 10.5061/dryad.4bb5849/3
title: Contigs attributed by HDplot

description: List of the 10,675 contigs that could be attributed to either single-copy or multi-copy contigs using HDplot in the individually sequenced populations EC-HJ and WC-HJ.
DOI: 10.5061/dryad.4bb5849/4
title: Population information

description: Environmental information of the seven studied populations.
DOI: 10.5061/dryad.4bb5849/5
title: RNA-Seq readcounts

description: Raw read counts of the transcripts (length is also given) in the different libraries of the RNA-Seq. A = Adult, J = Juvenile, S = Seedling, Number = Replicate, C = Control treatment, F = Frost treatment, D = Drought treatment.
DOI: 10.5061/dryad.4bb5849/6
title: Transcriptome annotation

description: Functional annotation of the 34,010 transcripts of the transcriptome that could be annotated. Given is the putative gene name and GO-term ID, type, and description.
DOI: 10.5061/dryad.60q6876/1
title: GIS shape files of male and female ramet location data

description: GIS shape files containing male and female ramet location data used to analyze mechanisms underlying sex ratio variation.
DOI: 10.5061/dryad.60q6876/2
title: Ramet production for male and female genotypes
DOI: 10.5061/dryad.60q6876/3
title: Survivorship and sex ratio of seed families in glasshouse experiment
DOI: 10.5061/dryad.6265g37/1
title: SwiSCI community survey 2012, Basic Module, employable age group

description: Data from the Swiss Spinal Cord Injury Cohort Study (SwiSCI) community survey 2012; Basic Module, persons in employable age
DOI: 10.5061/dryad.7264p69/2
title: Tolerance value of 70 taxa

description: This is a list of tolerance values (TV) for 70 macroinvertebrate taxa in the five assemblages, to general human disturbances in streams of Pacific Northwest US derived based on field data (Cao & Hawkins 2005).
DOI: 10.5061/dryad.7264p69/3
title: Fish diversity and environmental variables

description: This dataset includes the value of effective number of species (ENS) calculated at 21 q-levels (i.e., ENS_0 - ENS_20) and a set of predictor variables describing natural environment, land-uses and spatial connections for 937 stream sites in the State of Illinois, USA.
DOI: 10.5061/dryad.7264p69/4
title: Mussel diversity and environmental variables

description: This dataset includes effective number of species calculated at 21 q-levels (i.e., ENS_0 - ENS_20) for mussel samples collected from 915 stream sites in Illinois, USA, and a set of predictor variables describing natural environment, land-uses and spatial connections.
DOI: 10.5061/dryad.74hp1kt/1
title: dataset_Santos_et al. 2018 Ecol lett

description: Plant phenotypic data from experiments 1, and 2 as described in the manuscript.
DOI: 10.5061/dryad.77b2422/10
title: teak_repr_hc_models_HiC_con_sorted_modiGeneID.gff

description: GFF of representative high-confidence gene models
DOI: 10.5061/dryad.77b2422/11
title: teak_repr_hc_models_HiC.cdna_con_sorted_modiGeneID.fa

description: cDNA sequences of representative high-confidence gene models
DOI: 10.5061/dryad.77b2422/12
title: teak_repr_hc_models_HiC.cds_con_sorted_modiGeneID.fa

description: CDS of representative high-confidence gene models
DOI: 10.5061/dryad.77b2422/13
title: teak_repr_hc_models_HiC.pep_con_sorted_modiGeneID.fa

description: Peptide sequences of representative high-confidence gene models
DOI: 10.5061/dryad.77b2422/14
title: teak_working_gene_fpkm_matrix_con_sorted.txt

description: Expression abundances of the working gene set were estimated using cufflinks RNAseq experiment atlas from NCBI SRA BioProject PRJNA287604
DOI: 10.5061/dryad.77b2422/6
title: teak_hc_models_HiC_con_sorted_modiGeneID.gff

description: GFF of all high-confidence gene models
DOI: 10.5061/dryad.77b2422/7
title: teak_hc_models_HiC.cdna_con_sorted_modiGeneID.fa

description: cDNA sequences of all high-confidence gene models
DOI: 10.5061/dryad.77b2422/8
title: teak_hc_models_HiC.cds_con_sorted_modiGeneID.fa

description: CDS of all high-confidence gene models
DOI: 10.5061/dryad.77b2422/9
title: teak_hc_models_HiC.pep_con_sorted_modiGeneID.fa

description: Peptide sequences of all high-confidence gene models
DOI: 10.5061/dryad.7jr85rj/50
title: H5N1 MCCs

description: Maximum Clade Credibility (MCC) Trees for each model/sample of H5N1 in Egypt.
DOI: 10.5061/dryad.84rs783/1
title: Data of plant-insect interactions

description: Survey of plant-insect interactions in the experiment.
DOI: 10.5061/dryad.84rs783/2
title: R code
DOI: 10.5061/dryad.84rs783/3
title: R database
DOI: 10.5061/dryad.873r5r3/1
title: Hill&Winder-Baboon-biogeography-data-deposit

description: This file contains locality samples and model outputs, including average grids for current niche models. There is a ReadMe text file included explaining the naming, and the accompanying paper gives details of the environmental layer sources too. Further details and additional maps/grids are available on request from i.c.winder@bangor.ac.uk.
DOI: 10.5061/dryad.8dq043h/1
title: Racemiflorae_Chloroplast_ARLEQUIN

description: Chloroplast microsatellite data in ARLEQUIN format for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/2
title: Racemiflorae_Chloroplast_GENALEX

description: Chloropast microsatellite data in GENALEX format for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/3
title: Racemiflorae_Chloroplast_GENEPOP

description: Chloroplast microsatellite data in GENEPOP format for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/4
title: Racemiflorae_Chloroplast_CPssr input

description: Input file for CPssr software. Chloroplast microsatellite haplotype data for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/5
title: Racemiflorae_Nuclear_GENALEX

description: Nuclear microsatellite data in GENALEX format for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/6
title: Racemiflorae_Nuclear_GENEPOP

description: Nuclear microsatellite data in GENEPOP format for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.8dq043h/7
title: Racemiflorae_Nuclear_STRUCTURE

description: Input file for STRUCTURE of nuclear microsatellites for 49 populations of Quercus section Lobatae subsection Racemiflorae.
DOI: 10.5061/dryad.cm042k3/1
title: Effects of photoperiod on life-history and thermal stress resistance traits across populations of Drosophila subobscura

description: The data file contains the following traits: egg to adult viability, total productivity, thermal resistance (CTmax and CTmin), thermal tolerance based on the locomotor activity assay (CTmaxLMA), total locomotor activity, dry body weight (DBW) and starvation resistance.
DOI: 10.5061/dryad.dh6443h/1
title: Physical and chemical characteristics of stream water and diatom dataset

description: This file contains: (i) physical and chemical characteristics of stream water, (ii) diatom species identified in the studied streams and (iii) trait classification for the identified diatom species
DOI: 10.5061/dryad.f8qm2d7/1
title: Bg_byAnnual

description: Annual invertebrate biomass, by genus (or lowest practical taxonomic unit)
DOI: 10.5061/dryad.f8qm2d7/2
title: Bg_bySeason

description: Seasonal (autumn/winter and spring/summer) macroinvertebrate biomass, by genus (or lowest practical taxonomic unit)
DOI: 10.5061/dryad.f8qm2d7/3
title: Factors_byAnnual

description: Environmental data (DIN, SRP, leaf litter biomass and stoichiometry); annual means.
DOI: 10.5061/dryad.f8qm2d7/4
title: Factors_bySeason

description: Environmental data (DIN, SRP, leaf litter biomass and stoichiometry); seasonal (autumn/winter and spring/summer) means.
DOI: 10.5061/dryad.h07s9d1/10
title: Phylogenetic Supplementary Material

description: See readme file.
DOI: 10.5061/dryad.h07s9d1/12
title: FigS6

description: Figure S6. The evolution of body size and sexual size dimorphism (SSD) in nephilid spiders: an alternative optimization to Fig. 4. (a) Female body length shows 26 increases (+) and 28 decreases (-); (b) Male body length has 24 increases and 30 decreases; (c) SSD shows 24 increases and 30 decreases. An ultrametric tree was pruned to contain the 28 taxa with known size variation in both sexes. Sizes and SSD (ratio female/male body length) were optimized on the tree using square change parsimony in Mesquite. Clades are color coded by web type in (a).
DOI: 10.5061/dryad.h07s9d1/13
title: Figure S7

description: Figure S7. The evolution of sexual size dimorphism (SSD, as simple female to male body size ratio) on a genus level phylogeny, an alternative to Fig. 6. The genus level topology is from AHE analyses, the SSD ratios are optimizations for each nephilid genus (Fig. S6c) or exemplar SSD data for outgroups (Table S3). The reconstruction is linear parsimony in Mesquite. Inset image shows Trichonephila clavipes female (left) and male (right). The sizes of female and male symbols correspond to relative total body lengths (Table S3).
DOI: 10.5061/dryad.h07s9d1/5
title: Figure S1

description: Figure S1. Anchored Hybrid Enrichment topologies from the analyses of the concatenated datasets.
DOI: 10.5061/dryad.h07s9d1/6
title: Figure S2

description: Figure S2. Anchored Hybrid Enrichment species tree topologies.
DOI: 10.5061/dryad.h07s9d1/7
title: Figure S3

description: Figure S3. Maximum Likelihood inference of concatenated data from 367 loci (“loose” dataset). NEP = Nephilidae (shaded area), ARA = Araneidae, PHO = Phonognathidae, TET = Tetragnathidae, MIM = Mimetidae.
DOI: 10.5061/dryad.h07s9d1/8
title: Figure S4

description: Figure S4. Species-level phylogeny of Nephilidae: Concatenated phylogeny constrained for Anchored Hybrid Enrichment topology with node supports.
DOI: 10.5061/dryad.h07s9d1/9
title: Figure S5

description: Figure S5. Macroevolutionary patterns of nephilid size evolution. Reconstructed ancestral states are plotted over phyletic time (given as cladogenetic events on phylogeny). Male, but not female size, exhibits a significant phyletic increase, and sexual size dimorphism stagnates.
DOI: 10.5061/dryad.h46jr1k/1
title: Fossil eggshell SEM images

description: Elongatoolithus sp., Prismatoolithus levis and Gobioolithus minor secondary electron images. Note rugged grain boundaries in continuous layers.
DOI: 10.5061/dryad.h46jr1k/2
title: Modern avian eggshell SEM images

description: Rhea, chicken, duck, Japanese tit, Korean magpie eggshells in secondary electron mode. Note rugged grain boundaries in continuous layers.
DOI: 10.5061/dryad.h46jr1k/3
title: EBSD raw data for materials

description: Channel 5 files. Note that in case of Gobioolithus minor, a version that diagenetic calcite is removed is used for misorientation histogram. In each species, a complete EBSD data and a subset for mammillary layer analysis are included. A zero solution corrected version is provided as raw data.
DOI: 10.5061/dryad.h46jr1k/4
title: Misorientation (For Figure 9)

description: Misorientation angles for neighbour-pair (correlated) and random-pair (uncorrelated) distributions. These data were used for histograms in Figure 9.
DOI: 10.5061/dryad.h46jr1k/5
title: Misorientation (For Figure S2 and Table S2)

description: Misorientation angles for neighbour-pair (correlated) and random-pair (uncorrelated) distributions. These data were used for histograms in Figure S2 and for Table S2.
DOI: 10.5061/dryad.h46jr1k/6
title: Contrast maps

description: Contrast map of materials.
DOI: 10.5061/dryad.h46jr1k/7
title: 10 Grain boundary maps

description: These maps were used for measuring ruggedness of the grain boundaries in squamatic ultrastructure and an external layer.
DOI: 10.5061/dryad.kc40s9h/1
title: Heuring&Hughes data file

description: Each tab in datafile corresponds to a separate csv file in R code; variables explained within each.
DOI: 10.5061/dryad.kc40s9h/2
title: R code for publication

description: R code; references csv files that are tabs within uploaded datafile.
DOI: 10.17632/5n96btpg26.1
title: Data for: 2 μm Passively Q-switched all-solid-state laser based on WSe2 saturable absorber

description: Under the pump power of 8.84 W, the maximum single pulse energy of 12.8 μJ and peak power of 30 W can be obtained, corresponding to the perfect pulse duration and maximum repetition rate of 427 ns and 82 kHz, respectively. It is the first presentation of such kind of WSe2-SA employed in a solid-state Q-switched crystalline laser at 2 μm, to the best of our knowledge.
DOI: 10.5061/dryad.2rc8s7m/1
title: Isotope data of small mammals

description: Carbon and nitrogen isotope data in small mammals from the flooded meadow; this is excell file with raw values from all studied specimens
DOI: 10.5061/dryad.4n5929c/1
title: MV4_11_A

description: pair of 2D images (control + Pyr1-treated) of MV 4-11 cells
DOI: 10.5061/dryad.4n5929c/2
title: MV4_11_B

description: pair of 2D images (control + Pyr1-treated) of MV 4-11 cells
DOI: 10.5061/dryad.4n5929c/3
title: MV4_11_C
DOI: 10.5061/dryad.4n5929c/4
title: MV4_11_D
DOI: 10.5061/dryad.4n5929c/5
title: Kasumi_A
DOI: 10.5061/dryad.4n5929c/6
title: Kasumi_B
DOI: 10.5061/dryad.4n5929c/7
title: Kasumi_C
DOI: 10.5061/dryad.4n5929c/8
title: Kasumi_D

description: pair of 2D images (control + Pyr1-treated) of Kasumi-1 cells
DOI: 10.5061/dryad.5qc1jc3/1
title: harvest1

description: Dry masses of leaves, stems and roots (‘DM_leaf’, ‘DM_stem’ and ‘DM_root’) of M. bisulcata seedlings from the forest experiment using mesh bags at harvest H1. ‘LS’ is the Latin-square subplot, ‘trmt’ is treatment (1 to 4 being with 0.5, 35 and 250 µm mesh, and no mesh, respectively), ‘col’ and ‘row’ are the column and row numbers of each LS layout, and ‘tag’ the seedling identifier. Survivorship is shown as ‘ad’ (0 – died, 1 – alive). Total plant mass (‘DM_total’) is shown where leaves were present to harvest. Covariates (‘cov_’) ‘rootpen1’ and ‘rootpen2’ are the coarse and fine scales scorings for external root penetration of the bags, and ‘height1’ and ‘height2’ (cm), and ‘leafnr’ (leaf number), the starting size variables (see Methods of publication).
DOI: 10.5061/dryad.5qc1jc3/2
title: harvest2

description: Dry masses of leaves, stems and roots (‘DM_leaf’, ‘DM_stem’ and ‘DM_root’) of M. bisulcata seedlings from the forest experiment using mesh bags at harvest H2. Explanation of the variables and coding is the same as for 'harvest1.xls'.
DOI: 10.5061/dryad.5qc1jc3/3
title: nutrients

description: Concentrations of nutrients in the plant parts (L – leaf, R – root, S – stem) of M. bisulcata seedlings (survivors) from the forest experiment using mesh bags. N, P, Ca, K and Mg are in mg/g, and Al, Fe, Mn, Cu and Zn are in mg/100g, dry mass. Harvests are H1 and H2; LS is the Latin-square subplot, and trmt is treatment (1 to 4 being 0.5, 35 and 250 µm mesh, and no mesh, respectively). Means per harvest and plant part are shown as the bars under ‘LS’ in the panels of Figs 3 and 4 of the publication.
DOI: 10.5061/dryad.71638rk/1
title: Validation of the Hospital frailty risk score datafile

description: This file contains part of the data used for our analyses in our publication Validation of the hospital frailty risk score in a Swiss tertiary care hospital
DOI: 10.5061/dryad.77b2422/15
title: 2018.10.23-teak-data-readme.docx

description: Readme
DOI: 10.5061/dryad.7jr85rj/52
title: pdm09 MCCs

description: Maximum Clade Credibility (MCC) Trees for each model/sample of pdm09 in Mexico and USA.
DOI: 10.5061/dryad.7jr85rj/53
title: Empirical Tree for H5N1 MCMCs

description: Starting empirical tree used for H5N1 MCMCs. Use this for the H5N1 BEAST XMLs.
DOI: 10.5061/dryad.7jr85rj/54
title: Empirical Trees for pdm09 MCMCs

description: Starting empirical trees used for pdm09 MCMCs. Use this for the pdm09 BEAST XMLs.
DOI: 10.5061/dryad.7jr85rj/55
title: H5N1 XMLs

description: 41 XMLs for the H5N1 Scenario
DOI: 10.5061/dryad.7jr85rj/56
title: pdm09 XMLs

description: 41 XMLs for the pdm09 Scenario
DOI: 10.5061/dryad.7tg18mb/2
title: Supplementary video

description: An HDMI MP4 video file showing the visualisations during several different REvoSim runs.
DOI: 10.5061/dryad.7tg18mb/3
title: Supplementary figures

description: A PDF file with supplementary figures: a graph of fitness using alternative error bars, and numerous visualisations captured during an exemplar REvoSim run.
DOI: 10.5061/dryad.83g2024/1
title: haplotypes_males
DOI: 10.5061/dryad.8dm275k/1
title: Known Origin Birds

description: Claw isotope values for known migrant and resident bluebirds used in assignment.
DOI: 10.5061/dryad.8g5g6j4/1
title: UK Biobank custom height association statistics on ~700k genotyped SNPs

description: The zip file contains six files:

(1) ukb_cal_v2_height_allancestry_10pcs_assoc_linear.tsv
(2) ukb_cal_v2_height_allancestry_nopcs_assoc_linear.tsv
(3) ukb_cal_v2_height_britishancestry_10pcs_assoc_linear.tsv
(4) ukb_cal_v2_height_britishancestry_nopcs_assoc_linear.tsv
(5) ukb_cal_v2_height_sibs_perm_qfam.tsv
(6) ukb_cal_v2_height_wbsibs_perm_qfam.tsv

(1) - (4) are height GWAS estimates on all samples / white British samples using 10 PCs as covariates or no PCs as covariates. Sex was included as covariate in all analyses.
(3) is equivalent to the UK Biobank height GWAS from the Neale lab. The remaining small differences can be explained by genotype differences in the UK Biobank imputed data and genotyped data.

(5) and (6) are family based estimates from 20166 sibling pairs of any ancestry (5) and 17358 sibling pairs where both siblings are of white British ancestry (6) in the UK Biobank. Pairs of samples with IBS0 &gt; 0.0018 and Kinship coefficient &gt; 0.185 were identified as sibling pairs. For the analyses in Sohail, Maier et al., only the subset of ~300,000 SNPs with SDS scores was used.  

For a description of the columns in files (1)-(4) please see the PLINK documentation for the ‘--linear’ command. Column “A2” has been added and denotes the non-effect allele.
For a description of the columns in files (5) and (6) please see the PLINK documentation for the ‘--qfam’ command. Column “A2” has been added and denotes the non-effect allele. “EMP1” and “NP” refer to permutation p-value and number of permutations, respectively.

Please note: These data are derived from the UK Biobank Resource under Application Number 18597.
DOI: 10.5061/dryad.99s9r6b/1
title: R code for Evolutionary Associations

description: Contains the markdown file for the evolutionary associations. This has a list of the files used and the code used for the associations.
DOI: 10.5061/dryad.99s9r6b/2
title: averages

description: Averages for traits used in the evolutionary associations
DOI: 10.5061/dryad.99s9r6b/3
title: Combined_data_for_paper

description: Raw data for evolutionary associations
DOI: 10.5061/dryad.99s9r6b/4
title: pen06

description: Un-pruned phylogeny used for the evolutionary associations.
DOI: 10.5061/dryad.99s9r6b/5
title: TrichomeSize5cells

description: Cell width data.
DOI: 10.5061/dryad.99s9r6b/6
title: F2.avgs.KA

description: P. kunthii x P. amphorellae F2 averages for correlations.
DOI: 10.5061/dryad.99s9r6b/7
title: F2.trait.corrs

description: R script for P. kunthii x P. amphorellae F2 trait correlations.
DOI: 10.5061/dryad.9p47b7f/1
title: Daily visits dataset1_daily visits
DOI: 10.5061/dryad.9p47b7f/2
title: Dryad archive dataset 1_metadata_daily.visits
DOI: 10.5061/dryad.9p47b7f/3
title: Dryad archive dataset 2_total.feeders.and.visits
DOI: 10.5061/dryad.9p47b7f/4
title: Dryad archive dataset 2_metadata_total.feeders.and.visits
DOI: 10.5061/dryad.9p47b7f/5
title: Dryad archive dataset 3_vegetation
DOI: 10.5061/dryad.9p47b7f/6
title: Dryad archive dataset 3_metadata_vegetation
DOI: 10.5061/dryad.9p47b7f/7
title: Dryad archive dataset 4_visits.since.sunrise
DOI: 10.5061/dryad.9p47b7f/8
title: Dryad archive dataset 4_metadata_visits.since.sunrise
DOI: 10.5061/dryad.b47mj.2
title: Data from: Males harm females less when competing with familiar relatives
DOI: 10.5061/dryad.c538kq7/1
title: Fossen_JEXBIO2019_Raw_data

description: Data on metabolic rate (oxygen consumption) from a laboratory experiment used to quantify genetic and temperature effects on the scaling of metabolic rate with body size.
DOI: 10.5061/dryad.c5rs958/1
title: Rusty crayfish CPUE through time and trap locations

description: Worksheet 1: Study lakes with proportion rock and mean catch-per-unit effort of male Faxonius rusticus by year. Missing values are years where the lake was not sampled. Worksheet 2: Trap locations (WGS84 decimal degrees) for study lakes from baited trapping for rusty crayfish Faxonius rusticus.
DOI: 10.5061/dryad.h010451/1
title: Kodama_et_al_2018_Gene_Count_12Sep18

description: This file contains the raw gene counts for all samples used in Kodama et al. (2018). On the "count" tab, the data are organized as: Gene number, LOC ID, chromosome, start position of the gene, end position of the gene and the gene product.
DOI: 10.5061/dryad.h46jr1k/10
title: Raw data converted to Text files

description: These are CRC files converted into text files for users who can not access CRC files
DOI: 10.5061/dryad.h46jr1k/8
title: Supplementary Figures S1-S4

description: Supplementary Figures cited in the text.
DOI: 10.5061/dryad.h46jr1k/9
title: Supplementary Tables S1-S3

description: Supplementary Tables cited in the text.
DOI: 10.5061/dryad.h6q81d2/1
title: Bachofen-Shoot-and-Root-measurements

description: This file contains all measurements: shoot and root biomass, shoot height, vertical root length. All other variables (root biomass fraction, specific shoot height, specific vertical root length) are derived from this data as described in the publication.