cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k7c40/2
title: MakeNemoInputs_KurtoticDisp

description: R script to generate Nemo input files for simulations with leptokurtic dispersal kernels.
DOI: 10.5061/dryad.k7c40/3
title: MakeNemoInputs_NormalDisp_lowerFecundity_mimicMutationLoad

description: R script to generate Nemo input files for simulations with lower fecundity to mimic the presence of mutation load.
DOI: 10.5061/dryad.k7c40/4
title: PopulationSizes

description: Summarized simulation results data of population sizes
DOI: 10.5061/dryad.m5t70/1
title: Czech J Anim Sci-donkey microsatellite data
DOI: 10.5061/dryad.qd2nj/1
title: SHILD2012_cens_eng_16-64

description: Survey of a random sample of 19000 persons 16-64 years in Denmark autumn 2012.
DOI: 10.5061/dryad.sk6s0/10
title: Cybertype_Teratener nymeria_CASENT0053630_holotype worker_2

description: Cybertype dataset for Terataner nymeria (CASENT0053630) holotype worker 2: 3D PDF, 3D rotation video in mpg format, and montage photos (full-face view, body in profile, and dorsal view of body) in tif format
DOI: 10.5061/dryad.sk6s0/5
title: Cybertype_Terataner balrog_CASENT0472559_holotype worker_1

description: Cybertype dataset for Terataner balrog (CASENT0472559) holotype worker 1: complete micro-CT scanning raw dataset in DICOM format (993 slices)
DOI: 10.5061/dryad.sk6s0/6
title: Cybertype_Terataner balrog_CASENT0472559_holotype worker_2

description: Cybertype dataset for Terataner balrog (CASENT0472559) holotype worker 2: 3D PDF, 3D rotation video in mpg format, and montage photos (full-face view, body in profile, and dorsal view of body) in tif format
DOI: 10.5061/dryad.sk6s0/7
title: Cybertype_Terataner balrog_CASENT0426614_paratype queen_1

description: Cybertype dataset for Terataner balrog (CASENT0426614) paratype queen 1: complete micro-CT scanning raw dataset in DICOM format (993 slices)
DOI: 10.5061/dryad.sk6s0/8
title: Cybertype_Terataner balrog_CASENT0426614_paratype queen_2

description: Cybertype dataset for Terataner balrog (CASENT0426614) paratype queen 2: 3D PDF, 3D rotation video in mpg format, and montage photos (full-face view, body in profile, and dorsal view of body) in tif format
DOI: 10.5061/dryad.sk6s0/9
title: Cybertype_Teratener nymeria_CASENT0053630_holotype worker_1

description: Cybertype dataset for Terataner nymeria (CASENT0053630) holotype worker 1: complete micro-CT scanning raw dataset in DICOM format (993 slices)
DOI: 10.5061/dryad.t8016/5
title: Sarracenia alata sequences

description: Sequences used for Sarracenia alata
DOI: 10.5061/dryad.0sn63/6
title: EXP2premetabs

description: Contains data on plasma metabolite concentrations of birds in the preflight condition
DOI: 10.5061/dryad.0sn63/7
title: EXP2flightmetabs

description: Contains data on plasma metabolites during flight and time-matched fasting of birds eating different diets
DOI: 10.5061/dryad.15g78/2
title: NIL for interaction analysis
DOI: 10.5061/dryad.1gc03/1
title: data.plants

description: Morphological traits of plants used in the experiment described in the manuscript. Data include also mean number of visits and duration of each of the major insect groups.
DOI: 10.5061/dryad.1gc03/2
title: data.foraging

description: Data on individual visits for the plants by different insects.
DOI: 10.5061/dryad.1hs2m/1
title: AHE_BPP_alignments

description: Text file containing the alignments of all captured AHE loci used in the BPP analyses
DOI: 10.5061/dryad.1hs2m/2
title: AHE_concatenated_alignment_partitions

description: Partitions of the AHE concatenated dataset used in phylogenetic analyses, as estimated by PartitionFinder2
DOI: 10.5061/dryad.1hs2m/3
title: AHE_concatenated_alignment

description: Phylip file with concatenated AHE loci used in phylogenetic analyses
DOI: 10.5061/dryad.1hs2m/4
title: Cytb_aligment

description: Phylip file with cytb alignments
DOI: 10.5061/dryad.21tm5/1
title: RGB_RSOS

description: All figures
DOI: 10.5061/dryad.21tm5/2
title: Matlab code
DOI: 10.5061/dryad.27p4s/1
title: Starting models

description: Starting models for the iterative hybrid protocol. Based on the prefix you can determine where the models are coming from. (ab_v01) top10 denovo models using sigmoid only restraints. (ab_v02) top10 denovo models using bounded+sigmoid restraints during centroid, and sigmoid only during full atom stage.(mp) top10 map-align models from one round of hybrid.
DOI: 10.5061/dryad.27p4s/2
title: Initial models

description: Top models from initial experiments where only the (ab_v01+ab_v02) OR mp models are iteratively hybridized
DOI: 10.5061/dryad.27p4s/3
title: Top 30 models

description: Top 30 models across 30 iterations of hybrid of ab_v01+ab_v02 + map-align models.
DOI: 10.5061/dryad.27p4s/4
title: Final models

description: Single model for each target.
DOI: 10.5061/dryad.3c153/1
title: microbiome

description: The data contains tables in txt format with read counts for bacterial phyla (Phylum_level_readsCountTable.txt) and families (Family_level_readsCountTable.txt) in pooled samples from five different environments (nematodes, beetle gut, decaying beetle, native soil, and decaying beetle).
Zero read counts (no reads mapping to a taxonomic group) has been replaced by  a value of 1e-5 to facilitate downstream analysis, such as taking the logarithm.  We pooled the reads of technical replicates into one single sample by adding up the read counts, including 1e-5 values. For this reason some entries are floating point values rather than integers. Tables contain detailed information about each sample such as environment, 
sequencing year, decaying status, species and beetle parts information for nematode gut samples.
DOI: 10.5061/dryad.4gh7b/1
title: R scripts

description: Zipped archive of R scripts for simulation of samples and for analysis of simulated samples
DOI: 10.5061/dryad.4gh7b/2
title: Simulations for first iteration of the poulations-size change analyses:

description: The simulations output is stored as an R data file, to be loaded in an R session by the load() command.
DOI: 10.5061/dryad.5jc0t/2
title: SNP calls for Zonotrichia leucophrys nuttalli x Z. l. pugetensis hybrid zone

description: Dataset includes 6419 SNP loci for 169 individuals across the Zonotrichia leucophrys nuttalli x Z. l. pugetensis hybrid zone. Sampling information, including individual ID, locality, lat/long, sex, and whether song data is available is also provided. Songs are archived at the Borror Laboratory of Bioacoustics at Ohio State University.
DOI: 10.5061/dryad.65j02/1
title: Volpe et al-Fragmentation and_pollinator_movement_dataset

description: Hummingbird occurrence and movement data from Volpe et al. PLoS One
DOI: 10.5061/dryad.7717q.1
title: Data from: Expression of eukaryotic-like protein in the microbiome of sponges
DOI: 10.5061/dryad.7717q.2
title: Data from: Expression of eukaryotic-like protein in the microbiome of sponges
DOI: 10.5061/dryad.7717q.2/1.2
title: Eukaryotic transcriptomes and prokaryotic metatranscriptomes of three marine sponges.

description: Files Cym_Euk_165645.fasta, Sco_Euk_90948.fasta, Ted_Euk_113832.fasta are the eukaryotic transcriptomes for Cymbastella concentrica, Scopalina sp., Tedania anhelens respectively. Files Meta_Cym_RZ_228060.fasta, Meta_Sco_RZ_64649.fasta, Meta_Ted_RZ_56167.fasta are the prokaryotic metatranscriptomes of those same sponges. The numbers in the file names represent the number of transcripts within the file. See supporting table S1 C and D of the manuscript for details.
DOI: 10.5061/dryad.7717q.2/2.2
title: Eukaryotic transcriptomes and prokaryotic metatranscriptomes of three marine sponges (original assembly files).

description: These six files represent the original de-novo transcriptome assemblies obtained using Trinity software v2.0.6. Files Cym_Euk_184053.fasta, Sco_Euk_103013.fasta, Ted_Euk_129529.fasta are the eukaryotic transcriptomes for Cymbastella concentrica, Scopalina sp., Tedania anhelens respectively. Files Meta_Cym_RZ_383648.fasta, Meta_Sco_RZ_94173.fasta, Meta_Ted_RZ_85440.fasta are the prokaryotic metatranscriptomes of those same sponges. The numbers in the file names represent the number of transcripts within the file. See supplementary table S1 C and D of the manuscript for details.
DOI: 10.5061/dryad.7g978/2
title: All HTML files of VarVer.
DOI: 10.5061/dryad.8sk4r/1
title: Data with maximum number of bivalve individuals, including unidentified individuals (XNI approach)

description: This table provides the raw numbers of living and dead specimens of all mollusc taxa that were recovered in benthic assemblages, listed separately for all censuses. The dataset includes the few dead bivalve and gastropod specimens that could not be identified and were thus excluded from all analyses. Individual numbers are uncorrected for disarticulated valves of single bivalve individuals. As each empty bivalve valve was assumed to represent a unique individual ("XNI approach"), this dataset thus provides the maximum number of bivalve individuals.
DOI: 10.5061/dryad.8sk4r/2
title: Data with maximum number of bivalve individuals (XNI approach)

description: This table provides the raw numbers of living and dead specimens of all mollusc taxa that were recovered in benthic assemblages, listed separately for all censuses. Individual numbers are uncorrected for disarticulated valves of single bivalve individuals. As each empty bivalve valve was assumed to represent a unique individual ("XNI approach"), this dataset thus provides the maximum number of bivalve individuals.
DOI: 10.5061/dryad.8sk4r/3
title: Data with minimum number of bivalve individuals (MNI approach)

description: This table provides the numbers of living and dead specimens of all mollusc taxa that were recovered in benthic assemblages, listed separately for all censuses. Individual numbers are corrected for disarticulated valves of single bivalve individuals by assuming that both empty valves of all dead bivalve individuals were present in a sample ("the MNI approach"). This dataset thus provides the minimum number of bivalve individuals.
DOI: 10.5061/dryad.8sk4r/4
title: Data with corrected number of bivalve individuals (sampling domain 3x size of observed collections)

description: This table provides the numbers of living and dead individuals of all mollusc taxa that were recovered in benthic assemblages, listed separately for all censuses. Individual numbers are corrected for disarticulated valves of single bivalve individuals by assuming sampling domains three times the size of an observed collection. This dataset was used for all analyses presented in the manuscript.
DOI: 10.5061/dryad.b277d/1
title: evolution_16-0770

description: FiSSE analysis code, examples, testing datasets, analysis results, and batch processing scripts to accompany Rabosky & Goldberg (2017)
DOI: 10.5061/dryad.b5b4h/1
title: Above ground biomass in Nyungwe tropical montane forest

description: The data file contain the following information in separte sheets: (1) Plots, (2) Species, Breast height diameter classes, Above-ground biomass, Recruitment and mortality of trees, (3) Height vs DBH relationship, (4) Wood density, (5) Header definition, (6) Citations, (7) Data use policy.
DOI: 10.5061/dryad.bp76g/1
title: Survivorship data to acute heat stress.

description: temp= temperature of acute heat stress. pop= population of origin according to Suppl. Table 1; C demarks split broods reared in Control conditions (20C) and T demarks split broods reared in Treatment conditions (25C). alive/dead= number of individuals that were alive or dead 3 days after heat stress. prop= proportion of survivors.
DOI: 10.5061/dryad.bp76g/2
title: Summary statistics on heat tollerance.

description: Mean and SE estimated for LD50, LD10, and delta-LD50.
DOI: 10.5061/dryad.bp76g/3
title: raw_data_all_pops

description: data matrix for R analyses. stress_temp= heat-stress temperature; population= population; dev_temp= rearing condition; survived= number of individuals surviving to heat-stress after 3 days; died= number of individuals not surviving to heat-stress after 3 days; prop= proportion of survivorship.
DOI: 10.5061/dryad.c494p/1
title: Figure S2. Ancestral state reconstruction of viviparity for Liolaemidae using the uncorrected sample fraction

description: Figure S2. Ancestral state reconstruction of viviparity for Liolaemidae using the uncorrected sample fraction from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/2
title: Figure S1. Plot of the posterior and prior distributions from BAMM analysis using an expected number of shifts prior of 1.

description: Figure S1. Plot of the posterior and prior distributions from BAMM analysis using an expected number of shifts prior of 1.
DOI: 10.5061/dryad.c494p/3
title: Fig. S3 - BAMM net diversification

description: Figure S3. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are net diversification rates.
DOI: 10.5061/dryad.c494p/4
title: Fig. S4 - BAMM speciation

description: Figure S4. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are speciation rates.
DOI: 10.5061/dryad.c73q1/2
title: README

description: Instructions for supplementary data/source code
DOI: 10.5061/dryad.d4j55/5
title: TRP_on_OM_genes
DOI: 10.5061/dryad.d4j55/7
title: SuppMaterial_TraitRateProp
DOI: 10.5061/dryad.h6v7g.2/10.2
title: Matrix 1
DOI: 10.5061/dryad.h6v7g.2/7.2
title: Supplementary Table S1
DOI: 10.5061/dryad.h6v7g.2/8.2
title: Supplementary Table S2
DOI: 10.5061/dryad.j059v/1
title: All1Gamb

description: Genepop input file created by populations including all the markers used in the study
DOI: 10.5061/dryad.j059v/2
title: ADGamb

description: Genepop input file created by Populations. Only markers included in Anonymous Database (AD).
DOI: 10.5061/dryad.j059v/3
title: GDGamb

description: Genepop input file created by Populations. Only markers included in Associated-to-Genes Database (GD).
DOI: 10.5061/dryad.j059v/4
title: BLAST90_mRNA

description: BLASTN output file for the VM43 RADtags matching against the Xyphophorus maculatus mRNA sequences retrieved from GenBank using a word size of 90(BLAST90_mRNA.txt).
DOI: 10.5061/dryad.j059v/5
title: X_mac_mRNA

description: X_mac_mRNA.fasta: Fasta file including the Xyphophorus maculatus mRNA sequences retrieved from Ensembl (23,236 sequences) used for BLASTN analyses.
DOI: 10.5061/dryad.j059v/8
title: BayeScanGamb
DOI: 10.5061/dryad.j315n.1/10.1
title: Tableau-Genes retained  by each tests-dyad

description: This table contains all genes pointed by one list : PCA differentiating flor yeast from other strains (Allyeast-set), Dxy (VinVoile.VQSR.HighQualitybiall.vcf filtered for min genotype quality of 30 and sequence depth of 10), Da (same as Dxy), XPCLR (for Jura  and Spanish populations), 20% Best potentially damaging SNPs (according to SIFT) differentiating wine and flor PCA, codeml value. This table contains data for table S4 and for Figure 3.
DOI: 10.5061/dryad.j315n.1/11.1
title: DTdadi

description: Demographic  inferences (Figure S5a and b): SNP data set for wine and Jura/Hungary flor strains, and wine and Spain/Italy flor strains at dadi format for demographic inference. Obtained with script Vcf-to-dadi.pl
DOI: 10.5061/dryad.j315n.1/12.1
title: Vcf-to-dadi perl  script

description: Demographic  inferences (Figure S5a and b): Perl script that converts a vcf file including 2 or 3 pop with Ancestral Allele field (not necessary if folded)  to a file for diffusion approximation demographic inference (dadi,  Gutenkunst 2015, PLoS Genetics). Requires Bioperl, reference sequence fasta file, and variant file at VCF format (only with strains required for the analysis)
DOI: 10.5061/dryad.j315n.1/13.1
title: TranslocationsCompilation_outputs_delly

description: Compilation of delly  V 0.1.1 outputs  for each strain. This file contrains only events that occured more than 40 times.
DOI: 10.5061/dryad.j315n.1/14.1
title: XPCLR selection test: Script prepares ms data and run XPLCR
DOI: 10.5061/dryad.j315n.1/15.1
title: Data XPCLR of Wine and Spain Italy Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and Spain and Italy Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n.1/2.1
title: VinVoile.VQSR.HighQualitybiall.vcf

description: Compressed (tgz) Vcf file containing a subset of high quality biallelic variant filtered out from the genotyping output file  VQSR.vcf  produced by GATK, when filtering for only variants corresponding to the best genotyping scored (Indicated with PASS).  Population analysis measures (Dxy and Da) are performed on a second subset of this file after filtering  genotypes according to allelic depth and genotyping quality with vcftools, with  parameters: --minGQ 30 --minDP 10 --maf 0.001 . This filtered data set is used for figure 2C, and Figure S7.
DOI: 10.5061/dryad.j315n.1/4.1
title: Evaluation of variant impact on protein functions according to SIFT(4G)_ High quality biallelic variant set

description: Compressed file  containing the impact of each variant  on each annotated transcript, inferred with SIFT4G, for the file including all variant (VinVoile.VQSR.HighQualitybiall.vcf).
DOI: 10.5061/dryad.jv463/1
title: Garter snake telomeres and condition
DOI: 10.5061/dryad.k7c40/5
title: PopulationFitnesses

description: Summarized simulation results data of population fitness
DOI: 10.5061/dryad.k7c40/6
title: ExpansionSpeedResults

description: Summarized simulation results data for speed of expansion across simulations.
DOI: 10.5061/dryad.k7c40/7
title: EdgeLocation-FitnessResults

description: Summarized simulation results data for the location of the range edge in space across time points for simulations.
DOI: 10.5061/dryad.k7c40/8
title: SummaryFiles

description: Summarized simulation result files for deleterious mutations. Row 1 of each file contains column headers, row 2 contains the heterozygous of homozygous state effect sizes for each mutation, respectively, and rows 3 onward give the frequency of mutations across the landscape. Data is across generation times, as indicated by the file names.
DOI: 10.5061/dryad.m86k3/1
title: contigs

description: Whole genome sequencing reads for the 212 French Campylobacter jejuni isolates referred to in the associated publication.
DOI: 10.5061/dryad.nk35d/1
title: Result of full bibliometric search for ecology articles

description: We searched ISI web of knowledge (Core collection) for all ecology (Topic: Ecology) related papers published in leading journals for the time period 1990-2010. This was done on the 18th October 2016. We narrowed the dataset further down by restricting it to the following journals: ECOLOGY, FUNCTIONAL ECOLOGY, MARINE ECOLOGY PROGRESS SERIES, JOURNAL OF ECOLOGY, HYDROBIOLOGIA , OECOLOGIA , OIKOS , ECOLOGICAL MODELLING , SCIENCE , BIOLOGICAL CONSERVATION , JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY , PROCEEDINGS OF THE ROYAL SOCIETY B BIOLOGICAL SCIENCES , ANIMAL BEHAVIOUR , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , NATURE , MARINE BIOLOGY , ECOLOGICAL APPLICATIONS , LANDSCAPE ECOLOGY , AMERICAN NATURALIST, ECOLOGY LETTERS, and for the document type: Article and the ‘Web of science category’: Ecology. This yielded a total of 7415 articles.
DOI: 10.5061/dryad.nk35d/2
title: Subsetted bibliometric search for ecology articles

description: This dataset is a subset of a bibliometric search (see data description of full dataset). We choose every 5th article and used the information in the abstract, keywords and the title to manually classify each of those articles into 3 categories: Modelling article (MO, SM, MOFI, PHY, FI) , experimental article and articles that combined an experimental (EX) and a modelling approach (MIX) . The individual classification is described for each entry in the field code GR. We pooled the different modeling types (statistical modeling, phylogenetic modeling, individual based modeling, etc) into one category for the bibliometric analysis.
DOI: 10.5061/dryad.nk35d/3
title: List of highly cited ecologists

description: List of the top cited ecologists identified within the Clarivate analytics (formerly Thomson Reuters) list of “Highly cited researchers 2016 (http://hcr.stateofinnovation.thomsonreuters.com) in the category Environment/Ecology (n = 113) and sorted them into three groups: 1) researchers that only apply modelling approaches; 2) researchers that only apply experimental approaches in the laboratory or in the field; and 3) researchers that apply both modelling and experimental approaches. We further discriminated between researchers that collect their own observational data from non-manipulative descriptive studies (e.g. monitoring) and those that do not use observations or obtain them from other sources (e.g. databases). Information about research approaches was gathered by studying their publication lists and websites.
DOI: 10.5061/dryad.rj0h0/1
title: Sway and eye movements

description: The data in this file were used to generate figs 3-6.
DOI: 10.5061/dryad.s7q82/1
title: nSSR loci, the nuclear microsatellite data

description: The loci of nSSR, the nuclear microsatellite data
DOI: 10.5061/dryad.s7q82/2
title: species distribution localities of ENMs

description: The species distribution localities from the natural populations (56 populations), and other from CVH.
DOI: 10.5061/dryad.vg7h7/1
title: Chemnitz Bagrii Ayasse Steiger Data

description: Excel file contains data from the laboratory and the field experiments described in the article.
DOI: 10.5061/dryad.18p73/1
title: Alpine ibex behavioral and environmental data used in structural equation models

description: Data collected on male Alpine ibex behavior and environmental conditions in Gran Paradiso National Park, Italy, between May and October 2011.
DOI: 10.5061/dryad.18p73/2
title: Alpine ibex fecal crude protein and environmental data

description: Data collected on male Alpine ibex fecal crude protein content and environmental conditions in Gran Paradiso National Park, Italy, between May and October 2011.
DOI: 10.5061/dryad.21j0n/1
title: Plestiodon BEAST data set

description: Nexus file with concatenated UCE sequences. See ReadMe file to match sample names with species and locality.
DOI: 10.5061/dryad.3418j/1
title: HPLC - A.novae-angliae

description: HPLC characterization of leaves of A. novae-angliae grown in various soil microbial communities
DOI: 10.5061/dryad.3418j/2
title: HPLC - A.pilosus

description: HPLC characterization of leaves of A. pilosus grown in various soil microbial communities
DOI: 10.5061/dryad.3rc08/1
title: Arterial blood flow monitor

description: Arterial blood flow monitored in each rabbits model by Doppler flow during thrombolysis (L/min)
DOI: 10.5061/dryad.53k2d/1
title: SatoKudoh_AmNat_Data

description: The .xls file consists of separated sheets of the field survey data, the mesocosm experiment data, and README.
DOI: 10.5061/dryad.7gk6d/1
title: SM Dataset Giraudeau & Ducatez BL
DOI: 10.5061/dryad.8b146/2
title: Figure source data

description: Source data for results figures.
DOI: 10.5061/dryad.8b146/3
title: eeg_face_vs_noise

description: This is an EEG data set used in Section 4.1. Two classes of stimulus images were presented (faces or noise). Data are from a single subject.
DOI: 10.5061/dryad.8b146/4
title: meg_speech

description: This is an MEG data set used in Section 4.2. MEG was recorded during a 7.5 minute auditory presentation of speech. Data are from a single subject.
DOI: 10.5061/dryad.8b146/5
title: eeg_eye_visibility

description: This is an EEG data set used in Section 4.3. EEG was recorded while images of faces were presented sampled with bubbles (Gaussian apertures). We consider here the visibility of the eye region. Data are from a single subject.