cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2764/7
title: Phonotaxis data of the relative attractiveness(combined data)

description: Phonotaxis data of the relative attractiveness,combined data of 4,5,6 note numbers to E-F,N-F,or E-N
DOI: 10.5061/dryad.q3j73/3
title: Table S2

description: Matrix of geographic distance in km among all sampled sites estimated considering the minimum distance between sites, assuming the modern geological conformation, and circumnavigating lands.
DOI: 10.5061/dryad.q3j73/4
title: Alignments

description: S3 Fasta file including COI sequences used for the concatenated dataset. S4 Fasta file including 16S sequences used for the concatenated dataset. S5 Fasta file including 18S sequences used for the concatenated dataset. S6 Fasta file including 28S sequences used for the concatenated dataset. S7 Fasta file including all COI sequences used for the population structure analyses.
DOI: 10.5061/dryad.q3j73/5
title: Genetic and Geographic Matrices

description: Matrices of genetic (COI) and geographic (km) distances for each morphological group used for population structure analyses. S8-S14 Matrices of genetic distances. S15-S21 Matrices of geographic distances.
DOI: 10.5061/dryad.q3j73/6
title: Table S1

description: Table S1 (Supporting information). List of specimens, their geographical and genetic information used for this study, and GenBank accession numbers. H. = haplotype. Specimens followed by "*" were used only for the the population structure analyses. GenBank codes in between "|" are from Leasi and Norenburg 2014.
DOI: 10.5061/dryad.q3j73/7
title: Trees

description: Gene Trees obtained by single gene and concatenated alignments: S22 (BI COI); S23 (BI 16S); S24 (BI 18S); S25 (BI 28S); S26 (BI Concatenated); S27 (ML Concatenated); S28 (Ultrametric, BEAST Concatenated).
DOI: 10.5061/dryad.tj5f0/1
title: data_beirne et al

description: ID = Unique individual identity code; CD = focal capture date; SOCG = Social group of capture; AGE = Age in years (from 16th February); MEAN.AGE = Average age across all captures; DELTA.AGE = Deviation in age from MEAN.AGE; SEX = Male or Female; CONDITION = Scaled mass index condition estimate; DISEASE.EXCLUDED = bTB status excluding IFNγ-based ELISA test (1 = uninfected, 2 = exposed, 4 = excretor) ; DISEASE = bTB status including IFNγ-based ELISA test (1 = uninfected, 2 = exposed, 4 = excretor); IFN = Interferon-gamma response; IFN.PLATE = IFN test plate identity; TELOMERE = Telomere length estimate (Kb); TELOMERE.PLATE = Telomere plate identity
DOI: 10.5061/dryad.1d1t5/1
title: Fish abundance and climate data

description: This file includes data on species name, longitude and latitude of each population, log transformed abundance based on rarefaction estimates, as well as data for ten climate variables extracted at each site from the WorldClim dataset.
DOI: 10.5061/dryad.1tf8g/1
title: Cand_Thiosymbion_16SrRNA_phylogeny_mrBayes

description: Tree file of bayesian inference phylogenetic analysis of Candidatus Thiosymbion ecto- and endosymbionts
DOI: 10.5061/dryad.1tf8g/2
title: Cand_Thiosymbion_16SrRNA_phylogeny_RAxML

description: Tree file of RAxML phylogenetic analysis of Candidatus Thiosymbion ecto- and endosymbionts
DOI: 10.5061/dryad.1tf8g/3
title: Baysian_inference_phylogenies_Stilbonematinae_ectosymbioses

description: Tree files of bayesian inference (mrBayes) phylogenetic analysis of stilbonematine nematode hosts and Candidatus Thiosymbion ectosymbionts
DOI: 10.5061/dryad.1tf8g/4
title: RAxML_phylogenies_Stilbonematinae_ectosymbioses

description: Tree files of maximum likelihood (RAxML) phylogenetic analysis of stilbonematine nematode hosts and Candidatus Thiosymbion ectosymbionts
DOI: 10.5061/dryad.1tf8g/7
title: Bayesian_inference_phylogenies_gutless_Phallodrilinae_endosymbioses

description: Tree files of bayesian inference (mrBayes) phylogenetic analysis of gutless phallodriline annelid hosts and Candidatus Thiosymbion endosymbionts
DOI: 10.5061/dryad.1tf8g/8
title: RAxML_phylogenies_gutless_Phallodrilinae_endosymbioses

description: Tree files of maximum likelihood (RAxML) phylogenetic analysis of gutless phallodriline annelid hosts and Candidatus Thiosymbion endosymbionts
DOI: 10.5061/dryad.29h6k/1
title: Biatora
DOI: 10.5061/dryad.29h6k/2
title: Caloplaca
DOI: 10.5061/dryad.29h6k/3
title: Cladonia
DOI: 10.5061/dryad.29h6k/4
title: Dirina
DOI: 10.5061/dryad.29h6k/5
title: Flavoparmelia
DOI: 10.5061/dryad.486c0/10
title: Main analysis: analyses under transition model 4

description: The models were broken up by transition model, then diversification model, then focal area.
DOI: 10.5061/dryad.486c0/11
title: Main analysis: analyses under transition model 5

description: The models were broken up by transition model, then diversification model, then focal area.
DOI: 10.5061/dryad.486c0/5
title: Main analysis: source data

description: The data used in the main analysis of floral evolution.
DOI: 10.5061/dryad.486c0/6
title: Main analysis: summaries

description: Summaries of rates, likelihoods, and AIC values for the over 19K models analyzed.
DOI: 10.5061/dryad.486c0/7
title: Main analysis: analyses under transition model 1

description: The models were broken up by transition model, then diversification model, then focal area.
DOI: 10.5061/dryad.486c0/8
title: Main analysis: analyses under transition model 2

description: The models were broken up by transition model, then diversification model, then focal area.
DOI: 10.5061/dryad.486c0/9
title: Main analysis: analyses under transition model 3

description: The models were broken up by transition model, then diversification model, then focal area.
DOI: 10.5061/dryad.5ff80/23
title: Figure 1D

description: gif files for rotational views of 3D antigenic maps in Figure 1
DOI: 10.5061/dryad.5jt25/1
title: Complement_gene_alignments

description: Primates Multispecies alignments used in the evolutionary analyses
DOI: 10.5061/dryad.5jt25/2
title: omegaMap_alignments

description: complement bacterial-encoded interactors alignment files
DOI: 10.5061/dryad.5jt25/3
title: gammaMap_input

description: input files for the human lineage gammaMap analysis
DOI: 10.5061/dryad.706df/1
title: CT scans of Icacinaceae fossils: Faboidea and Palaeophytocrene

description: X-Ray micro-CT scans of Faboidea and Palaeophytocrene fossils (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.706df/2
title: CT scans of Icacinaceae fossils: Icacinicarya spp. 1

description: X-ray micro-CT scans of Icacinicarya spp. (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.706df/3
title: CT scans of Icacinaceae fossils: Icacinicarya spp. 2

description: X-ray micro-CT scans of Icacinicarya fossils (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.706df/4
title: CT scans of Icacinaceae fossils: Iodes spp. 1

description: X-ray micro-CT scans of Iodes fossil (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.983r5/1
title: Data: Spatial distribution of D. discoideum in soil

description: Abundance of Dictyostelium discoideum isolates in small soil samples collected along transects. See Fortunato et al (2003) Mol Ecol 12:1031 and Gilbert et al (2012) Proc Roy Soc Lond B 279:2619.
DOI: 10.5061/dryad.983r5/10
title: Data: Germination of D. discoideum spores on bacterial lawns

description: Number of plaques observed on bacterial lawns inoculated with known number of Dictyostelium discoideum spores.
DOI: 10.5061/dryad.983r5/2
title: Analysis: Spatial distribution of D. discoideum in soil

description: Analyze and visualize spatial distribution of Dictyostelium discoideum amoebae among soil samples. Script for use with R environment for statistical computing.
DOI: 10.5061/dryad.983r5/3
title: Data: D. discoideum plaque growth

description: Growth of Dictyostelium discoideum plaques on bacterial lawns
DOI: 10.5061/dryad.983r5/4
title: Analysis: D. discoideum plaque growth

description: Analyze and visualize growth of Dictysotelium discoideum plaques on Klebsiella lawns. Script for use with R environment for statistical computing.
DOI: 10.5061/dryad.983r5/5
title: Data: Transect of D. discoideum fruiting bodies across two intersecting plaques

description: Distribution of genotypes along transect of D. discoideum fruiting bodies across two intersecting plaques.
DOI: 10.5061/dryad.983r5/6
title: Analysis: Transect of D. discoideum fruiting bodies across two intersecting plaques

description: Analyze and visualize distribution of genotypes along transect of Dictyostelium discoideum fruiting bodies across two intersecting plaques. Script for use with R environment for statistical computing.
DOI: 10.5061/dryad.983r5/7
title: Analysis: D. discoideum flow cytometry

description: Parse flow cytometry .fcs files to determine number and proportion of fluorescent/nonfluorescent Dictyostelium discoideum cells. Script for use with R environment for statistical computing.
DOI: 10.5061/dryad.983r5/8
title: Data: D. discoideum fruiting bodies sampled from petri plate

description: Genotype composition of individual Dictyostelium discoideum fruiting bodies sampled from across surface of petri plate. Generated by analysis of flow cytometry data.
DOI: 10.5061/dryad.b1k26/1
title: Emergence data

description: Data used to perform the GLM analysis.
DOI: 10.5061/dryad.cd2pk/1
title: FullData_MustonenEtAl_EcolAppl_2016

description: This data file includes all data used in the article. Please see the attached ReadMe file for more detailed information.
DOI: 10.5061/dryad.d18m1/1
title: Traversia lyalli Sequence Data

description: FASTQ file containing filtered, de-mulitplexed and collapsed MiSeq (Illumina) sequencing reads corresponding to the Traversia lyalli (S27777) enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.d18m1/2
title: Pachyplichas yaldwyni Sequence Data

description: FASTQ file containing filtered, de-mulitplexed and collapsed MiSeq (Illumina) sequencing reads corresponding to the Pachyplichas yaldwyni (Av18213) enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.d18m1/3
title: Xenicus longipes Sequence Data

description: FASTQ file containing filtered, de-mulitplexed and collapsed MiSeq (Illumina) sequencing reads corresponding to the Xenicus longipes (Av37320) enriched genomic library. See main publication for full details on data processing.
DOI: 10.5061/dryad.d18m1/4
title: BEAST_files

description: BEAST files, including input .xml and final maximum clade credibility tree.
DOI: 10.5061/dryad.d18m1/5
title: Morphology_files

description: Files for re-analysis of Worthy et al.'s (2010) morphological matrix, including .nex for PAUP* and MrBayes, and final trees.
DOI: 10.5061/dryad.d18m1/6
title: MrBayes_files

description: MrBayes files, including input .nex and final tree.
DOI: 10.5061/dryad.d18m1/7
title: RAxML_files

description: RAxML files, including input alignment & partition file and final tree.
DOI: 10.5061/dryad.d18m1/8
title: NGS_pipeline_scripts

description: Scripts for analysis of high-throughput sequencing data.
DOI: 10.5061/dryad.hk82b/1
title: Panero & Crozier 2016

description: Nexus file used to generate phylogeny of Asteraceae
DOI: 10.5061/dryad.m8k24/5
title: Additional file 5_14dpf_FMRF_aTub_DAPI_apical

description: Confocal z-stack showing FMRFamide-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 14 dpf stage. Apical view. Note that the staining of peripheral nerves is scarce.
DOI: 10.5061/dryad.m8k24/6
title: Additional file 6_14dpf_FMRF_aTub_DAPI_lateral

description: Confocal z-stack showing FMRFamide-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 14 dpf stage. Lateral view. Note that the staining of peripheral nerves is scarce.
DOI: 10.5061/dryad.m8k24/7
title: Additional file 7_14dpf_5HT_aTub_DAPI_lateral

description: Confocal z-stack showing 5-HT-LIR (purple), aTub-LIR (cyan) and DAPI staining (dark blue) of the 14 dpf stage. Lateral view. Note that the staining of peripheral nerves is scarce.
DOI: 10.5061/dryad.pk20h/1
title: configuration files and admix'em input file for neutral simulations

description: Required files to run neutral simulations including three admix'em configuration files for neutral hybrid swarm (admixsimul.cfg), neutral bottleneck hybrid swarm (admixsimul_bottle.cfg), and neutral hybrid swarm with migration simulations (admixsimul_mig.cfg) and other input files to admix'em called by these configuration files
DOI: 10.5061/dryad.pq624/1
title: Data and code for fitting multi-species occupancy model.

description: Camera trap detection / non-detection data for bobcats, coyotes, gray foxes, and red foxes from 6 mid-Atlantic states and the District of Columbia, USA; associated site-level covariates; and R and Stan code for fitting a multi-species occupancy model.  See ReadMe for detailed file descriptions.
DOI: 10.5061/dryad.sp45r/1
title: R-code

description: The code generates niche overlap matrices and gradient of species evenness, and calculates relative biomass production and species survival probability. It reproduces figures 1 and 4.
DOI: 10.5061/dryad.tg37f/1
title: Simulations under CR and DD models - part 2

description: Second batch of .RData files of the tree simulations under the CR and DD models.
DOI: 10.5061/dryad.tg37f/2
title: Simulations under CR and DD models - part 1

description: First of two batches of .RData files of the trees simulation under the CR and DD models and the R-script that generated both batches.
DOI: 10.5061/dryad.tg37f/3
title: Maximum likelihood results under CR model

description: RData files with maximum likelihoods and corresponding parameter estimates under the constant-rate (CR) model, and the R-script that generated them.
DOI: 10.5061/dryad.tg37f/4
title: Maximum likelihood results under DD model - 1

description: RData files with maximum likelihoods and corresponding parameter estimates under the diversity-dependent model, and the R-script that generated them. The starting values of the optimization are the simulation values.
DOI: 10.5061/dryad.tg37f/5
title: Maximum likelihood results under DD model - 2

description: RData files with maximum likelihoods and corresponding parameter estimates under the diversity-dependent model, and the R-script that generated them. The starting values of the optimization are the results from the CR models fits with a large but finite carrying capacity..
DOI: 10.5061/dryad.tg37f/6
title: R-script to make plots from results

description: R-script to make plots from simulation results
DOI: 10.5061/dryad.tg37f/7
title: Bootstrap likelihood ratio test results of the Dendroica case study

description: RData file of the bootstrap likelihood ratio test results of the Dendroica case study.
DOI: 10.5061/dryad.1h669/1
title: PasserineClocks.MitochondrialDNA

description: Nexus-formatted nucleotide alignments of 12 protein-coding genes from the mitochondrial genomes of 183 passerine species
DOI: 10.5061/dryad.1tf8g/5
title: Phylogenetic_marker_sequence_alignments_Stilbonematinae_ectosymbioses

description: Phylogenetic marker sequence alignments of stilbonematine nematode hosts and Candidatus Thiosymbion ectosymbionts
DOI: 10.5061/dryad.1tf8g/6
title: Phylogenetic_marker_sequence_alignments_gutless_Phallodrilinae_endosymbioses

description: Phylogenetic marker sequence alignments of gutless phallodriline annelid hosts and Candidatus Thiosymbion endosymbionts
DOI: 10.5061/dryad.1tf8g/9
title: Sequence_alignment_Cand_Thiosymbionts_16SrRNA

description: 16S rRNA gene sequence alignment of Candidatus Thiosymbion ecto- and endosymbionts
DOI: 10.5061/dryad.29h6k/10
title: Lobariella
DOI: 10.5061/dryad.29h6k/11
title: Melanohalea
DOI: 10.5061/dryad.29h6k/12
title: Miriquidica
DOI: 10.5061/dryad.29h6k/13
title: Montanelia
DOI: 10.5061/dryad.29h6k/14
title: Parmotrema
DOI: 10.5061/dryad.29h6k/6
title: Fulgensia
DOI: 10.5061/dryad.29h6k/7
title: Lecania
DOI: 10.5061/dryad.29h6k/8
title: Lecanora
DOI: 10.5061/dryad.29h6k/9
title: Letharia
DOI: 10.5061/dryad.2gf23/4
title: Social networks for 10 cities

description: The giant component for Tweets during October 1st 2014 through to October 28th 2014, separated by city. The first column relates to the city (1:Edinburgh; 2:Glasgow; 3:Cardiff; 4:Bristol; 5:Nottingham; 6: Birmingham; 7:Sheffield; 8:Leeds; 9:Manchester; 10:London), and the other two columns indicate an edge between the two listed nodes.
DOI: 10.5061/dryad.316s7/1
title: Data for paper: Different food sources elicit fast changes to bacterial virulence

description: Data includes death occurrence data of Galleria mellonella (wax moth) after injection of different doses of bacteria that had grown 48 hours in plant or animal based mediums, in high or low concentrations. ResourceType (1=plant, 2=animal), ResoureLevel (1=low concentrations, 2=high concentration), Dead =observation of death (1) (0 =alive), at time of death/observation (ToD). Treatment equals 1 level factor of treatments (plant low, plant high, animal low, animal high, 1,2,3,4, respectively). CFU =colony forming units in 1 ml of bacterial diluted suspension injected to bacteria. LogCFU = log transformed CFU. Filter = is used to exclude observations of which logCFU&lt;1.96, and &gt;6.59.
DOI: 10.5061/dryad.6r9q6.2
title: Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).
DOI: 10.5061/dryad.6r9q6.2/1.2
title: Dryad Tables 1 and 2

description: This data file contains the hormone concentrations (in ng/g feces) for 26 adult males, 25 pregnant females, and 29 non-pregnant females, determined by radioimmunoassays (RIA) and/or liquid chromatography combined with triple quadropole mass spectrometry (LC/MS/MS). The following hormones were measured: testosterone (T), androstendione, 5α-dihydrotestosterone (DHT), dehydroepiandrosterone (DHEA), androsterone, estrone (E1), 17β-estradiol (E2) and total estrogens (E). Note that a few individuals were represented by two samples, in which case we calculated the mean hormone value and this mean was used for the analyses.
DOI: 10.5061/dryad.6r9q6.2/2.2
title: Dryad Fig. 1

description: This data file contains the testosterone (T) concentrations, the logarithm-transformed T concentrations and the number of days from the onset of sex skin deturgescence for all the fecal samples collected between September 2009 and June 2013, for pregnant and non-pregnant females. See manuscript for more information.
DOI: 10.5061/dryad.6r9q6.2/3.2
title: Dryad Fig. 2

description: This data file contains the testosterone (T) concentrations, the logarithm-transformed T concentrations and the number of weeks into pregnancy for all the pregnant female’s fecal samples collected between September 2009 and June 2013.
DOI: 10.5061/dryad.6s0s8/1
title: latency of responses
DOI: 10.5061/dryad.706df/5
title: CT scans of Icacinaceae fossils: Iodes spp. 2

description: X-ray micro-CT scans of Iodes fossils (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.706df/6
title: CT scans of Icacinaceae fossils: Spaeriodes and Stizocarya

description: X-ray micro-CT scans of Spaeriodes and Stizocarya fossils (Icacinaceae) from the Early Eocene London Clay flora
DOI: 10.5061/dryad.7sj32/1
title: data_property_scale
DOI: 10.5061/dryad.7sj32/2
title: data_village_scale
DOI: 10.5061/dryad.7sj32/3
title: data_landscape_scale
DOI: 10.5061/dryad.864bv/1
title: Supplementary material file_raw data

description: Data for a nitrogen balance study and immune studies
DOI: 10.5061/dryad.9008g/1
title: Dryad data jellyfish-fish association

description: supporting data
DOI: 10.5061/dryad.983r5/11
title: Data: D. discoideum inocula

description: Genotype composition of Dictyostelium discoideum samples used to inoculate bacterial lawns. Generated by analysis of flow cytometry data.
DOI: 10.5061/dryad.983r5/12
title: Data: Flow cytometry of fruiting bodies from transect across plaques

description: Raw flow cytometry data (FCS format) from Dictyostelium discoideum fruiting bodies sampled along transect crossing two plaques.
DOI: 10.5061/dryad.983r5/13
title: Data: Flow cytometry of D. discoideum inocula and all-RFP controls

description: Raw flow cytometry data (FCS format) of Dictyostelium discoideum spores (1) inoculated onto bacterial lawns and (2) sampled from fruiting bodies on plates only inoculated with RFP-labelled amoebae.
DOI: 10.5061/dryad.983r5/14
title: Data: Flow cytometry of D. discoideum fruiting bodies sampled from across plate

description: Raw flow cytometry data (FCS format) of Dictyostelium discoideum spores sampled from fruiting bodies on plates inoculated with mix of wild type and RFP-labelled amoebae.
DOI: 10.5061/dryad.983r5/15
title: Data: D. discoideum microscopy

description: Individual and composited images of Dictyostelium discoideum fruiting bodies.
DOI: 10.5061/dryad.983r5/9
title: Analysis: D. discoideum fruiting bodies sampled from petri plate

description: Analyze and visualize distribution of Dictyostelium discoideum genotypes in individual fruiting bodies sampled from across surface of petri plates. Script for use with R environment for statistical computing.
DOI: 10.5061/dryad.c715s/1
title: Raw data from occurrence records and experiments performed to quantify strength and species- and morph-dependent asymmetries of reproductive isolation between Primula elatior and P. vulgaris.

description: The excel file contains raw data of (i) number of 1x1 km grid cells from occurrence data of Switzerland that was used to estimate ecogeographic isolation (RIecogeo); (ii) number of pollen grains, diameter of pollen grains, anther and stigma positions, and anther-stigma distance from the pollen-transfer experiment that was used to estimate mechanical isolation (RImech); (iii) number of seeds, filled seeds, seedlings, and flowers, and proportion of fruits and survivors from the hand-pollination experiment that was used to estimate F1 seedling formation (RIseedling) and F1 survivorship (RIsurvivorship); (iv) number of plants and open flowers per census day, date of onset, peak, and end of flowering time, number of flowers,  number of seeds and filled seeds from the common garden experiment that was used to estimate phenological isolation (RIphenoP), F1 phenology (RIphenoF1), F1 flower production (RIflower), and F1 seed set (RIseed set); and (v) number of seeds, filled seeds, and seedlings from the hand-pollination backcross experiment that was used to estimate F1 male sterility (RImale). Data for occurrence records and each experiment are presented in an individual worksheet. Names of column headings correspond with terms used in the original paper (Table 1).
DOI: 10.5061/dryad.fn627/1
title: 'Agalma best' alignments

description: The alignments representing a subset of the output of Agalma, run on 21 eupulmonate transcriptomes. This subset is the 546 orthologous clusters identified by Agalma, where each orthologous cluster was the only one produced from the respective homolog cluster and had sequences for at least 18 taxa. The alignments contain dummy sequences for missing taxa.
DOI: 10.5061/dryad.fn627/2
title: 'Agalma equivalent' alignments

description: The alignments representing a subset of the output of Agalma, run on 21 eupulmonate transcriptomes.This subset is the 635 orthologous clusters identified by the automated pipeline Agalma, which correspond to the 500 nuclear single copy, orthologous genes identified by manual curation. The alignments contain dummy sequences for missing taxa.
DOI: 10.5061/dryad.fn627/3
title: Manual curation: 500 gene alignments

description: The alignments for 500 single copy, orthologous, nuclear genes across 21 representatives of the eupulmonates. Orthology was assessed through manual curation and gene tree assessment. Each alignment contains a mask, 'x' denotes regions that were masked out (i.e. remove from further analyses). The alignments contain dummy sequences for missing taxa.