cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2tg34/2
title: Figure S2 - Prior and posterior probabilities for shifts

description: Figure S2. Frequency distribution of distinct macroevolutionary rate regimes estimated for the Dictyoptera using BAMM with a Poisson prior of 10. A scenario including five shifts of diversification has the highest posterior probability Similar results are obtained with different values of the Poisson prior (Fig. S6).
DOI: 10.5061/dryad.2tg34/3
title: Figure S3 - Marginal probabilities and marginal odds ratios of the BAMM run

description: Figure S3. Two different metrics of weighing the relative evidence of a diversification shift occurring along any individual branch. (a) The phylogenetic tree has its branch lengths been replaced by the branch-specific marginal shift probabilities, i.e. the length of a given branch is equal to the percentage of samples from the posterior that contain a rate shift on that particular branch. (b) The phylogenetic tree has the branch lengths scaled to equal the corresponding marginal odds ratio accounting for the effects of the prior and branch length. The longest branch length, in both trees, is labelled for reference. In both cases, the longest branch is within the termites.
DOI: 10.5061/dryad.2tg34/4
title: Figure S4 - Credible set of diversification shifts in Dictyoptera

description: Figure S4. Credible set of configuration shifts for net diversification of Dictyoptera inferred with BAMM. Phylogenies show the distinct shift configurations with the highest posterior probability. For each shift configuration, the locations of rate shifts are shown as black circles, with circle size proportional to the marginal probability of the shift. Text labels (e.g. f=0.11) denote the posterior probability of each shift configuration.
DOI: 10.5061/dryad.2tg34/5
title: Figure S5 - Best shift configuration in diversification shifts in Dictyoptera

description: Figure S5. The best shift configuration for net diversification shifts inferred with BAMM. The phylogeny indicates five core rate shifts (indicated by red-filled circle) within the termites, two within the Mantodea, and two within the cockroaches (notably in Blaberidae, Panesthiinae). The first shift in mantises occurred early (166.8 Ma) and includes most of the mantises but leaves out all ancient and depauperate lineages near the root of the tree. The second shift within mantises is located at the base of a clade including notably the plant-mimicking mantises (Empusidae), the flower mantises (Hymenopodidae), and the core of praying mantises (Mantidae). The first shift in cockroaches is ancient (243 Ma), just after the Permian-Triassic extinction, corresponds to the divergence of the termite lineage (including Cryptocercidae and Lamproblattidae, two species-poor families of cockroaches) and the lineage leading to Blattidae. The second shift occurred at the K-Pg event (66 Ma), and involves an offshoot of the blaberid radiation (Panesthiinae, ca. 150 species). The most important shift occurred within termites, 66 Ma, at the node sustaining the radiation of Termitidae and a part of Rhinotermitidae. Interestingly this lineage is composed only by eusocial species with true workers (Fig. S1).
DOI: 10.5061/dryad.2tg34/6
title: Figure S6 - BAMM analyses to check for prior effect

description: Figure S6. All the results for the BAMM analyses using a range of values for the Poisson prior process (0.1/0.5/1/5/10/50). The figures are ranked as follows: (1) prior and posterior distribution, and (2) best configuration. Overall, the results indicate a similar macroevolutionary mixture of rate shifts and diversification rates, with a significant shift within termites and a higher net diversification for termites.
DOI: 10.5061/dryad.4qh45/1
title: Positive fire severity feedback in SE Australia

description: This data file contains R code for the statistical analysis of severity feedbacks between fires in South-East Australia.
DOI: 10.5061/dryad.4qh45/2
title: Severity feedback data

description: This is the original data used for the analysis of severity feedbacks.
DOI: 10.5061/dryad.75625/1
title: Data from MV and microMA experiments

description: A description of the data can be found in the readme file.
DOI: 10.5061/dryad.86634/1
title: dryad_datasets_2010_2016_update_2017

description: We downloaded the reference information for all packages published between 2010-2016 on datadryad.org. This information was retrieved in January-February 2017.
DOI: 10.5061/dryad.86634/2
title: webofscience_update_2017

description: We gathered citation information from Thomson Reuters™ Web of Science Core Collection (http://apps.webofknowledge.com/) for a total of more than sixteen thousands scientific publications between the years 2010 and 2016 from the top ten journals submitting data to Dryad (Molecular Ecology, PLOS ONE, Evolution, Proceedings of the Royal Society B, Journal of Evolutionary Biology, The American Naturalist, Heredity, Molecular Ecology Resources, Biology Letters, Ecology and Evolution). From Web of Science online search page, we excluded reviews, perspectives, corrections, erratums and editorials. In addition, given the multidisciplinary nature of PLOS ONE and Proceedings of the Royal Society B, we limited searches for those two journals with the keywords “ecology”, “evolution” or “genetics”. For PLOS ONE (&gt;10k results), we only kept 3,000 random publications and accompanying citation records to keep the study design balanced. This amounted to a total of 16,771 references and their corresponding citation information that could be downloaded (per journal) that was exported in text format. This information was retrieved in January-February 2017.
DOI: 10.5061/dryad.8vm8d/1
title: False SNPs caused by batch effect

description: This file is a vcf file containing the SNP calls at the eight SNPs identified as outliers. Seven of these SNPs were false variants caused by differences in read length.
DOI: 10.5061/dryad.8vm8d/2
title: demultiplexing.file.Alpine.ibex.Capra.ibex

description: The demultiplexing file. Includes the sample name, population, sex, the barcodes used, sequencing length and data generator.
DOI: 10.5061/dryad.8vm8d/3
title: VCF_filterPolym.Lischer.H.E.L

description: Script to remove SNPs only polymorphic relative to the genome. This was used to remove SNPs when aligning Capra ibex RADseq to the Capra domestica genome.
DOI: 10.5061/dryad.gh0q91j/1
title: Supplementary Data 1 - Eodicynodon AZ

description: Specimens from the Eodicynodon assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/2
title: Supplementary Data 2 - Tapinocephalus AZ

description: Specimens from the Tapinocephalus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/3
title: Supplementary Data 3 - Pristerognathus AZ

description: Specimens from the Pristerognathus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.mr070/1
title: LOM et al JXB_PHENO_GENO-2

description: Genotypic and phenotypic data for the HEB-25 barley mapping population grown under well-watered (WW) and water-limited (WL) environments for two years (2015 and 2016). The genotypic data: 11, homozygous for the cultivated Hordeum vulgare allele; 12, heterozygous; 22, homozygous for the wild donor (H. spontaneum). Phenotype: Heading time (HEA), defined as the time between sowing to time at which the first spike of 50% of the plants in a plot reaches BBCH49 (first awns visible), was recorded based on daily inspection. Days from sowing to stage BBCH87 (hard dough: grain content solid: fingernail impression held) was recorded as maturity (MAT). At maturity, plant height (HEI) was measured from the soil surface to the base of the three first spikes per plot. 
At full grain maturity and after plants were fully dried, all aboveground biomass was harvested and weighed to determine total dry matter (TDM). Notably, all the free-thrashing material (app. ¼ of the material) was caged between BBCH49 and BBCH87 to avoid loss of spikes. Spikes were then threshed and weighed to determine plant grain yield (PGY). Finally, grains were counted to estimate grain number per mini-plot (GN) and average grain weight (GW). Harvest index (HI) was calculated as the ratio between PGY and TDM. Vegetative dry matter (VDW) was calculated by subtracting PGY from TDM. The grain-filling period (GFP) was calculated by subtracting HEA from MAT.  Trait values were adjusted based on the ratio between population mean values in the two years. The adjusted HEB means across years were used in the GWAS.
DOI: 10.5061/dryad.r9n52/10
title: Marks Point Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Marks Point' (MP) in Lake Macquarie
DOI: 10.5061/dryad.r9n52/11
title: Palm Beach Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Palm Beach' (PB) in Pittwater
DOI: 10.5061/dryad.r9n52/12
title: Quibray Bay Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Quibray Bay' (QB) in Botany Bay
DOI: 10.5061/dryad.r9n52/13
title: Seaplane Wharf Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Seaplane Wharf' (SW) in Pittwater
DOI: 10.5061/dryad.r9n52/14
title: Yacht Club North Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Yacht Club North' (YN) in Lake Macquarie
DOI: 10.5061/dryad.r9n52/15
title: Yacht Club South Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Yacht Club South' (YS) in Lake Macquarie
DOI: 10.5061/dryad.r9n52/16
title: Before-After polygon attributes

description: Data generated from shapefiles to compare seagrass meadow size (as polygons) in 2009/2010 and 2014
DOI: 10.5061/dryad.r9n52/9
title: Manly Wharf Shapefiles

description: Shapefiles and images for the Posidonia australis meadow located at site 'Manly Wharf' (MW) in Sydney Harbour
DOI: 10.5061/dryad.rr3667m/1
title: combined_chloroplast_collection

description: Systematic sample of Bayesian trees. Every 1,000th post-burnin tree from the four runs was included, for a total of 600 trees.
DOI: 10.5061/dryad.rr3667m/2
title: Volvocine tree, ultrametric

description: Volvocine phylogenetic tree, created from the phylogram using a penalized likelihood function.
DOI: 10.5061/dryad.rr3667m/3
title: Volvocine tree, phylogram

description: Bayesian phylogram of volvocine and outgroup taxa.
DOI: 10.5061/dryad.rr3667m/4
title: Chloroplast data matrix

description: Data matrix for volvocine chloroplast phylogenetic tree.
DOI: 10.5061/dryad.rr3667m/5
title: Dataset 1

description: Genbank accession numbers of chloroplast genes for ingroup and outgroup taxa.
DOI: 10.5061/dryad.t04k1/2
title: Fig. 2

description: Data sheet Fig 2
DOI: 10.5061/dryad.t04k1/3
title: Fig. 3

description: Data sheet Fig 3
DOI: 10.5061/dryad.t04k1/4
title: Fig. 4

description: Data sheet Fig. 4
DOI: 10.5061/dryad.t04k1/5
title: Fig5.

description: Data sheet Fig. 5
DOI: 10.5061/dryad.t04k1/6
title: Fig. 6

description: data sheet Fig. 6
DOI: 10.5061/dryad.t04k1/7
title: Fig. 7

description: Data sheet Fig. 7
DOI: 10.5061/dryad.t04k1/8
title: Fig. 8

description: Data sheet Fig. 8
DOI: 10.5061/dryad.v7g08/1
title: CarrierReitzel_RawData_Dryad

description: All samples associated with the study
DOI: 10.5061/dryad.vg089/10
title: OTUs fasta file
DOI: 10.5061/dryad.vg089/11
title: Genetic data

description: Includes files with various QC and summary information as well as the genotype estimate matrix
DOI: 10.5061/dryad.vg089/3
title: Mass spec features not placed in a putative chemical class

description: The first field has focal plant information in the form "MesaJH.01" where 01 refers to the first plant. Values in the file are intensities. Data were combined into putative parent compounds using CAMERA (see methods) and normalized by sample mass.
DOI: 10.5061/dryad.vg089/5
title: Saponin mass spec. features normalized by sample weight
DOI: 10.5061/dryad.vg089/6
title: Phenolic mass spec. features normalized by sample mass
DOI: 10.5061/dryad.vg089/7
title: PlantLocations

description: Locations of plants in terms of bearing and meters from origin
DOI: 10.5061/dryad.vg089/8
title: Warcup taxonomic placement of each fungal OTU
DOI: 10.5061/dryad.vg089/9
title: OTU table for fungi

description: Normalized to counts per million, see methods
DOI: 10.5061/dryad.vp955/1
title: Supporting Info - Dataset for BMJ Open

description: Anonymous DataBase
DOI: 10.5061/dryad.2tg34/16
title: Figure S8 - Differences MuSSE worker states macroevolutionary rates MCMC

description: Differences in rates computed from the MCMC analyses using the best MuSSE model for the ‘true’ workers. The compound figure shows: 1) the differences between speciation rates as made by pair comparisons; 2) the differences between extinction rates; and 3) the differences between net diversification rates. Only the lineages with ‘true’ workers have a significant different speciation, extinction, and net diversification rates (i.e. no posterior distribution overlaps with the red line). Eusocial lineages with ‘true’ workers diversified faster than non-eusocial lineages and eusocial lineages with pseudergates.
DOI: 10.5061/dryad.2tg34/17
title: Figure S9 - Differences MuSSE hindgut microbiota macroevolutionary rates MCMC

description: Differences in rates computed from the MCMC analyses using the best MuSSE model for the gut microbiota. The compound figure shows: 1) the differences between speciation rates as made by pair comparisons; 2) the differences between extinction rates; and 3) the differences between net diversification rates. Only the lineages with an entirely prokaryotic gut microbiota have a significant different net diversification rates (i.e. no posterior distribution overlaps with the red line). Eusocial lineages with an entirely prokaryotic hindgut microbiota diversified faster than other lineages (cellulolytic flagellates or no specialized microbiota for lignocellulose digestion).
DOI: 10.5061/dryad.2tg34/18
title: Figure S10 - Simulations with SSE models

description: Randomization tests for (a) BiSSE, (b) MuSSE on the worker state, and (c) MuSSE on the hindgut microbiota. The difference of fit between the best model and the reference model is shown with the red vertical line for real data, and in vertical coloured bars for the distribution of simulated data. The tests show that our results are robust to type-I error.
DOI: 10.5061/dryad.2tg34/19
title: Figure S11 - MuSSE hindgut microbiota Wood-feeding non-eusocial

description: Results for the MuSSE analyses with the wood-feeding non-eusocial lineages re-coded as cellulolytic flagellates along with plots of the differences in rates computed from the MCMC analyses using the best MuSSE model. The compound figure shows: 1) the differences between speciation rates as made by pair comparisons; 2) the differences between extinction rates; and 3) the differences between net diversification rates. Only the lineages with an entirely prokaryotic hindgut microbiota have a significant different net diversification rates (i.e. no posterior distribution overlaps with the red line). Eusocial lineages with an entirely prokaryotic hindgut microbiota diversified faster than other lineages (cellulolytic flagellates or no specialized microbiota for lignocellulose digestion).
DOI: 10.5061/dryad.2tg34/20
title: Table S1 - BAMM analyses

description: Summary of diversification models in BAMM compared across a gradient of values for the Poison process governing the number of rate shifts. The analyses show that a scenario with either four, five or six shifts of diversification best explained the macroevolution of Dictyoptera. Although it might suggest that the Poison prior has some effect on the analyses, it is important to note that all shifts are in common between the analyses (see Fig. S6 for more details). Based on the effective sample size (ESS) and the highest posterior distribution per number of shifts for the Poisson rate prior, we selected the model with a Poison prior of 10 (highlighted in bold). In addition this model represents an intermediary among the analyses (i.e. we did not favour a model with more shifts or a model with few shifts).
DOI: 10.5061/dryad.2tg34/21
title: Table S2 - SSE analyses

description: Supports for eusociality, eusocial lineages with ‘true’ workers, and eusocial lineages with entirely prokaryotic microbiota as driver(s) of diversification. Tables (a), (c) and (e) report the means for each value estimated based on 100 dated trees, for each diversification model applied under the BiSSE approach, their number of parameters (NP), the log-likelihood (logL), the corrected Akaike Information Criterion (AICc), the difference of AICc (ΔAIC) between the best model (lowest AIC) and a given model. The best model is highlighted in bold and determined by ∆AIC. Tables (b), (d) and (f) report the standard errors for each parameter estimated by the diversification models and listed in the tables (a), (c) and (e).
DOI: 10.5061/dryad.4v23b/1
title: DRYAD Database for South African Adolescent study

description: Age and sexual debut data was generated from questionnaires. Sexual transmitted infection was generated from the laboratory from the specimens provided by study participants
DOI: 10.5061/dryad.58j041n/1
title: Supplemental Data 1

description: Methods used in generating 3D rendering and μCT scans
DOI: 10.5061/dryad.58j041n/2
title: Supplemental Data 2

description: Micro-CT slices of Rautangaroa aotearoa n. gen. and comb. nov
DOI: 10.5061/dryad.58j041n/3
title: Supplemental Data 3

description: 3 D rendering of Rautangaroa aotearoa n. gen. and comb. nov
DOI: 10.5061/dryad.5ff8194/1
title: Air Pressure Soleus Fig. 4

description: This file includes the data of air pressue data showed in Fig. 4 in the manuscript.
DOI: 10.5061/dryad.5vn76/1
title: RAD data processing files
DOI: 10.5061/dryad.5vn76/2
title: Cline_analysis
DOI: 10.5061/dryad.5vn76/3
title: STRUCTURE
DOI: 10.5061/dryad.5vn76/4
title: USA_map
DOI: 10.5061/dryad.6fm12/1
title: Genotype Data for oyster spat (C. gigas) from early and late settlement

description: This excel sheet contains microsatellite marker genotypes for oyster spat settling on day 19 or day 24. Genotypes were called by eye (and compared to parent genotypes) on a ABI 377 prism instrument using the Genescan software. These data form the basis of the QTL mapping analyses and chi-square comparisons of early vs. late settlement in Plough 2018. Column A contains the individual Spat ID, and columns C through BK contain the genotype data. Microsatellite marker names are prefixed by "Cg" and are presented in pairs of columns for each marker: one for spat settling on day 19, the other for day 24 (Row 1). Row 2 contains the cross-type of the parents (e.g. abxab) and Row 3 contains the C. gigas linkage group (LG) information  for a given marker (LGs 1-10).
DOI: 10.5061/dryad.c5b7t/1
title: These are the data in origin program for the paper titled Modification of Wheat Gluten for Improvement of Binding Capacity with Keratin in Hair
DOI: 10.5061/dryad.fd1tf/1
title: Recovery data for Bayesian CMR model

description: Contains information on year and location (area) of ringing and recovery for 4511 cormorants
DOI: 10.5061/dryad.gd788/1
title: IBI duration

description: This dataset was used to conduct our first analysis, which examined the duration of IBIs and their component phases. For this analysis we used 36 years of data (collected between 1977 and 2012) on reproductive states, demographic events, dominance rank, and rainfall for 160 wild-feeding females. Specifically, we had a total of 490 IBIs for 160 females that fit our analysis criteria (see Methods - Data Analysis), with each female contributing an average of 3 IBIs to the dataset (range: 1-10). 
Note that female identity and pregnancy identity have been anonymized and the ID given were identical across tables.
DOI: 10.5061/dryad.gd788/2
title: Fat Score

description: This dataset included the body fat scores, which were used to conduct our second analysis. For this analysis, we had 345 body fat scores for 105 females during 260 IBIs (collected between 2008 and 2014). Scores were collected during July, August, or November of each year, and the timing of the score within the IBI varied across females. 183 fat scores were assessed during PPA, 70 during cycling, and 92 during pregnancy. For any given phase of a given IBI, females were usually assessed once, but in a few cases females were assessed twice during a given PPA (n=11). For these 11 cases an average body fat score was calculated so that each female contributed only one score for each PPA.
DOI: 10.5061/dryad.gd788/3
title: Fecal hormones

description: This dataset includes the data for our third analysis, which examined fecal glucocorticoids (fGC), fecal estrogens (fE), and fecal progestogens (fP) during PPA as a function of the number of months to sexual cycle resumption, or during the various phases of the sexual cycles (early or late follicular and luteal) as a function of the number of cycles to conception. For fGC and fE we had a total of 5,470 hormone samples collected between 2000 and 2014 for 138 females during 549 IBIs. Of these samples, 4,150 fecal samples were collected during PPA, and 1,320 were collected during cycling. Each female contributed fecal samples from an average of 4 IBIs (range: 1-11) with an average of 10 hormone samples per IBI (range: 1-55) and an average total number of 40 samples per female (range: 1-145). For fP, we had a smaller sample size of 4,095 hormone samples collected between 2003 and 2014 for 130 females during 456 IBIs; 2,922 were collected during PPA and 1,173 during cycling. Each female contributed samples from an average of 3.5 IBIs (range 1-8), with an average of 9 (range 1-47) samples per IBI, for an average total number of 32 (range 1-141) samples per female.
DOI: 10.5061/dryad.gh0q91j/10
title: Instructions for RAC Function

description: Instructions for calculating the RAC Beta Diversity estimate using the R function (supplementary data 9)
DOI: 10.5061/dryad.gh0q91j/11
title: Example dataset

description: The example dataset for use in the example analyses
DOI: 10.5061/dryad.gh0q91j/4
title: Supplementary Data 4 - Tropidostoma AZ

description: Specimens from the Tropidostoma assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/5
title: Supplementary Data 5 - Cistecephalus AZ

description: Specimens from the Cistecephalus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/6
title: Supplementary Data 6 - Daptocephalus AZ

description: Specimens from the Daptocephalus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/7
title: Supplementary Data 7 - Lysterosaurus AZ

description: Specimens from the Lystrosaurus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/8
title: Supplementary Data 8 - Cynognathus AZ

description: Specimens from the Cynognathus assemblage zone, their locality of provenance and taxonomic assignment
DOI: 10.5061/dryad.gh0q91j/9
title: Supplementary Data 9_revised

description: R functions for calculating the modified Forbes distance metric and calculating the Relative-abundance-corrected beta diversity
DOI: 10.5061/dryad.j7n42/1
title: Female TPS file

description: This TPS file contains the aligned and scaled landmark coordinates for the female specimens used in the analyses. This file can be read using TPS software and/or the "geomorph" R package (Adams & Otarola-Castillo, 2013).
DOI: 10.5061/dryad.j7n42/2
title: Male TPS file

description: This TPS file contains the aligned and scaled landmark coordinates for the male specimens used in our analyses. This file can be read using TPS software and/or the "geomorph" R package (Adams & Otarola-Castillo, 2013).