cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2108pm6/2
title: Bicyclus_anynana_Wildtype_Ventral

description: Eyespots image of Bicyclus anynana Wildtype dorsal side
DOI: 10.5061/dryad.2108pm6/3
title: exon 2 mutants

description: Images for Exon 2 mutants
DOI: 10.5061/dryad.2108pm6/4
title: exon 3 mutants

description: Images for Exon 3 mutants
DOI: 10.5061/dryad.2294qd9/2
title: Which haplotypes were grouped as 'species'?

description: List of haplotypes included in each of the GMYC species assignment groups, and sites they were collected.
DOI: 10.5061/dryad.2294qd9/3
title: Where was each haplotype found?

description: Collection details for each haplotype. Corresponding Barcode Identification Numbers (BIN) are also provided
DOI: 10.5061/dryad.2294qd9/4
title: Negative sites

description: List of samples where no springtails were found
DOI: 10.5061/dryad.2294qd9/5
title: Failed samples

description: List of samples where springtails were extracted but failed to sequence
DOI: 10.5061/dryad.2294qd9/6
title: Sequence alignment

description: Final alignment of unique sequences that was used for analyses, trimmed to 582 bp
DOI: 10.5061/dryad.231m570/1
title: Kalamazoo flora extinction_dataset

description: This file contains species names, species characteristics, and species names formatted to work with the Phylomatic program for all species included in the Kalamazoo flora extinction dataset. The README file includes variable descriptions.
DOI: 10.5061/dryad.231m570/2
title: Kalamazoo flora extinction_prairie phylogenetic data

description: This file contains the branch length for all species from the Kalamazoo flora extinction dataset, pulled from Phylomatic.
DOI: 10.5061/dryad.2df87g2/1
title: Genetic diversity of Dendrolimus punctatus

description: Locations of populations of Dendrolimus punctatus sampled, including the sample sizes (N), frequencies of COI and Ribotypes per population (Nh), and estimates of haplotype diversity (h) and nucleotide diversity (π) for each populations.
DOI: 10.5061/dryad.2g1f4n5/2
title: Concateneated dataset 3534 loci

description: Primary dataset composed of 3534 loci concateneated. This file in combination with the all_stats.xls and the corresponding partition file can be used to produce all data subsets described in the manuscript.
DOI: 10.5061/dryad.2g1f4n5/3
title: Partition file of the 3534 loci dataset
DOI: 10.5061/dryad.2g1f4n5/4
title: MARE reduced dataset with 721 loci
DOI: 10.5061/dryad.390js8n/1
title: lophelia_8loci_13pops

description: The samples originate from numerous sampling campaigns, in the Mediterranean Sea, Northeast Atlantic (Bay of Biscay, Irish Sea and South of Iceland). 13 populations in total. Samples were genotyped with 8 microsatelite markers (D3, C44, A105, C91, C61, ,C120, C142, A5). The geographical coordinates are provided in columns X,Y.
DOI: 10.5061/dryad.390js8n/2
title: madrepora_genalex

description: The samples originate from numerous sampling campaigns, in the Mediterranean Sea, Northeast Atlantic (Azores, Bay of Biscay, Irish Sea and South of Iceland). 13 populations in total. Samples were genotyped with 6 microsatelite markers (c016, g028, g025, g016, C7, C6). The geographical coordinates are provided in columns X,Y.
DOI: 10.5061/dryad.3ds9484/1
title: 16S and 18S FASTA files

description: 16S and 18S amplicon sequencing files for microbial network analysis. Files are in FASTA format. One 18S and one 16S file is provided for each of the 18 samples in the study. Codes in the file name identify the species (VV), the region (NZ for New Zealand and EU for Belgium) and the life stage (Q for queen, L for larva and W for worker).
DOI: 10.5061/dryad.5t37q5f/2
title: Vombatus ursinus SNP data

description: Vombatus ursinus SNPs (from DArT technology) - 28,088 SNPs for 166 individuals (unfiltered)
DOI: 10.5061/dryad.6140j/10
title: Crocodyliformes

description: Analysis files for the Crocodyliformes dataset including BI, MP, BEAST2, and ghost lineage time scaling.
DOI: 10.5061/dryad.6140j/8
title: Archosauria

description: Analysis files for the Archosauria dataset including BI, MP, BEAST2, and ghost lineage time scaling.
DOI: 10.5061/dryad.63q3283/1
title: Weather annotated foraging data

description: Flight heights and wingbeat frequency are derived from atmospheric pressure radio transmitters. Weather data were collected from the German weather service, Deutscher Wetterdienst (DWD), and interpolated to the timestamps of the observed altitude data. Additional movement data are available at the Movebank Data Repository: doi:10.5441/001/1.7t4b97qf. Please see the README for data definitions.
DOI: 10.5061/dryad.70dn712/1
title: Figure 2 code

description: This file includes the code used to create Figure 2. It includes the life cycle loop iterated over multiple generations.
DOI: 10.5061/dryad.70dn712/2
title: Figure 3 code

description: This file includes the code used to create Figure 3. It includes  data (in form of matrices) that was generated using separate files. One such data generating file is provided separately here. See "Note" at the top of the code in this file.
DOI: 10.5061/dryad.70dn712/3
title: Figure 3 data generation file Sc=0.05

description: This file includes the code used to create one of the panels in Figure 3. It includes the life cycle loop iterated over multiple generations across a large number of combinations of parameter values.
DOI: 10.5061/dryad.782s82b/1
title: fireSense

description: SpaDES modules and data to estimate the parameters for the fire ignition, escape and spread module and to run the fire and vegetation succession models on the initial landscape are provided, including the annual fire weather data for the 21st century as used in the manuscript.  This data and code is sufficient to reproduce the results in the paper, although some SpaDES code would need to be written: see http://predictiveecology.org/SpaDES/ for downloads and tutorials.
DOI: 10.5061/dryad.82vs647/10
title: z_MPI-ESM-P.7z

description: Three of four 7z compressed files for the downscaled 30-yr climatologies for each GCM from 850-1850 CE. These are separated into individual files due to their large storage size (~5 GB). Each of these compressed files should be extracted into the following directories to recreate the analyses:  ..\results\⁩3_gcm_30yr_climatologies⁩\used_in_analysis\[GCM]\
DOI: 10.5061/dryad.82vs647/11
title: z_MRI-CGCM3.7z

description: Four of four 7z compressed files for the downscaled 30-yr climatologies for each GCM from 850-1850 CE. These are separated into individual files due to their large storage size (~5 GB). Each of these compressed files should be extracted into the following directories to recreate the analyses:  ..\results\⁩3_gcm_30yr_climatologies⁩\used_in_analysis\[GCM]\
DOI: 10.5061/dryad.82vs647/4
title: Data

description: Contains the ancillary data, pre-processed data, and citations for the raw datasets needed to conduct the analyses described in the manuscript.
DOI: 10.5061/dryad.82vs647/5
title: Figures

description: Contains the figures from the publication in three different formats at 600 dpi resolution (MATLAB .fig, .jpeg, and .tif formats).
DOI: 10.5061/dryad.82vs647/6
title: Metadata

description: Documentation/description of this archive using FGDC standards in an xml format, including geographic metadata for the raster datasets generated during the workflow of the analysis. This metadata was originally generated using Tkme (version 3.0.5) by Peter N. Schweitzer and updated using the USGS Metadata Wizard (version 2.0.3). The thesaurus used for keyword selection was the Global Change Master Directory (version 8.6, 2018).
DOI: 10.5061/dryad.82vs647/7
title: Results

description: Series of results produced from processing the raw data stored in the '\data\' directory using the code provided.
DOI: 10.5061/dryad.82vs647/8
title: z_GISS-E2-R.7z

description: One of four 7z compressed files for the downscaled 30-yr climatologies for each GCM from 850-1850 CE. These are separated into individual files due to their large storage size (~5 GB). Each of these compressed files should be extracted into the following directories to recreate the analyses:  ..\results\⁩3_gcm_30yr_climatologies⁩\used_in_analysis\[GCM]\
DOI: 10.5061/dryad.82vs647/9
title: z_MPI-ESM-LR.7z

description: Two of four 7z compressed files for the downscaled 30-yr climatologies for each GCM from 850-1850 CE. These are separated into individual files due to their large storage size (~5 GB). Each of these compressed files should be extracted into the following directories to recreate the analyses:  ..\results\⁩3_gcm_30yr_climatologies⁩\used_in_analysis\[GCM]\
DOI: 10.5061/dryad.cb8gd26/1
title: Maximum credibility BEAST tree

description: Maximum credibility tree from the BEAST analysis. Node values represent medians.
DOI: 10.5061/dryad.cb8gd26/2
title: Congruified BEAST tree -- matched to environmental data

description: "Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with environmental data.
DOI: 10.5061/dryad.cb8gd26/3
title: Congruified BEAST tree -- matched to trait data

description: "Congruified" BEAST tree. Result from treePL with BEAST dates used as node constraints. This tree contains taxa matched with trait data.
DOI: 10.5061/dryad.cb8gd26/4
title: treePL tree -- matched to environmental data

description: treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with environmental data.
DOI: 10.5061/dryad.cb8gd26/5
title: treePL tree -- matched to trait data

description: treePL tree. Result from treePL with fossil node constraints. This tree contains taxa matched with trait data.
DOI: 10.5061/dryad.dg5fd33/1
title: Quadrat_plant_community_data

description: Percent cover data of each plant species recorded in all quadrats from all four regional datasets.
DOI: 10.5061/dryad.dg5fd33/2
title: Site_environmental_data.csv

description: Environmental characteristics of each site from all four regional datasets.
DOI: 10.5061/dryad.dq444fr/1
title: Genetic_dataset_Coenonympha

description: File with the individuals names and genotypes for the 1,047 SNPs used for the analyses.
DOI: 10.5061/dryad.f32p4/48
title: RAD-seq raw reads Swertia_site13-2
DOI: 10.5061/dryad.f32p4/49
title: RAD-seq raw reads Swertia_site13-3
DOI: 10.5061/dryad.f32p4/50
title: RAD-seq raw reads Swertia_site14-1
DOI: 10.5061/dryad.f32p4/51
title: RAD-seq raw reads Swertia_site14-2
DOI: 10.5061/dryad.f32p4/52
title: RAD-seq raw reads Swertia_site14-3
DOI: 10.5061/dryad.f32p4/53
title: RAD-seq raw reads Swertia_site18-1
DOI: 10.5061/dryad.f32p4/54
title: RAD-seq raw reads Swertia_site18-2
DOI: 10.5061/dryad.f32p4/55
title: RAD-seq raw reads Swertia_site18-3
DOI: 10.5061/dryad.f32p4/56
title: RAD-seq raw reads Swertia_site21-1
DOI: 10.5061/dryad.h7d11cd/1
title: Online Supplemental Material
DOI: 10.5061/dryad.kb79121/79
title: pha-1_EMBD0025_MS
DOI: 10.5061/dryad.kb79121/80
title: pha-4_EMBD0002_GLS
DOI: 10.5061/dryad.kb79121/83
title: README_movie_files
DOI: 10.5061/dryad.kb79121/84
title: lit-1_EMBD0387_MS
DOI: 10.5061/dryad.kb79121/85
title: let-502_EMBD0007_GLS
DOI: 10.5061/dryad.kb79121/86
title: aph-1_EMBD0022_GLS-1
DOI: 10.5061/dryad.kb79121/87
title: control_EMBD0000_MS_long
DOI: 10.5061/dryad.kb79121/88
title: control_EMBD0000_GLS_long
DOI: 10.5061/dryad.kb79121/91
title: arx-3_EMBD0055_GLS-2
DOI: 10.5061/dryad.kb79121/92
title: arx-1_EMBD0006_GLS-2
DOI: 10.5061/dryad.sd69mc7/1
title: Tetraglochin ITS alignment

description: Nuclear ribosomal ITS aligned matrix in nexus format
DOI: 10.5061/dryad.sd69mc7/2
title: Tetraglochin trnLF alignment

description: Chloroplast trnL-F aligned matrix in nexus format
DOI: 10.5061/dryad.sd69mc7/3
title: TETRAGLOCHIN_species_BEAST1.8.2

description: xml file for species tree analyses in BEAST v1.8.2 under the coalescent-based method implemented in *BEAST extension, using ribosomal ITS and chloroplast trnL-F regions,  uncorrelated lognormal relaxed clock models, a yule process for the species tree prior, the piecewise linear and constant root for the population size model, and three calibrations points.
DOI: 10.5061/dryad.sd69mc7/4
title: Tetraglochin_MCCT

description: Maximum clade credibility species tree (MCCT) estimated in BEAST v1.8.2 from nuclear ribosomal ITS  and chloroplast trnL-F, using the multispecies coalescent method implemented in *BEAST, uncorrelated lognormal relaxed clock models, a yule process for the species tree prior, the piecewise linear and constant root for the population size model, and three calibrations points.
DOI: 10.5061/dryad.sd69mc7/5
title: Tetraglochin_1000trees

description: 1000 randomly subsampled posterior trees from the Bayesian species tree analyses in BEAST v1.8.2 using ribosomal ITS and the chloroplast trnL-F,  uncorrelated lognormal relaxed clock models, a yule process for the species tree prior, the piecewise linear and constant root for the population size model, and three calibrations points.
DOI: 10.5061/dryad.sd69mc7/6
title: Tetraglochin_MCCT_pruned

description: Maximum clade credibility species tree (MCCT) estimated in BEAST v1.8.2 from nuclear ribosomal ITS and chloroplast trnL-F, pruned to include only the species of Tetraglochin
DOI: 10.5061/dryad.t429r75/1
title: Genotypic data from 10 populations of Ailanthus altissima in Eastern Austria

description: The file contains genotypic data of 298 trees from 10 populations of Ailanthus altissima in eastern Austria. Samples were collected in the field and genotyped according to the methods described in the cited research. The file contains genotypes of five (5) microsatellite loci scored using fragment length analysis (Aa22, Aa69, Aa75, Aa76 and Aa82) and further twelve (12) microsatellite loci scored based on an SSR-GBS approach (loci loci HT2, HT7, HT9, HT10, HT16, HT19, HT22, HT24, HT27, HT30, HT31 and HT35). Genotypes of the same population assigned to a particular multilocus lineage (MLL) are marked with a capital letter (from A-F).
DOI: 10.5061/dryad.th725q8/2
title: Patient groups and funding recommendations

description: Complete data set for article
DOI: 10.5061/dryad.tt6v3jg/1
title: SGH

description: Colony forming units of e.coli and total in various treatments. Rows 1-6 used for analysis, remaining rows are additional information
DOI: 10.5061/dryad.v22901d/1
title: Little_Altermatt_Aquatic_Ecology_data

description: This data is organized by experimental replicate, and includes the biomass of amphipods used in each replicate, as well as the biomass of leaf litter consumed in each replicate. Code to run the analyses and produce the figures based on this data is available at https://github.com/chelseajlittle/CAGE2
DOI: 10.17632/3cx23k2b88.1
title: Data for: Phylogenomic analyses and divergence time estimation of Elateroidea (Coleoptera) based on RNA-Seq data
DOI: 10.17632/btgysd8r5b.1
title: Experiment

description: Reinforcement Learning Experiment
DOI: 10.17632/jkhw8k6m5k.1
title: Data for: Numerical investigation of gas separation in the system of filaments with different temperatures

description: Complete set of obtained molar fractions, pressure at the right end (near the wall) along with dimensionless heat fluxes to the filaments for all 64 configurations are presented in table in supplementary materials.
DOI: 10.17632/w8x33fgk42.1
title: Data for: In vivo diagnosis of large cell acanthoma by cellular resolution optical coherent tomography

description: calculation of nucleus size
DOI: 10.5061/dryad.298rn73/1
title: Top-down heterotrophic respiration

description: This file includes top-down estimates of heterotrophic resolution at 4 degrees by 5 degrees spatial resolution and monthly temporal resolution, covering the period January 2010 to December 2012. The data are gridded on the CMS-Flux grid (also the 4x5 GEOS-Chem grid). Each dataset is a 3-dimensional matrix with dimensions longitude, latitude, and time (in order). Datasets included are the derived top-down heterotrophic respiration mean, standard deviation, 25th percentile of the distribution, and 75th percentile of the distribution, as well as the mean and standard deviation of the input datasets: net ecosystem productivity, gross primary productivity, and vegetation carbon use efficiency.
DOI: 10.5061/dryad.2g1f4n5/10
title: droptips

description: Script to prune a reference tree (species tree) from leaves not present in a given alignment. The script is used as a preliminary for Dellta GLS calculations.
DOI: 10.5061/dryad.2g1f4n5/11
title: splitDist

description: Script  and functions to list and count the bipartitions present in a collection of trees.
DOI: 10.5061/dryad.2g1f4n5/14
title: matrices.xlxs

description: Spreadsheet listing all partitions, general properties, amino acid substitution models and results of Delta GLS and TtreSpEx LB scores. This file can also be used to filter dataset and reproduce the matrices in the manuscript.
DOI: 10.5061/dryad.2g1f4n5/15
title: Supplemental_Tables_and_Figures

description: Suplemental Tables and Figures including full annotated trees
DOI: 10.5061/dryad.2g1f4n5/16
title: datbacoca_pca

description: Modified BaCoCa output used for PCA analyses.
DOI: 10.5061/dryad.2g1f4n5/17
title: part_1499

description: Nexus file defining partitions and amino acid substitution models for the decisive dataset
DOI: 10.5061/dryad.2g1f4n5/5
title: partition file MARE
DOI: 10.5061/dryad.2g1f4n5/8
title: functions for gene tree simulations
DOI: 10.5061/dryad.2g1f4n5/9
title: mpsi

description: Script for calculating mean pair-wise sequences identity metric
DOI: 10.5061/dryad.2j1d35d/1
title: RAxML-matrices

description: The file contains the nine .phy formatted data matrices for use in RAxML to construct the phylogenomic trees. The nine matrices were generated using ipyrad. Files are named by the similarity threshold (85, 90, or 95%) and taxon coverage used (75, 50, or 25%).
DOI: 10.5061/dryad.2j1d35d/2
title: ipyrad-parameter-files

description: The file contains the nine parameter files used by ipyrad to generate all data matrices for downstream analyses. We used three similarity threshold values (85, 90, and 95%) and three different taxon coverages (75, 50, and 25% of individuals).
DOI: 10.5061/dryad.2j1d35d/3
title: mrbayes-data-matrix

description: This file contains the data matrix from the 90% similarity threshold including 75% of individuals used for analysis in MrBayes. The nexus file was generated by ipyrad.
DOI: 10.5061/dryad.2j1d35d/4
title: Single SNP VCF file

description: This is the single SNP file in vcf format that was used to generate inputs for Structure, treemix, and DAPC analyses in the manuscript. File was created using the python code vcf_single_snp.py (Bongaerts 2018).
DOI: 10.5061/dryad.2j1d35d/5
title: SVDquartets input file

description: This is the file used to generate the species estimation tree in SVDquartets
DOI: 10.5061/dryad.2j1d35d/6
title: Treemix input

description: This is the input file used to conduct the f3 admixture tests. The file contains seven "populations" based on the structure analyses.
DOI: 10.5061/dryad.2j1d35d/7
title: DAPC input files

description: This file contains all of the input files used for the DAPC analyses in the manuscript. They are in genepop format and were generated from the single SNP vcf file.
DOI: 10.5061/dryad.2j1d35d/8
title: structure-input

description: This file contains all of the inputs used for the five different structure analyses. The input files were generated from the single SNP vcf and converted to the structure format using PGDspider.
DOI: 10.5061/dryad.6140j/11
title: Sauria

description: Analysis files for the Sauria dataset including BI, MP, BEAST2, and ghost lineage time scaling.
DOI: 10.5061/dryad.6140j/12
title: Yule_BEAST1.8

description: Contains tree files from exploratory BEAST1.8 analysis examining Yule tree priors.
DOI: 10.5061/dryad.6d2h8bp/1
title: scripts

description: Python scripts used to test direct ancestor arrangements
DOI: 10.5061/dryad.6d2h8bp/2
title: ranges

description: stratigraphic ranges of hominin taxa
DOI: 10.5061/dryad.6d2h8bp/3
title: clade_best_strat.jitter

description: final hominin tree inferred from stratophylogenetic rearrangements and AIC comparisons
DOI: 10.5061/dryad.6rp36b6/1
title: analysis-steps-for-manuscript

description: These are the are the rough analysis steps for the manuscript. If you find these steps helpful, please cite the manuscript!
DOI: 10.5061/dryad.6rp36b6/11
title: CamDro2 gene annotations in GFF format (zipped)
DOI: 10.5061/dryad.6rp36b6/12
title: cDNA transcripts used to train Augustus for the second round of MAKER

description: cDNA transcripts used to train Augustus for the second round of MAKER
DOI: 10.5061/dryad.6rp36b6/2
title: CamDro2 predicted proteins

description: CamDro2 genome predicted proteins produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).
DOI: 10.5061/dryad.6rp36b6/3
title: CamDro2 predicted mRNA

description: CamDro2 genome predicted mRNA transcripts produced by a single round of MAKER (Holt and Yandell: MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 2011 12:491).
DOI: 10.5061/dryad.6rp36b6/4
title: RH-alpaca-probe-sequences

description: RH alpaca probe sequences for Steps 20, 28, and 33 of analysis-steps-for-manuscript.txt. RH probe sequences are in 37 different files contained in the master zip file (chromosome 1,2,...,36,and X). Even though files are named with .txt format, they are FASTA formatted files.
DOI: 10.5061/dryad.6rp36b6/5
title: CamDro1 assembly (GCA_000803125.1) improved by Dovetail Genomics Chicago and Hi-C libraries gzipped (www.gzip.org) FASTA file

description: Dovetail Genomics created Chicago and Dovetail Hi-C libraries from a low passage cell culture line (Perelman et al. 2018) derived from ear fibroblasts of the same dromedary used in CamDro1 (GCA_000803125.1). Dovetail Genomics created both Chicago and Hi-C libraries with the DpnII restriction enzyme, sequenced these libraries on six lanes of an Illumina HiSeq sequencer, and then scaffolded the CamDro1 assembly using the HiRise pipeline (Putnam et al. 2016). First, the CamDro1 assembly was split at gaps and scaffolded using Dovetail Chicago data. Then, the Chicago assembly was improved by scaffolding with Hi-C data creating a Hi-C assembly. Assembly is a gzipped (www.gzip.org) FASTA file.
DOI: 10.5061/dryad.6rp36b6/6
title: CamDro2 genome gzipped FASTA file

description: CamDro2 genome gzipped (www.gzip.org/
 ) FASTA file, chromosomes are identified by &gt;1,&gt;2,...,&gt;36,&gt;X (for chromosomes 1,2,...,36,X). There is no Y chromosome as the sequenced dromedary was female.
DOI: 10.5061/dryad.70dn712/4
title: Figure 4 code

description: This file includes the code used to create Figure 4. It includes  data (in form of matrices) that was generated using separate files. One such data generating file is provided separately here. See "Note" at the top of the code in this file.
DOI: 10.5061/dryad.70dn712/5
title: Figure 4 data generation file Sc=0.05

description: This file includes the code used to create one of the panels in Figure 4. It includes the life cycle loop iterated over multiple generations across a large number of combinations of parameter values.
DOI: 10.5061/dryad.70dn712/6
title: Figure 5 code

description: This file includes the code used to create Figure 5. It includes the life cycle loop iterated over multiple generations.
DOI: 10.5061/dryad.70dn712/7
title: Figure 6 code

description: This file includes the code used to create Figure 6. It includes  data (in form of matrices) that was generated using separate files. One such data generating file is provided separately here. See "Note" at the top of the code in this file.
DOI: 10.5061/dryad.70dn712/8
title: Figure 6 data generation file Sp=0.05

description: This file includes the code used to create one of the panels in Figure 6. It includes the life cycle loop iterated over multiple generations across a large number of combinations of parameter values.