cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tg469/6
title: Supplementary Table 4

description: Correspondence analysis data of samples and taxa using logarithmically transformed sporomorph relative abundances (refers to Fig. 6A).
DOI: 10.5061/dryad.5f017/1
title: Lönnqvist et al._2015_data

description: The file represents the original SPSS data base we used for our analyses based on the experiments we run in Germany, Israel and the West Bank.
DOI: 10.5061/dryad.7ct1n/1
title: Nexus file - phenotypic and ancestral state reconstruction characters

description: Phenotypic characters (766 total) represent latest revision of the Gauthier et al. (2012) AToL squamate matrix. Ancestral state reconstruction characters (11 total) collected based on literature searches (see Additional file 8). Matrix generated using Mesquite v. 2.75 (build 566).
DOI: 10.5061/dryad.7ct1n/2
title: Nexus file - genetic data only

description: Genetic data compiled from NCBI GenBank database (see Additional file 9 for accession numbers) for 21 nuclear loci and one mitochondrial locus. Generated using TextWrangler v. 4.0.1 (build 3152).
DOI: 10.5061/dryad.7ct1n/3
title: Nexus file - combined phenotypic and genetic characters

description: Dataset combining phenotypic characters (777 total) and genetic characters (18,320 total). Generated using TextWrangler v. 4.0.1 (build 3152).
DOI: 10.5061/dryad.7n1q4/3
title: Photographs of Cuvierina shells in an apertural orientation.

description: Photographs of 550 Cuvierina shells in an apertural orientation used for geometric morphometric analyses in this study.
DOI: 10.5061/dryad.88kj7/1
title: GenBank acession numbers

description: Table containing the GenBank accession numbers of the sequences from Adenomera, Leptodactylus and Lithodytes used in phylogenetic
DOI: 10.5061/dryad.88kj7/2
title: Character states

description: Table with the character states for the six life-history traits (reproductive mode, clutch size, habitat, tadpole environment, buptial pads or spines and egg pigmentation) for 35 Leptodactylinae species. Characters coded as in "ReadMe file"
DOI: 10.5061/dryad.88kj7/3
title: State probability

description: State probability of the six reconstructed life-history traits at each ancestral node of the 50% majority-rule consensus cladogram. Life-history traits reconstructed were reproductive mode, clutch size, habitat, tadpole environment, buptial pads or spines and egg pigmentation. Characters coded as in "ReadMe file"
DOI: 10.5061/dryad.88kj7/4
title: Nexus file

description: Nexus file used in MrBayes software to generate Bayeasian molecular phylogenetic hypothesis
DOI: 10.5061/dryad.8kb37/1
title: Phenotypes

description: Tree ID (Site, Family, Tree), height, diameter, volume, velocity, Resistograph, Xray (wood density), MoE (modulus of elasticity)
DOI: 10.5061/dryad.8kb37/2
title: SNP MI 30%

description: Genotyping-by-sequence imputated SNP file with 30% missing data using the mean imputation method
DOI: 10.5061/dryad.8kb37/3
title: SNP MI 60%

description: Genotyping-by-sequence imputated SNP file with 60% missing data using the mean imputation method
DOI: 10.5061/dryad.9f878/1
title: Adsl_alignment
DOI: 10.5061/dryad.9f878/2
title: Atub_alignment
DOI: 10.5061/dryad.9f878/3
title: clpC_alignment
DOI: 10.5061/dryad.9f878/4
title: coxI_alignment
DOI: 10.5061/dryad.9f878/5
title: cytB_alignment
DOI: 10.5061/dryad.9f878/6
title: EF2_alignment
DOI: 10.5061/dryad.9f878/7
title: HisH3_alignment
DOI: 10.5061/dryad.9f878/8
title: HSP70_alignment
DOI: 10.5061/dryad.bt21d/1
title: Patch-scale summary data

description: Contains data for each 900 square-meter patch (patches were the primary units of analysis in the study). These data are the basis of Figures 1 and 2, and Tables 1 and S1, in the paper. Data include the experimental treatment of each patch; gecko (lizard) abundances and densities in July 2013, March 2014, and July 2014; the number and density of trees per patch; mean tree height and basal circumference; abundance and length of insects (gecko prey) captured in sticky traps within each patch; number and density of elephant damaged trees in each patch; and number of trees in each patch occupied by four different symbiotic acacia-ant species (along with unoccupied trees and trees other than Acacia drepanolobium, which do not have ants).
DOI: 10.5061/dryad.bt21d/2
title: July 2013 gecko habitat selection data

description: Contains attribute data for each of 559 unique Acacia drepanolobium trees surveyed in July 2013. These data are the basis for Tables 2 and S2 in the paper. Attributes included are: (A) presence/absence of geckos (0,1); (B) presence/absence of elephant damage (0,1); (C) species of symbiotic ant occupant (categorical, with 6 categories); and (D) tree basal circumference.
DOI: 10.5061/dryad.d4863/8
title: MLSA Borrelia ML tree alignment

description: This is the alignment file for the tree that shows the relationships of a number of Borrelia strains, including a subset of the Bbsl strains included in our PCR screen. A plus sign (+) next to the strain designation indicates that gene(s) from the Bor TOMM biosynthetic cluster (borB/borC/borD) was/were detected. WGS: whole genome sequence.
DOI: 10.5061/dryad.fj429/1
title: Study subjects, including feeding condition, age, maturation status, social rank, and canine length

description: Study subjects  (N=5 food-enhanced and 75 wild-feeding male baboons), including feeding condition, age, maturation status, social rank, and canine length. *Birthdate status indicates whether the birthdate is known or estimated, and what the error interval around the estimate is.  0 indicates an age known to within a few days; 1 indicates an estimate to within  ± 1 year, 2 indicates within ± 2 years, and so on.  ** ‘Researcher’ indicates who measured the canines: JA: Jeanne Altmann, and JG: Jordi Galbany.
DOI: 10.5061/dryad.h9m07/1
title: alignments_for_phylogeny

description: The data folder contains three sequence alignments used to construct phylogenetic trees of Geraniales, Gymnospermae and Orchidaceae in this study.
DOI: 10.5061/dryad.hd922/1
title: Raw_counts_data

description: Read counts for all 152 samples and 33,496 contigs.
DOI: 10.5061/dryad.hd922/2
title: Full experimental design

description: Experimental design for DESeq analysis.
DOI: 10.5061/dryad.hd922/3
title: DESeq Analysis 5h

description: R commands for DESeq analysis on 5 hr data.
DOI: 10.5061/dryad.hd922/4
title: DESeq Analysis 20h

description: R commands for DESeq analysis on 20 hr data.
DOI: 10.5061/dryad.hd922/5
title: 33,496 Acropora hyacinthus contigs

description: Fasta file of the 33,496 assembled contiguous sequences from Acropora hyacinthus type E from Ofu Island, American Samoa.
DOI: 10.5061/dryad.hd922/6
title: 33496 Acropora hyacinthus Contigs Annotation

description: Annotations for the 33,496 contigs from Acropora hyacinthus.
DOI: 10.5061/dryad.hd922/7
title: Read counts for 5 hr samples

description: Input file for DESeq analysis on 5 hr samples.
DOI: 10.5061/dryad.hd922/8
title: Read counts for 20 hr samples

description: Input file for DESeq analysis on 20 hr samples.
DOI: 10.5061/dryad.mf1ck/1
title: RadtagCounter

description: Perl script that counts the number of RADtags in each*.matches file within a directory
DOI: 10.5061/dryad.mf1ck/2
title: SNPCounter

description: Counts the number of potential variable sites in a .vcf file generated by populations in the stacks program
DOI: 10.5061/dryad.mf1ck/3
title: genotypecounter.pl

description: perl script to determine how many genotype calls within the same individual are the same as the 0 hour muscle call
DOI: 10.5061/dryad.mf1ck/4
title: compressposition.pl

description: perl script to remove multiple entries for a variable site position and determine the total coverage of each position
DOI: 10.5061/dryad.mf1ck/5
title: coveragecounter.pl

description: perl script to determine if a call in the 12, 48 or 96 file is present in the 0 file and if it is it determines the coverage at that position. The output is the average coverage per snp position
DOI: 10.5061/dryad.mf1ck/7
title: AdapterInfo

description: This file contains the internal and external adapters for each sample as well as the reverse compliment for the i7 tags.
DOI: 10.5061/dryad.mf1ck/8
title: D1FastqFiles

description: Fastq files for the first restriction enzyme pair, EcoRI-NheI
DOI: 10.5061/dryad.mf1ck/9
title: D2FastqFiles

description: Fastq files for the second restriction enzyme pair, EcoRI-ClaI
DOI: 10.5061/dryad.n0qr5/10
title: Partitions file for Matrix 5

description: Partitions file for Matrix 5.
DOI: 10.5061/dryad.n0qr5/11
title: Matrix 6

description: Supermatrix of 453 orthologs and 98,370 sites. Occupancy: 87.1%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 2.
DOI: 10.5061/dryad.n0qr5/4
title: Partitions file for Matrix 2

description: Partitions file for Matrix 2.
DOI: 10.5061/dryad.n0qr5/5
title: Matrix 3

description: Supermatrix of 1,557 orthologs and 346,260 sites. Occupancy: 80.1%. Criterion: At least 29 taxa present for every ortholog.
DOI: 10.5061/dryad.n0qr5/6
title: Partitions file for Matrix 3

description: Partitions file for Matrix 3.
DOI: 10.5061/dryad.n0qr5/7
title: Matrix 4

description: Supermatrix of 5,025 orthologs and 1,113,796 sites. Occupancy: 64.2%. Criterion: At least 19 taxa present for every ortholog.
DOI: 10.5061/dryad.n0qr5/8
title: Partitions file for Matrix 4

description: Partitions file for Matrix 4.
DOI: 10.5061/dryad.n0qr5/9
title: Matrix 5

description: Supermatrix of 131 orthologs and 41,615 sites. Occupancy: 81.0%. Criterion: Minimal compositional heterogeneity.
DOI: 10.5061/dryad.ns7pv/1
title: Species and environmental data

description: This compiled (zip) file consists of 7 matrices of data: one species data matrix, with abundance observations per visited plot; and 6 environmental data matrices, consisting of land cover classification (Class), simulated EnMAP and Landsat data (April and August), and a 6 time-step Landsat time series (January, March, May, June, July and September). All data is compiled to the 125m radius plots, as described in the paper.
DOI: 10.5061/dryad.s2r1c/1
title: Dryad ID14-0403R1

description: Data from inoculation experiment.
DOI: 10.5061/dryad.tg469/10
title: Supplementary Table 8

description: Correspondence analysis data of taxa and samples using logarithmically transformed sporomorph relative abundances (refers to Fig. 7A).
DOI: 10.5061/dryad.tg469/7
title: Supplementary Table 5

description: Correspondence analysis data of samples and taxa using sporomorph presence–absences (refers to Fig. 6B).
DOI: 10.5061/dryad.tg469/8
title: Supplementary Table 6

description: Nonmetric multidimensional scaling data of samples using logarithmically transformed sporomorph relative abundances (refers to Fig. 6C).
DOI: 10.5061/dryad.tg469/9
title: Supplementary Table 7

description: Nonmetric multidimensional scaling data of samples using sporomorph presence–absences (refers to Fig. 6D).
DOI: 10.5061/dryad.23h73/1
title: Nestling growth all data incl flower scores

description: Data on growth trajectory of individual nestlings and the availability of food nearby
DOI: 10.5061/dryad.23h73/2
title: simple_nestling_code

description: R code for building nestling growth curves
DOI: 10.5061/dryad.23j81/1
title: Genotypes of Asellus aquaticus on 8 microsatellite loci

description: Dataset contains genotypes of surface and subterranean ecomorph pairs of Asellus aquaticus from Slovenia and Romania. 324 individuals were genotyped on 8 microsatellite loci. Columns in the table: sampling site – site code on Figure 1 in the article; Voucher ID – sample name from the SubBioDatabase; alleles at each locus are recorded in separate columns. Missing data is recorded as "?".
DOI: 10.5061/dryad.23j81/2
title: Morphometric data ecomorphs Asellus aquaticus

description: Morphometric data: List of 60 traits used in morphometric analysis of surface and subterranean Asellus aquaticus ecomorphs from Slovenia and Romania. Means, standard deviations (SD) and standard errors (SE) of 60 morphometric traits (listed in Table A) in the surface and subterranean ecomorph pairs of Asellus aquaticus from Slovenia (PP/PR*) and Romania (MD/AW*). Asterisk (*) denotes the subterranean ecomorph relative to its ancestral surface form.
DOI: 10.5061/dryad.23j81/3
title: Population genetics results

description: Population genetics analysis: number of alleles, observed and expected heterozygosity, tests of Hardy-Weinberg equilibrium for each locus separately and linkage disequilibrium. Included are also results from Structure analysis of the Romanian samples.
DOI: 10.5061/dryad.390t3/1
title: Data Set providing the recordings of time (in seconds) of birds attacking either models in two-choice based experiments

description: The excel sheet contains raw data from 5 two-choice experiments as described in the article. The data has been collected from field observations and have been entered manually in the excel sheet. Each trial/test of an experiment describes the time (in seconds) taken by a bird to attack both models. A trial was terminated either after the bird had attacked both models or after the completion of 5 minutes, so the time does not exceed 300s in any trial. The column headings have been described in accordance with the article. Experiment 1: i. 0 vs 1 ii. 1 vs 5 & iii. 0 vs 5 eyespots per hindwing; Experiment 2: Natural-sized eyespots (Area)  vs eyespots with reduced area (Area/2); Experiment 3: A pair of natural eyespots (Eyespot) vs a pair of non-eyelike patterns with the same total area (Fan); Experiment 4: A pair of symmetric eyespots (Sym = OO) vs a pair of asymmetric patterns consisting of an eyespot and a fan (Asym = OF/FO); Experiment 5: A pair of natural eyespots (Paired) vs a single eyespot with twice the area (Unpaired)
DOI: 10.5061/dryad.4kg4c/1
title: internexum_data_deposit

description: This is a zipped folder that contains the input files for molecular analyses conducted as part of this study.
DOI: 10.5061/dryad.7ct1n/4
title: List of phenotypic characters and state names

description: Complete list of phenotypic characters updated from Gauthier et al.'s (2012) AToL squamate matrix.
DOI: 10.5061/dryad.879c0/1
title: IJIDF_ABIA_Towards_a_Framework_supplement

description: The Supplement contains: a short description file, the rule set of the simulation executable with eCognition 9.2 or higher (Trial Version) which can be downloaded from www.ecognition.com; the image data, elevation data and further derived data used in ERDAS Imagine Format; JPEG and ESRI shape files containing all intermediate results. The Shape files additionally contain object feature values and membership degrees.
DOI: 10.5061/dryad.8mr56/1
title: Count data

description: Table of count data from processed reads. Columns are samples. Rows are genes.
DOI: 10.5061/dryad.9h569/1
title: Consensus sequences

description: Consensus sequences of all loci used in analyses. Loci identifier numbers match those of other uploaded files.
DOI: 10.5061/dryad.9h569/2
title: SNPs

description: SNPs of each individual, with the top row containing the identifier locus for each SNP. Individual names match those in the publication. Missing data coded as 0.
DOI: 10.5061/dryad.9h569/3
title: Summary Statistics

description: Output of STACKS for the 30% coverage dataset. Populations identified as north or south (lines 1 & 2). Locus ID matches identifiers of other uploaded files. BP indicates location of each SNP (starting at bp 0), allowing placement of SNPs into consensus sequences.
DOI: 10.5061/dryad.dc02b/1
title: Puckett_etal-MaxEntInput

description: Geographic coordinates used as input in MaxEnt species distribution model.
DOI: 10.5061/dryad.dc02b/2
title: Puckett_etal-mtDNA_HaplotypeList

description: List of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den Bussche et al 2009), KJ406324-KJ406336 (Puckett et al 2014), and KM230048-KM230113 (this paper).
DOI: 10.5061/dryad.dc02b/3
title: Puckett_etal-SSR_Data

description: Microsatellite genotypes (15 loci) used for inference of effective population size by regional cluster.
DOI: 10.5061/dryad.dc02b/4
title: Puckett_etal-U_amer_29k_SNPs

description: PED file with 29,213 SNPs for Ursus americanus. Data were clustered the following way: 1- AK-East, 2- Central Interior Highlands, 3- Great Lakes, 4- Northeast, 5- Southeast, 6- AK-West, 7- West, 8- Southwest, 9- Pacific Coast.
DOI: 10.5061/dryad.dc02b/5
title: Puckett_etal-U_amer_29k_SNPs

description: MAP file that accompanies PED file for analyzing SNP data in PLINK.
DOI: 10.5061/dryad.fm466/1
title: Geographic and haplotype information for Araneus omnicolor samples

description: .xlsx file containing the voucher, sex, locality, collection date and haplotypes of each A. omnicolor individual used in the present study.
DOI: 10.5061/dryad.fm466/2
title: Araneus omnicolor occurrence records

description: .xls file containing the geographical coordinates of the 52 unique occurrence points used in the species distribution modelling.
DOI: 10.5061/dryad.fm466/3
title: BEAST XML input file of the COI Bayesian Inference analysis

description: .xml input file used for the COI Bayesian Inference analysis in the software BEAST 1.8.
DOI: 10.5061/dryad.fm466/4
title: BEAST XML input file of the multilocus EBSP analysis

description: .xml input file used for the multilocus Extended Bayesian Skyline Plot analysis in the software BEAST 1.8.
DOI: 10.5061/dryad.fm466/5
title: ms Python scrips used for data simulations in the ABC analyses

description: .rar compressed file containing the ms Python scripts used for data simulations in the Approximate Bayesian Computation (ABC) analyses. Simulation 1: data simulation for model comparison within each scenario with flat prior parameters; Simulation 2: data simulation for model comparison within each scenario with restricted prior parameters (restriction based on simulation 1); Simulation 3: data simulation for comparison among scenarios.
DOI: 10.5061/dryad.gd8m9/1
title: Jacobetal_JAE_Data

description: Zip file containing the datasets of all five experiments (immigrant density, number, cooperation strategy, corridor diameter and habitat quality) with dispersal rates.
DOI: 10.5061/dryad.jt1fb/1
title: DataDryad_mixed_model_290415

description: Raw data for mixed model analysis, plotting and creating case studies for further analysis.  See Read me section in r script "mixed_model_DataDryad_290415.r"
DOI: 10.5061/dryad.jt1fb/2
title: All_lines_030515

description: .csv file for plotting case study plot using r script "mixed_model_DataDryad_290415.r"
DOI: 10.5061/dryad.jt1fb/3
title: mixed_model_DataDryad_290415

description: R script for mixed model analysis of raw data supplied and plotting.
DOI: 10.5061/dryad.jt1fb/4
title: Simulation

description: The effect of sampling from a finite number of possible environmental drivers was explored using a simulation written in R
DOI: 10.5061/dryad.mf1ck/10
title: SamplingInfo

description: File containing the treatment time, tissue type and restriction enzyme pair of each sample
DOI: 10.5061/dryad.n0qr5/12
title: Partitions file for Matrix 6

description: Partitions file for Matrix 6.
DOI: 10.5061/dryad.n0qr5/13
title: Matrix 7

description: Supermatrix of 2,580 orthologs and 565,648 sites. Occupancy: 72.0%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 4.
DOI: 10.5061/dryad.n0qr5/14
title: Partitions file for Matrix 7

description: Partitions file for Matrix 7.
DOI: 10.5061/dryad.n0qr5/15
title: Matrix 8

description: Supermatrix of 500 orthologs and 118,851 sites. Occupancy: 81.1%. Criterion: Slowest-evolving (as measured by percent pairwise identity) tertile of ortholog set in Matrix 3.
DOI: 10.5061/dryad.n0qr5/16
title: Partitions file for Matrix 8

description: Partitions file for Matrix 8.
DOI: 10.5061/dryad.n0qr5/17
title: Matrix 9

description: Supermatrix of 500 orthologs and 118,260 sites. Occupancy: 80.1%. Criterion: Middle tertile of evolutionary rate (as measured by percent pairwise identity) of ortholog set in Matrix 3.
DOI: 10.5061/dryad.n0qr5/18
title: Partitions file for Matrix 9

description: Partitions file for Matrix 9.
DOI: 10.5061/dryad.n0qr5/19
title: Matrix 10

description: Supermatrix of 577 orthologs and 109,149 sites. Occupancy: 78.5%. Criterion: Fastest-evolving (as measured by percent pairwise identity) tertile of ortholog set in Matrix 3.
DOI: 10.5061/dryad.n0qr5/20
title: Partitions file for Matrix 10

description: Partitions file for Matrix 10.
DOI: 10.5061/dryad.q5j65/1
title: Database of Vertebrate Home Range Sizes

description: Database of mean species masses and corresponding empirically measured home range sizes for 569 vertebrate species from across the globe, including birds, mammals, reptiles, and fishes.
DOI: 10.5061/dryad.r473b/1
title: Xa -no gaps- all data

description: Excel coded microsatellite repeat number data for Megalagrion xanthomelas across all loci, populations, and individuals.
DOI: 10.5061/dryad.r473b/2
title: pacificum all data

description: Excel coded microsatellite repeat number data for Megalagrion pacificum across all loci, populations, and individuals.
DOI: 10.5061/dryad.r473b/3
title: Genepop formating- xa&pc - All data

description: Excel coded microsatellite repeat number data for Megalagrion xanthomelas and M. pacificum across all loci, populations, and individuals, with formatting prepared for GenePop.
DOI: 10.5061/dryad.vf0t2/1
title: Yellow perch larvae and juvenile microsatellite data

description: GenePop file of genotypes (12 microsatellites) for larval and juvenile Yellow perch collected from the Detroit and Maumee River plumes, and Western Lake Erie in 2006, 2007, 2008
DOI: 10.5061/dryad.vf0t2/2
title: Geneland_06_coords

description: Geographic coordinates (decimal degrees) for Yellow perch larvae 2006, Geneland format
DOI: 10.5061/dryad.vf0t2/3
title: Geneland_07_coords

description: Geographic coordinates (decimal degrees) for Yellow perch larvae 2007, Geneland format
DOI: 10.5061/dryad.vf0t2/4
title: Geneland_08_coords

description: Geographic coordinates (decimal degrees) for Yellow perch larvae 2008, Geneland format
DOI: 10.5061/dryad.vf0t2/5
title: Geneland_06_data

description: Microsatellite data (12 loci) for Yellow perch larvae 2006, Geneland format
DOI: 10.5061/dryad.vf0t2/6
title: Geneland_07_data

description: Microsatellite data (12 loci) for Yellow perch larvae 2007, Geneland format
DOI: 10.5061/dryad.vf0t2/7
title: Geneland_08_data

description: Microsatellite data (12 loci) for Yellow perch larvae 2008, Geneland format
DOI: 10.5061/dryad.202f5/1
title: Data from SanJose et al

description: Zip file including data on melanin content, plumage color traits per body part, and plumage color traits at different ages and body parts.
DOI: 10.5061/dryad.7tb72/1
title: Table_1

description: Table_1 contains the locus sequences and coded genotypes of each individual used to recreate genomic composition of the Alpine x Baltic cross and their offspring. SNPs that were fixed between parents (following standard genetic mapping procedure) were used in the Structure analysis. Each individual contains two columns per locus with their genotype. Numbers refer to the four different DNA bases: A = 1, C = 2, G = 3, T = 4. 0 = missing data.
DOI: 10.5061/dryad.8mr56/2
title: DESeq2 script

description: DESeq2 script to analyze gene expression from count data. This script will call for the counts file.
DOI: 10.5061/dryad.8mr56/3
title: Principal coordinate analysis script

description: Script for principal coordinate analysis of gene expression data with the R package vegan. This script will call for variance stabilized data generated in DESeq2.