cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb40v/29
title: Data used in phylogenetic analyses

description: Data used in phylogenetic analyses, in column separated text format. First column is species name, second column is name of data partition, third column is a unique id for the species/partition data (ie GenBank GI number), fourth column is sequence or morphological data. The sequence data are derived from the raw 454 data, or from other sources. Raw 454 data was assembled using Newbler. We pulled genes from transcriptomes using Hamstr. We then aligned sequences with MUSCLE, and cut out ambiguously aligned regions with AliScore/AliCut. Unique identifiers with "Voucher" in the name are previously unpublished, and will be placed in GenBank. This 4-column data format can be used with many tools developed in the Osiris package for conducting phylogenetics in Galaxy.
DOI: 10.5061/dryad.8b414/11
title: 110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.004
DOI: 10.5061/dryad.8sc8b/1
title: Flaxman_Data

description: .zip archive of raw data used in publication figures
DOI: 10.5061/dryad.b78g9/1
title: Tropheus moorii male courtship data
DOI: 10.5061/dryad.bh581/1
title: Supplimentary data

description: Procrustes coordinates data used for wing morphology analyses. This file contains information such as genotype, individual ID, sex and procrustes coordinates for eight landmarks.
DOI: 10.5061/dryad.bk58j54t/1
title: AFLP data structure #1
DOI: 10.5061/dryad.j2d6v/1
title: Goldin Zvonok Ukraine Supplemental Data File 1 Character list 20120913
DOI: 10.5061/dryad.j2d6v/2
title: Goldin_Zvonok_Ukraine_Supplemental_Data_File_2_Character_codings_20120913
DOI: 10.5061/dryad.j2d6v/3
title: Goldin_Zvonok_Ukraine_Supplemental_Data_File_3_list_of_taxonomical_identifications_20120913
DOI: 10.5061/dryad.j2d6v/4
title: Goldin_Zvonok_Ukraine_Supplemental_Data_File_4_age_data_for_phylogeny_20120913
DOI: 10.5061/dryad.k2qc1/1
title: Data_file_MEC-12_0649

description: Data_file_MEC-12-0649 contains the microsatellite data, coordinates and landscape genetics data (univariate and bivariate) associated with study entitled 'Landscape genetics of a top neotropical predator'
DOI: 10.5061/dryad.nv5v1v59/13
title: Intron 11 of GRIN1 gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 11 of GRIN1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/14
title: Intron 2 of LCAT gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 2 of LCAT gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/15
title: Intron 2 of LDHB gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 2 of LDHB gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/16
title: Intron 2 of MSTN gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 2 of MSTN gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/17
title: Intron 12 of NCL gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 12 of NCL gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/18
title: Intron 5 of ODC1 gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 5 of ODC1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/19
title: Intron 9 of PCK1 gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 9 of PCK1 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/20
title: Intron 2 of SAA gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 2 of SAA gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/21
title: Intron 12 of SOAT1 gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 12 of SOAT gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.nv5v1v59/22
title: Intron 2 of SOX9 gene

description: Contains DNA sequences for 100 phased and aligned alleles from intron 2 of SOX9 gene sampled from gadwalls (Anas strepera). The first 50 alleles were sampled from Eurasia, and the second set of 50 alleles were sampled from North America. The sequences were aligned in Sequencher.
DOI: 10.5061/dryad.q8b18/2
title: feeding rate for DRYAD

description: These data are for feeding rates of different Ddc genotypes
DOI: 10.5061/dryad.q8b18/3
title: Field Attack Rate Data for DRYAD

description: These data are for the attack rates of wasps on the different Ddc genotypes in the field.
DOI: 10.5061/dryad.q8b18/4
title: Foraging Assay for DRYAD

description: Foraging rates of different Ddc genotypes
DOI: 10.5061/dryad.q8b18/5
title: Laboratory Attack Rate Data for DRYAD

description: Attack rate of Leptopilina and Aphaereta on different Ddc genotypes
DOI: 10.5061/dryad.q8b18/6
title: Laboratory Encapsulation ability for DRYAD

description: Encapsulation ability of different Ddc genotypes exposed to Leptopilina and Aphaereta wasps
DOI: 10.5061/dryad.td18m/1
title: Eb'Vlent' H22011_PrefFunctions

description: Mate preference function data used in the analysis. Each female has multiple data points, one for each playback stimulus.
DOI: 10.5061/dryad.td18m/2
title: Eb'Vlent' H2_PrefFunctionTraits

description: Traits describing variation in the shape of mate preference functions used in the analysis
DOI: 10.5061/dryad.10kd4/1
title: Genotypes_Dryad
DOI: 10.5061/dryad.10kd4/2
title: appendix_S1_Mathematica_notebook_Bermond_et_al

description: This file shows how we realized our analyses from genetic and genotypic data. Both methods that we used to estimate Sigma (methods of Endler and Linkage Disequilibrium) are detailed. Details on simulations are also given.
DOI: 10.5061/dryad.10kd4/3
title: appendix_S2_R_script_simulations_Bermond_et_al

description: R script of the simulations that we used in this paper to evaluate the effect of dispersal kernel and heterogeneity of population density on the estimation of dispersal and time since contact.
DOI: 10.5061/dryad.1pg07/1
title: egg-to-adult viability data
DOI: 10.5061/dryad.2h4n301t/1
title: Rattlesnakes

description: The file "Rattlesnakes" is a .tps file of landmark coordinates taken from .jpg images of rattlesnake dorsal head views. In addition to geometric morphometrics software, the file can be opened as a text or excel file. The letter in the identifier (M or F) indicates that the coordinates originate from male or female snakes, respectively. The number in the identifier is arbitrary and refers to the individual snake. The images used for collecting landmark data originate from subadult and adult individuals of Mexican Lance-headed Rattlesnakes (Crotalus polystictus) from a single population near Atlacomulco, Estado de Mexico, Mexico. All photographs used in this study were collected between June-July 2006.
DOI: 10.5061/dryad.3372j/1
title: Supplementary table 1.-Investigated fossil localities.

description: Angular shell fragments: absent or exceedingly rare (-); present (+); abundant (++).
DOI: 10.5061/dryad.615sc2rv/1
title: Wild-caught individuals

description: Wild data. Deme indicates the sub-population to which an individual belongs (see McCairns and Bernatchez 2008 Mol. Ecol. 17:3901-3916 for further clarification regarding demes). Env is a coding variable indicating the salinity at the sampling site (FW=freshwater; SW=saltwater); note that BW indicates a site which experiences ‘atypical’ salinity fluctuations relative to other sites within the geographic location of a given deme. Site is code corresponding to map locations (this article & McCairns and Bernatchez 2008 Mol. Ecol. 17:3901-3916). Sex distinguishes females (F) and males (M) and Ind is the unique individual identifier. Individual size measurements include standard length (SL, mm), total weight (Total.Wt, g) and somatic weight (i.e. total weight less gonad weight; Somatic.Wt, g). Plate.No indicates the total number of lateral plates counted along the left side.
DOI: 10.5061/dryad.615sc2rv/2
title: Growth (lab-reared families)

description: Growth data. The Family column indicated the environment-specific full-sib family group to which individuals belong. Dam & Sire indicate the individuals used as broodstock, and Mat.Deme & Pat.Deme denote their deme of origin, respectively (see McCairns and Bernatchez 2008 Mol. Ecol. 17:3901-3916 for further clarification regarding demes). Cross denotes the maternal x paternal lineage. Env indicates the rearing environment, either FW (&lt; 1 parts-per-thousand salinity), or SW (20 parts-per-thousand). Day is the number of days post-fertilization when the measurement was taken, and SL denotes the standard length (mm).
DOI: 10.5061/dryad.615sc2rv/3
title: Geometric morphometrics

description: Morphological data. Geometric morphometric landmark data for wild-caught (wild) and lab-reared (qg) fish combined – the respective data sets are indicated in the Data.Set column. All missing or irrelevant data points and coding variables are marked NA. Deme indicates the sub-population to which an individual belongs (see McCairns and Bernatchez 2008 Mol. Ecol. 17:3901-3916 for further clarification regarding demes). Site is code corresponding to map locations (see Fig. 1). Sex distinguishes females (F) and males (M). SL corresponds to individual standard length (mm) and Plate.No indicates the total number of lateral plates counted along the left side. Dam & Sire indicate the individuals used as broodstock, and Mat.Deme & Pat.Deme denote their deme of origin, respectively. Cross denotes the maternal x paternal lineage. For lab-reared fish (Data.Set=qg), Env indicates the rearing environment, either FW (&lt; 1 parts-per-thousand salinity), or SW (20 parts-per-thousand); for wild-caught individuals (Data.Set=wild), Env is acoding variable indicating the salinity at the sampling site (FW=freshwater; SW=saltwater); note that BW indicates a site which experiences ‘atypical’ salinity fluctuations relative to other sites within the geographic location of a given deme. Columns x1 to y14 contain the raw coordinates of the 14 landmarks (see Methods for details). Cent.Size is the individual’s centroid size. Shear & Compr are the scores corresponding to affine (i.e. uniform) shape deformations, whereas columns Warp1 to Warp22 are the partial warp scores.
DOI: 10.5061/dryad.9f8q91q3/1
title: PDvsPD.SHR4_RTPCR

description: Raw data and results for real-time PCR verification of microarray comparison of hepatic expression between PD and PD. SHR4 rat strains.
DOI: 10.5061/dryad.b9q73/2
title: Kershawetal_TableS2_HaplotypeInformation

description: Table S2: Table of corresponding accession (ACCN) numbers for haplotypes H01-H49 included in the study. From the 299 bp mitochondrial consensus sequence (bp position 15545-15843 in the mtDNA genome of B. e. edeni [ACCN: AB201258]), H01-H45 were identified as B. e. brydei, and H46-H48 were identified as B. e. edeni. The B. e. edeni haplotype H49 was identified from the 407 bp consensus sequence (bp position 15500-15906 in the mtDNA genome of B. e. edeni [ACCN: AB201258]). The total number of individuals (N) for each haplotype is shown and, when two accession numbers are listed, the number of individuals represented by each is indicated in parentheses. * indicates the five new haplotypes described by the current study. The remaining forty-four haplotypes have been previously described and published (Kanda et al. 2007; Yoshida & Kato 1999). For details of haplotype frequencies across sampling locations, see Figure 2 of the main article.
DOI: 10.5061/dryad.bk58j54t/2
title: AFLP data structure #2
DOI: 10.5061/dryad.bk58j54t/3
title: R syntax for gene diversity for AFLPs
DOI: 10.5061/dryad.dk625/1
title: Evolution 2012 summary data

description: These are summary data from laboratory experiments described in the paper in Driscoll et al. (2012). Most data were collected as simple cell counts with a hemacytometer. A few are based on automated cell size measurements using ImageJ. D4 and D5 are short for Dunaliella started at 10^4 cells mL^-1 and 10^5 cells mL^-1, respectively. (So 'TOX1 and D4' means TOX1 initiated at 10^3 with Dunaliella at 10^4.) Corresponding figures are shown somewhere relatively obvious on each worksheet in blue.
DOI: 10.5061/dryad.f13r3/1
title: 12-033R Rhenberg Supplemental-1

description: Locality information for collecting sites. M localities were collected by Dr. Macurda, Laudon numbers collected by Dr. Laudon, and FC localities were collected by the authors.
DOI: 10.5061/dryad.f13r3/2
title: 12-033R Rhenberg Supplemental-2

description: Township and range information for the Macurda localities.
DOI: 10.5061/dryad.f13r3/3
title: 12-033R Rhenberg Supplemental-3

description: Material examined from the Nunn Member of the Lake Valley Formation in New Mexico. UMMP numbers are those illustrated and types for new species which are housed at the University of Michigan Museum of Paleontology. M localities are those collected by Brad Macurda and students while he was at the University of Michigan. KNM specimens were donated by Barry Kues of the University of New Mexico. LNM specimens come from the Lowell Laudon collection, also donated by Barry Kues. IU specimens were collected by A. S. Horowitz and J. H. Johnson of Indiana University, which came with Macurda's collection. FC specimens were those collected by the authors. All these specimens are housed with the University of Michigan. All other specimens are part of the Springer Collection of the U.S. National Museum of Natural History (USNM).
DOI: 10.5061/dryad.f13r3/4
title: 12-033R Rhenberg Supplemental-4

description: Interradial plate counts of all Nunnacrinus dalyanus studied, including the type specimens of Nunnacrinus mammillatus from the Smithsonian Institution.
DOI: 10.5061/dryad.g1gd8/1
title: Data matrix for likelihood analysis

description: Data matrix of 44 genes for 161 squamate reptile species and 10 outgroup species.  The matrix is used for maximum likelihood analysis with RAxML.  A separate file specifies the models and data partitions.
DOI: 10.5061/dryad.g1gd8/2
title: Models and partitions for likelihood analysis

description: This file specifies the models and partitions used in the likelihood analysis (with RAxML).
DOI: 10.5061/dryad.g1gd8/3
title: Data matrix for concatenated Bayesian analysis

description: Data matrix used for concatenated Bayesian analysis of 44 genes and 161 squamate species (and 10 outgroup species), utilizing MrBayes.
DOI: 10.5061/dryad.g1gd8/4
title: Data matrix for Bayesian species-tree analysis

description: Data matrix of 44 genes and 29 squamate species (and 2 outgroup species) for Bayesian species-tree analysis utilizing *BEAST.
DOI: 10.5061/dryad.gs048/1
title: Microsatellite genotypes for Peromyscus maniculatus

description: Contains original individual genotypes: see ReadMe file.
DOI: 10.5061/dryad.gs048/2
title: Null-adjusted genotypes for Peromyscus maniculatus

description: Contains population-level genotypes after adjusting for null alleles, in tab-delimited text format.  See ReadMe file for full description.
DOI: 10.5061/dryad.gs048/3
title: Structure clustering data for Peromyscus maniculatus

description: Clustering data for Peromyscus maniculatus after adjusting for the presence of null alleles, in a tab-delimited text file.  See ReadMe for full description.
DOI: 10.5061/dryad.gs048/4
title: Geographical distances for Peromyscus maniculatus populations

description: Contains distances, in km, between Peromyscus maniculatus populations in the Great Lakes region.
DOI: 10.5061/dryad.hc257/1
title: Eleutherodactylus  antillensis beta-crystallin intron 1 (CRYBA) alignment
DOI: 10.5061/dryad.hc257/2
title: Eleutherodactylus antillensis mtDNA control region (CR) alignment
DOI: 10.5061/dryad.m329j/1
title: All data

description: This is an Excel workbook containing spreadsheets on restoration of fertility (female egg count), Spiroplasma density (qPCR-Spiroplasma), Howardula motherworm size (Motherworm size), and maternal transmission (Maternal transmission). These data were collected in either the Perlman (University of Victoria) or Jaenike (University of Rochester), as indicated in the file.
DOI: 10.5061/dryad.mt60p/1
title: Pilliod_et_al_2013_MER_DryadData_7-31-13

description: We handled, stored, and extracted eDNA from 0.45 nm Cellulose Nitrate filter paper the same way for each experiment using protocols described in Pilliod et al. (2013). We extracted DNA from half of each filter paper using the Qiashredder/DNeasy Blood & Tissue DNA extraction kit method described in Goldberg et al. (2011). We used the quantitative PCR assay described in Pilliod et al. (2013) to estimate the amount of eDNA in each sample. We used the QuantiTect Multiplex PCR Mix (Qiagen, Inc., Gaithersburg, Maryland, USA) with recommended multiplexing concentrations and parameters on an Applied Biosystems 7500 Fast Real-Time PCR System to conduct the assay. We used 2 µL of DNA extract in each reaction and ran all reactions in triplicate. Standard curves were constructed from whole genomic DNA extracted from tail tissue and diluted to 0.001, 0.01, and 0.1 ng. Average r2 for curves used in this study was 0.99. We considered a test result negative if there was no exponential phase at any point during 50 cycles. See Pilliod et al. (2013) for additional methodological details.
DOI: 10.5061/dryad.nv5v1v59/23
title: IM input file, 22 loci, 2 populations of gadwall

description: Contains the input file used in IM analysis with sequences truncated to meet the assumption of no intralocus recombination. Data were filtered using IMgc to optimally remove base pairs and/or chromosomes (a maximum of 5% of chromosomes, N = 5 copises) for each locus.
DOI: 10.5061/dryad.nv5v1v59/24
title: Characteristics and primers of loci sequenced

description: This table contains full locus names, locus abbreviations, location of each locus within the chicken and zebra finch genomes, length of the intron, and primer sequences used for amplifying each locus.
DOI: 10.5061/dryad.nv5v1v59/27
title: Input for *BEAST - 8 taxa, 22 loci

description: Input file for analyses of relative substitution rates in *BEAST. This file contains 8 deeply divergent taxa of Anseriformes sequenced at 22 nuclear introns. The command lines direct *BEAST to use a relaxed lognormal clock and the multispecies coalescent for rate calculations.
DOI: 10.5061/dryad.nv5v1v59/28
title: ms.out.v4.2

description: This contains the R-script used to analyze data simulated using the coalescent program MS. This script contains detailed annotations describing the code. Also see the readme file for more details.
DOI: 10.5061/dryad.r47q769s/1
title: Toc75_allignment_Topel_PSB_2011

description: Alignment of the C-terminal end of 48 Toc75 amino acid sequences. The alignemnt has been truncated so that only the part corresponding to residues 651-818 of atToc75-III remains and was used for the phylogenetic analysis. Also included in the file are the instructions to MrBayes, that was used to analyze the data.
DOI: 10.5061/dryad.r47q769s/2
title: Toc75_trees_Topel_PSB_2011

description: The resulting 50% majority rule consensus trees (with and without branch length data) from the analysis of the data in "Toc75_allignment_Topel_PSB_2011.nex". The tree with branch lengths was used for figure 1 in the paper.
DOI: 10.5061/dryad.sh487/1
title: Laine_etal_2012_HBC-DATA

description: Standardised heterozygosity values calculated from different marker groups and principal components from behavioural measurements. More details in ReadMe file.
DOI: 10.5061/dryad.sq63c/1
title: Host acceptance for mtDNA lineages

description: Results of experiments showing population growth for different WCM mtDNA lineages when transferred from source host plants to test plants. Column headings: host.org - original host, host.nov - novel host, feme - no. of females settled, progeny - no. of progeny found after 14 days, lineage - mtDNA lineage
DOI: 10.5061/dryad.15np2/1
title: Carrara_2013
DOI: 10.5061/dryad.15np2/2
title: Adjacency_matrix

description: Adjacency Matrices for the five different river networks topologies adopted in the dendritic connectivity -habitat capacity experiment.
DOI: 10.5061/dryad.1rd2p/1
title: microsatellite genotyping data for 455 horses from 17 locations in eastern Eurasia

description: Dna was extracted from hair root samples collected in the field between 2006 and 2011 and amplified using 26 microsatellite markers. PCR products were run on an ABI 3730 Genetic Analyser (Applied Biosystems) and alleles were called using GENEMAPPER software v37 (Applied Biosystems).
DOI: 10.5061/dryad.1rd2p/2
title: landscape.data

description: This folder contains  RData objects and R scripts used to carry out the least-cost path analyses described in the ms
DOI: 10.5061/dryad.250c3s47/1
title: all the data_dryad3

description: 18 Microsatellite loci. Alleles coded by three digits, six digits for the diploid organism are in each cell. Collected in the field. Columns are: subpopulation (pop), Subspecies, Ecotype, Individual ID, followed by the 18 markers.
DOI: 10.5061/dryad.2sr417nv/1
title: BiSSE-ness

description: Contains the directories of data files and R code to complete BiSSE-ness using the R package diversitree.
DOI: 10.5061/dryad.44sf1/1
title: s_1_1_sequence_AATTC_start.txt
DOI: 10.5061/dryad.44sf1/2
title: s_1_2_sequence_CACTCC_start.txt
DOI: 10.5061/dryad.4q34p37b/1
title: Alignment ITS sequences

description: Fasta (txt) file with all the aligned ITS sequences of all strains from our culture collection and isolated from dung, used in the analysis to detect correlated evolution between substrate and (rapid) senescence.
DOI: 10.5061/dryad.524t4v16/1
title: 20120202_microsatellite_Structure_Xiphophorus
DOI: 10.5061/dryad.524t4v16/3
title: Data summary spreadsheet_Jones et al. 2012
DOI: 10.5061/dryad.524t4v16/4
title: MtDNA seqs_alignment_Jones et al.

description: Sequence alignment of the main mtDNA haplotypes found in this study.
DOI: 10.5061/dryad.5892n/1
title: Punzalan et al 2013_Dryad

description: Fitness data (i.e. wildtype and mutant offspring number) from laboratory crosses of inbred lines against (inbred) reference lines, when reared in 4 novel environments (C = corn, R = rice, S = salt, Y = yeast).  "Trait" is simply a merger of "Sex" and "Environment" columns.  Each row corresponds to a replicate cross (vial).
DOI: 10.5061/dryad.85pd5/1
title: asm_TlongiContigsFB_IFB_Q_W-MIRA

description: The transcriptome of four T. longispinosus female castes was sequenced on an Illumina HiSeq 2000. After read trimming, caste specific contigs were assembled using the CLC software package. With these contigs as input a meta-assembly was conducted with MIRA to obtain the final contig set.