cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7sq5c/13
title: Supplemental Data Set 13

description: Amino acid sequence alignment used to produce Supplemental Figure 7B.
DOI: 10.5061/dryad.7sq5c/14
title: Supplemental Data Set 14

description: Amino acid sequence alignment used to produce Supplemental Figure 8B.
DOI: 10.5061/dryad.7sq5c/15
title: Supplemental Data Set 15

description: Amino acid sequence alignment used to produce Supplemental Figure 10B.
DOI: 10.5061/dryad.7sq5c/16
title: Supplemental Data Set 16

description: Amino acid sequence alignment used to produce Supplemental Figure 13B.
DOI: 10.5061/dryad.88dj4/1
title: Fitzpatrick et al_MSMR data

description: Monthly multistate mark recapture histories for every individual included in this study. These data were collected in the field in Trinidad over a 1 year period between June 2009-June 2010. The format is intended for use in the capture-mark-recapture Program Mark.
DOI: 10.5061/dryad.fb6qg/1
title: Finnsheep coat colour phenotypes
DOI: 10.5061/dryad.fb6qg/2
title: Finnsheep 50K SNP genotypes
DOI: 10.5061/dryad.j6676/1
title: Annotation spreadsheet for transcriptome assembly of Lithobates clamitans

description: An Excel spreadsheet of contig sequence similarity for the Lithobates clamitans assembly. BLASTX hits to Xenopus tropicalis, HMMER matches to the Pfam-A database (for predicted ORFs), and other annotation information is given. The column headings are as follows:
Contig: contig name
Length (bp): length in base pairs
%GC content: percent of contig sequence that is C or G
Longest ORF (min 50 amino acids): the longest ORF identified on the contig that was at least 50 amino-acids long
Pfam (E-value threshold 0.1): A colon-delimited list of matched Pfam accessions, E-values, and domain descriptions
Xenopus.tropicalis BLASTX E-value: E-value of the best BlastX match to X. tropicalis proteins.
bit: bit score of this match
id%: percentage identity (protein sequence) of this match to the query contig
description: descriptive text in the fasta header of the best match
RefSeq ID: associated RefSeq ID for best match
Entrez gene ID: associated Entrez gene ID for best match
UniProt ID: associated UniProt ID for best match
DOI: 10.5061/dryad.k3bh40bg/10
title: 61V96_s_5_1_qual_trimmed.fqab
DOI: 10.5061/dryad.k3bh40bg/2
title: s_1_1_trimmed5nt.fq
DOI: 10.5061/dryad.k3bh40bg/3
title: s_1_2_trimmed8nt.fq
DOI: 10.5061/dryad.k3bh40bg/4
title: s_2_1_sequence.fq
DOI: 10.5061/dryad.k3bh40bg/5
title: s_2_2_sequence.fq
DOI: 10.5061/dryad.k3bh40bg/6
title: 61V96_s_3_1_qual_trimmed.fqaa
DOI: 10.5061/dryad.k3bh40bg/7
title: 61V96_s_3_1_qual_trimmed.fqab
DOI: 10.5061/dryad.k3bh40bg/8
title: 61V96_s_3_1_qual_trimmed.fqac
DOI: 10.5061/dryad.k3bh40bg/9
title: 61V96_s_5_1_qual_trimmed.fqaa
DOI: 10.5061/dryad.kp79t/1
title: Sample_data

description: New sequence data and sequence data retrieved from GenBank for all loci analysed. Details on sampling locality are given for each specimen analysed. Haplotype names as well as GenBank accession numbers are detailed for each loci per specimen, as well as source of previously published data. Information on where samples are held in is also displayed.
DOI: 10.5061/dryad.kp79t/2
title: BRCA1_genotype_alignment

description: Alignment of BRCA1 genotypes of all individuals used for species tree inference. This data set corresponds to the largest non-recombining blocks obtained with software IMgc (Woener et al. 2007). Two sequences are given per individual.
DOI: 10.5061/dryad.kp79t/3
title: BRCA1_haplotype_alignment

description: Alignment of BRCA1 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003). Dataset used for gene tree inference.
DOI: 10.5061/dryad.kp79t/4
title: DBX5_genotype_alignment

description: Alignment of DBX5 genotypes of all individuals used for species tree inference.
DOI: 10.5061/dryad.kp79t/5
title: DBX5_haplotype_alignment

description: Alignment of DBX5 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.
DOI: 10.5061/dryad.kp79t/6
title: CYTB_haplotype_alignment

description: Alignment of cytochrome b haplotypes used for gene tree inference.
DOI: 10.5061/dryad.kp79t/7
title: DBX6_genotype_alignment

description: Alignment of DBX6 genotypes of all individuals used for species tree inference.
DOI: 10.5061/dryad.kp79t/8
title: DBX6_haplotype_alignment

description: Alignment of DBX6 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.
DOI: 10.5061/dryad.nk151/1
title: Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation.

description: fFsta file Ranunculus sequences
DOI: 10.5061/dryad.nk151/2
title: Presence/absence SNPs matrix

description: Presence absence SNPs matrix. Nexus File
DOI: 10.5061/dryad.rp4q6/8
title: Digestion time of Oculina arbuscula fed Brachionus plicatilis based on the prey DNA content estimated by qPCR

description: Concentration of Brachionus plicatilis prey DNA ingested by Oculina arbuscula after 0, 1, 2, 3, 4, 6, 8 and 10 days.  Prey DNA concentration is shown for different amplicon sizes amplified with different primer sets.
DOI: 10.5061/dryad.s0885/1
title: AFLPdata_HR_73loci

description: AFLP genotypes of 721 plant individuals of Trifolium montanum,  31 sampling sites, 73 loci, sampled in Hinterrheintal (HR)
DOI: 10.5061/dryad.s0885/2
title: AFLPdata_VL_78loci

description: AFLP genotypes of 695 plant individuals of Trifolium montanum,  30 sampling sites, 78 loci, sampled in Val Lumnezia (VL)
DOI: 10.5061/dryad.327v0/1
title: DFTD samples 2006-2011

description: Tumour tissue samples used in the study were collected between 2006 and 2011 at 12 sites within the DFTD affected areas of Tasmania.
DOI: 10.5061/dryad.57vh3/2
title: RobinsonEtAl2012_TransectLocations
DOI: 10.5061/dryad.61cj4/1
title: Periphyton Spatial Biomass distribution

description: Tiff Images of biomass spatial distribution of periphyton colonization at different times. The brigthness of each pixel represent the chlorophyl-a content estimated using the method described in:  Saravia LA, Giorgi A, Momo FR (1999) A photographic method for estimating chlorophyll in periphyton on artificial substrata. Aquatic Ecology 33: 325–330. The initial letter of the file name correspond to the different tanks used in the experiment, then the number of the plate, and finally the date YYMMDD.
DOI: 10.5061/dryad.61cj4/2
title: Output of multifractal analysis software mfSBA

description: This is the output of multifractal analysis applied to each imageThe software used mfSBA is available at: . The output are ASCII files pasted in an spreadsheet. The output for each image is labeled as the file name. The columns named R- are the coefficient of determination. The columns named SD are the standard deviations. Tau is the slope of log(Zq) vs log(epsilon) and is used to calculate Dq.
DOI: 10.5061/dryad.6b2t6/1
title: Lonicera japonica phenotypic data

description: Raw data collected for L. japonica common gardens from fall 2006 to spring 2009. Readme has description of trait codes, as well as locations where populations were collected.
DOI: 10.5061/dryad.79kh0/1
title: Trimmed Un-mapped Data assembly

description: Resultant BAM file from a pool of rRNA-depleted, non-normalized cDNA of six white-tailed deer from the University of Saskatchewan's Specialized Livestock Research Facility that was assembled de novo in CLC Genomics Workbench 6.0.1.
DOI: 10.5061/dryad.79kh0/2
title: BLAST results

description: Top BLAST results of consensus contigs extracted from the .bam file.  blastx+ 2.2.27 was used with an e-value threshold of 0.000001 against a custom database of RefSeq eutherian protein sequences.
DOI: 10.5061/dryad.79kh0/3
title: dbSNP ss Accession Numbers

description: List of SNP ss accession numbers detected in the assembly using CLC Genomics Workbench 6.0.1. These SNPs will be available online in the next dbSNP update, currently scheduled for Oct. 2013.
DOI: 10.5061/dryad.79kh0/4
title: White-tailed deer SNPs (VCF file)

description: We detected SNPs using CLC’s quality-based variant detection algorithm (min. average quality of five flanking bases on either side of SNP = 15; min. quality of central base = 20; min. coverage = 20; max. coverage = 1000; min. variant frequency = 15%; min. variant count = 4), discarding all reads with non-specific alignments.  Multiallelic SNPs were discarded as they may result from incorrect alignment of reads from paralogous genes in the transcriptome data.  All SNPs have been submitted to dbSNP and will be available online in the October 2013 update.  This VCF file is available in the interim.
DOI: 10.5061/dryad.8f191/1
title: Genotypes, pedigree and phenotype files for Scottish Blackface population

description: SNP, nematode and body weight data
DOI: 10.5061/dryad.cp723/1
title: The 15 reference transcriptome assemblies of Compositae crops and their wild relatives
DOI: 10.5061/dryad.ff1g6/1
title: Maximum likelihood phylograms and their alignment files for ectomycorrhizal fungi associated with Salix arctica and Dryas integrifolia across the North American Arctic.

description: Maximum-likelihood phylograms (pdf) of (1) Tomentella1, (2) Tomentella 2, (3) Pseudotomentella, (4) Inocybe 1, (5) Inocybe 2, (6) Inocybe 3, (7) Inocybe 4, (8) Inocybe 5, (9) Sebacina 1, (10) Sebacina 2, (11) Sebacina 3, (12) Cortinarius 1, (13) Cortinarius 2, (14) Cortinarius 3, (15) Cortinarius 4, (16) Clavulina, (17) Russula, (18) Tulasnella, (19) Ceratobasidium, (20) Entoloma, (21) Hebeloma, (22) Lactarius, (23) Laccaria, (24) Pyronemataceae, (25) Tuber, (26) Tuberaceae, (27) Sordariaceae, (28) Phialocephala, (29) Cenococcum, (30) Angulospora, (31) Hymenoscyphus, (32) Leohumicola, (33) Cadophora, (34) Leptodontidium, (35) Peziza, (36) Balsamia, (37) Tetracladium.
taxa inferred from the ITS rDNA datasets showing the phylogenetic spread of the OTUs observed in our study (highlighted by a grey box), including their presence across the bioclimatic subzones of the Arctic among representatives of congeneric taxa in GenBank. Branches with ≥ 90% bootstrap support are highlighted. Each phylogram is accompanied by the sequence alignment files (nex) used for each phylogram.
DOI: 10.5061/dryad.j6676/10
title: Conserved signal peptides of AMPs

description: Sequence logos of the highly conserved signal peptide and acidic propiece region for each species, based on aligned cluster sequences. Standard amino-acid symbols are used, with dark font representing more acidic residues. The predicted cleavage site is C-terminal of the conserved cysteine residue. Position 24 of the P. regilla alignment is blank because the majority of sequences had a gap at this alignment position.
DOI: 10.5061/dryad.j6676/2
title: Annotation spreadsheet for transcriptome assembly of Pseudacris regilla

description: A spreadsheet of contig sequence similarity for the Pseudacris regilla assembly. BLASTX hits to Xenopus tropicalis, HMMER matches to the Pfam-A database (for predicted ORFs), and other annotation information is given. Column headings are:Contig: contig name
Length (bp): length in base pairs
%GC content: percent of contig sequence that is C or G
Longest ORF (min 50 amino acids): the longest ORF identified on the contig that was at least 50 amino-acids long
Pfam (E-value threshold 0.1): A colon-delimited list of matched Pfam accessions, E-values, and domain descriptions
Xenopus.tropicalis BLASTX E-value: E-value of the best BlastX match to X. tropicalis proteins.
bit: bit score of this match
id%: percentage identity (protein sequence) of this match to the query contig
description: descriptive text in the fasta header of the best match
RefSeq ID: associated RefSeq ID for best match
Entrez gene ID: associated Entrez gene ID for best match
UniProt ID: associated UniProt ID for best match
DOI: 10.5061/dryad.j6676/3
title: antimicrobial-peptide-clusters

description: A FASTA-formatted file containing aligned representative sequences for each cluster of antimicrobial peptide reads and/or contigs. The sequence headers correspond to the phylogeny in Figure 1.
DOI: 10.5061/dryad.j6676/4
title: antimicrobial-peptide-cluster-reads

description: The raw reads that mapped to each sequence cluster given in antimicrobial-peptide-clusters.fasta. This file provides the raw data underlying our clustering of antimicrobial peptide transcripts.
DOI: 10.5061/dryad.j6676/5
title: Rana-assembly
DOI: 10.5061/dryad.j6676/6
title: 3-way-orthologs

description: A simple list of contigs from each of three transcriptome assemblies that were reciprocal-best TBLASTX matches. Each row represents a triplet of putatively orthologous sequences that may be useful for comparative genomics, primer design, etc.
DOI: 10.5061/dryad.j6676/7
title: 3-way-aligned-orthologous-segments

description: This FASTA-formatted file is a series of 56 sequence alignments. Each alignment contains one sequence from each frog transcriptome studied. The sequences were aligned at the protein level using MUSCLE (Edgar 2004) and then converted to nucleotide alignments. Annotation information for each set of contigs can be found in the two annotation.xls spreadsheets. This file provides the expected amplicons from each reference sequence for the primers listed in conserved-primer-candidates-for-orthologous-segments.xls, for the purposes of guiding the selection of sequences that may be useful for a given population-genetic or phylogenetic study.
DOI: 10.5061/dryad.j6676/8
title: conserved-primer-candidates-for-orthologous-segments

description: A spreadsheet containing sets of forward and reverse PCR primers in successive rows, for each of the 56 segments in 3-way-aligned-orthologous-segments.fas. The primers were predicted with BatchPrimer3 (You et al. 2008) and the principal output such as expected product size and Tm is included. We also include the estimated dN/dS ratio for each pairwise comparison of the three frog transcriptomes, as an index of the overall conservation of each set of predicted cDNAs. The primer sets have not been systematically evaluated on either cDNA or genomic DNA, and may or may not bridge intronic sequence.
DOI: 10.5061/dryad.j6676/9
title: Summary-figure-of-nucleotide-distance-conserved-regions

description: This figure summarizes the nucleotide distances from the spreadsheet "conserved-primer-candidates-for-orthologous-segments.xls" in order to better guide the selection of loci for molecular phylogenetics. Loci with greater nucleotide distances may be more informative for analysis of closely related species.
DOI: 10.5061/dryad.k2q95/1
title: HoodCanalSummerChumSalmonGenotypes

description: Summer Chum salmon microsatellite genotypes in GenePop format
DOI: 10.5061/dryad.k3bh40bg/11
title: 61V96_s_5_1_qual_trimmed.fqac
DOI: 10.5061/dryad.k3bh40bg/12
title: s_1_1_qual_trimmed.fqaa
DOI: 10.5061/dryad.k3bh40bg/13
title: s_1_1_qual_trimmed.fqab
DOI: 10.5061/dryad.k3bh40bg/14
title: s_1_1_qual_trimmed.fqac
DOI: 10.5061/dryad.k3bh40bg/15
title: s_2_1_qual_trimmed.fqaa
DOI: 10.5061/dryad.k3bh40bg/16
title: s_2_1_qual_trimmed.fqab
DOI: 10.5061/dryad.k3bh40bg/17
title: s_2_1_qual_trimmed.fqac
DOI: 10.5061/dryad.k3bh40bg/18
title: README
DOI: 10.5061/dryad.kp79t/10
title: DBY7_haplotype_alignment

description: Alignment of DBY7 haplotypes used for gene tree inference.
DOI: 10.5061/dryad.kp79t/11
title: RAG1_genotype_alignment

description: Alignment of RAG1 genotypes of all individuals used for species tree inference. This data set corresponds to the largest non-recombining blocks obtained with software IMgc (Woener et al. 2007). Two sequences are given per individual.
DOI: 10.5061/dryad.kp79t/12
title: RAG1_haplotype_alignment

description: Alignment of RAG1 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003). Dataset used for gene tree inference.
DOI: 10.5061/dryad.kp79t/13
title: SMCY7_genotype_alignment

description: Alignment of SMCY7 sequences of all individuals used for species tree inference.
DOI: 10.5061/dryad.kp79t/14
title: SMCY7_haplotype_alignment

description: Alignment of SMCY7 haplotypes used for gene tree inference.
DOI: 10.5061/dryad.kp79t/15
title: CYTB_genotype_alignment

description: Alignment of cytochrome b sequences of all individuals used for species tree inference.
DOI: 10.5061/dryad.kp79t/9
title: DBY7_genotype_alignment

description: Alignment of DBY7 sequences of all individuals used for species tree inference.
DOI: 10.5061/dryad.m247bg66/1
title: Limborg et al. 2012_Sprattus sprattus_microsatellite data

description: Microsatellite data for eight loci and 17 samples of Sprattus sprattus.
DOI: 10.5061/dryad.n65k2/1
title: Ephydra_packardi_read-pair_set1

description: A gzip file containing one of two fastq files associated with the data set. Each gzip file contains a large FASTQ sequence file. Files contain congruent sequences from the paired-end run. For example, the first entry from file set 1 contains the first half of the read pair, while the first entry from file set 2 contains the second half of the read pair. There are 9015656 sequences in each file, and each sequence uses 4 lines in the file (consistent with the FASTQ format). These data can be used to reproduce the "Benchmarking and Code Performance" section of the manuscript associated with this Dryad submission.
DOI: 10.5061/dryad.s55c4/1
title: Bjorklund et al Dryad explanations

description: Explanations to the data files
DOI: 10.5061/dryad.s55c4/2
title: Bjorklund_et_al_data

description: Data
DOI: 10.5061/dryad.s55c4/3
title: Bjorklund_et_al_dryad_pedigree

description: Pedigree
DOI: 10.5061/dryad.1kk2k/1
title: sampling locations and environmental variables

description: Geographical coordinates of sampling locations and environmental data for the 711 Iberian honey bee individuals
DOI: 10.5061/dryad.1kk2k/2
title: SNP genotypes
DOI: 10.5061/dryad.1nt11/1
title: Roche SFF sequence files for all 16 Oli populations

description: These are the SFF files from Roche 454 titanium sequencing of the Oli populations. Populations were barcode indexed using the Roche MIDs, sequenced on the 454 titanium, base-called using the Roche pipeline version 2.53, then split into the 16 separate populations using the MID index. These sff files have been bzip2'ed into one tar archive for easier upload and download.
DOI: 10.5061/dryad.3280v/1
title: data_for dryad

description: Main data file. Please contact mz338@cam.ac.uk for more information
DOI: 10.5061/dryad.42577/1
title: ValentineEtAl-PaleoDB download

description: Pliocene bivalve data downloaded from Paleobiology Database 4 September 2011 (Valentine et al. Fig. 5)
DOI: 10.5061/dryad.4vk85.1
title: Data from: The evolution of males: support for predictions from sex allocation theory using mating arrays of Sagittaria latifolia (Alismataceae)
DOI: 10.5061/dryad.4vk85.2
title: Data from: The evolution of males: support for predictions from sex allocation theory using mating arrays of Sagittaria latifolia (Alismataceae)
DOI: 10.5061/dryad.5856q415/1
title: TopographicBarrierModel_v1.0

description: Complete results from the topographic model of ring barriers published in BMC Biology (2012) -- Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species, Monahan, William B., Pereira, Ricardo J., Wake, David B.
DOI: 10.5061/dryad.5p91k
title: Data from: Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus)
DOI: 10.5061/dryad.70np2513/1
title: Luttikhuizen_et_al_MolEcol_2012_datadryad

description: AFLP data for field collected marine bivalves in shallow intertidal locations in NW Europe. The species is Macoma balthica, the Baltic clam. Please refer to the original publication for further information such as exact locations and local habitat characteristics. File contains data on 644 individuals from 21 different locations scored (presence/absence) for 90 AFLP markers.
DOI: 10.5061/dryad.76ks0/1
title: Genotype data

description: Individual ID, sex, and 15 microsatellite loci
DOI: 10.5061/dryad.8j486/1
title: BAPS_input_files

description: These files are GenePop files that were used for the BAPS analyses.  Each file reflects whether it contains 'Known' or 'Unknown' individuals incorporated in the BAPS analysis, along with the year and training set.  Those with just a year in the file name are for the 'Update' training set, whereas those ending with '12years' were part of the '12 years' training set.
DOI: 10.5061/dryad.8j486/2
title: Canid_genotypes_Dryad

description: This file contains microsatellite genotypes of all individuals used in the simulation study.  The first column contains the identification number for each individual.  Column two indicates which group the individual was assigned to as part of our study (note: this matches the 'Founders' training set in our publication).  The third column indicates whether the individual was included as a 'known' individual in the STRUCTURE analysis.  A '1' indicates that an individual's genotype was included in estimating the allele frequencies, a '0' means is was not.  All the remaining columns contain genotypic information, with each column containing genotyped alleles.  There are two columns per microsatellite locus.
DOI: 10.5061/dryad.8j486/3
title: STRUCTURE_input_files

description: This contains all the input files used for the STRUCTURE analyses. Each file represents a separate year and training set.  See our publication for more details. The ReadMe file contains the details of the parameter settings and input files.
DOI: 10.5061/dryad.8rf538cp/1
title: IMa2 input files

description: Input files for sequence analysis in IMa2. Files in the archive include 3 pairwise comparisons of populations from Smith et al data and 3 from Machado et al (2007), labelled by population comparison (see manuscript) and data source. The last file is for comparison of all populations for the Smith et al data. All files contain locus ID, DNA sequence (aligned using MAFFT - see manuscript for details) and locus specific mutation rates. Line 1= general info, line 2 = number of populations, line 3 = tree topology, line 4 = number of loci, thereafter = sequence data.
DOI: 10.5061/dryad.92p3p/1
title: LeinoetalPisum

description: Microsatellite data from genotypings of eight individuals each of in total 40 extant and historical accessions. Microsatellite markers are from Loridon et al 2005.
DOI: 10.5061/dryad.9hd71135/1
title: Phylogeography_populations_cpSSRs

description: Data of alleles scores of the chloroplast microsatellites ccmp2 and ccmp5, comprising 59 populations of Populus alba, P. nigra, and P. xcanescens, of Spain and one population of Morocco. n=628 trees. Collected by D. Macaya-Sanz, M. Heuertz, N. Alba, U. Lopez-de-Heredia, A.I. de-Lucas, E. Hidalgo, C. Maestro, A. Prada, R. Alia, and S.C. Gonzalez-Martinez. For contact, please email: santiago@inia.es. | Column headings | ID: Identity code of the individual collected; Population: Populations where the individual is located and its subsequents; Province: Administrative province were populations are sited; ccmp2 & ccmp5: Allele scores of these regions. Missing data are represented by a hyphen '-'. Additional information for the data can be found in the related publication.
DOI: 10.5061/dryad.9hd71135/2
title: nuSSRs for Clonality within population assessment

description: Data of alleles scores of the five nuclear microsatellites PMGC2852, ORPM312, ORPM344, ORPM127, and ORPM30, comprising 5 populations of Populus alba and P. xcanescens, of Spain. n=200 trees. Collected by D. Macaya-Sanz, M. Heuertz, N. Alba, U. Lopez-de-Heredia, A.I. de-Lucas, E. Hidalgo, C. Maestro, A. Prada, R. Alia, and S.C. Gonzalez-Martinez. For contact, please email: santiago@inia.es. | Column headings | ID: Identity code of the individual collected; Population: Populations were the individual is located; UTM_X & UTM_Y: UTM coordinates in ED50; Remaining columns: Allele scores of these regions. Missing data are represented by '-999'. Additional information for the data can be found in the related publication.