cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jr233/1
title: Alignments of C. gigas in silico sequences

description: For the in silico SNPs, we investigated in 2009 the 6th assembly of the Crassostrea gigas EST database (http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html). The database contained results of the assembly of 55,851 public ESTs from dbEST and 417 Genbank mRNA sequences. The assembly, performed with TGICL (http://compbio.dfci.harvard.edu/tgi/software/; parameters -l 60 -p 96 -s 100000 -O '-p 75 -s 500'), produced an alignment file from which 1370 SNPs were extracted. We looked for SNPs that complied with the initial criteria: a minimum depth of seven sequences, with a minimum allele count of three, and the absence of any other SNP in the 60 bp segment flanking the analyzed SNP to the left or right. As these conditions appeared too stringent, and did not produce many SNPs, we relaxed the criteria to a minimum depth of five sequences with a minimum allele count of two, and allowed there to be a SNP within 120 bp of the SNP of interest, as long as there was only one and it was not close.
DOI: 10.5061/dryad.jr233/2
title: Alignments of O. edulis in silico sequences

description: For the in silico SNPs, we investigated O. edulis transcriptome sequence data from eight individuals from the natural range (Cahais et al. 2012, Gayral et al. 2011). For the present study, the 454 and Illumina reads were assembled using a multi-kmer strategy (kmers: 37, 41, 45, 49, 53, 57 and 61, assembled with Velvet version 1.1.03). Contigs longer than 100 bp from every assembly were then meta-assembled with TGICL (http://compbio.dfci.harvard.edu/tgi/software/). The Illumina reads were remapped on the contigs using BWA (0.5.9-r16) and a compressed alignment file was produced using SAMtools view (version 0.1.11). The alignment file was then used to call the SNPs with SAMtools pileup and varFilter (version 0.1.11). In this database, we looked for SNPs that represented different contigs, with a depth ranging from 20 to 500 at the position and no other SNPs in the surrounding 120 bp. The SNP quality score was initially set at 20 but finally, due to the high number of SNPs available, we only used SNPs with the highest score of 227.
DOI: 10.5061/dryad.jr233/3
title: Alignments of O. edulis in vitro sequences

description: For the European flat oyster, in vitro sequencing investigated 40 loci from two EST libraries (Morga et al. 2011, 2012). Primers were designed using Primer3 software package (Rozen and Skaletsky 2000). A total of 22 oysters, 16 from four different natural populations collected on the Atlantic and Mediterranean coasts and six belonging to the first generations of three selected families for resistance to bonamiosis were used to investigate polymorphisms. The PCR and sequencing protocols used were the same as those given in Harrang et al. (2013). Sequence alignment was performed with ClustalW via the BioEdit interface (Hall 1999). The validity of each SNP was checked individually on nucleotide sequences and sequence alignments. A total of 420 in vitro SNPs were detected in the dataset of 40 sequenced fragments. Among them, the indels (n = 34) were discarded. Moreover, 347 SNPs were also discarded because of neighboring polymorphisms or low functionality scores. However, as we wanted some genes of interest to be represented in the SNP dataset, we kept some (n = 13) that had neighboring polymorphisms. To favor genotyping, those polymorphic nucleotides were treated as degenerated nucleotides. In total, 52 in vitro SNPs were included in the array, representing 35 different gene fragments.
DOI: 10.5061/dryad.jr233/4
title: Alignments of C. gigas in vitro sequences

description: For the Pacific oyster, in vitro sequencing investigated 103 loci from ESTs retrieved from the Genbank database (http://www.ncbi.nlm.nih.gov/) or from specific libraries that had been obtained to detect genes differentially regulated during summer mortality events (Fleury et al. 2009). Primers were designed using the Primer3 software package (Rozen and Skaletsky 2000). For a first set of ESTs (n = 61), 24 oysters belonging to a third generation of selection for summer mortality resistance were used in the SNP discovery phase (Sauvage 2008; Sauvage et al. 2007). A second set of ESTs (n = 42) was then added and 10 of the 24 oysters were used for sequencing, as described in Sauvage et al. (2007), together with a third set of five SNPs from the 20 developed by Bai et al. (2009). Sequence alignment was performed with ClustalW via the BioEdit interface (Hall 1999) and DNAMAN version 4.1 (www.lynnon.com). The validity of each SNP was checked manually on the chromatograms and sequence alignments. A total of 321 in vitro SNPs were detected in the first dataset of 61 sequenced fragments, and 380 in the second dataset of 42 sequenced fragments. Among those 701 SNPs, 72 were selected (39 and 33 from the two datasets, respectively) because they had high functionality scores and no neighboring polymorphisms. However, as we wanted to be sure that some genes of interest were represented in the SNP dataset, for several ESTs we kept two SNPs. Therefore, our 72 selected in vitro SNPs were obtained from 65 different ESTs.
DOI: 10.5061/dryad.k90m7/1
title: Locations of Lama guanicoe across Chile
DOI: 10.5061/dryad.m3v72/1
title: SNP_Genotyping

description: Genotyping at 3 SNPs found in AMY1 and AMY2 genes, on 112 horses sampled in Italy and belonging to different breeds.
DOI: 10.5061/dryad.ms5q038t/1
title: Cypholoba localities

description: List of collecting localities for Cypholoba species in the Republic of South Africa, based on museum specimen data from the following collections: Field Museum of Natural History, Chicago, Illinois (FMNH); Kruger National Park Museum (Scientific Services), Skukuza, South Africa (KNPC); South African National Collection of Insects, Pretoria, South Africa (SANC); National Museum of Natural History, Smithsonian Institution, Washington, D.C. (NMNH); Transvaal Museum, Pretoria, South Africa (TMSA).
DOI: 10.5061/dryad.nf591/1
title: Simulated metacommunities

description: For each speciation scenario, each folder contains characteristics of each metacommunity simulated. Each file is a R binary object stored as a list with 5 elements: $tree: the phylogenetic tree of extant species in 'phylo' format ; $land: a raster map of the climatic variable; $niche: the mean niche of each species ; $meta: an array that identifies the species each individual in the metacommunity belongs to (NAs are empty slots), which dimensions are (landscape length, landscape width, carrying capacity in each pixel) ; $Res gives the parameter used to simulate each metacommunity.
DOI: 10.5061/dryad.ns7v7/1
title: Reichenbach_etal_Cochlostoma_supplemetary_datafile

description: Datafile used for quantitative analyses of males and females Cochlostoma septemspirale. It contains the measurements for each individual. The file is saved in a tabbed text format. The readme file contains abbreviations used in the datafile. Datafile as well as read me file should best be opened with spread sheet program such as Excel.
DOI: 10.5061/dryad.p0t0b/1
title: IRBP-Pages-2012

description: Fasta alignment of IRBP sequences used in Pages et al., 2012
DOI: 10.5061/dryad.p0t0b/2
title: Mito-Pages-2012

description: Fasta alignment of mitochondrial data used in Pages et al., 2012
DOI: 10.5061/dryad.p0t0b/3
title: Microsat-Pages-2012

description: Microsatellite data used in Pages et al., 2012
DOI: 10.5061/dryad.p0t0b/4
title: Morphological data

description: We assessed the morphological differences between 328 adult specimens from the R3 and R. tanezumi mt lineages. Five linear measurements were considered: head + body length, tail length, hind-foot length, ear length and head length. All measurements were made with a ruler (precision 1 mm), with the exception of head length, which was measured with a caliper (precision 0.1 mm). Specimens were sexed and classified as adults on the basis of both complete development of the mandibular row of teeth and sexual maturity (full development of seminal vesicles and vulva opening, for males (M) and females (F), respectively)
DOI: 10.5061/dryad.pk24v/1
title: 12S-16S Data flie

description: 12-16S data file used for Myrmekiaphila species delimitation.  Nexus file includes Bayes block with models and run parameters.
DOI: 10.5061/dryad.pk24v/2
title: Consensus tree file from Bayesian analysis
DOI: 10.5061/dryad.pk24v/3
title: 12S-16S Phylip file

description: Phylip formatted file for RAxML run
DOI: 10.5061/dryad.pk24v/4
title: RAxML_bestTree
DOI: 10.5061/dryad.qm636/2
title: Alignment of ITS sequences

description: The ITS sequences of Romanian niphargids obtained in the course of this study were aligned using MAFFT's E-INS-i option. Some individuals had more than one sequence type, hence the suffixes a, b and c appended to their names.
DOI: 10.5061/dryad.qm636/3
title: Alignment of COI sequences

description: The COI sequences of Romanian niphargids obtained in the course of this study were aligned by hand.
DOI: 10.5061/dryad.qm636/4
title: Alignment of Thiothrix 16S rRNA gene sequences

description: The Thiothrix 16S rRNA gene sequences isolated from Romanian niphargids in the course of this study were aligned with Thiothrix sequences present in GenBank using MAFFT's Q-INS-i option.
DOI: 10.5061/dryad.r8ns3/1
title: FASTA file of CAP3 assembly

description: Assembly in fasta format of white-footed mouse 454 cDNA libraries from in and around New York City (NYC) using the CAP3 assembler with default setting.
DOI: 10.5061/dryad.r8ns3/2
title: FASTA file of Newbler cDNA assembly

description: Assembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the cDNA option.
DOI: 10.5061/dryad.r8ns3/3
title: FASTA file of Newbler genome assembly

description: Assembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the large genome option.
DOI: 10.5061/dryad.r8ns3/4
title: Sequence alignment file (SAM) of 454 reads from Central Park population

description: Sequence alignment file of fastq files from Central Park 454 sequencing.  Fastq Files were aligned to Newbler cDNA assembly.
DOI: 10.5061/dryad.r8ns3/5
title: Sequence alignment file (SAM) of 454 reads from Flushing Meadows population

description: Sequence alignment file (SAM) of fastq files from Flushing Meadows 454 sequencing.  Fastq Files were aligned to Newbler cDNA assembly.
DOI: 10.5061/dryad.r8ns3/6
title: Sequence alignment file (SAM) of 454 reads from Harriman State Park population

description: Sequence alignment file (SAM) of fastq files from Harriman State Park 454 sequencing.  Fastq Files were aligned to Newbler cDNA assembly.
DOI: 10.5061/dryad.r8ns3/7
title: Sequence alignment file (SAM) of 454 reads from New York Botanical Garden population

description: Sequence alignment file (SAM) of fastq files from New York Botanical Garden 454 sequencing.  Fastq Files were aligned to Newbler cDNA assembly.
DOI: 10.5061/dryad.r8ns3/8
title: Sequence alignment file (SAM) of 454 reads from Ridgewood Reservoir population

description: Sequence alignment file (SAM) of fastq files from Ridgewood Reservoir sequencing.  Fastq Files were aligned to Newbler cDNA assembly.
DOI: 10.5061/dryad.r8ns3/9
title: BLAST and gene ontology annotations for white-footed mouse cDNA sequences

description: Output file from software program BLAST2GO.  Must be opened in BLAST2GO.  Contains full BLAST and GO annotations for Newber assembly of all Peromyscus leucopus 454 sequences
DOI: 10.5061/dryad.rc515/9
title: Incidence data

description: Incidence data for seasonal influenza viruses A/H3N2, A/H1N1, B/Vic and B/Yam.  Each row represents a USA winter influenza season.  The column "flu" gives the frequency of influenza positive isolates from all isolates tested.  The columns "typeA" and "typeB" give the relative frequencies of influenza A and influenza B in samples that tested positive.  The columns "subtypeH3", "subtypeH1", "subtypeH1pdm" give the relative frequencies of A/H3N2, A/H1N1 and pandemic A/H1N1 among type A samples.  The columns "subtypeVic" and "subtypeYam" give the relative frequencies of B/Vic and B/Yam among type B samples.  The column "ili" gives the influenza-like illness (ILI) frequency over the same season.
DOI: 10.5061/dryad.rc5tb/3
title: Structure

description: Input files for Structure
DOI: 10.5061/dryad.rc5tb/4
title: Simapse

description: Input files for Simapse
DOI: 10.5061/dryad.rc5tb/5
title: Simulated

description: Hybridlab generated data for NewHybrids and Structure
DOI: 10.5061/dryad.rk204/2
title: Passerines_CleanReads

description: Contains the cleaned reads for the Passerine samples.
DOI: 10.5061/dryad.rm8jf564/16
title: Meliaceae_psbB-psbN_Muellner-etal_2011
DOI: 10.5061/dryad.rm8jf564/17
title: Moraceae_ITS-Roy-etal-2010
DOI: 10.5061/dryad.rm8jf564/18
title: Moraceae_trnH-psbA-Roy-etal-2010
DOI: 10.5061/dryad.rm8jf564/19
title: Orobanchaceae_ITS_Dong-etal-2011
DOI: 10.5061/dryad.rm8jf564/20
title: Orobanchaceae_matK_Dong-etal-2011
DOI: 10.5061/dryad.rm8jf564/21
title: Potamogetonaceae_ITS_Du-etal-2011
DOI: 10.5061/dryad.rm8jf564/22
title: Potamogetonaceae_matK_Du-etal-2011
DOI: 10.5061/dryad.rm8jf564/23
title: Primulaceae_ITS_Yan-etal-2011
DOI: 10.5061/dryad.0157d/1
title: Hypothesis 2 dryad data 1

description: data on shoot length, shoot mortality and cone production used to test hypothesis 2.
DOI: 10.5061/dryad.0157d/4
title: Hypothesis 1 ascomycota and spp richness dryad b

description: Data on the percentage of fungi from the division ascomycota and ectomycorrhizal fungal species richness used to test hypothesis 1.  This file includes GenBank accession numbers and species identity information for the species richness data.
DOI: 10.5061/dryad.0157d/5
title: Hypothesis 2 dryad data 2b

description: Data on the relative abundance of ectomycorrhizal fungi used to test hypothesis 2.  This file includes species names and GenBank accession numbers.
DOI: 10.5061/dryad.056r5/1
title: Arachidonic acid content of individual spawns of eggs from captive red drum after a diet-shift.

description: Data were manually entered into a Microsoft Excel spreadsheet then imported into Systat statistical software for analysis and graphing. Data extracted from Systat to create this file. Variable names and descriptions are provided in ReadMe.txt.
DOI: 10.5061/dryad.056r5/2
title: Regression statistics for changes in arachidonic acid concentration of red drum eggs over time after a diet shift. Regression statistics are estimates of initial concentration and incorporation rate of arachidonic acid in eggs.

description: Data were derived from linear regressions computed by Systat statistical software and exported to create this file. Variable names and descriptions are provided in ReadMe.txt.
DOI: 10.5061/dryad.056r5/3
title: Arachidonic acid content of individual spawns of eggs and the diet of captive red drum during irregular diet variations

description: Data were manually entered into a Microsoft Excel spreadsheet then imported into Systat statistical software for analysis and graphing. Data extracted from Systat to create this file. Variable names and descriptions are provided in ReadMe.txt.
DOI: 10.5061/dryad.180n7/1
title: Typhlopidae_10_5

description: DNA Sequence Matrix. See partitions in README.parts
DOI: 10.5061/dryad.180n7/2
title: RAxML_bipartitions

description: RAxML Tree.
DOI: 10.5061/dryad.1sr5c/1
title: Raw host use data: H. melpomene, H. cydno and hybrids

description: Raw  data collected from insectary host use assays as described in the manuscript.
DOI: 10.5061/dryad.25kd9/1
title: Amblyopsis-Final-ND2

description: mitochondrial ND2, Nexus format
DOI: 10.5061/dryad.25kd9/2
title: Amblyopsis-Final-S7

description: nuclear S7 intron, Nexus format
DOI: 10.5061/dryad.25kd9/3
title: Amblyopsis-Final-RAG1

description: nuclear RAG1 gene, coding region, Nexus format
DOI: 10.5061/dryad.25kd9/4
title: Amblyopsis-Final-RHO

description: nuclear RHO (rhodopsin), coding region, Nexus format
DOI: 10.5061/dryad.25kd9/5
title: Amblyopsis-Final-TBR

description: nuclear TBR gene, coding region, Nexus format
DOI: 10.5061/dryad.31072/1
title: The developmental plasticity and functional significance of an additional sperm storage compartment in female yellow dung flies

description: The data files contain information on maternal and offspring spermatheca phenotype, offspring development time, body size, growth rate and survival from five artificial selection lines of Scathophaga stercoraria. The data are provided based on family means and individual female offspring.
DOI: 10.5061/dryad.325vm/1
title: Sample Information

description: Information and results (microsatellite data analyses and control region - CR - haplotypes) for the samples analysed in the study and respective GenBank Accession Numbers for mtDNA data.
DOI: 10.5061/dryad.325vm/2
title: Microsatellite Dataset

description: Microsatellite dataset used in the study. Genotypes recovered for 302 samples analysed for 11 microsatellite loci.
DOI: 10.5061/dryad.3f765/1
title: DLoop_alignment

description: alignment of DLoop sequences from 172 specimens for Bayes Factor analyses, PhiST calculation and construction of a haplotype network.
DOI: 10.5061/dryad.3f765/2
title: Morphometric_Data

description: Landmark data from 16 morphometric landmarks for 315 specimens
DOI: 10.5061/dryad.3h1c4/1
title: Alleles of the melanocortin 1 receptor

description: DNA sequences of the MC1R genes of sciurus carolinensis, niger and vulgaris
DOI: 10.5061/dryad.46n9h/2
title: BehaviorandMateChoiceData131024R1

description: Spreadsheet containing both the mating outcome and the trainer behavior for all behavior/mating trials reported in the manuscript. Treatments are abbreviated: WS/DS=seasonal form, M/F=sex of trainer or trainee for naive trials, 0/2/naive=exposure. Behaviors are counts of trainer behaviors.
DOI: 10.5061/dryad.4rk06/1
title: MonstersBL_final_stats

description: Eye Movement Data
DOI: 10.5061/dryad.54c7h/1
title: Kronauer et al. 2012 microsatellite genotypes

description: This file contains multilocus microsatellite genotypes for female individuals of the ant Cerapachys biroi.
DOI: 10.5061/dryad.5qs11/1
title: Compressed repository of Nematode Argonaute phylogenetic analyses

description: The repository contains a NEXUS format protein alignment, the outputs from MrBayes analyses of this alignment, and a figure describing the analyses.
DOI: 10.5061/dryad.6j13r/7
title: Supplemental Data 7

description: PLY 3D file of the partial endocast of of Kentuckia deani MCZ 5226.
DOI: 10.5061/dryad.75j12/1
title: Mochras Borehole Foraminifera Distribution Charts (Supplementary Data)

description: The data file comprises two large scale charts, in pdf format, showing the distribution and abundances of all recorded foraminifera from the Lower Jurassic section of the Llanbedr (Mochras Farm) Borehole, North Wales, United Kingdom.  These data are supplementary to the publication COPESTAKE, P & JOHNSON, B. 2014. Lower Jurassic Foraminifera from the Llanbedr (Mochras Farm) Borehole, North Wales, UK. Monograph of the Palaeontographical Society, London: 1-000, pls 1-21. (Publ.641, part of Vol. 000 for 2013).
DOI: 10.5061/dryad.77r3p/1
title: data and matrices
DOI: 10.5061/dryad.7gg70/4
title: Tremadocian 3 dataset

description: Abundance dataset. Samples were collected from restricted 10-20 cm shale intervals. Localities and depositional environments are indicated. Individuals were counted using the MNI protocol. The dataset was taxonomically standardized by the authors.
DOI: 10.5061/dryad.7mt1t/1
title: Cheetah MHC class I sequences

description: Cheetah MHC class I alpha 1 domain sequences
DOI: 10.5061/dryad.7mt1t/2
title: Lion MHC class I sequences

description: Gir Lion MHC class I alpha 1 domain sequences
DOI: 10.5061/dryad.7mt1t/3
title: Domestic cat microsatellite data

description: Domestic cat microsatellite data for 6 MHC-linked and 5 neutral microsatellites in two breeds, domestic mixed breed (DSH) and Burmese (BUR)
DOI: 10.5061/dryad.7mt1t/4
title: Cheetah microsatellite data

description: Cheetah microsatellite data for 3 MHC-linked microsatellite markers in two cheetah subspecies, jubatus and raineye.
DOI: 10.5061/dryad.842n6/1
title: FUNCTIONS AND EXAMPLES
DOI: 10.5061/dryad.8b3d1/1
title: VegetationPlots_Saponaria bellidifoliaHabitat_Apuseni Mts

description: Vegetation data sampled within Saponaria bellidifolia habitat in the Apuseni Mountains (Carpathian Mountains, Romania).
DOI: 10.5061/dryad.8b3d1/2
title: RAPD_Saponaria bellidifolia_Apuseni Mts

description: RAPD analysis of 10 plants/population for 7 Saponaria bellidifolia populations within Apuseni Mountains.
DOI: 10.5061/dryad.8dc30/1
title: Phenotypic means, between and within male coefficients of variation and variance estimates for testis area and sperm length

description: Phenotypic means (±SE), along with between and within male coefficients of variation and variance estimates for the male characters (testis area and sperm length) used in the analyses. NA = no value. * Indicates species that could not be used for phylogenetic analysis and ° indicates those species for which between-male data could not be calculated. TA= testis area in mm2; MSL = mean sperm length (mm); BMVAR = between male variance; WMVAR = within male variance; BMCV = between male coefficient of variation and WMCV = within male coefficient of variation.
DOI: 10.5061/dryad.8kk36/1
title: Primary data for all figures and analyses

description: This file contains all primary data used to generate the figures and analyses in the article. The file is in Excel format, with separate sheets for each figure.
DOI: 10.5061/dryad.8p2f7/1
title: Wild_bird_isolates_concatenated_alignment

description: A fasta-file alignment containing the concatenated MLST sequences from each wild bird C. jejuni isolate presented in the article.
DOI: 10.5061/dryad.96k0t/1
title: SUPPLEMENTAL DATA FIGURE 1

description: BSE-Z images showing locations of EDS point analyses on P. simplex vanes and matrix. Data are shown in Table 1. Scale bar in 1=500 µm, in 2=100 µm, in 3 and 4=1 mm, in 5 and 6=400 µm, and in 7 and 8=100 µm.
DOI: 10.5061/dryad.9cf75/1
title: JoinmapInputGenotypeFile

description: JoinMapGenotypeInputFile:  Contains the microsatellite genotypes for each of the 198 F2 in the mapping cross.  The genotypes are coded according to the JoinMap segregation types.Rows at the top are wrapped around in this tab-delimited text file, but will load into Excel properly.  These 5 rows are: Markername, segregationType, Phase,  Markertype, marker#The left-most column contains the F2 ID numbers.  These data were classified as "CP" for Joinmap, since they came from an outcrossed population.
DOI: 10.5061/dryad.9cf75/2
title: TraitsFileF2

description: Phenotypic values for each of the 198 F2 used in the QTL map. Values are BLUPs from a mixed model ANOVA.  File is tab delimited.
DOI: 10.5061/dryad.9cf75/3
title: MarkerIDcodes

description: MarkerIDcodes.txt:  This file matches the marker id codes used on the map in Fig1 to the markerNames used in the Joinmap datafiles.  Columns are markerName, code used in Fig. 1, LinkageGroup,location on LG in cM.
DOI: 10.5061/dryad.9cf75/4
title: FDIST_Summary195markers_msat&AFLP&codom

description: Contains the output of Fdist2 for all markers-- microsatellites, AFLPs and sequence-tagged codoms.  Columns are:markerName, outlier?(0 = non-outlier, 1= marginal outlier, 2 = significant outlier),Fst,(1-p) at Round1,(1-p) at Round2, (1-p) at Round3, heterozygosity
DOI: 10.5061/dryad.9cf75/5
title: STRUCTURE data Class1Rep1

description: STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA.  Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields.  Columns in each dataset are:  CloneID, Marker1, Marker2, Marker3, Marker4, Marker5.  All markers are unlinked.  To findthe markers on the map,  use the ID codes in the file called "MarkerIDcodes.txt"