cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7vj03/6
title: Metamorphosis of Acropora millepora at different temperatures

description: "age" is larval age (h); "temp" is temperature; "rep" is the replicate number; "meta" is the number of larvae that metamorphosed that day; "larvae" is the number of larvae used to start the experiment; "cum" is the cumulative number of larvae that have metamorphosed until that day; "propmeta" is the proportion of larvae that have metamorphosed that day, calculated as "meta"/"larvae"; "propcum" is the cumulative proportion of larvae that have metamorphoses, calculated as "cum"/"larvae"
DOI: 10.5061/dryad.7vj03/7
title: Larval survival of Cyphastrea japonica at different temperatures

description: "temp" is the temperature the larvae were raised in; "age" is the larval age (h), "surv" is the number of larvae alive (swimming as no settlement cue was provided), "larvae" is the  number of embryo/larvae in the beginning of the experiment; "propsurv" is the proportion of larvae alive, calculated as "surv"/"larvae"
DOI: 10.5061/dryad.7vj03/8
title: Larval survival of Favites stylifera at different temperatures

description: "temp" is the temperature the larvae were raised in; "age" is the larval age (h), "surv" is the number of larvae alive (swimming as no settlement cue was provided), "larvae" is the  number of embryo/larvae in the beginning of the experiment; "propsurv" is the proportion of larvae alive, calculated as "surv"/"larvae"
DOI: 10.5061/dryad.841k6/1
title: advertisement and reward traits in Salvia flowers

description: Include morphological and nectar measurements from 3251 flowers belonging to 503 individual plants and 18 Salvia species.
DOI: 10.5061/dryad.841k6/2
title: data for repeatability

description: Include data for ten randomly chosen flowers per species, in which area measurements (frontal area of the lower lip and area of corolla tube) were taken three times.
DOI: 10.5061/dryad.8m30f/1
title: Aquasplatche network simulation settings

description: Ten folders corresponding to the ten networks described in Fourcade et al. Simulations can be performed using Aquasplatche.
DOI: 10.5061/dryad.98m0m/1
title: SAM files containing RNA-seq reads supporting fusion transcripts in Providence and Rush cohorts

description: These SAM files consist 2 directories, one for Providence cohort, and another for Rush cohort. Each sample has one individual SAM file under each cohort directory. The data were generated by gFuse, a RNA-seq fusion detection bioinformatics method, from archived FFPE human breast cancer patients. As a part of gFuse pipeline, the SAM files were generated by GSNAP via mapping supporting RNA-seq reads against the fasta sequences of 5 template sets of 100 unique fusion junctions in the length of 100bp, which are available here in the file “100fusiontemplates.fa”. The sequences and sample IDs are also described in Supplementary Table 1 of the manuscript titled “Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression”.
DOI: 10.5061/dryad.9mg16/1
title: Data from 6 turtles exposed to light during anoxia and reoxygenation.zip

description: The data consists of wav files, which contain the recorded data of evoked potential measurements performed on anoxic (labeled Anoxi) and reoxygenating (labeled Reox) turtles exposed to light stimulation. Each recording was performed after one ventilation, during anoxia and reoxygenation.
DOI: 10.5061/dryad.9mg16/2
title: Data from 6 turtles exposed to light during temperature change

description: The data consists of wav files containing recorded data from 6 turtles exposed to light stimulation during cooling, from 25 C to 3 C, and during reheating from 5 C to 25 C.
DOI: 10.5061/dryad.9mg16/3
title: Data from 6 turtles exposed to vibration during anoxia and reoxygenation

description: The data consists of wav files containing data recorded from 6 turtles exposed to vibration during anoxia (labeld Anoxi) and reoxygenation (labeled Reox). A recording was performed after each ventialtion during anoxia and reoxygenation.
DOI: 10.5061/dryad.9rf5m/1
title: Phylogenetic tree from cytb sequences of common voles, Microtus arvalis

description: TreeBase entry containing DNA sequence alignment of mitochondrial cytb gene, phylogenetic tree from the Bayesian inference analysis, details of the analysis. This constitutes Figure 2 in the paper.
DOI: 10.5061/dryad.9rf5m/7
title: GenBank population set information

description: Ancient DNA sequences of cytb from common voles, Microtus arvalis,are in GenBank under PopSet: 302202495. Modern complete sequences of the cytb gene from common voles, Microtus arvalis, are in GenBank under PopSet: 304634227.
DOI: 10.5061/dryad.b0qn5/4
title: microsatellites data for migrate

description: input file of migrate(11pops, 30 neutral loci, 384samples)
DOI: 10.5061/dryad.b0qn5/5
title: microsatellites data for Bayesass

description: input file of bayesass (neutral loci)
DOI: 10.5061/dryad.b0qn5/6
title: microsatellites data for DIYABC

description: input file of DIYABC (neutral loci, 3 groups+1outgroup)
DOI: 10.5061/dryad.b0qn5/7
title: DIYABC settings

description: The scenarios, parameters and settings of DIYABC (6 different scenarios are including)
DOI: 10.5061/dryad.d18r8/1
title: DNA.alignments

description: The zip file contains the DNA alignments used for analyses. This submission includes the original unedited alignments plus the gap-coded alignments (with gaps removed). See the original publication for details regarding collection, DNA extraction, amplification and sequencing.
DOI: 10.5061/dryad.g8d5h/1
title: Fertility of Sex-ratio and Standard male Drosophila neotestaea

description: offspring counted in the laboratory
DOI: 10.5061/dryad.g8d5h/2
title: Mating frequencies for Drosophila neotestacea females

description: Mating observations were performed in the laboratory
DOI: 10.5061/dryad.g8d5h/3
title: Autosomal microsatellite loci for 5 populations of Drosophila neotestacea

description: Flies were collected in the field, sacrificed and genotyped in the laboratory.
DOI: 10.5061/dryad.pf5cg/1
title: Genotype_data_Jaquiery_et_al_2012_Mol_Ecol

description: Multilocus genotypes for pea aphids (Acyrthosiphon pisum) individuals sampled in France & Switzerland on three host plants. Precise sampling locations are indicated under the 'latitude' & 'longitude' columns. The 'pop_name' column indicates the population labels used during the analyses. Multilocus genotypes start from column G. For each microsatellite marker, two columns with a unique label (i.e. marker name) indicate the two alleles. Missing data are labelled '999'.
DOI: 10.5061/dryad.pf5cg/2
title: Arlequin_input_Jaquiery_et_al_2012_Mol_Ecol

description: Arlequin input file
DOI: 10.5061/dryad.pf5cg/3
title: Structure_input_Jaquiery_et_al_2012_Mol_Ecol

description: Structure input file.
DOI: 10.5061/dryad.ph8s5/10
title: Reference database Arctic (ITSAst)

description: Fasta file of the Arctic reference database (ITSAst)
DOI: 10.5061/dryad.ph8s5/11
title: Reference database Arctic (ITSCyp)

description: Fasta file of the Arctic reference database (ITSCyp)
DOI: 10.5061/dryad.ph8s5/12
title: Reference database Arctic (ITSPoa)

description: Fasta file of the Arctic reference database (ITSPoa)
DOI: 10.5061/dryad.ph8s5/13
title: Reference database Boreal (gh)

description: Fasta file of the Boreal reference database (P6 loop of the trnL)
DOI: 10.5061/dryad.ph8s5/14
title: Reference database EMBL (gh)

description: Fasta file of the EMBL reference database (P6 loop of the trnL)
DOI: 10.5061/dryad.ph8s5/15
title: Reference database EMBL (ITSAst)

description: Fasta file of the EMBL reference database (ITSAst)
DOI: 10.5061/dryad.ph8s5/16
title: Reference database EMBL (ITSCyp)

description: Fasta file of the EMBL reference database (ITSCyp)
DOI: 10.5061/dryad.ph8s5/9
title: Reference database Arctic (gh)

description: Fasta file of the Arctic reference database (P6 loop of the trnL)
DOI: 10.5061/dryad.r406f/1
title: P. ramosa estimated haplotypes in STRUCTURE format

description: P. ramosa estimated haplotypes in STRUCTURE format
DOI: 10.5061/dryad.r406f/2
title: P_ramosa_allele_presence_absence

description: P. ramosa presence/absence data for each allele at each locus
DOI: 10.5061/dryad.tk400/1
title: Matching Model Simulations Alpha = 0.02

description: Simulation data for generation 2000 for the phenotype matching model where alpha has been set to 0.02.
DOI: 10.5061/dryad.tp979/1
title: Half-sib genetic design data

description: This file contains CHC log contrast data of male Drosophila serrata and their pedigree from a half-sib genetic design. The flies came from a lab-adapted population derived from a natural population in Brisbane, Australia.
DOI: 10.5061/dryad.tp979/2
title: Selection experiment data

description: This file contains the CHC log contrast data of Drosophila serrata males from the artificial selection experiment.
DOI: 10.5061/dryad.tp979/3
title: Selection indices

description: This file contains the eight indices (T1 to T8) used in the artificial selection experiment on the CHC log contrasts.
DOI: 10.5061/dryad.v55p5/10
title: Part of image archive
DOI: 10.5061/dryad.v55p5/11
title: Part of image archive
DOI: 10.5061/dryad.v55p5/4
title: Part of image archive
DOI: 10.5061/dryad.v55p5/5
title: Part of image archive
DOI: 10.5061/dryad.v55p5/6
title: Part of image archive
DOI: 10.5061/dryad.v55p5/7
title: Part of image archive
DOI: 10.5061/dryad.v55p5/8
title: Part of image archive
DOI: 10.5061/dryad.v55p5/9
title: Part of image archive
DOI: 10.5061/dryad.v6st3/1
title: Multicolor flow cytometry for healthy and uveitides patients

description: Multicolor flow cytometry datasets from 22 fresh peripheral blood patient samples. Please see attached ReadMe file.
DOI: 10.5061/dryad.0sd41/1
title: Female Song Data - Odom Et al. 2014

description: Female song scored for 1,141 oscine passerine species (all oscine passerine species except those within Passerida). The README.rtf file contains information on columns and scoring of female song.
DOI: 10.5061/dryad.18j3d/19
title: c38_TamaulipasProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/2
title: c1_IsthmusOfTehuantepec-ChiapasProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/20
title: c40_SouthesternMexicoProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/21
title: c44_GulfOfCaliforniaProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/22
title: c45_MexicanPlateauProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/23
title: c48_Chiapas-Central AmericaProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/24
title: c49_NevadianProvince

description: Shapefile for SIG
DOI: 10.5061/dryad.18j3d/26
title: c54_SierraMadreDelSur

description: Shapefile for SIG
DOI: 10.5061/dryad.1f217/1
title: rajon_plotkin_prsb_2013_code

description: The folders starting with "Simul_" contain C++ and R code for obtaining and analyzing simulation results. The two remaining folders contain R and Sweave code for making the figures in the manuscript. See the enclosed README.txt file for more information.
DOI: 10.5061/dryad.1pp2c/1
title: Dataset Vézilier et al. 2012 wild mosquitoes

description: qPCR data for the wild-caught mosquitoes experiment described in "The impact of insecticide resistance on Culex pipiens immunity"
DOI: 10.5061/dryad.1pp2c/2
title: Dataset Vézilier et al 2012 Isogenic

description: qPCR data for the isogenic mosquitoes experiment described in Vézilier et al. 2012, "The impact of insecticide resistance on Culex pipiens immunity"
DOI: 10.5061/dryad.215jd/1
title: BIGS_sequences

description: Whole genome sequencing reads for BIGSdb isolates 1-30 (isolates 26,27,28,29 are already published with accession numbers: NC_009839; NC_008787; NC_003912; NC_002163). For isolates 1-3 de novo 454 sequencing was assembled using Newbler (April 2009). For isolates 4-25 and 30 de novo illumnia sequencing was assembled using Velvet 1.0.
DOI: 10.5061/dryad.2m854/1
title: Alignment of 16S rRNA sequences of the 50 most abundant bacterial OTUs associated with the hindgut of carrion beetles (Coleoptera, Silphidae)

description: Genomic DNA was extracted from the hindguts of males and females of eight species of carrin beetles (Coleoptera, Silphidae), respectively, and subjected to bacterial tag-encoded FLX amplicon pyrosequencing. Reads were quality-trimmed and analyzed using QIIME (Caporaso et al. 2010). After a multi-step OTU picking strategy with cdhit (Li & Godzik 2006) and uclust (Edgar 2010), an OTU table was generated describing the occurrence of bacterial phylotypes within the samples, and all OTUs that amounted to less than 0.1% in all of the samples (=2166 OTUs) were excluded from further analysis. Of the remaining OTUs, 23 were removed due to their likely chimeric origin as identified by UCHIME, which left 522 OTUs for the final analysis. For phylogenetic reconstruction, the 50 most abundant OTUs across host taxa were selected, and their representative sequences (picked with –m longest using pick_rep_set.py in QIIME) were trimmed to 300 bp in order to remove low-quality end regions. The resulting sequences as well as closely related sequences identified by BLASTn against the NCBI nr database were aligned to the SILVA SSU database (Pruesse et al. 2007) using the SINA aligner (Pruesse et al. 2012) and imported into ARB (Ludwig et al. 2004). Further representative relatives were included, and the final alignment was exported, and common gaps were removed.
DOI: 10.5061/dryad.2m854/2
title: Alignment of LSU rRNA sequences of fungi associated with the hindgut of carrion beetles (Coleoptera, Silphidae)

description: Genomic DNA was extracted from the hindguts of males and females of eight species of carrin beetles (Coleoptera, Silphidae), respectively, and part of the fungal large subunit ribosomal RNA gene (LSU) was amplified for the different species and sexes, respectively, with primers LS1 and LR5 (Gibson & Hunter 2009). Amplicons were cloned into E. coli using the StrataClone PCR Cloning Kit (Agilent Technologies, USA) according to the manufacturer’s instructions. For Ni. humator, Ni. vespillo, Ni. orbicollis, Ni. puctulatus, Ni. tomentosus, Ne. americana, and O. noveboracense, inserts of 16 clones per species were amplified with the flanking primers M13fwd and M13rev and sequenced bidirectionally with M13fwd and M13rev. For Ni. vespilloides, 53 clones were sequenced unidirectionally with primer M13fwd. All sequences were blasted against the NCBI nr database for taxonomy assignment. Representative sequences were aligned with SINA (Pruesse et al. 2012) and imported into ARB (Ludwig et al. 2004). Closely related fungal reference sequences were selected from the SILVA LSU reference database and included in the alignment.
DOI: 10.5061/dryad.2m854/3
title: Alignment of two mitochondrial and two nuclear markers across eight species of carrion beetles (Coleoptera, Silphidae) and an outgroup taxon (Tribolium castaneum), in nexus format with MrBayes block

description: For an analysis of the evolutionary history of microbial communities across the Silphidae, the host phylogeny was reconstructed based on two mitochondrial (cytochrome oxidase I and II, COI and COII hereafter) and two nuclear genes (28S rRNA gene and carbamoylphosphate synthetase, 28S and CAD hereafter). Most sequences for Nicrophorus spp., Ne. americana, and the outgroup species Tribolium castaneum were obtained from the NCBI database. The dataset was completed by sequencing CAD for Ne. americana, COI/COII for Ni. tomentosus, and CAD, COI, and 28S rRNA for O. noveboracense. COII could not successfully be amplified and sequenced for O. noveboracense, so it was coded as missing data for the analysis. Amplicons were sequenced bidirectionally with (CAD, some COI/II) or without (28S, most COI/II fragments) prior subcloning with the StrataClone PCR Cloning Kit (Agilent Technologies, USA). Curated protein-coding sequences (CAD, COI, and COII) were aligned based on their amino acid translation in Geneious Pro 5.4 (Drummond et al. 2011), and partial 28S rRNA gene sequences were aligned using the SINA aligner (Pruesse et al. 2012). The alignments were concatenated, and phylogenetic relationships were reconstructed using approximately-maximum-likelihood (ML, FastTree) and Bayesian algorithms (MrBayes 3.1.2, Huelsenbeck & Ronquist 2001; Huelsenbeck et al. 2001; Ronquist & Huelsenbeck 2003). For the ML analysis, the general time-reversible (GTR) model was used. For the Bayesian analysis, the dataset was partitioned into the four genes. For the three protein-coding genes, six substitution rates were allowed (GTR model), whereas all substitutions were restricted to the same rate (JC model) for the ribosomal gene. Due to saturation, third codon positions were excluded from the analysis for the two mitochondrial genes (COI and COII). We ran the analysis with four chains and a temperature of 0.2 for 10,000,000 generations (1,000,000 generations for the reduced dataset, see below) and confirmed that the standard deviation of split frequencies was consistently less than 0.01. Trees were sampled every 1000 generations, and a “burnin” of 1000 was used. We computed a 50% majority rule consensus tree with posterior probabilities for every node. We ran all analyses with the complete set of taxa as well as with a reduced set containing only the species analyzed in this study. In both cases, T. castaneum was included and defined as the outgroup to root the tree.
DOI: 10.5061/dryad.2m854/4
title: Alignment of two mitochondrial and two nuclear markers across 30 species of carrion beetles (Coleoptera, Silphidae) and an outgroup taxon (Tribolium castaneum), in nexus format with MrBayes block

description: For an analysis of the evolutionary history of microbial communities across the Silphidae, the host phylogeny was reconstructed based on two mitochondrial (cytochrome oxidase I and II, COI and COII hereafter) and two nuclear genes (28S rRNA gene and carbamoylphosphate synthetase, 28S and CAD hereafter). Most sequences for Nicrophorus spp., Ne. americana, and the outgroup species Tribolium castaneum were obtained from the NCBI database. The dataset was completed by sequencing CAD for Ne. americana, COI/COII for Ni. tomentosus, and CAD, COI, and 28S rRNA for O. noveboracense. COII could not successfully be amplified and sequenced for O. noveboracense, so it was coded as missing data for the analysis. Amplicons were sequenced bidirectionally with (CAD, some COI/II) or without (28S, most COI/II fragments) prior subcloning with the StrataClone PCR Cloning Kit (Agilent Technologies, USA). Curated protein-coding sequences (CAD, COI, and COII) were aligned based on their amino acid translation in Geneious Pro 5.4 (Drummond et al. 2011), and partial 28S rRNA gene sequences were aligned using the SINA aligner (Pruesse et al. 2012). The alignments were concatenated, and phylogenetic relationships were reconstructed using approximately-maximum-likelihood (ML, FastTree) and Bayesian algorithms (MrBayes 3.1.2, Huelsenbeck & Ronquist 2001; Huelsenbeck et al. 2001; Ronquist & Huelsenbeck 2003). For the ML analysis, the general time-reversible (GTR) model was used. For the Bayesian analysis, the dataset was partitioned into the four genes. For the three protein-coding genes, six substitution rates were allowed (GTR model), whereas all substitutions were restricted to the same rate (JC model) for the ribosomal gene. Due to saturation, third codon positions were excluded from the analysis for the two mitochondrial genes (COI and COII). We ran the analysis with four chains and a temperature of 0.2 for 10,000,000 generations (1,000,000 generations for the reduced dataset, see below) and confirmed that the standard deviation of split frequencies was consistently less than 0.01. Trees were sampled every 1000 generations, and a “burnin” of 1000 was used. We computed a 50% majority rule consensus tree with posterior probabilities for every node. We ran all analyses with the complete set of taxa as well as with a reduced set containing only the species analyzed in this study. In both cases, T. castaneum was included and defined as the outgroup to root the tree.
DOI: 10.5061/dryad.2m854/5
title: Quality-trimmed bTEFAP sequences of bacterial 16S rRNA from the hind-guts of eight species of carrion beetles (Coleoptera, Silphidae)

description: DNA from adult hind-guts of 3-6 males and females per species was extracted individually using the SoilMasterTM DNA Extraction Kit (Epicentre, Madison, USA), according to the manufacturer’s instructions (including lysozyme treatment to break up Gram-positive bacterial cells). Identical volumes of the samples for each sex and species, respectively, were pooled for bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). DNA was sent to an external service provider (Research & Testing Laboratories, Lubbock, USA) for bTEFAP with 16S rRNA primers Gray28F and Gray519R (Sun et al. 2011) (Table S1). A sequencing library was generated through one-step PCR with 30 cycles, using a mixture of HotStar and HotStar HiFidelity Taq polymerases (Qiagen). Sequencing extended from Gray28F, using a Roche 454 FLX instrument with Titanium reagents and procedures at Research and Testing Laboratory (RTL, Lubbock, TX, USA, http://www.medicalbiofilm.org/). All low quality reads (quality cut-off = 25) and sequences &lt; 200 bp were removed following sequencing, which left 223,470 sequences for analysis (mean ± SD = 13,967 ± 5,946 per sample). Sample abbreviations are as follows: #SampleID Host species NvspFhind Nicrophorus vespillo NvspMhind Nicrophorus vespillo NhumFhind Nicrophorus humator NhumMhind Nicrophorus humator NvesFhind2 Nicrophorus vespilloides NvesMhind2 Nicrophorus vespilloides NorbF_ED Nicrophorus orbicollis NorbM_ED Nicrophorus orbicollis NpusF_ED Nicrophorus pustulatus NpusM_ED Nicrophorus pustulatus NtomF_ED Nicrophorus tomentosus NtomM_ED Nicrophorus tomentosus NameF_ED Necrophila americana NameM_ED Necrophila americana OnovF_ED Oiceoptoma noveboracense OnovM_ED Oiceoptoma noveboracense
DOI: 10.5061/dryad.2m854/6
title: Mapping file for the quality-trimmed bTEFAP sequences of bacterial 16S rRNA from the hind-guts of eight species of carrion beetles (Coleoptera, Silphidae)

description: Mapping file containing sample IDs, barcode and primer sequences from 454 sequencing, and host species.
DOI: 10.5061/dryad.3rn6323d/1
title: Microsatellite data for all populations in presence-absence format

description: This comma-delimited file contains microsatellite data for all 411 individuals from 18 populations of Phlox amabilis and P. woodhousei that were surveyed with five microsatellite loci.
DOI: 10.5061/dryad.3rn6323d/2
title: Microsatellite data for diploid populations

description: This comma-delimited file contains microsatellite data for 144 diploid individuals from 6 populations of Phlox amabilis and P. woodhousei that were surveyed with five microsatellite loci.
DOI: 10.5061/dryad.4h071/1
title: BolundetalDATA

description: Data file and pedigree file used for analyses.
DOI: 10.5061/dryad.4qq0v/1
title: transcripts.fa
DOI: 10.5061/dryad.4qq0v/2
title: transcripts_over_500_bp
DOI: 10.5061/dryad.4qq0v/3
title: contig-ordering
DOI: 10.5061/dryad.4qq0v/4
title: splicing_events
DOI: 10.5061/dryad.4t7h2/1
title: Red deer endocranial volume measurements

description: Endocranial volume data were collected on 33 red deer (Cervus elaphus) skulls using four different methods: 1) CT scanning and calculating the endocranial volume with OsiriX software, 2) pouring beads into the skull and measuring their volume in a graduated cylinder, 3) taking linear measurements (length, width, and height of the brain case) using calipers, and 4) entering the skull width into an equation developed by Finarelli (2011) for estimating brain volume.
DOI: 10.5061/dryad.4v875/13
title: Appendix 13

description: Posterior distributions and parameters of τ1, τ2, and τ 3 (BPBP model) used in BEAST.
DOI: 10.5061/dryad.4v875/15
title: NEWAppendix 4_morpho_FINAL

description: Phylogenetic tree based on 156 morphological characters