cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.93js1254/1
title: mitochondrial 16S

description: Sequence data from the mitochondrial 16S gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.93js1254/2
title: mitochondrial COI

description: Sequence data from the mitochondrial COI gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.93js1254/3
title: mitochondrial COII

description: Sequence data from the mitochondrial COII gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.b98m6/4
title: Phys_chem_data

description: Physico-chemical data from monitoring overlying water paramaters within a benthic mesocosm; including pH, temp., salinity, nutrients and carbonate system outputs from CO2SYS. See the ReadMe file for column headers and units.
DOI: 10.5061/dryad.dp380n8s/1
title: Koffi_AJB-D-12-00041R1_Supplemental Online Material

description: The file is the Supplemental Online Material of the "AJB Primer Notes & Protocols" manuscript published by Guillaum Koffi et al. This manuscript presents a microsatellite primer set to be used in Santiria trimera, an African tropical tree species. The SOM present: the tested sequences that proved amplifiable with polymorphism described in the article; the tested sequences that did not lead to a readable product; the untested sequences containing a microsatellite motif (more than 400 different sequences).
DOI: 10.5061/dryad.f4586/1
title: SupplementalTable1

description: Supplemental Table 1. Proportional abundances of foraminifera from 58 samples from Newport Member of the Astoria Formation with sample age, DCA site scores used in this paper, and MDS, NMDS and CA site scores for comparison. NMDS analyses were done with three axes and at a stress of 10.28. * denotes which foraminiferal samples were selected to more directly compare to the molluscan data.
DOI: 10.5061/dryad.f4586/2
title: SupplementalTable2

description: Supplemental Table 2. Proportional abundances of molluscs from 18 samples from the Newport Member of the Astoria Formation with sample age, DCA site scores used in this paper, and PCO, NMDS, and CA site scores for comparison. NMDS analyses were done with two axes and at a stress of 8.57.
DOI: 10.5061/dryad.f4586/3
title: SupplementalTable3

description: Supplemental Table 3. Foraminifera species identified in the Newport Member of the Astoria Formation with life habit information and DCA species scores. Life habit assignments are based on modern congenerics and are from Murray (1991, 2006).
DOI: 10.5061/dryad.f4586/4
title: SupplementalTable4

description: Supplemental Table 4. Molluscan species identified in the Newport Member of the Astoria Formation with life habit information and DCA species scores. Trophic group assignment made following Todd (2001). Taxonomy follows Moore (1963). Modern water depth distributions are given where possible and follow Keen (1937).
DOI: 10.5061/dryad.f4586/5
title: SupplementalTable5

description: Supplemental Table 5. Environmental proxy data from 36 samples where all proxies were available, PCA site scores used to examine environmental gradients this paper, and NMDS ordination scores based on the Euclidian distances among sites from proxy data for comparison. * denotes environmental data associated with foraminiferal samples that were selected to more directly compare to the molluscan data.
DOI: 10.5061/dryad.h32m962j/1
title: CONCATENATE_rbcLS_COI_ITS_for_DRYAD

description: The data represent the alignment of rbcLS, COI, and ITS in 29 algae samples.
DOI: 10.5061/dryad.h32m962j/2
title: Concatenate_NJ_tree_Saccharina_rbcLS_COI_ITS

description: The tree shows relationships between morphological forms of Saccharina japonica.
DOI: 10.5061/dryad.kt062/10
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/3
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/4
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/5
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/6
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/7
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/8
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/9
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.m04j9/10
title: Giant Alignment.zip

description: Contains the FASTA format sequence alignments for the IAV sequence data preparation.
DOI: 10.5061/dryad.m04j9/8
title: Figure3.zip

description: Contains (1) the nexus format sequence alignments, (2) the BEAST XML input files and (3) the resulting maximum clade credibility (MCC) tree files for the HA and NA diversity analyses reported in Figure 3.
DOI: 10.5061/dryad.mc4s1/1
title: GEO GSE29133

description: Link to GEO. Primary ATII cells were isolated from lung tissues obtained from thoracic surgery using FACS. We profiled the gene expression of ATII cells from three non-COPD and three COPD patients. This study was approved by the Ethics Committee at Tohoku University School of Medicine and Ishinomaki Red Cross Hospital. All subjects gave informed consent.
DOI: 10.5061/dryad.p9c00/1
title: Amson_Supplementary_tables_methods

description: Methods are described, specimens studied are listed, and bone compactness data are provided in a text file (rtf format).
DOI: 10.5061/dryad.p9c00/2
title: Amson_ESM_compactness_data_matrix

description: Mesquite Nexus file including the bone compactness data and the trees used for the analyses. This is a simple text file that can be read by any text editor, but for full functionality, you should open it in Mesquite.
DOI: 10.5061/dryad.q3s66/1
title: Salgado-Salazar-PlosOne-2013

description: Fused alignment of 6 loci used in this study.
DOI: 10.5061/dryad.s8c2c/1
title: Environmental data
DOI: 10.5061/dryad.s8c2c/2
title: MID#-Sample

description: MID numbers corresponding to the samples. These MID numbers were used in the analysis input files.
DOI: 10.5061/dryad.s8c2c/3
title: R input files

description: R input files for Mantel and Partial Mantel tests
DOI: 10.5061/dryad.s8c2c/4
title: CANOCO input files

description: CANOCO input files for community CCA analysis
DOI: 10.5061/dryad.s8c2c/5
title: GENE-E input files

description: GENE-E input files for heatmaps
DOI: 10.5061/dryad.s8c2c/6
title: Network input files

description: Network input files for network analysis
DOI: 10.5061/dryad.tb50m/1
title: blue cardinalid full mtDNA data set

description: Nexus file with aligned ND2 sequences generated from 166 samples. See ReadMe file to match sample names with species and voucher specimens.
DOI: 10.5061/dryad.tb50m/2
title: blue cardinalid phased MYC data set used in *BEAST analyses

description: Nexus file with final alignment of phased MYC sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.
DOI: 10.5061/dryad.tb50m/3
title: blue cardinalid phased FGBI5 data set used in *BEAST analyses

description: Nexus file with final alignment of phased FGBI5 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.
DOI: 10.5061/dryad.tb50m/4
title: blue cardinalid phased ACO1 data set used in *BEAST analyses

description: Nexus file with final alignment of phased ACO1 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.
DOI: 10.5061/dryad.v55p5/29
title: Part of image archive
DOI: 10.5061/dryad.v55p5/30
title: Part of image archive
DOI: 10.5061/dryad.v55p5/31
title: Part of image archive
DOI: 10.5061/dryad.v55p5/32
title: Part of image archive
DOI: 10.5061/dryad.v55p5/33
title: Part of image archive
DOI: 10.5061/dryad.v55p5/34
title: Part of image archive
DOI: 10.5061/dryad.v55p5/35
title: Part of image archive
DOI: 10.5061/dryad.v55p5/36
title: Part of image archive
DOI: 10.5061/dryad.v55p5/37
title: Part of image archive
DOI: 10.5061/dryad.v55p5/38
title: Part of image archive
DOI: 10.5061/dryad.19856/1
title: Koala ID, sample location, and MHCII (DAB and DBB) genotypes

description: DNA from koala blood and tissue samples were collected from 12 locations across Australia, and MHCII DAB and DBB variants were characterised. A key is provided to define the MHCII variants that each genotype is composed of.
DOI: 10.5061/dryad.1k4gq/1
title: NC field site data

description: Measurement data from the NC field site, including samples from four populations and F1/F2 progeny from Spiterstulen-Mayodan cross. Column headings are explained in ReadMe file.
DOI: 10.5061/dryad.1k4gq/2
title: QTL analysis data from North Carolina field site

description: Marker and trait data for F2 progeny from Spiterstulen-Mayodan cross grown at NC field site.  Data are formatted for reading into R/qtl.  Detailed explanation of column headings is in ReadMe file.
DOI: 10.5061/dryad.1k4gq/3
title: QTL analysis data from Norway field site

description: Marker and trait data for F2 progeny from Spiterstulen-Mayodan cross grown at Norway field site.  Data are formatted for reading into R/qtl.  Detailed explanation of column headings is in ReadMe file.
DOI: 10.5061/dryad.1k4gq/4
title: Scripts for NC field data analysis

description: This file contains the R scripts used for analysis of the NC field data (non-QTL analyses).  Use of the various scripts is described in comment lines within the file.  Some of the scripts require loading the lme4 and Hmisc packages.
DOI: 10.5061/dryad.1kn38/3
title: qPCR Statistical Analyses

description: This file contains normalized qPCR data for both the short-term and long-term gene candidates, as described in the paper, in addition to an R script for analyzing and plotting data.
DOI: 10.5061/dryad.1kn38/4
title: Pilot RNAseq Data

description: This file contains cleaned SOLiD reads (in colorspace) and a table of read counts mapping to the Porites astreoides transcriptome as described in the paper.
DOI: 10.5061/dryad.1m166/1
title: Elnagdy et al data

description: Experimental data collected to test impact of various male-killing bacteria on the fitness of their ladybird hosts.
DOI: 10.5061/dryad.1m2p3/1
title: Single-cell high-content dataset - Golgi reference set

description: Raw features and SVM features (phenotypic features) for each channel of each cell in the Golgi reference set
DOI: 10.5061/dryad.1m2p3/2
title: Single-cell high-content dataset - Kinome and phosphatome set

description: Raw features and SVM features (phenotypic features) for each channel of each cell in the kinome and phosphatome set
DOI: 10.5061/dryad.1mj31/1
title: RAD data for bamboos: phy and fa files
DOI: 10.5061/dryad.1mj31/2
title: RAD data for bamboos: paired reads
DOI: 10.5061/dryad.1p145/1
title: Genetic and spatial data for individuals of Acacia woodmaniorum

description: Genetic data for genotyping at 15 microsatellite loci and spatial data for individuals of Acacia woodmaniorum collected in the field. The data file is provided in a format suitable for use by theGenAlEx (Peakall and Smouse, 2006) computer program and can be opened using Microsofts Excel computer program.Peakall R, Smouse P (2006). GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
DOI: 10.5061/dryad.1qp42/7
title: Nucleosome MNase-seq data aligned to Haloferax genome (BAI file)
DOI: 10.5061/dryad.25gn8/1
title: Microsatellite allele lengths

description: The data file consists of microsatellite allele lengths for 13 loci described in the paper. The data file has individuals organized in rows, with the abbreviation of the district in the first column. The subsequent 26 columns correspond to microsatellite data (two columns per locus). Missing data are coded as zeros.
DOI: 10.5061/dryad.3003f/1
title: All data: Binding of anti-HSA antibody to Array 1

description: Datafile from peptide microarray measuring Human Serum Albumin(HSA) antibody binding to peptides from HSA and variations of these peptides.
DOI: 10.5061/dryad.3003f/2
title: All data: Binding of anti-HSA antibody to Array 2 (Identical to/Repeat of Array 1)

description: Datafile from peptide microarray measuring Human Serum Albumin(HSA) antibody binding to peptides from HSA and variations of these peptides.
DOI: 10.5061/dryad.3gm8c/1
title: LACL1

description: Benthic sample from Lay river on Mainland France that usually displays high diversity of diatom taxa.Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs.After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions.Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
DOI: 10.5061/dryad.3gm8c/2
title: BDNA

description: Benthic sample from Saint-Denis river on French tropical islands in the Indian Ocean (la Réunion) that usually displays low diversity of diatom taxa.Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs.After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions.Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
DOI: 10.5061/dryad.3gm8c/3
title: LACL2

description: Benthic sample from Lay river on Mainland France that usually displays high diversity of diatom taxa.Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs.After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions.Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
DOI: 10.5061/dryad.4j07v/1
title: Table S3. Strain growth phenotypes under five conditions.

description: This table contains the doubling time value of all strains under five conditions. For each strain, replicate measurements are included.
DOI: 10.5061/dryad.4j07v/2
title: Table S4. Growth phenotype of the 7 x 37 BC1 population.

description: This file contains the mean doubling time of parents, hybrid and each BC1 strain under two temperatures.
DOI: 10.5061/dryad.4j07v/3
title: Table S5. Growth phenotype of the 38 x 37 BC1 population.

description: This file contains the mean doubling time of parents, hybrid and BC1 strains under two temperatures.
DOI: 10.5061/dryad.50070/1
title: Species-diagnostic mtDNA assignment data - BanII and BstBI
DOI: 10.5061/dryad.50070/2
title: Microsatelite data - base pair sizes Sceloporus woodi and S. undulatus Ocala FL
DOI: 10.5061/dryad.50070/3
title: Results of Structure analysis - assignment to Sceloporus woodi, Sceloporus undulatus, or Hybrid q-values
DOI: 10.5061/dryad.50070/4
title: Morphology, phenetics and scale counts, with assignments to Sceloporus undulatus, Sceloporus woodi, or hybrid z-scores

description: Sex, scale counts and species assignment data. Followed methods by Jackson 1973 Evolution 27:58-68
DOI: 10.5061/dryad.5ns57/10
title: ND4 data set used in bioinformatic analysis

description: 237 species included
DOI: 10.5061/dryad.5ns57/11
title: rag1 data set used in bioinformatic analysis

description: 1078 species included
DOI: 10.5061/dryad.5ns57/12
title: rag2 data set used in bioinformatic analysis

description: 642 species included
DOI: 10.5061/dryad.5ns57/13
title: rhod data set used in bioinformatic analysis

description: 792 species included
DOI: 10.5061/dryad.5ns57/9
title: ND2 data set used in bioinformatic analysis

description: 1309 species included
DOI: 10.5061/dryad.615tj/1
title: isotope data from: Identifying the African wintering grounds of hybrid flycatchers using a multi–isotope (δ2H, δ13C, δ15N) assignment approach

description: δ2H, δ13C, δ15N isotope data
DOI: 10.5061/dryad.615tj/2
title: isotope data from: Does migration of hybrids contribute to post-zygotic isolation in flycatchers? Veen T, Svedin N, Forsman JT, Hjernquist MB, Qvarnström A, et al. (2007)  Proceedings of the Royal Society B: Biological Sciences 274: 707–712. doi:10.1038/35075000.

description: δ13C, δ15N isotope data
DOI: 10.5061/dryad.865s4/10
title: Kay et al RSPB-2013-2374 worker survival, metapleural blockage experiment, 5-ant groups

description: In January 2012, we tested whether secretions from the metapleural gland (a specialized gland on the thorax of ants that produces antibiotic secretions) influences diet-related immunity. To do this, we reared 12 colonies on either the 1P:3C or 3P:1C diet for 18 days. We then blocked the metapleural gland (using nail polish) on 10 ants per colony, created 5 solitary-ant or 1 worker-group sets, and treated all ants with Metarhizium as described above. We assessed survivorship as above. We used workers sampled from field colonies to show that blocking metapleural glands per se did not affect survivorship (Cox Proportional Hazards: L-R χ2 = 0.087, d.f. = 1, p = 0.762, n=40).
DOI: 10.5061/dryad.865s4/11
title: Kay et al RSPB-2013-2374 mortality in colony level experiment

description: In June 2011 and January 2012, we tested how nutrition affects colony-level immunity, and whether nutritional immunity depended on the presence of larvae in colonies. Given that nutritional feedbacks between workers and larvae influence protein:carbohydrate regulation in ant colonies (Dussutour & Simpson 2009), we predicted that larval presence would enhance nutritional effects on colony immunity.For this test, we used 16 colonies in June 2011 and 10 in January 2012. We assigned colonies (blocked by size as above) to the 1P:3C or 3P:1C diet, and removed larvae from half of the colonies in each treatment; we removed and returned larvae for control colonies. We reared colonies for 21 days. During the rearing period, we challenged colonies with Metarhizium by placing headless ant corpses covered in Metarhizium spores in each nest every 2 days. We used this approach to challenge colonies (rather than direct application to workers of spores in solution, as above) because we wanted to sufficiently challenge colonies to test for differences among diet treatments; spore-covered corpses could be added at regular intervals, whereas periodic solution application to workers would have considerably disturbed colonies. We counted the number of dead ants in each colony (easily distinguishable from headless ant additions) every 2 days, and monitored each for signs of infection.
DOI: 10.5061/dryad.865s4/8
title: Kay et al RSPB-2013-2374 worker survivorship experiment, untreated ants

description: For survival assays, we measured responses of solitary and social ant groupings to treatment with M. anisopliae (strain KVL02-73 collected at this site (Hughes et al. 2004)). After the 18-day diet manipulation, we created 1-ant (solitary ants) or 5-ant (worker groups) sets from each colony. In Jan 2012, we assigned 5 solitary ants and 1 worker group per colony to  a control treatment (not challenged with Metarhizium).
DOI: 10.5061/dryad.865s4/9
title: Kay et al RSPB-2013-2374 worker survival, metapleural blockage experiment, solitary

description: In January 2012, we tested whether secretions from the metapleural gland (a specialized gland on the thorax of ants that produces antibiotic secretions) influences diet-related immunity. To do this, we reared 12 colonies on either the 1P:3C or 3P:1C diet for 18 days. We then blocked the metapleural gland (using nail polish) on 10 ants per colony, created 5 solitary-ant or 1 worker-group sets, and treated all ants with Metarhizium as described above. We assessed survivorship as above. We used workers sampled from field colonies to show that blocking metapleural glands per se did not affect survivorship (Cox Proportional Hazards: L-R χ2 = 0.087, d.f. = 1, p = 0.762, n=40).
DOI: 10.5061/dryad.93js1254/4
title: ANTintron

description: Sequence data from the nuclear ANT intron gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.93js1254/5
title: EF1intron

description: Sequence data from the nuclear EF1 Intron gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.93js1254/6
title: EF1exon122

description: Sequence data from the nuclear EF1 exon gene obtained from samples of Aegla neuquensis. Sequences names are sampleID/population name/major river(abbreviation).
DOI: 10.5061/dryad.b2534/2
title: d_phen_N=488

description: Phenotype data set for Berner et al. (2014) Evolution: Genetic architecture of skeletal evolution in European lake and stream stickleback
DOI: 10.5061/dryad.b2534/3
title: d_gen_N=488_M=2011

description: Genotype data set for Berner et al. (2014) Evolution: Genetic architecture of skeletal evolution in European lake and stream stickleback
DOI: 10.5061/dryad.b2534/4
title: SNP.positions

description: Details on the genome positions of the SNP markers used in Berner et al. (2014) Evolution: Genetic architecture of skeletal evolution in European lake and stream stickleback
DOI: 10.5061/dryad.bk827/1
title: 26S_profile
DOI: 10.5061/dryad.bk827/2
title: 26S_de novo
DOI: 10.5061/dryad.bk827/3
title: 18S_profile
DOI: 10.5061/dryad.bk827/4
title: 18S_de novo
DOI: 10.5061/dryad.bk827/5
title: 18S_26S_conc_strict_profile
DOI: 10.5061/dryad.bk827/6
title: 18S_26S_conc_strict_de novo
DOI: 10.5061/dryad.c9h41/1
title: Floral traits measurements and phylogenetic distance matrices of Bignonieae.

description: Worksheets: 1- traits description; 2- traits measurements (herbarium specimens;) 3- genus phylogenetic distances matrix; 4- species phylogenetic distances matrix.
DOI: 10.5061/dryad.f4586/6
title: SupplementalTable6

description: Supplemental Table 6. Nitrogen isotope values measured from bulk sediment.