cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n1506/3
title: Climate data

description: Climate data for 13 Berthelot's pipits populations, used to make geographical and ecological distance matrices.
DOI: 10.5061/dryad.pg2kb/1
title: Table_S4_large_table_of_expression_data_-_checked_-_final
DOI: 10.5061/dryad.r0056/63
title: plots_microbes_MapDamage

description: Map Damage profile of bacteria
DOI: 10.5061/dryad.r634p/3
title: Sample description - (age,sex,location,time of capture)

description: Sample number codes = Location - year of capture - month of capture - trap number, S(M) = mainland, SI=Secretary Island
DOI: 10.5061/dryad.r634p/4
title: Sample data

description: The age, sex, date of capture and location of capture is given for the stoat samples used in the study.
DOI: 10.5061/dryad.rm5v5/52
title: Supplemental Figure 52: Traits significantly correlated with a distinct cluster of genes.

description: Supplemental Figure 52: Traits significantly correlated with a distinct cluster of genes. A histogram of the traits significantly correlated with the group of genes forming a distinct cluster marked by “*” in Figure 5A. Classes of traits are denoted by color (“DEV”, black; “ENZ”, yellow; “MET”, blue; “MOR”, magenta; and “SED”, orange). Note the preponderance of traits of the “DEV” class concerning leaf development phenotypes. The most abundant trait correlating with this group of genes of a class other than “DEV” is glucose levels (“MET”) in the fruit pericarp.
DOI: 10.5061/dryad.rm5v5/53
title: Supplemental Table 1: Summary of cv. M82 vs. S. pennellii SNP/indel distribution for RNAseq and RESCAN analyses.

description: Supplemental Table 1: Summary of cv. M82 vs. S. pennellii SNP/indel distribution for RNAseq and RESCAN analyses. Provided are the summary statistics for base pairs and genes between SNPs and indels derived from RNA-Seq, RESCAN, and combined RNA-Seq and RESCAN datasets.
DOI: 10.5061/dryad.rm5v5/54
title: Supplemental Table 2: Chromosomal positions of the S. pennellii introgression boundaries for all 76 ILs.

description: Supplemental Table 2: Chromosomal positions of the S. pennellii introgression boundaries for all 76 ILs. Boundaries were deduced by combining RNAseq and RESCAN analyses and are represented graphically in Supplemental Figure 1 online. The last cv. M82 polymorphism position preceding the introgression (“M82 (last)”) and the first cv. M82 polymorphism following (“M82 (first)”) are provided, in addition to the first (“PEN (first)”) and last (“PEN (last)”) S. pennellii polymorphism. “-1” indicates that the S. pennellii genotype extends to the beginning or end of a chromosome.
DOI: 10.5061/dryad.rm5v5/55
title: Supplemental Dataset 1: Polymorphism database.

description: Supplemental Dataset 1: Polymorphism database. A set of flat-file databases of polymorphisms identified between cv. M82 and S. pennellii using RNA-Seq (SNPs/indels) or RESCAN (SNPs) sequence data. Column titles: (1) chromosome, (2) position, (3) reference base, (4) SNP base, (5) genotype SNP/indel in which SNP/indel was identified, (6) insert position.
DOI: 10.5061/dryad.rm5v5/56
title: Supplemental Dataset 2: Unique IL combinations define bins.

description: Supplemental Dataset 2: Unique IL combinations define bins. Provided is a binary matrix showing the combinations of ILs (top row) that define unique bins (left column). “1” indicates that the given bin is defined by the presence of the corresponding IL, whereas “0” indicates that the bin is defined by the absence of the IL.
DOI: 10.5061/dryad.rm5v5/57
title: Supplemental Dataset 3: Genes per bin.

description: Supplemental Dataset 3: Genes per bin. A list of the number of annotated genes present within each bin.
DOI: 10.5061/dryad.rm5v5/58
title: Supplemental Dataset 4: Annotation of genes present in each bin.

description: Supplemental Dataset 4: Annotation of genes present in each bin. Provided is a list of annotated genes in the tomato genome. For each gene, the chromosome (“chromosome”) and bin (“bin”) within which it resides is given. “Subset.bin” indicates the specific sub-bin (if the bin is non-contiguous) within which the gene resides. “Gap” indicates that the gene is not represented by any IL. Also shown is the beginning (“begin”) and ending (“end”) coordinates of the gene in the tomato genome, the linear order of genes in the genome (“sort.order”), a description of the gene (“Human.readable.description”), the best BLAST Arabidopsis hit (“Subject.ID”, “AGI”), a description of the best Arabidopsis hit (“Description”), as well as BLAST hit statistics (“Score,” “E.Value,”, and “Identities”).
DOI: 10.5061/dryad.rm5v5/59
title: Supplemental Dataset 5: Modeled trait values and significance values.

description: Supplemental Dataset 5: Modeled trait values and significance values. For each trait studied, the model-fitted deviation for each IL from the estimated cv. M82 value is given (under the column “Estimate”). Additionally, standard error (“SE”), t-values (“t.value), and p-values (“p.value”) for the estimates are provided.
DOI: 10.5061/dryad.rm5v5/60
title: Supplemental Dataset 6: Graphs of fitted values for each trait, their distributions, and significance values.

description: Supplemental Dataset 6: Graphs of fitted values for each trait, their distributions, and significance values. Provided is a graph corresponding to each trait. The x-axis of each graph is IL identity, and the y-axis represents modeled trait values for each IL. Modeled trait values are expressed as deviation from cv. M82, which by definition is set to “0” and represented by a bold horizontal line. For each IL, its modeled value is accompanied by standard error bars. Additionally, p-values representing significant deviation from cv. M82 are denoted by color. Red, p &lt; 0.0001; orange, 0.0001 ≤ p &lt; 0.001; yellow, 0.001 ≤ p &lt; 0.01; green, 0.01 ≤ p &lt; 0.05. Trait values represent transformed values, as indicated in Supplemental Dataset 7 online.
DOI: 10.5061/dryad.sd845/1
title: Ibrev_Ifulva

description: Data provided here are diploid Single nucleotide polymorphisms (SNPs) used in the analysis to determine population structure and hybridization for two iris species. In addition, to the SNP calls, collection information is also provided.
DOI: 10.5061/dryad.t72kr/1
title: DRYAD DATA FARM V WILD

description: Raw data supporting all analyses and Figures 1 to 4
DOI: 10.5061/dryad.t838p/1
title: data

description: Contains (1) genotypic data for each of the five contact zones and (2) data used to estimate divergence history for (a) S. basiliscus / S. lewisi in IMa2 and (b) all other lineage-pairs in dadi
DOI: 10.5061/dryad.v8q6c/1
title: HetSim function for Simulating Offspring Heterozygosity
DOI: 10.5061/dryad.v8q6c/2
title: White-Browed Sparrow Weaver Genotypes
DOI: 10.5061/dryad.v8q6c/3
title: R Code for Analysis of Paired Data by Randomisation Test
DOI: 10.5061/dryad.v8q6c/4
title: Mean Heterozygosity by Locus Data for HetSim function
DOI: 10.5061/dryad.0179t/1
title: Contig data for modern-1

description: FASTA file of all contigs considered during the metagenomic analysis of sample modern-1. Use with 'BLAST assignment data for modern-1' in MEGAN v4.70.
DOI: 10.5061/dryad.0179t/2
title: Contig data for modern-2

description: FASTA file of all contigs considered during the metagenomic analysis of sample modern-2. Use with 'BLAST assignment data for modern-2' in MEGAN v4.70.
DOI: 10.5061/dryad.0179t/22
title: BLAST assignment data for modern-1

description: Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-1. Use with 'Contig data for modern-1' in MEGAN v4.70. See attached readme file for column headers.
DOI: 10.5061/dryad.0179t/23
title: BLAST assignment data for modern-2

description: Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample modern-2. Use with 'Contig data for modern-2' in MEGAN v4.70. See attached readme file for column headers.
DOI: 10.5061/dryad.0179t/24
title: BLAST assignment data for museum-1

description: Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-1. Use with 'Contig data for museum-1' in MEGAN v4.70. See attached readme file for column headers.
DOI: 10.5061/dryad.0179t/25
title: BLAST assignment data for museum-2

description: Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample museum-2. Use with 'Contig data for museum-2' in MEGAN v4.70. See attached readme file for column headers.
DOI: 10.5061/dryad.0179t/26
title: BLAST assignment data for ancient-1

description: Unfiltered BLAST assignment file of contigs identified during the metagenomic analysis of sample ancient-1. Use with 'Contig data for ancient-1' in MEGAN v4.70. See attached readme file for column headers.
DOI: 10.5061/dryad.0179t/3
title: Contig data for museum-1

description: FASTA file of all contigs considered during the metagenomic analysis of sample museum-1. Use with 'BLAST assignment data for museum-1' in MEGAN v4.70.
DOI: 10.5061/dryad.0179t/4
title: Contig data for museum-2

description: FASTA file of all contigs considered during the metagenomic analysis of sample museum-2. Use with 'BLAST assignment data for museum-2' in MEGAN v4.70.
DOI: 10.5061/dryad.0179t/5
title: Contig data for ancient-1

description: FASTA file of all contigs considered during the metagenomic analysis of sample ancient-1. Use with 'BLAST assignment data for ancient-1' in MEGAN v4.70.
DOI: 10.5061/dryad.0179t/6
title: Contig data for ancient-2

description: FASTA file of all contigs considered during the metagenomic analysis of sample ancient-2. Use with 'BLAST assignment data for ancient-2' in MEGAN v4.70.
DOI: 10.5061/dryad.08m6t/1
title: Coordinates
DOI: 10.5061/dryad.08m6t/4
title: Individual_genotypes
DOI: 10.5061/dryad.23j8n/2
title: Funnel plots of ego-depletion data

description: Funnel plots for ego-depletion effect sizes from our meta-analysis (see Hagger, M. S., Wood, C., Stiff, C., & Chatzisarantis, N. L. D. (2010). Ego depletion and the strength model of self-control: A meta-analysis. Psychological Bulletin, 136(4), 495-525. doi: 10.1037/a0019486). There are two separate plots: Standard - this is the effect size (standardized mean difference, Cohen's d) against the standard error of each study; Precision - this is the effect size plotted against the study precision (1/standard error). For  description see: Duval, S., & Tweedie, R. L. (2000). Trim and fill: A simple funnel plot based method of testing and adjusting for publication bias in meta-analysis. Biometrics, 56, 455–463. Files are MS word format.
DOI: 10.5061/dryad.23j8n/3
title: Small-study effect and bias reports

description: Word files from CMA summarising bias statistics for the ego-depletion data from our meta-analysis (Hagger, M. S., Wood, C., Stiff, C., & Chatzisarantis, N. L. D. (2010). Ego depletion and the strength model of self-control: A meta-analysis. Psychological Bulletin, 136(4), 495-525. doi: 10.1037/a0019486). There are separate files for the overall effect and each separate set of data for depleting task domain (see our meta-analysis or main ego-depletion data file in this data set for description of depleting task domains). Each file contains a description of the funnel plot, the Classic fail-safe N, Begg and Mazumdar's Rank Correlation Test, Egger's Test of the Intercept, Duval and Tweedie's Trim and Fill, and an important caveat about the interpretation of bias, which we also outline in our commentary: Hagger, M. S. (2014). Avoiding the ‘déjà-variable’ phenomenon: Social psychology needs more guides to constructs. Frontiers in Psychology, 5, 52. doi: 10.3389/fpsyg.2014.00052. It is also important to note that almost all of these data files indicate substantial heterogeniety, so may question the validity of the use of these statistics to make definitive decisions on small-study or publication bias.
DOI: 10.5061/dryad.23j8n/4
title: Ego depletion meta-analysis full raw data files

description: Full raw data sets for our meta-analysis (Hagger, M. S., Wood, C., Stiff, C., & Chatzisarantis, N. L. D. (2010). Ego depletion and the strength model of self-control: A meta-analysis. Psychological Bulletin, 136(4), 495-525. doi: 10.1037/a0019486) including data for all moderator variables, additional dependent variable, and tests of additional 'Strength Model' hypotheses. See accompanying readme for details.
DOI: 10.5061/dryad.2mg29/2
title: English version of the study questionnaire

description: Copy of the English version of the study questionnaire filled by patients.
DOI: 10.5061/dryad.2mg29/5
title: DiPCare dataset

description: Source file in text format, tab delimited
DOI: 10.5061/dryad.2mg29/6
title: DiPCare Stata do file

description: Contains all the commands to run the entire analysis for the publication on forgoing healthcare.
DOI: 10.5061/dryad.2mg29/7
title: DiPCare stata log file

description: Contains the Stata statistical report exported after running the do file and the description of all variables used in the analysis.
DOI: 10.5061/dryad.504636cd/15
title: ALN3

description: Alignment based on ALN2.fas with the deletion of the E gene and the region of NS3 identified as a possible recombinant fragment.
DOI: 10.5061/dryad.504636cd/16
title: E_161

description: Alignment compiled from the 161 longest E-sequences from Tick-borne encephalitis virus species available in Genbank (1033 to 1491 nt in length) endowed with sampling dates (from 1931 to 2008) retrieved in January 2011.
DOI: 10.5061/dryad.504636cd/17
title: Beast_inference1_C

description: Beast xml file used in Beast inference 1 for the C-gene.
DOI: 10.5061/dryad.504636cd/18
title: Beast_inference1_E

description: Beast xml file used in Beast inference 1 for the E-gene.
DOI: 10.5061/dryad.504636cd/19
title: Beast_inference1_NS1

description: Beast xml file used in Beast inference 1 for the NS1-gene.
DOI: 10.5061/dryad.504636cd/20
title: Beast_inference1_NS2A

description: Beast xml file used in Beast inference 1 for the NS2A-gene.
DOI: 10.5061/dryad.504636cd/21
title: Beast_inference1_NS2B

description: Beast xml file used in Beast inference 1 for the NS2B-gene.
DOI: 10.5061/dryad.504636cd/22
title: Beast_inference1_NS3

description: Beast xml file used in Beast inference 1 for the NS3-gene.
DOI: 10.5061/dryad.504636cd/23
title: Beast_inference1_NS4A

description: Beast xml file used in Beast inference 1 for the NS4A-gene.
DOI: 10.5061/dryad.51696/1
title: Raw_coordinates

description: X and Y coordinates of each landmark
DOI: 10.5061/dryad.522cm/5
title: Tree2: Less_constained_chronogram

description: Chronogram of alternative phylogenetic tree used to corroborate results from fully constrained tree. See journal article for details.
DOI: 10.5061/dryad.522cm/6
title: Supplementary tables: Linear model results based on unconstrained tree

description: Same as tables presented in the full publication except these analyses are based on the less constrained phylogenetic tree.
DOI: 10.5061/dryad.522cm/7
title: Supplementary Figure: Probability (P-value) curves for reproductive strategy factor in PGLS models from Table 1 with varying degrees of freedom

description: Probability (P-value) curves for reproductive strategy factor in PGLS models from Table 1 with varying degrees of freedom. As the true phylogeny is unknowable, all statistical estimates are best guesses. Because there are five clades with the benthic guarding reproductive strategy, the most conservative choice for degrees of freedom would be d.f. = 4, shown as a dotted vertical line; d.f. = 4 is certain to be an underestimate of the true degrees of freedom as benthic guarding is common among freshwater fishes suggesting many character state changes along the full acanthomorph tree. An upper bound to degrees of freedom might be set by adjusting for polytomies (following Purvis and Garland 1993; Garland and Díaz-Uriarte 1999) as shown as vertical dotted lines. Finally the phylogenetic degrees of freedom determined by GEE is shown as a solid vertical line. The true degrees of freedom for our PGLS analyses are likely to fall somewhere within this bounded range for degrees of freedom.
DOI: 10.5061/dryad.522cm/8
title: Full reference list for sources of original Fst estimates

description: Bibliography corresponding to entries in the "Database of Fst data for benthic fishes"
DOI: 10.5061/dryad.6cn04/1
title: data for dryad

description: Data file includes individual genotypes at the mapped loci in the first tab and individual phenotypes for the floral traits in the second tab. Individuals are in the same order in each tab.
DOI: 10.5061/dryad.6hs29/3
title: Input and output files BEASTdating

description: Beauty input files of the two runs of BEAST and resulting combined tree
DOI: 10.5061/dryad.71nv1/1
title: Gene details for Cerapachys biroi chemosensory genes, UGTs and CYPs

description: Tab 1 contains details of all manually annotated chemosensory genes from Cerapachys biroi. Tab 2 contains all sequenced ant UDP glycosyltransferases, organised by clade (as described in supplemental data of Oxley et al.). Tab 3 contains all sequenced ant cytochrome P450 genes, organised by clade (as described in supplemental data of Oxley et al.).
DOI: 10.5061/dryad.71nv1/2
title: MUSCLE alignment of insect UDP glycosyltransferases

description: Alignment of UDP glycosyltransferases containing conserved signature motif (Mackenzie et al. Pharmacogenetics (1997) 7,255-269). Sequence includes motif and 100 amino acids up- and downstream. Details can be found in supplemental data: UDP Glycosyltransferases (UGTs) in Oxley et al.
DOI: 10.5061/dryad.71nv1/3
title: NEXUS file of maximum likelihood tree for insect UGTs

description: Maximum likelihood tree was constructed using Garli 2.0 (Poisson+G+I evolutionary model; best tree of five runs chosen), using the alignments provided in this repository.
DOI: 10.5061/dryad.71nv1/4
title: MUSCLE alignment of insect cytochrome P450 genes

description: MUSCLE alignment of all sequenced ant CYPs and representative dipteran, hymenopteran and lepidopteran CYPs. All genes were manually checked for presence of conserved motifs (Nelson, D. Methods Mol. Biol. (2006) 320, 1-10). The alignment was further edited to remove the hypervariable non-conserved N-terminal up to (but not including) the N-terminal anchor sequence, as well as the region between the C-helix and I-helix. Further details can be found in Supplemental Data: Cytochrome P450 Genes of Oxley et al.
DOI: 10.5061/dryad.71nv1/5
title: NEXUS file of maximum likelihood tree for insect CYPs

description: Maximum likelihood phylogeny was constructed using Garli 2.0 (Poisson+G+I evolutionary model; best tree of two runs chosen) using protein alignment provided in this repository. For further details see Supplemental Data: Cytochrome p450 Genes in Oxley et al.
DOI: 10.5061/dryad.7f297/1
title: Data and computer code

description: Contains readme file, comma separated data files, and R codes for analyses reported in the paper.
DOI: 10.5061/dryad.7kp90/1
title: msdirTBS_SB.tar

description: Compress file containing the c++ code modified from Hudson's mstbs to include coalescent simulations with seed banks. When extracting the content of the tar file, you find 3 pdfs with description of ms and mstbs options (msdoc, msTBSdoc), and one for the seed bank extension (msTBS_SBdoc).
DOI: 10.5061/dryad.7kp90/2
title: seed bank - notebook

description: Mathematica notebook to compute the main analytical results in the article (Zivkovic and Tellier).
DOI: 10.5061/dryad.8h350/1
title: PRC_archive
DOI: 10.5061/dryad.8vn5d/1
title: Ovule number, pollen viability, and sex ratio by cross type

description: The data are counts of ovule number, pollen viability, and sex ratio (by family) for 15 different crosses between Silene latifolia and Silene diclinis used to investigate the genetic basis of Haldane's rule between these two flowering plant species.  Cross type is as in Table 1 of the paper these data are associated with.
DOI: 10.5061/dryad.dp78p/1
title: Altitudinal cumulative distribution of malaria cases (Debre Zeit)

description: Yearly cumulative distribution of malaria cases (P. falciparum) with altitude for each year from 1994 to 2004 for the study region in Ethiopia.  Cases are aggregated for the transmission season as explained in the Supplement of the paper.
DOI: 10.5061/dryad.dp78p/2
title: Altitudinal cumulative distribution of malaria cases (Antioquia)

description: Yearly cumulative distribution of malaria cases (P. falciparum) with altitude from 1990 to 2006 for the transmission season in the study region of Antioquia, Colombia. See section on "epidemiological data' in Supplementary Information of the paper.
DOI: 10.5061/dryad.dp78p/3
title: Time series of mean temperatures (Ethiopia)

description: Monthly time series of mean temperatures.  Four meteorological stations in Ethiopia situated in close proximity to the study areas were selected. Monthly averages of daily minimum and maximum temperature data for the stations in Ethiopia were obtained from the Ethiopian National Meteorological Agency (NMA).The four climate stations in Ethiopia (namely Addis Ababa (Bole), Addis Ababa (Obs), Adama and Debre Zeit) were selected based on their proximity to Debre Zeit town (within 50 km) and their high correlation with Debre Zeit’s station readings. Missing data were filled by the lagged 5 year climatology (average for the same month in the preceding five years). Data for the four stations were then averaged for the two variables, and monthly mean temperature were generated by taking the average of the monthly minimum and maximum temperature.
DOI: 10.5061/dryad.dp78p/4
title: Total malaria cases during transmission season (Debre Zeit)

description: The reported (falciparum and vivax) malaria cases aggregated for the study region and for the epidemic season for each year between 1980 and 2004.
DOI: 10.5061/dryad.f5t56/1
title: Population survey and genotypic classification of Melanoides tuberculata snails in Israel

description: See "Materials and Methods" in the published paper.
DOI: 10.5061/dryad.f789n/1
title: Microsatellite data collected from L. marinus and L. smithsonianus

description: Data collected from 12 microsatellite loci : Hg16, Hg18, Hg25 (Crochet et al. 2003), K16 (Tirard et al. 2002), LarZAP12, LarZAP19, LarSNX24, LarZAP26 (Gregory and Quinn 2006), Rbg13, Rbg18, Rbg27 and Rbg29 (Given et al. 2002).  Museum accession numbers and collection locality are included.
DOI: 10.5061/dryad.fk444/1
title: Stockley et al Phil Trans 2013

description: Excel data file. Sheet 1: Data from experiment to investigate if urinary protein output of female house mice predicts total number of aggressive or submissive behaviours recorded during a 30 min encounter with an unfamiliar female conspecific (Section 5(c) and Table 1 in paper). Sheet 2: Data on urinary protein output, paternity outcomes of mating and reproductive success for female house mice captured from four large semi-natural enclosures (Sections 5(b) & (c), Figure 1 in paper).
DOI: 10.5061/dryad.fv94v/1
title: Global island dataset

description: The data are described in detail in SI Materials and Methods in the supporting information of the paper (Weigelt et al. 2013, PNAS) and in the ReadMe file.
DOI: 10.5061/dryad.k60kb/1
title: Concatenated sequences

description: Concatenated sequences of 63 individuals of two genes mitochondrial ND2 and RC
DOI: 10.5061/dryad.k60kb/2
title: Arlequin plus matrix

description: Infile for software Arlequin, contain sequences of haplotype, Distance Matrix generated in PAUP
DOI: 10.5061/dryad.p083b/1
title: Zebra capture data

description: Individual, season, parasite and genetic data from zebras captured in Etosha National Park, Nambia.
DOI: 10.5061/dryad.qc580/1
title: Supplement_genera and species

description: Matrixes