cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2m3v4/3
title: Nucleotide sequence data used for mitogenome analyses

description: This zip file contains 26 nucleotide sequence alignment files in fasta format, representing protein-coding genes spanning the mitogenome of 24 salmonid species and 3 related outgroup species. Each of 13 clearly named protein-coding genes is represented by two files, representing codon position 1 and 2, which are stated as P1 and P2. This data was combined in a time calibrated BEAST analysis, dating major divergence times in salmonid evolution and in a range of other phylogenetic analyses described in the paper (see Figures S21-S26 and Figure S28 in the electronic supplementary material).
DOI: 10.5061/dryad.2m3v4/4
title: Protein sequence data for mitogenome analyses

description: This zip file contains 13 protein sequence alignment files in fasta format, representing 13 proteins coded in the mitogenomes of 24 salmonid species and 3 related outgroup species. This data was used in a range of other phylogenetic analyses described in the paper (see Figures S21-S26 and Figure S28 in the electronic supplementary material).
DOI: 10.5061/dryad.38v59/3
title: Models

description: Coeffiecients and summary statistics for all models and all subsets of the data.
DOI: 10.5061/dryad.3k88t/1
title: All relevant datasets are included in the zip file

description: The zip file contains 5 files: 1) Precipitation dependence data 2) Carbon fluxes 3) Volumetric water content vs carbon fluxes 4) Volumetric water content vs photosystem II efficiency and 5) Recovery: carbon fluxes at wet and rewetted treatment. See for detailed file description in the ReadMe file
DOI: 10.5061/dryad.4vk85.2/1.1
title: FieldData

description: Data collected from natural populations of S. latifolia, as described in the paper. Column names refer to the following information: Site (sampling location); SS (sexual system - monoecious or dioecious); Mopen (number of open male flowers per inflorescence); Mtotal (total number of male flowers per inflorescence); MVL (leaf mid-vein length for the leaf subtending the inflorescence, cm); Petal (petal width, cm).
DOI: 10.5061/dryad.4vk85.2/2.1
title: ArrayDataPlantFlowerSize

description: Plant size and flowering data for the plants used in the mating arrays. Column labels refer to: Array (the array number; nb. these do not correspond with the labels in Fig. 2, see data file description for the cumulative siring data set for a key); Treatment (high vs. low nutrient resource additions); Plant (code name for the genotype included in the array); Sex (H - hermaphrodite, M - male); MVL (leaf mid vein length for the leaf subtending the inflorescence); Nflowers (total number of flowers produced per inflorescence); Year (year the genotype had been sampled from natural populations).
DOI: 10.5061/dryad.4vk85.2/3.1
title: Cumulative_floweringBYsiring

description: The data set contains the data used to generate Figure 1, and to analyse the association between flower production and siring success. Column names are as follows: Treatment (levels of the nutrient resource addition treatment - High and Low); Array (label for the mating array); CumFlws (cumulative number of male flowers produced by the focal male per day for the duration the array was set up); CumSire (cumulative number of seeds sired by the focal male over the course of the array).
DOI: 10.5061/dryad.4vk85.2/4.1
title: PropSiring

description: These data correspond with those presented in Fig. 2. Column labels: Array (label for array); Trt (level of the nutrient resource addition treatment - High vs. Low); Mflws (the total number of flowers produced by the focal male in the array); Hflws (the total number of hermaphrodite flowers produced by all hermaphrodites per array); Totflws (the sum of Mflws and Hflws); Mprog(the total number of seeds sired by the focal male per array); TotProg (the total number of seeds genotyped per array).
DOI: 10.5061/dryad.4vk85.2/5.1
title: SiringCountData

description: These data were used to evaluate overall differences in the number of seeds sired by males vs. hermaphrodites. Column labels are: Array (label for the mating array); Treatment (level of the nutrient resource addition treatment - High vs. Low); SexofSire (plant sex (male or hermaphrodite) to correspond with the data in the next column; Progeny (the number of seeds sired by the focal male, or the average number of seeds sired by the hermaphrodites in each array); Fflowers (the total number of female flowers available for siring opportunities in each array).
DOI: 10.5061/dryad.4vk85.2/6.1
title: MomType

description: These data were used to conduct an analysis of deviance between the identity of the father (male vs. hermaphrodite) and identity of the mother (female vs. hermaphrodite) using a contingency table approach. The column labels are: Treatment (levels of the nutrient resource addition treatment - High vs. Low); Father (the sex of the father that sired the seeds genotyped in the paternity analysis - M for male, H for hermaphrodite); Mother (the sex of the mother that produced the seeds genotyped for paternity analysis); Count (the total number of seeds screened for each treatment and sex combination).
DOI: 10.5061/dryad.54722/2
title: Spigler_etalEVOL_DRYAD_HermGenotypes

description: Genotypic data for male fertile individuals (males and hermaphrodites)
DOI: 10.5061/dryad.6h822/16
title: Figure_5_Tank11(A27A)

description: Paternity analysis for Tank 11 (A27A). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/17
title: Figure_5_Tank12(A29B)

description: Paternity analysis for Tank 12 (A29B). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/18
title: Figure_5_Tank13(A210B)

description: Paternity analysis for Tank 13 (A210B). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/19
title: Figure_5_Tank14(B16B)

description: Paternity analysis for Tank 14 (B16B). Study Day indicates the day on which each embryo analysed was spawned. The first 3 rows in the table are the parent fish and below that are the 20 selected offspring. The microsatellite loci used for analysis are listed along the top of the table and corresponding allelles are detailed below.
DOI: 10.5061/dryad.6h822/5
title: Figure_4_24hr Viability

description: Embryo viability assessed at 24 hours post fertilisation, across the 10 day study periods of Experiment I and II (as indicated in table)
DOI: 10.5061/dryad.6nr73/1
title: Raw sequencing data

description: Raw and processed high-throughput sequencing data, including both ribosome profiling and mRNA-seq experiments, for 0-2 hour Drosophila embryos and S2 cells. Reduced genomic alignments are additionally supplied as Wiggle files. See sample description at GEO for additional information.
DOI: 10.5061/dryad.6s444/1
title: Crown rust trait-measurements

description: The excel file contains P. coronata life history measurements of all 348 individual inoculated plants.  The data for each individual replicate is shown in a single row.  A description of the column names can be found in the second excel sheet.
DOI: 10.5061/dryad.6vd8p/1
title: AdjacencyAnalysisAndExample

description: This zip file contains a MATLAB .m file with a function to convert a zone map to all of the adjacency statistics in my paper.  A subdirectory contains all the material I used to do the Anolis example in the paper.  Thanks to Manuel Leal for supplying the photo.
DOI: 10.5061/dryad.77tm4/1
title: Carnivore Postcranial Morphology Data Samuels et al. 2013
DOI: 10.5061/dryad.78p90/1
title: script_chloro

description: UNIX script used for plastid reconstruction. The following tools must be installed: VELVET, PLAST, COPE, OBITOOLS
DOI: 10.5061/dryad.78p90/2
title: alignments

description: Plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only. Alignments were performed using MAFFT and cleaned using Gblocks. Files are in fasta format.
DOI: 10.5061/dryad.78p90/3
title: trees

description: Trees obtained with plastid DNA, mitochondrial DNA and nuclear ribosomic regions alignments, including the complete sequences or the non-intronic transcribed sequences only, using RAxML and MrBayes. Files are in NEXUS format.
DOI: 10.5061/dryad.bh051/1
title: CHONe_MB-18_NevesB_data

description: Substrate types and biotopes identified from the video analysis, with corresponding geographic coordinates, bathymetry, backscatter and slope values. A classification criteria based on the last three variables was used to produce substrate and biotope maps as seen in the article. The table includes a list of codes and the corresponding biotopes. Finally, the results from the accuracy analysis are also presented. A Canadian Healthy Oceans Network (CHONe) Marine Biodiversity Project, MB-18.
DOI: 10.5061/dryad.cb098/10
title: 59_Sciomyzidae_Shoreline2_constrained
DOI: 10.5061/dryad.cb098/11
title: 59_Sciomyzidae_Slug_constrained
DOI: 10.5061/dryad.cb098/12
title: 59_Sciomyzidae_Succineid_constrained
DOI: 10.5061/dryad.cb098/13
title: 59_Sciomyzidae_Terrestrial_constrained
DOI: 10.5061/dryad.cb098/7
title: 59_Sciomyzidae_Aquatic1_constrained
DOI: 10.5061/dryad.cb098/8
title: 59_Sciomyzidae_Aquatic2_constrained
DOI: 10.5061/dryad.cb098/9
title: 59_Sciomyzidae_Shoreline_constrained
DOI: 10.5061/dryad.cc47h/1
title: Island Biogeography Supporting Information
DOI: 10.5061/dryad.d4s1k/1
title: Focal male tapping behaviour by line (original plus validation data combined)

description: SAS file with line, temperature and binary response.
DOI: 10.5061/dryad.d4s1k/2
title: Data for blind validation

description: Tapping behaviour in subset of 8 lines. SAS data file contains line, temperature, block (0 = original, 1 = validation) and binary tapping response.
DOI: 10.5061/dryad.d4s1k/3
title: Inter-lab validation of startle response

description: File contains startle response data from Mackay et al. (2012) compared to startle response data collected in the present study, for a subset of 3 high and 3 low lines. For "block", (0 = Mackay et al. (2012) data, 1 = data collected for validation).
DOI: 10.5061/dryad.d4s1k/4
title: Line means for multiple regression

description: Line means from this study and from DGRP database used in multiple regression analysis.
DOI: 10.5061/dryad.f058c/2
title: CytB_reference

description: Cyt b reference generated as consensus sequences from the Leiopelma hochstetteri Cyt b sequences available in GenBank
DOI: 10.5061/dryad.gh317/3
title: Nasutitermes and outgroup ITS2 sequences

description: Internal Transcribed Spacers 2 (ITS2) sequences for Nasutitermes samples and two outgroups. Genbank Accession Numbers and putative species are indicated.
DOI: 10.5061/dryad.gh317/4
title: Total combined alignment (COII/16S/ITS2)

description: Total combined alignment (1784bp) for COII, 16rDNA and ITS2 sequences. Samples with at least one missing locus were discarded from the analyses, resulting in datasets of 64 Nasutitermes and two outgroup samples.
DOI: 10.5061/dryad.gh317/5
title: Morphological dataset

description: Taxonomic notes on the identification of the Nasutitermes species
DOI: 10.5061/dryad.gs3r8/1
title: elevation

description: The elevation of the field sites across New Zealand
DOI: 10.5061/dryad.gs3r8/2
title: field.data

description: This spreadsheet records the dependent variables (abundance and process) across trophic levels (plants, herbivore and parasitoid) across field sites in New Zealand.
DOI: 10.5061/dryad.gs3r8/3
title: interaction.nature

description: This speadsheet records the effect sizes of generalized mixed effect models. Effects were classified by calculating the difference between the sum of individual effect sizes and the interactive effect sizes, with positive values representing synergistic effects and negative values representing antagonistic effects.
DOI: 10.5061/dryad.gs3r8/4
title: slopes

description: This spreadsheed records slope values of the relationship between the biotic measure and either fragment area or distance from edge, as calculated at each location ranging from the warmest (Auckland; 36°S) to the coolest (Banks Peninsula; 43°S).
DOI: 10.5061/dryad.j5r33/1
title: am nat dryad ctdata
DOI: 10.5061/dryad.k41qk/11
title: 8_RpL27A_R_110713
DOI: 10.5061/dryad.kh7sc/1
title: Sample IDs

description: Individual IDs for 621 samples; columns give individual number; species (P. alba (AL), hybrid (HY), P. tremula (TR), or family sample (FA)); mom or progeny (MO, PR, NA); family ID; individual ID.
DOI: 10.5061/dryad.kh7sc/2
title: Genotype likelihoods, 32 912 SNPs

description: Genotype likelihoods in vcf file format for the full data set including all 621 individuals.
DOI: 10.5061/dryad.kh7sc/3
title: Genotype likelihoods, 64 649 SNPs

description: Genotype likelihoods in vcf file format for the reduced data set without seedlings, 137 individuals.
DOI: 10.5061/dryad.kh7sc/4
title: Input file, 11 979 SNPs

description: Formatted input file to run ancestry model.
DOI: 10.5061/dryad.kh7sc/5
title: Input file, 5 226 SNPs

description: Formatted input file to run ancestry model.
DOI: 10.5061/dryad.kh7sc/6
title: Additional input file, 11 979 SNPs

description: Initial q values to run ancestry model.
DOI: 10.5061/dryad.kh7sc/7
title: Additional input file, 5 226 SNPs

description: Initial q values to run ancestry model.
DOI: 10.5061/dryad.m3752/1
title: Zélé et al. Full dataset Proc. R. Soc. B 2014
DOI: 10.5061/dryad.pr1jf/1
title: qPCR data (Tabatadze et al., 2014)
DOI: 10.5061/dryad.qt3j5/4
title: Vignette for "resamplediversity" package.

description: User friendly, hands-on, example based tutorial to the data and functions provided in resamplediversity package. Includes a walk-through through the analyses presented in the manuscript.
DOI: 10.5061/dryad.rf161/2
title: Appendix 2: Cytb, 173 taxa

description: A nexus file having mitochondrial cytochrome b gene sequences (1140 bp) from 169 house mice (Mus musculus) and four from outgroup taxa. This nexus file was used for the maximum likelihood, Neighbor Net and BEAST analyses.
DOI: 10.5061/dryad.rf161/3
title: Appendix 3: Cr, without DOM

description: A nexus file having mitochondrial control region sequences from 213 house mice (Mus musculus) and one from outgroup taxon Mus macedonicus being modified for alignment. This nexus file was created by removing sequences genotyped for Mus musculus domesticus from the input file of Appendix 1 and used to construct Neighbor-Net networks.
DOI: 10.5061/dryad.rf161/4
title: Appendix 4: Concatenated, 30 taxa

description: A nexus file having concatenated mitochondrial DNA haplotypes (control region and cytochrome b gene) representing the four major haplogroups of Mus musculus and a outgroup taxon M. macedonicus. This nexus file was used to construct phylogenetic trees using the maximum likelihood, maximum parsimonious and neighbor joining methods.
DOI: 10.5061/dryad.rf161/5
title: Appendix 5: Cr, MUS

description: A nexus file having mitochondrial control region sequences from 132 house mice (Mus musculus) belong to the subspecies group Mus musculus musculus (MUS). This nexus file was used to construct Neighbor-Net networks.
DOI: 10.5061/dryad.rf161/6
title: Appendix 6: Cr, DOM

description: A nexus file having mitochondrial control region sequences from 561 house mice (Mus musculus) belong to the subspecies group Mus musculus domesticus (DOM). This nexus file was used to construct Neighbor-Net networks.
DOI: 10.5061/dryad.rf161/7
title: Appendix 7: cytb, CAS

description: A nexus file having mitochondrial cytochrome b gene sequences from 38 house mice (Mus musculus) belong to the subspecies group Mus musculus castaneus (CAS). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.
DOI: 10.5061/dryad.rf161/8
title: Appendix 8: Cytb, DOM

description: A nexus file having mitochondrial cytochrome b gene sequences from 88 house mice (Mus musculus) belong to the subspecies group Mus musculus musculus (MUS). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.
DOI: 10.5061/dryad.rf161/9
title: Appendix 9: Cytb, Mus

description: A nexus file having mitochondrial cytochrome b gene sequences from 53 house mice (Mus musculus) belong to the subspecies group Mus musculus domesticus (DOM). This nexus file was used for construction of Neighbor-Net networks and further analyses using DnaSP v5 and Arlequin version 3.5.
DOI: 10.5061/dryad.rt950/1
title: ChoiceExperimentData_7mar13
DOI: 10.5061/dryad.s8v7q/1
title: script

description: python script to establish the genomic position of candidate SNPs based on the gene predictions for the European eel genome
DOI: 10.5061/dryad.s8v7q/2
title: Raw_SNP_Data

description: RAW SNP data on Genepop format for all individuals
DOI: 10.5061/dryad.s903c/1
title: Giese et al 2013_suppl_temperature and precipitation IMGERS 1982-2003

description: Monthly mean values of precipitation and temperature 1982-2003
DOI: 10.5061/dryad.vq587/14
title: Appendix_C_Intersection_All

description: List of correspondences found in common between all included ontologies.
DOI: 10.5061/dryad.1hk59/1
title: ILOE for DRYAD

description: Initial loss of equilibrium of X. birchmanni, X. malinche and hybrids in thermal tolerance trials. Data collected at the CICHAZ field station in Mexico.
DOI: 10.5061/dryad.1vv8v/3
title: age3

description: results of third life table experiment
DOI: 10.5061/dryad.1vv8v/4
title: age4

description: results of hybrid experiment, also labelled experiment 4
DOI: 10.5061/dryad.270b7/1
title: Cat_mtDNA

description: Fasta File containing mtDNA sequences of wild- and domestic cats
DOI: 10.5061/dryad.276j5/1
title: Predator and prey survival data

description: This file describes the initial density and survival (and mortality) of a shared prey (copepods) and predators (Buenoa), how many predators were added (initial + replaced dead individuals), and the experimental treatments which manipulated the size class of both predator species. Method details are given in the main manuscript.
DOI: 10.5061/dryad.2jv25/1
title: allometry

description: This is the matlab m-file containing the code used for the simulations of our paper.
DOI: 10.5061/dryad.2jv25/2
title: run_allometry

description: This is matlab m-file contains a code that runs the main simulation code ("allometry.m", contained in a separate file) with different parameter values.
DOI: 10.5061/dryad.2k55t/4
title: Pathology and Path_Load

description: Please see README file for description of all data files.
DOI: 10.5061/dryad.2k55t/5
title: Tolerance and Cytokine Data

description: Please see README file for description of all data files.
DOI: 10.5061/dryad.2m5c4/1
title: Effects of amides on insect feeding choice and fungal growth
DOI: 10.5061/dryad.32b88/4
title: meadow.tar.gz

description: Raw RAD sequencing data in fastq format for Meadow population.
DOI: 10.5061/dryad.35321/15
title: Ctenotus phylogenetic tree

description: Ctenotus phylogenetic tree used in community phylogenetic analyses
DOI: 10.5061/dryad.38v59/1
title: Raw data

description: Raw data and species averages of all measurements made.
DOI: 10.5061/dryad.4qg5k/1
title: Genotype and habitat type data
DOI: 10.5061/dryad.5j56v/1
title: Analysis code

description: R code for analysis conducted in our study
DOI: 10.5061/dryad.5j56v/2
title: Data file for birds

description: Comma separated text file of the bird data
DOI: 10.5061/dryad.5j56v/3
title: Data file for mammals

description: Comma separated text file of mammal data
DOI: 10.5061/dryad.63qp0/1
title: Antimicrobial response

description: Data from lytic zone assay, where inhibition zones created by heamolymph was measured in (mm). PlateNumber describes the individual agar plate.
DOI: 10.5061/dryad.63qp0/2
title: Early Surival both sexes

description: Data describing 72 h survival in males and females
DOI: 10.5061/dryad.63qp0/3
title: Binary egg success

description: Data describing whether females laid and egg or not
DOI: 10.5061/dryad.63qp0/4
title: EggtoAdult viability data

description: Number of eggs that hatch out to adults.
DOI: 10.5061/dryad.63qp0/5
title: Female fecundity data

description: Total number of eggs for each female, including individuals laying no eggs.
DOI: 10.5061/dryad.63qp0/6
title: Sperm competition

description: Including data on sperm competition and on sperm competition success as binary data (yes or no).
DOI: 10.5061/dryad.63qp0/7
title: SurvivalFemales

description: Long-term survival females (used in proportional hazard model).
DOI: 10.5061/dryad.63qp0/8
title: Survival Males

description: Long-term survival males (used in proportional hazard model).
DOI: 10.5061/dryad.63qp0/9
title: Correlations Fitness Immunity

description: Overall means (n=5) of fitness and immune data used for supporting material.
DOI: 10.5061/dryad.7194t/1
title: Mauritius genotypes

description: This data file contains the microsatellite (STR) genotypes for 35 Pristionchus pacificus strains collected from Mauritius Island.
DOI: 10.5061/dryad.77j02/1
title: Microsatellite genotypes (from 7 nuSSR) of 849 Milicia individuals

description: Microsatellite genotypes (from 7 nuSSR) of 849 Milicia individuals sampled in almost the entire range of this African genus
DOI: 10.5061/dryad.7c7q0/3
title: lcb 27

description: fasta files for genes in LCB27
DOI: 10.5061/dryad.7c7q0/4
title: lcb 156

description: fasta files for genes in LCB 156
DOI: 10.5061/dryad.7d2g2/6
title: Supplementary Table 4

description: Supplementary Table 4
DOI: 10.5061/dryad.7q341/1
title: SeedPredationDataForSouthHills

description: The data represent for 87 trees their mean cone traits and the percent of seeds eaten from a sample of cones by each of 3 seed predators. I used JMP software to estimate tree means.
DOI: 10.5061/dryad.7q341/2
title: MothPredationLittleRockyMtns

description: The file contains data on the percent of seeds eaten by moths and the mean cone traits of 34 lodgepole pine trees.
DOI: 10.5061/dryad.7vs2c/1
title: Machado_et_al_ND2alignment

description: Fasta format DNA sequence alignment of 180 cichlid ND2 gene sequences
DOI: 10.5061/dryad.9c568/6
title: flu H1 Beast data file
DOI: 10.5061/dryad.cp6gg/1
title: Lycodon Alignment File

description: This is the nexus alignment file used for phylogenetic analyses. The character set for each of the three genes is at the bottom of the file.
DOI: 10.5061/dryad.f4211.1
title: Data from: Pulsing hydrology determines top-down control of basal resources in a tropical river-floodplain ecosystem
DOI: 10.5061/dryad.f4211.2
title: Data from: Pulsing hydrology determines top-down control of basal resources in a tropical river-floodplain ecosystem
DOI: 10.5061/dryad.f4211.2/1.1
title: 3-Cinaruco AFDM Sand Exp

description: samples and calculations for particulate organic matter accumulations in sand during fish exclosure/enclosure experiments
DOI: 10.5061/dryad.f4211.2/2.1
title: 1-Cinaruco AFDM Tiles Exp

description: samples and calculations for particulate organic matter accumulations on tiles during fish exclosure/enclosure experiments
DOI: 10.5061/dryad.f4211.2/3.1
title: 2-Cinaruco CHLA Tiles Exp

description: samples and calculations for chlorophyll a accumulations on tiles during fish exclosure/enclosure experiments