cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.34621/3
title: López-Fernández et al Cichlinae1000 chronograms

description: This file contains 1000 Newick-formatted trees of Neotropical cichlids obtained by randomly sampling the posterior distribution of trees obtained from the BEAST search performed using the XML file provided. African, Indian and Madagascan taxa used for cichlid dating in the BEAST run have been pruned for analysis of Neotropical taxa. This file is directly readable in the relevant R packages used in the paper. These chronograms were pruned to generate 1000-tree sets for the clades Geophagini, Cichlasomatini and Heroini as needed for analysis presented in the paper.
DOI: 10.5061/dryad.36md8/1
title: Data from: Genetics of gene expression responses to temperature stress in a sea urchin gene network

description: This archive contains scripts and data files to duplicate all analyses in the accompanying paper. To run, open the file README.R in R, and follow the included instructions. Of particular interest is the script labeled "Run_uantitative_genetics_models_MCMC.R". This scripts implements the hierarchical Bayesian mixed-effect modelwe describe to robustly estimate genetic parameters from the gene expression data.
DOI: 10.5061/dryad.3v39m/1
title: fierer_tallgrass

description: All data pertaining to this study are in this archive.
DOI: 10.5061/dryad.43vg5/1
title: Microsatellite Genotypes

description: A text file containing all the genotypes (11 loci) used
DOI: 10.5061/dryad.4g832/4
title: HUWE1_BEAST_imput
DOI: 10.5061/dryad.4g832/5
title: LSUa_BEAST_imput
DOI: 10.5061/dryad.4g832/6
title: LSUb_ITS2_BEAST_imput
DOI: 10.5061/dryad.4g832/7
title: Pronotum_outlines_Harmonics_297_Mesocarabus
DOI: 10.5061/dryad.51b94/2
title: Richardson 2012_MolEcol_RASY genotype file

description: Genepop formatted genotype file for the wood frog (Rana sylvatica) dataset. File consists of a title line followed by the 15 microsatellite loci names and then full genotypes for each individual within each population (coded corresponding to Supplementary Table 1 from the manuscript).
DOI: 10.5061/dryad.53t4c/1
title: Analysis of high throughput sequencing data from spo11 hypomorphs using ReCombine
DOI: 10.5061/dryad.57vg4/1
title: Short PCR product - all cycles with fusion primers

description: Sequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCGCTGTTATCCCTAGGGTAACT-3').
DOI: 10.5061/dryad.57vg4/2
title: Short PCR product - last 5 cycles with fusion primers

description: Sequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCGCTGTTATCCCTAGGGTAACT-3').
DOI: 10.5061/dryad.6764jd6d/1
title: Data amphibian

description: presence-absence matrix showing the distribution of 268 anuran species among 27 sites in the Brazilian Atlantic Forest.
DOI: 10.5061/dryad.6n9d5/1
title: Data_Ant

description: Species incidence frequency counts for ant samples from five elevations in northeastern Costa Rica (Longino and Colwell 2011)
DOI: 10.5061/dryad.6vk48/2
title: NBR_SNP

description: Genotype matrix for SNPloci in National Bison Range. Individual genotypes are presented as either homozygous (0), heterozygous (1), or missing (NA) at each locus. Loci numbers correspond to those presented in the supplementary tables.
DOI: 10.5061/dryad.6vk48/3
title: RM_MICROS

description: Genotype matrix for microsatellite loci in Ram Mountain. Individual genotypes are presented as either homozygous (0), heterozygous (1), or missing (NA) at each locus. Loci numbers correspond to those presented in the supplementary tables.
DOI: 10.5061/dryad.6vk48/4
title: RM_SNP

description: Genotype matrix for SNP loci in Ram Mountain. Individual genotypes are presented as either homozygous (0), heterozygous (1), or missing (NA) at each locus. Loci numbers correspond to those presented in the supplementary tables.
DOI: 10.5061/dryad.7bn22/1
title: Milano et al 2013 Merluccius merluccius SNP data
DOI: 10.5061/dryad.862h5/1
title: AvianMalariaSequences-Ecuador

description: List of locations, hosts, and sequences of each positive malaria positive found in Ecuador, South America.
DOI: 10.5061/dryad.8cp33/1
title: all data

description: These data were obtained using experimental matings conducted in Plexiglas chambers in the field. Male mating attempts were recorded (Attempt/No attempt), latency to attempt (min), outcome of attempt (Copulation/Rejection), capture success (Yes/No), female resistance (Yes/No), female resistance duration (sec), and male displacement when faced with resistance (Yes/No). Raw measures of body size are also included in reticle units (at 32x mag). Finally, female egg development was recorded as either nongravid or gravid (meaning female clutch visually appeared mature).
DOI: 10.5061/dryad.92kg0/2
title: Simulation code of the evolution of frugivory with frugivore's discrimination

description: This is a Python script to do the simulations of the evolution of frugivory when frugivores disperse only to empty patches. Approximate time of each simulation is 2 hours in a 50x50 lattice.
DOI: 10.5061/dryad.b5k4s/1
title: Table-DRYAD

description: Data file contains a list of cheilostome bryozoan species and their reproductive patterns describing their oogenesis mode, absence and presence of brooding and its mode (placental vs non-placental)
DOI: 10.5061/dryad.b9q73/1
title: Kershawetal_TableS1_SampleInformation

description: Table S1: Details of new Bryde’s whale samples. Sample ID corresponds to original field sample code as managed by the American Museum of Natural History. Taxon was designated as a result of the phylogenetic analysis carried out in the current study. Sampling sites are as follows: BAN, Swatch-of-No-Ground, Bangladesh; BAN (CB), Cox’s Bazaar, Bangladesh; MAL, Maldives; OMA, Oman. Latitude and Longitude are in decimal degrees; N, North; E, East. Body length is given in meters or, if this information wasn’t available, as life history stage. Sex is coded as: M, male; F, female. ND, no data.
DOI: 10.5061/dryad.c3p08/1
title: Counts of all passive and aggressive interactions

description: Counts of all passive and aggressive interactions for all species pairs
DOI: 10.5061/dryad.c3p08/2
title: aggression_analysis

description: Data for the analysis of heterospecific aggression
DOI: 10.5061/dryad.c3p08/3
title: dominance_analysis

description: Data used for the analysis of behavioural dominance
DOI: 10.5061/dryad.c4f03/1
title: OTUclassification

description: Following 454 sequencing of the 16s rDNA region of bacterial communities of 59 samples of attine ants, 993 bacterial OTUs (operational taxonomic units) were identified. The file contains the taxonomic classification of these OTUs. Each OTU is denoted by a number (1-993), the number of reads contributing to the OTU and its taxonomic classification.
DOI: 10.5061/dryad.c4f03/2
title: ReadDistributionAllOTUs

description: Following 454 sequencing of the 16s rDNA region of bacterial communities of 59 samples of attine ants, 993 bacterial OTUs (operational taxonomic units) were identified. The file shows the distribution of sequencing reads for all OTUs across the 59 samples.
DOI: 10.5061/dryad.c4f03/3
title: Alignment

description: Following 454 sequencing of the 16s rDNA region of bacterial communities of 59 samples of attine ants, 35,063 unique sequences were identified after data quality check. The file contains the alignment of these sequences to a SILVA reference alignment (v.102 from www.mothur.org).
DOI: 10.5061/dryad.c4f03/4
title: RepSeqsOTUs

description: Following 454 sequencing of the 16s rDNA region of bacterial communities of 59 samples of attine ants, 993 bacterial OTUs (operational taxonomic units) were identified. The file contains the representative sequences for the 993 OTUs. Each sequence is denoted by a number (1-993) and the original name of the read.
DOI: 10.5061/dryad.c4f03/5
title: mothur commands

description: Commands used for analysis of 454 sequencing datasets NCBI Sequence Read Archive acc.no. SRA050635.2; 16S rDNA bacterial communities of attine ants. Analyses performed in mother following the Schloss SOP (mothur.org)
DOI: 10.5061/dryad.c5097/1
title: Biometry of Cantabrian mountain Grasshoppers

description: Several morphometric measurements of male and female grasshoppers of nine species of Cantabrian Mountains. Climatic data and geographic coordinates are also provided. details can be found in the paper.
DOI: 10.5061/dryad.fb8tk/1
title: Environmental data used in MANOVA

description: Data were collected at each experimental pool to investigate abiotic conditions across roadside and woodland pools.
DOI: 10.5061/dryad.fb8tk/2
title: Survival, growth, and development from embryo to hatchling.

description: These data report the survival from embryo to hatchling in the reciprocal transplant experiment. Additionally, container level averages are provided for embryo size, embryo developmental stage, hatchling size, and hatchling developmental stage. The derived estimates for both logistic growth and logistic developmental rates are also provided.
DOI: 10.5061/dryad.fb8tk/3
title: Survival following acute exposure to road salt.

description: These data report the number of animals stocked into and surviving the acute exposure to road salt experiment.
DOI: 10.5061/dryad.fb8tk/4
title: Survival and malformation of hatchlings following chronic exposure to road salt.

description: These data report the number of animals that survived from embryo to hatchling, and the number of hatchlings with malformations, following chronic exposure to three concentrations of road salt.
DOI: 10.5061/dryad.fb8tk/5
title: Size and developmental stage of hatchlings following chronic exposure to road salt.

description: Size and developmental stage of hatchlings following chronic exposure to road salt.
DOI: 10.5061/dryad.fb8tk/6
title: Fecundity of female wood frogs

description: Each gravid wood frogs in this dataset were collected from the wild, paired with a male, and position to oviposit in an enclosure. The data reported here show the size of each female and the number of eggs laid.
DOI: 10.5061/dryad.g2p5g/1
title: Microsatellite genotypes for Clarkia xantiana
DOI: 10.5061/dryad.g2qp5/16
title: Supplementary File S9_Sipuncula outside Annelida

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/17
title: Supplementary Files S10_MorphologicalMatrix_Likelihood

description: Morphological matrix of the ancestral reconstruction using the likelihood criterion.
DOI: 10.5061/dryad.g2qp5/18
title: Supplementary Files S11_MorphologicalMatrix_Parsimony

description: Morphological matrix of the ancestral reconstruction using the parsimony criterion.
DOI: 10.5061/dryad.g2qp5/19
title: lophotrochozoa_hmmer3.tar

description: Core-ortholog set used for orthology prediction with HaMStR. The set was generated using proteomes from seven primer taxa (Helobdella robusta, Capitella teleta, Lottia gigantea, Schistosoma mansoni, Daphnia pulex, Apis mellifera and Caenorhabditis elegans) and comprises 2,33 orthologous genes.
DOI: 10.5061/dryad.j44hf20s/1
title: Dryad_CSV_rawdata_Alldata_2011_03_18

description: These are the size measurements and counts on the plants and the dates on which they were taken
DOI: 10.5061/dryad.j44hf20s/2
title: Dryad_CSV_data4analysis_Alldata_2011_03_18

description: These are the data as they were analysed: molecular S-genotyping and microsatellite verification and growth measures (based on raw measurements)
DOI: 10.5061/dryad.jj3s0/1
title: Fruit, seed predator, and parasitoid abundance

description: Data were collected in the field from a common garden experiment conducted in 2011, near the town of Molas (Yucatan, México). These data include the number of fruits, seed predators, and parasitoids recorded per plant, used to analyze and describe insect functional responses.  Abbreviated headlines are as follows (from left to right): plant maternal family ("genotype"), fertility treatment (NF = not fertilized, F = fertilized, "treatment"), individual plant sampled ("plant"), number of sampled fruits ("fruit#"), number of fruits with a seed predator or seed predator abundance ("seedpredator#"), and number of attacked fruits by the seed predator with a parasitoid or parasitoid abundance ("parasitoid#"). Data were collected over a two-month period (November-December) in 2011.
DOI: 10.5061/dryad.jj3s0/2
title: seedsrescued_fitness

description: Data were collected in the field from a common garden experiment conducted in 2011, near the town of Molas (Yucatan, México). These data include the number of fruits, seed predators, and seeds rescued by parasitoids from seed predator consumption, used to calculate relative fitness under scenarios of: one trophic level (potential seed number, i.e. fruit#*mean # of seeds per fruit), two trophic levels (potential seed # - seeds consumed by seed predators assuming no seed rescue [seed predator #*mean # of seeds per fruit]), and three trophic levels ([potential seed # - seeds consumed] + seeds rescued by parasitoids). Abbreviated headlines are as follows (from left to right): plant maternal family ("genotype"), fertility treatment (NF = not fertilized, F = fertilized, "treatment"), individual plant sampled ("plant"), number of recorded fruits ("fruit#"), number of fruits with a seed predator (i.e. seed predator abundance, "seedpredator#"), number of seeds consumed by seed predators assuming no seed rescue ("consumedseed#(no rescue)"), and the number of rescued seeds by parasitoids ("rescuedseed#"). Data were collected over a two-month period (November-December) in 2011.
DOI: 10.5061/dryad.jj3s0/3
title: Seeds per fruit per genotype

description: Data were collected in the field from a common garden experiment conducted in 2011, near the town of Molas (Yucatan, México). Data are the mean number of seeds per fruit for each of 14 maternal plant families, shown separately for each of two levels of soil fertilization. These means were used to calculate the potential number of seeds produced per plant (# of fruits recorded*mean # of seeds for the appropriate family-treatment combination). Abbreviated headlines are as follows (from left to right): plant maternal family ("genotype"), mean number of seeds per fruit in fertilized conditions ("#seedsperfruitF"), and mean number of seeds per fruit in unfertilized conditions ("seedsperfruitNF"). Data were collected over a two-month period (November-December) in 2011.
DOI: 10.5061/dryad.mf3gd/14
title: real-model6

description: settings and output for migrate-N model 6
DOI: 10.5061/dryad.mf3gd/15
title: real-model7

description: settings and output for migrate-N model 7
DOI: 10.5061/dryad.mf3gd/16
title: totalfile

description: Input file for Migrate-N model comparison
DOI: 10.5061/dryad.mj3v6/1
title: Concatenated Alignment File

description: This is the alignment file used in phylogenetic analyses.  A character block is provided at the bottom of the file defining the gene and codon datasets within the alignment.
DOI: 10.5061/dryad.mj3v6/2
title: AppendixS1

description: This appendix provides information relating to specimens used in phylogenetic and population genetic analyses.  For each individual listed, field collector numbers and museum voucher numbers are provided as well as general localities.
DOI: 10.5061/dryad.nf7697j6/1
title: Ord_TJ-2011-0215R1_readme
DOI: 10.5061/dryad.nf7697j6/2
title: Ord_TJ-2011-0215R1_accession-numbers
DOI: 10.5061/dryad.nf7697j6/3
title: Ord_TJ-2011-0215R1_ants
DOI: 10.5061/dryad.nh3d2/3
title: Microsatellite_Data_Runemark_et_al.txt

description: Microsatellite data which was used to calculate expected heterozygosity for the populations. Population abbreviations are as in the manuscript.
DOI: 10.5061/dryad.nh3d2/4
title: Patch_size_He_population_level_Runemark_et_al

description: Data on patch size, expected heterozygosity and morphological traits per population.
DOI: 10.5061/dryad.p3878/2
title: Table S2 - Selection gradients

description: Contains the raw data for calculating selection gradients for each generation, as well as the population mean for each generation. Includes a key identifying the variables.
DOI: 10.5061/dryad.p3878/3
title: Supplement - ASReml data and pedigree from Galloway et al 2009

description: Contains the raw data for calculating the results of Galloway et al. (2009, New Phytologist 183: 826–838), which were used extensively in the current paper. This includes the M matrix in Table S1, the G matrices in Table S3-S4, and the various matrices used here and originally reported in Galloway et al. (2009). Includes a key identifying the variables.
DOI: 10.5061/dryad.q5570/2
title: COI alignment
DOI: 10.5061/dryad.rd304/4
title: Tyler_et_al_triad_data

description: Detail of the individuals used in mating trials, male success in sperm storage and siring offspring, the number of eggs laid, and the percentage of nymphs that hatched.
DOI: 10.5061/dryad.rt01f/1
title: Varying FML
DOI: 10.5061/dryad.rt01f/2
title: Coordination Knockout Experiments
DOI: 10.5061/dryad.v3144/2
title: IGR

description: fasta file of noncoding intergenic region (IGR) sequences
DOI: 10.5061/dryad.v7370/1
title: female.data.dryad.final

description: Phenotypic data for quantitative genetic analysis of female liability for extra-pair reproduction
DOI: 10.5061/dryad.v7370/2
title: female.Ainv.final

description: Inverse A matrix for quantitative genetic analysis of female liability for extra-pair reproduction
DOI: 10.5061/dryad.v7370/3
title: male.data.dryad.final

description: Phenotypic data for quantitative genetic analysis of male liability for within-pair paternity success
DOI: 10.5061/dryad.v7370/4
title: male.Ainv.final

description: Inverse A matrix for quantitative genetic analysis of male liability for within-pair paternity success
DOI: 10.5061/dryad.v7370/5
title: male.female.data.dryad.final

description: Phenotypic data for joint quantitative genetic analysis of female liability for extra-pair reproduction and male liability for within-pair paternity success
DOI: 10.5061/dryad.v7370/6
title: male.female.Ainv.final

description: Inverse A matrix for joint quantitative genetic analysis of female liability for extra-pair reproduction and male liability for within-pair paternity success
DOI: 10.5061/dryad.023s6/1
title: Dryad_Sanders_etal_MolEcol_2013

description: DIRECTORY: ./example_scriptsThese are generalized example scripts that should help you to recreate thesesanalyses using your own data. They are just guides, and will not run withoutsome (limited) modification. There are four files.1) ./example_scripts/final_parameters.txt	QIIME parameters file2) ./example_scripts/qiime_script_example.sh	bash shell script for Qiime 1.4.0 analysis pipeline3) ./example_scripts/bdiv_summary_example.sh	bash shell script for summarizing jacknifed beta diversity results using the	QIIME tree_compare.py script.4) ./example_scripts/bdiv_rugs.py	simple python script for creating SVG images to visualize the results from	the beta diversity sensitivity analysis performed in (3) above.
DOI: 10.5061/dryad.023s6/2
title: figures

description: DIRECTORY: ./figuresThis directory contains R code used to generate the alpha rarefaction curves(./figures/alpha), beta diversity box plot comparisons (./figures/box_plots),mantel tests (./figures/mantel), and principle coordinate plots (./figures/PCoA)used in the paper.
DOI: 10.5061/dryad.023s6/3
title: ochman_original_data

description: DIRECTORY: ./ochman_original_data./ochman_original_data contains the original sequencedata as supplied by Prof. Howard Ochman (Personal Communication, July 12, 2013).This is in the format of a combined fasta file (primer_trimed.fasta) and asample mapping file (sample_map.txt). Additionally, the folder contains a simplepython script used to convert the sequence file to Qiime post-split_libraries.pyformat; the result of this script is ./ochman_example_analysis/seqs.fna.
DOI: 10.5061/dryad.023s6/4
title: ochman_example_analysis

description: DIRECTORY: ./ochman_example_analysisThis contains example scripts and analysis similar to the Cephalotes exampleabove. In addition to example output for four OTU widths(./ochman_example_analysis/93, 95, 97, 99), example scripts for analysis at twolevels of rarefaction (1000 and 15000 sequences/sample), metadata mapping(./ochman_example_analysis/ochman_split_map.txt), results from the betadiversity sensitivity analysis(./ochman_example_analysis/bdiv_sensitivity_grids), and example host trees(./ochman_example_analysis/ape_phylogram_ILS_relabeled_furcated.tre,ape_cladogram_relabeled_relabeled_furcated.tre), there are several additionalfiles. ape_sample_locations.txt are Lat/Lon values estimated from Figure 1 ofOchman et al 2010, used to estimate geographic distances for the partial Manteltests.
DOI: 10.5061/dryad.023s6/5
title: cephalotes_example_analysis

description: DIRECTORY: ./cephalotes_example_analysisThis contains the denoised sequence data used in the analysis of Cephalotes antgut microbiota (./cephalotes_example_analysis/seqs.fna), metadata mapping info(cephalotes_map.txt), host trees with individual samples (ceph_guide_tree.tre)and colonies (ceph_species_tree_SpeciesColony.tre) as leaves, and an exampleanalysis script (cephalotes_script_example). It also contains example outputfrom four different OTU clustering thresholds (./cephalotes_example_analysis/93,95, 97, and 99), results from the beta diversity sensitivity analysis(./cephalotes_example_analysis/bdiv_sensitivity_grids), and the results of thecompute_core_microbiome.py script in Qiime 1.6.0(./cephalotes_example_analysis/core_otus).
DOI: 10.5061/dryad.12c6b/1
title: Frequency dependence

description: Fitness data for frequency dependence determination obtained after competition experiments at two initial volumetric ratio (1:9 and 9:1)
DOI: 10.5061/dryad.12c6b/2
title: Generic Fitness

description: Fitness values obtained after direct competition experiments (1:1 ratio)
DOI: 10.5061/dryad.12c6b/3
title: Growth in L Supernatant

description: Values of OD after growth of S in L supernatant
DOI: 10.5061/dryad.12c6b/4
title: Metabolic Flux Analysis

description: Measurements of metabolic flux
DOI: 10.5061/dryad.12c6b/5
title: Stable.Coexistence

description: Measurement of co-existence between clones after co-cultures
DOI: 10.5061/dryad.12ck0.2/4.1
title: Data of the laboratory experiment

description: This dataset contains the following variables: MHCIIb gene expression values, physiological parameters (weight, length and Fulton condition index), Minisatellites groups (either long or short based on the number of repeat), family and temperature.
DOI: 10.5061/dryad.12ck0.2/5.1
title: 454 raw MHC2b sequences

description: This file contains raw 454 sequences of the MHC2b gene.
DOI: 10.5061/dryad.12ck0.2/6
title: MHC_alleles_sequences

description: Sequences of the 29 MHC2b alleles described in the study. These sequences were aligned with muscle, using MEGAv5 and are in the fasta format.
DOI: 10.5061/dryad.1786p/3
title: Data report, A Canadian Healthy Oceans Network Ecosystem Function Project, EF-03

description: Data report file in MS Word
DOI: 10.5061/dryad.2f1k3/9
title: Anas crecca PCK1 alleles.fas

description: FASTA file containing 100 resolved alleles from intron 8 of the phosphoenolpyruvate carboxykinase (PCK1) gene sampled from 50 Common (Green-winged) Teal (Anas crecca). The first 50 alleles were sampled from Eurasia, and the next 50 were sampled from North America.