cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.443g2/2
title: pedigree

description: File contains the pedigree (ID of individual, sire, dam) associated with the datafile
DOI: 10.5061/dryad.4b815/1
title: Pacific Zooplankton

description: Samples of zooplankton from the ballast water of ships arriving to Pacific Canada
DOI: 10.5061/dryad.4b815/2
title: Atlantic Zooplankton

description: Samples of zooplankton from the ballast water of ships arriving to Atlantic Canada
DOI: 10.5061/dryad.650cn/4
title: Onset of metamorph feeding

description: This file contains information on the rate at which Agalychnis callidryas metamorphs initiated feeding upon emergence from mesocosms where they were reared at different larval densities.  Data include size at emergence and the time required for tail resorption and the production of the first fecal pellet.  The file also contains the number of insect heads egested in each fecal pellet for varying periods of time post-metamorphosis.
DOI: 10.5061/dryad.650cn/5
title: Froglet Mean Retention Time

description: This file contains data for mean retention time for Agalychnis callidryas froglets reared at different larval densities.  The data include froglet ID, tank number, rearing density, and froglet size.  We maintained froglets on a fruit fly (Drosophila sp.) diet and inserted a single meal of leafhopper insects (Cicadellidae) followed by additional fruit flies.  We used the leafhoppers as a diet marker and counted the number of leafhopper and fruit fly heads egested each day to determine mean diet retention time.
DOI: 10.5061/dryad.650cn/6
title: Froglet metabolic rates

description: This file contains metabolic rates of Agalychnis callidryas froglets that were reared as larvae in mesocosms at different densities.  The data include metamorph ID, tank (mesocosm) number, body size, and rates of oxygen consumption.
DOI: 10.5061/dryad.6rg87/1
title: Reyer_et_al_Fig-3

description: This file provides the data base for Table 1 and Fig. 3, namely the absolute numbers and proportions of 7 genotypes (LL, LLR, LLRR, LR, LRR, RR and uncertain) sampled in natural ponds at 5 developmental stages (eggs, tadpoles, metamorphs, juveniles and adults).
DOI: 10.5061/dryad.6rg87/2
title: Reyer_et_al_Fig-4

description: This file presents the numbers of gamete types produced by the crossed LR, LLR and LRR males and females. Data base for Table 2 and Fig. 4.
DOI: 10.5061/dryad.6rg87/3
title: Reyer_er_al_Fig-5

description: Fertilization success and hatching rates of offspring from different crossing types. Data base for Table 3 and Fig. 5.
DOI: 10.5061/dryad.76k4j/1
title: Genotypic data for the ten validation populations of coho salmon

description: Genotypes for 91 novel SNPs from ten populations of coho salmon from the West Coast of North America in standard GENEPOP format (two-digit). Data were generated using TaqMan assays (Applied Biosystems) and a Fluidigm EP1.
DOI: 10.5061/dryad.76k4j/2
title: Tree file for Supplemental Figure 1

description: NEXML tree file for the ten validation populations genotyped with the 91 SNP markers described in the paper.
DOI: 10.5061/dryad.8g0v3/1
title: Details of characteristics of the 29 virtual species

description: * Method to generate the virtual species - A virtual species is a group of occurrences, which are selected by an ellipsoid in a 3D environmental space. In this case, we did a principal component analysis (PCA) on the 19 bioclimatic variables, and used the first 3 principal components to create a 3D environmental space. The x, y, z axes are the first three principal components. All of these processes were implemented via Niche Analyst (http://biodiversity-informatics-training.org/software-data-sources/nichea/). Using Niche Analyst, we created two groups of virtual species with different volumes. The volume of ‘big’ group was 143.69, and the ‘small’ one was 2.14. Each group had 7 virtual species with the same centroid and same directions of semi-axes. * The distribution maps of virtual species - Once niches were created, we explored their projections into geographic space, and created different scenarios of abiotic factors in relation to dispersal. Specifically, we created a scenario in which all suitable conditions were accessible (“Hutchinson’s Dream,” or HD), one in which distributional limitation was driven by dispersal/access exclusively and not by abiotic conditions (“Wallace’s Dream,” or WD), and one in which both abiotic and dispersal considerations act to limit distributions in different areas (“Classic BAM,” or CB).
DOI: 10.5061/dryad.b56n0/1
title: Calo_µsats

description: Raw micosatellite genotypes
DOI: 10.5061/dryad.b56n0/2
title: Calo_IMa2

description: Input file of IMa2 analysis
DOI: 10.5061/dryad.c5m42.2/1.2
title: codon_all_genes

description: Nexus file for the codon-based analyses.
DOI: 10.5061/dryad.c5m42.2/10.2
title: SI_Fig2
DOI: 10.5061/dryad.c5m42.2/2.2
title: Dryad_BASEML_results_summary

description: Outputs from BASEML runs (part of the PAML package).
DOI: 10.5061/dryad.c5m42.2/3.2
title: Dryad_CODEML_results_summary

description: Outputs from CODEML (part of the PAML package).
DOI: 10.5061/dryad.c5m42.2/4.2
title: nucleotide_all_data

description: Nexus file for nucleotide-model based analyes (including a block of recoded indels).
DOI: 10.5061/dryad.c5m42.2/5.2
title: SI_Appendix1

description: PAMLparser, a Python script for organizing PAML outputs (from both CODEML and BASEML) and reformated them in tab-delimited files.
DOI: 10.5061/dryad.c5m42.2/6.2
title: SI_Fig1

description: Phylogeny of the gapCp "retained clones." Includes gapC, gapCp "short," and gapCp "long" sequences.
DOI: 10.5061/dryad.c5m42.2/7.2
title: SI_Table1

description: Primers used in amplification and sequencing.
DOI: 10.5061/dryad.c5m42.2/8.2
title: SI_Table2

description: Voucher table and sequence data for the broad gapCp and gapC family sequences.
DOI: 10.5061/dryad.c5m42.2/9.2
title: SI Table 3
DOI: 10.5061/dryad.dn7b8/1
title: BrownBear_historicalsamples_microsats
DOI: 10.5061/dryad.dn7b8/2
title: Alignment_Scandinavian_Brown_Bear_Modern_and_Historical_Samples

description: Sequence alignment including individuals from the historical and modern sample set. Code names with "SC" and "MB" correspond to the historical and modern samples respectively.
DOI: 10.5061/dryad.f5124/1
title: Geographic Distances Between Study Sites

description: This file contains a matrix of geographic distances between study sites in kilometers.
DOI: 10.5061/dryad.f5124/2
title: Helminth Species And Host Characteristics

description: This file contains the identity and number of helminths discovered in each individual host as well as the demographic characteristics of each host.
DOI: 10.5061/dryad.f5124/3
title: Study Site Nonspatial Explanatory Variables

description: This file contains landcover and climatic data relevant to each study site.
DOI: 10.5061/dryad.fd3m4/1
title: Doyle_etal_SystBiol_SuppInfo
DOI: 10.5061/dryad.fd3m4/2
title: repMissPatterns

description: A python script to find the pattern of missing data in an empirical data set and replicate it in simulated datasets.
DOI: 10.5061/dryad.hs593/1
title: cro_functional_annotation.final.txt
DOI: 10.5061/dryad.hs593/2
title: cro_scaffolds.min_200bp
DOI: 10.5061/dryad.hs593/3
title: cro_scaffolds.min_1000bp
DOI: 10.5061/dryad.hs593/4
title: cro_std_maker_anno.final.cds
DOI: 10.5061/dryad.hs593/5
title: cro_std_maker_anno.final
DOI: 10.5061/dryad.hs593/6
title: cro_std_maker_anno.final.pep
DOI: 10.5061/dryad.hs593/7
title: cro_std_maker_anno.final.transcripts
DOI: 10.5061/dryad.jk2jm/1
title: cooperation under time pressure vs time delay in India

description: This sheet contains the data of the 1558 subjects who participated in our experiment investigating the effect of promoting intuition versus deliberation on cooperative decision-making in India.
DOI: 10.5061/dryad.jk2jm/2
title: Data India 20150409

description: This file contains the data of the 450 participants of our experiment.
DOI: 10.5061/dryad.k1m1g/1
title: All_individuals_Grapholita_molesta_cox1

description: Mitochondrial cox1 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/2
title: All_individuals_Grapholita_molesta_cox2

description: Mitochondrial cox2 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/3
title: All_individuals_Grapholita_molesta_atp8

description: Mitochondrial atp8 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/4
title: All_individuals_Grapholita_molesta_atp6

description: Mitochondrial atp6 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/5
title: All_individuals_Grapholita_molesta_nad5

description: Mitochondrial nad5 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/6
title: All_individuals_Grapholita_molesta_nad1

description: Mitochondrial nad1 gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/7
title: All_individuals_Grapholita_molesta_lrna

description: Mitochondrial lrna gene sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/8
title: All_individuals_Grapholita_molesta_all_genes

description: Combined mitochondrial genes of cox1, cox2, atp8, atp6, nad5, nad1 and lrna sequences of the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.kb110/1
title: Moult files for Dryad

description: 12 separate files in a zip folder: BREEDERF/M = comparing breeders v non-breeders for each sex. Clutchegg = analyses of clutch size and egg mass. DISP = dispersal distance analysis. FIVEF/M comparing age of partner in first year birds. hatched_in_wytham= natal effects data file. RES-IMM = comparison of residents v immigrants. SEX_DIFFERENCES = comparison of moult extent by sex. YRMALES/FEMALES = analysis of young ringed by moult extent for both sexes. All headings self-explanatory. PC1_F is our synthetic measure of moult extent.
DOI: 10.5061/dryad.n1mn9/1
title: Pavey_2015_eel_genotypes

description: Genepop file containing all raw genotypes for 16 sampling sites (8 freshwater 8 saltwater) for 42,424 SNPs
DOI: 10.5061/dryad.n1mn9/2
title: 325 contigs that contain the 331 important SNPs

description: 325 contigs that contain the 331 important SNPs most important for distinguishing freshwater and brackish/saltwater ecotypes of American eel
DOI: 10.5061/dryad.pd790/1
title: Questionnaire_Round1

description: Questionnaire sent to the expert panel for the 1st round of the Delphi process.
DOI: 10.5061/dryad.q8q44/1
title: FireLoggersCombinedData_DRYAD

description: Data for time and temperature during fire from 48 burned sampling plots divided evenly among two burn-units, along with data for subsequent vegetation response in each of the 48 plots. Time and temperature data were measured by K-type thermocouples attached to HOBO dataloggers. A subset of plots (N=18) include time and temperature measurements in vertical profile taken: 1) 1 cm aboveground, 2) at the soil surface, 3) 1 cm belowground, 4) 2 cm belowground, and 5) 4 cm belowground.
DOI: 10.5061/dryad.q8q44/2
title: SeedBankProjectData_Dryad

description: We examined effects of increased-fuels on post-fire germination from the soil seed-bank in a concurrent experiment at the same study site. This file contains identification information (species, family, growth habit, functional group) for the plants that germinated from seed-bank samples.
DOI: 10.5061/dryad.r6b0p/1
title: Rosengren_Cronberg_Sporegermination
DOI: 10.5061/dryad.22vs3/1
title: Neonicotinoid exposure and sex allocation data
DOI: 10.5061/dryad.23hs1/4
title: InputFilesForFastsimcoal.zip

description: A set of folders containing the input files for analyses with fastsimcoal2, including the calculated joint Site Frequency Spectrum for each of the focal population pairs. Folder and file names follow the population codes used consistently throughout the manuscript.
DOI: 10.5061/dryad.3k502/1
title: Barrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-geographic-tabular

description: Geographic tabular data in tab-separated text format (.tsv) and Python Pandas format (.pandas), for both stocks and time series, at several spatial scales, combined together using ZIP format.
DOI: 10.5061/dryad.3k502/4
title: Barrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-graphs-in-GML-format

description: Road network (graph) files in GML format.  Numerous files (one per metro region) are compressed with GNU gzip, and then combined with GNU tar, and again compressed with GNU gzip.
DOI: 10.5061/dryad.3k502/5
title: Barrington-Leigh-Millard-Ball-PNAS2015-Century-of-sprawl-shapefiles

description: A collection of geographic information files in ESRI SHP format ("shapefiles"), one for each geographic level (state, metro and country), combined in ZIP format.
DOI: 10.5061/dryad.3m680/1
title: OTU representative sequences

description: Representative sequences for all OTUs for the forward (Euk20F) and Reverse (Euk302r) sequencing directions
DOI: 10.5061/dryad.3m680/2
title: Bioinformatic scripts

description: Full scripts for bioinformatic pipeline as applied for sequence data analysis for Geisen et al. 2015 Mol. Ecology
DOI: 10.5061/dryad.3m680/3
title: Amoebozoa alignment

description: Allignment of 18S sequences (NEXUS-file), as used for phylogenetic analysis on Amoebazoa, as presented in Fig.3 of Geisen et al. 2015, Mol Ecology. Allignment includes OTUs recovered in this study, as well as sequences associated with those OTUs (downloaded from NCBI).
DOI: 10.5061/dryad.4b815/3
title: Great Lakes Zooplankton

description: Samples of zooplankton from the ballast water of ships arriving to the Laurentian Great Lakes
DOI: 10.5061/dryad.4b815/4
title: Ship-trip data

description: Ship-trips between source and recipient regions, including corresponding ballast water volume
DOI: 10.5061/dryad.4mt34/1
title: Table_S1:  Raw HPLC data

description: This files contains the raw HPLC peak abundance data for all of our samples.  The columns are as follows: Venom:  unique venom sample identifier. Tissue:  Unique animal identifier (one animal may have several venom samples; KW0719a is the same animal as KW0719b). Peak1a to Peak21: area under each HPLC peak (not a percentage). MaturityFactor:  the age class each animal belongs to based on the 102 cm SVL cut-off. GeographyFactor:  population of each animal. Eglin is Ca1, ANF is Ca2, ONF is Ca3, ENP is Ca4, LSG is Ca5, CAL is Ca6, SAP is Ca7. The last two columns indicate whether the sample was used in all analyses or only in the PCA and cluster analysis (i.e., removed prior to non-parametric MANOVA because it lacked size data and/or was a duplicate sample from an individual already present in the data set).
DOI: 10.5061/dryad.4mt34/2
title: Table_S2_raw_qPCR_data

description: This file contains the raw qPCR data.  For the “Results edited” and “Results” sheets:  the sample name corresponds to the unique tissue identifier in Table S1.  Each sample was run in duplicate at two different concentrations (e.g., 529 and 529-10).  The CT is the cycle threshold, the CT mean is the cycle threshold mean, the CT SD is the cycle threshold standard deviation, and Tm corresponds to the melting temperature.  The “pics” sheet shows the melting curve graph for northern individuals on the right and southern individuals on the left with the red line representing the standard (i.e., control).  The “sheet1” sheet shows a draft of Figure 6 from the manuscript.
DOI: 10.5061/dryad.4mt34/3
title: Table_S3_Raw_Morphological_Data

description: This table contains the raw morphological data.  The “All Data” sheet contains the raw measurements for each individual.  The columns are the following:  “Museum ID” is the unique specimen identifier for the Florida Museum, SVL is snout-vent length in mm, HL is head length in mm, HW is head width in mm, IF is inter-fang distance in mm, and FL is fang length in mm.  The “PCA_Kruskal_Wallis” sheet contains the data from the Kruskal-Wallis tests.  The “Shapiro-Wilk” sheet contains the Shapiro-Wilk normality test data for each variable.
DOI: 10.5061/dryad.4mt34/4
title: Table_S4_PCA

description: This file contains the loadings for the first 3 principal components broken down by RP-HPLC peak.
DOI: 10.5061/dryad.4mt34/5
title: Table_S5_PCA_Loadings

description: This file contains all PCA loadings.
DOI: 10.5061/dryad.54v2q.2
title: Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species
DOI: 10.5061/dryad.575p1/1
title: Sampling locations, dates, and coordinates

description: File is a tab-delimited text file that contains sampling locations (abbreviations and geographic coordinates) and sample collection dates for abalone.
DOI: 10.5061/dryad.575p1/2
title: Total Data Genepop

description: File contains genotypes for abalone from for 27 locations using 9 microsatellite loci (labeled as total data in the manuscript). File is a text file in Genepop format. See Sampling_Information-2012-04-10.txt for geographic coordinates and sampling dates.
DOI: 10.5061/dryad.575p1/3
title: 5-Loci Data Genepop

description: File contains genotypes for abalone from for 27 locations using 5 microsatellite loci (labeled as 5-loci data from the manuscript). Loci AB22, AB31, AB75, EDN91 were excluded due to null alleles. File is a text file in Genepop format. See Sampling locations, dates, and coordinates (Sampling_Information-2012-04-10.txt) for geographic coordinates and sampling dates.
DOI: 10.5061/dryad.6rg87/4
title: Reyer_et_al_Fig-6+7a

description: This file provides the data basis for Table 4a and Figs. 6 and 7a, which analyze and depict tadpole development under different food treatments from the start of the raising Experiment (SURVA0) to shortly before metamorphosis (SURVA10).
DOI: 10.5061/dryad.6rg87/5
title: Reyer_et_al_Fig-7b

description: Number of surviving froglets from shortly after metamorphosis (Aug 04) to the next summer (July 05). The category "Hyb" includes all hybrid types (LR, LLR, LRR) and the category "Par" the two parental species (LL, RR). Data base for Table 4b and Fig. 7b.
DOI: 10.5061/dryad.6t9p3/1
title: Data for Birth date predicts alternative life history pathways in a fish with sequential reproductive tactics

description: The data refer only to males whose pathways were possible to identify in the cohorts 2000-2004. Comments to the excel table: On sheet "TL pathways": Pathway - life-history pathway followed by the male; TL switch - total length at the moment of switch from Sneaker to Nest-holder morphotype (the average TL value estimated  for the last time the male was seen as Sneaker and the first time that it was seem as Nest-holder ); switch month - mid point between the month in which the male was last seen as sneaker and the first month in which it was seen as a Nest -holder as long as these 2 dates were not more than 2 months apart; For each male the value of TL in presented for each of the census in which that male was captured and measured. Values are presented in cm. On sheet "reproductive success pathways": Pathway - life-history pathway followed by the male; TL 1st breeding season - average of total length during the first breeding season, age 0+/1; Lifetime eggs - sum of all eggs present inside the nest of the male for the whole time in which it was a Nest-holder (not corrected for the eggs that are ind^side the nest but are actually fertilized by other males, sneakers; also not taken into account ).
DOI: 10.5061/dryad.87478/1
title: for Dryad

description: file in Structure format with the coloration, the sex, population ID where the sample was collected, and the length of 9 microsatellite markers
DOI: 10.5061/dryad.b56n0/3
title: Calo_CAD_haplos.trees

description: BEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the nuclear genes cad.
DOI: 10.5061/dryad.c5m42.1
title: Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection
DOI: 10.5061/dryad.c5m42.2/11.2
title: SI_Fig3
DOI: 10.5061/dryad.h5971/1
title: Data from: The Implications of Stratigraphic Compatibility for Character Integration among Fossil Taxa

description: These include the data matrices, first and last appearances, and character-ordering files analyzed within this paper.
DOI: 10.5061/dryad.h5971/2
title: SOM Appendix
DOI: 10.5061/dryad.h5971/3
title: Wagner_&_Estabrook_Data_2014
DOI: 10.5061/dryad.j69p2/1
title: Orthology groups for Methanosarcinaceae species

description: This archive contains initial groups of orthologues proteins (GOPs) utilized in the research.Here you can find GOPs for 3 Methanosarcina species (Methanosarcina acetivorans CA, Methanosarcina barkeri Fusaro, and Methanosarcina mazei Go1) and 6 Methanosarcinaceae species: 3 Methanosarcina and ﻿Methanococcoides burtonii DSM 6242, Methanohalobium evestigatum Z-7303, and Methanohalophilus mahii DSM 5219. GOPs were calculated by bidirectional best hits (BBHs) approach. The detailed description of method is provided in the original manuscript.
DOI: 10.5061/dryad.j69p2/2
title: Horizontally transferred genes in Methanosarcina spp.

description: This archive contains detailed information about horizontally transferred genes in Methanosarcina, such as list of genes of bacterial origin in 3 Methanosarcina species, corresponding alignments (produced by MUSCLE), neighbor-joining (NJ) trees with 100 bootstrap replicas generated by ClustalW software with default parameters (BLOSUM distance matrix), and a maximum-likelihood (ML) cladograms produced with PhyML v3.0 with default parameters.
DOI: 10.5061/dryad.k1m1g/10
title: All_haplotypes_Grapholita_molesta_cox2_42

description: Haplotypes of the mitochondrial cox2 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164168 - KF164208)
DOI: 10.5061/dryad.k1m1g/11
title: All_haplotypes_Grapholita_molesta_atp8_11

description: Haplotypes of the mitochondrial atp8 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164062 - KF164071)
DOI: 10.5061/dryad.k1m1g/12
title: All_haplotypes_Grapholita_molesta_atp6_40

description: Haplotypes of the mitochondrial atp6 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164022 - KF164061)
DOI: 10.5061/dryad.k1m1g/13
title: All_haplotypes_Grapholita_molesta_nad5_57

description: Haplotypes of the mitochondrial nad5 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF163966 - KF164021)
DOI: 10.5061/dryad.k1m1g/14
title: All_haplotypes_Grapholita_molesta_nad1_45

description: Haplotypes of the mitochondrial nad1 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164084 - KF164127)
DOI: 10.5061/dryad.k1m1g/15
title: All_haplotypes_Grapholita_molesta_lrna_13

description: Haplotypes of the mitochondrial lrna gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164072 - KF164083)
DOI: 10.5061/dryad.k1m1g/16
title: All_haplotypes_Grapholita_molesta_all_genes_197

description: Haplotypes of the combined mitochondrial genes of cox1, cox2, atp8, atp6, nad5, nad1 from the 794 Grapholita molesta specimens
DOI: 10.5061/dryad.k1m1g/9
title: All_haplotypes_Grapholita_molesta_cox1_41

description: Haplotypes of the mitochondrial cox1 gene from the 794 Grapholita molesta specimens (GenBnak NOs: KF164072 - KF164083)
DOI: 10.5061/dryad.m1g3v/1
title: concatenated mtDNA dataset

description: NEXUS file containing the 'concatenated mtDNA' dataset alignment, which includes 171 mtDNA subsamples sequenced for the mitochondrial cytochrome b and/or cytochrome oxidase 1 genes.
DOI: 10.5061/dryad.m1g3v/2
title: 50tax_plus8out_mtDNAonly

description: NEXUS file containing mtDNA locus data matching samples in the 50-sample 'concatenated nDNA' dataset.
DOI: 10.5061/dryad.m1g3v/3
title: concatenated nDNA dataset - LDHA alignment

description: NEXUS file containing the muscle-type lactate dehydrogenase (ldh-A) sequences in the concatenated nDNA dataset.
DOI: 10.5061/dryad.m1g3v/4
title: concatenated nDNA dataset - RPS7 alignment

description: NEXUS file containing the sequences of nuclear ribosomal protein S7 (RPS7) introns and exons in the concatenated nDNA dataset.