cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f7mb0/3
title: LakeSoundscapes_Morton24Hours_Data

description: Acoustic data collected at Morton Lake over 24 hours; reported in manuscript using multivariate analysis of temporal trends. Data is summarized by hour of day (field=HourOfDay) and includes average power of the sound sample for each 1 kHz frequency interval (e.g. 3to4kHz_Power). All power is in decibels (db) calculated in Raven Pro 1.4.
DOI: 10.5061/dryad.g3v15/2
title: Known and novel transcripts' cDNA, protein and expression information

description: Known and novel transcripts' cDNA, protein and expression information
DOI: 10.5061/dryad.g3v15/3
title: Novel transcripts which gained or lost miRNA target sites relative to their most similar known isoform

description: Novel transcripts which gained or lost miRNA target sites relative to their most similar known isoform
DOI: 10.5061/dryad.g3v15/4
title: Expression of genes with Gene Ontology (GO) categories associated with alternative splicing

description: Expression of genes with Gene Ontology (GO) categories associated with alternative splicing
DOI: 10.5061/dryad.g3v15/5
title: Expression and mapping results for genes with statistically significant (q &lt; 0.05) genotype-dependent alternative splicing variations

description: Expression and mapping results for genes with statistically significant (q &lt; 0.05) genotype-dependent alternative splicing variations
DOI: 10.5061/dryad.g3v15/6
title: Expression of genes with statistically significant expression differences in tissue and genotypic tests

description: Expression of genes with statistically significant expression differences in tissue and genotypic tests
DOI: 10.5061/dryad.g3v15/7
title: Primers used to amplify known and novel isoforms

description: Primers used to amplify known and novel isoforms
DOI: 10.5061/dryad.h1n02/10
title: 2007-11-01_141000_HF_Clip10

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/5
title: 2007-11-02_101000_HF_Clip5

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/6
title: 2007-11-01_113000_HF_Clip6

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/7
title: 2007-11-02_101000_HF_Clip7

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/8
title: 2007-11-01_160549_HF_Clip8

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.h1n02/9
title: 2007-10-31_162000_HF_Clip9

description: DIDSON data file. See Table 1 in Hightower et al.
DOI: 10.5061/dryad.k30sg/1
title: TransportBenchmark

description: This benchmark contains 8600 images for comparing methods to solve transportation problems and to compute the Earth Mover's Distance (EMD).
DOI: 10.5061/dryad.nd2mb/8
title: Supplementary Figure 8

description: Completeness metrics. A. Several species accumulation curves from samples of various ages. B. Species-accumulation curve on a typical sample (sample 120-751A-6H-6, 98/102cm, Late Miocene). Bold black curve is the species accumulation curve; light grey curve and dashed light grey line are, respectively, the de Caprariis et al. (1976, 1981) curve-fitting and its asymptote.
DOI: 10.5061/dryad.nf757/1
title: Flow Cytometery Data for Figures 2 and 3a
DOI: 10.5061/dryad.nf757/2
title: Flow Cytometery Data for Figure 5
DOI: 10.5061/dryad.nf757/3
title: Flow Cytometery Data for Figures 6 and S11

description: File names are: __.xxx
DOI: 10.5061/dryad.nf757/4
title: Flow Cytometery Data for Figure S3
DOI: 10.5061/dryad.pp0q1/10
title: Input file for simple mantel tests

description: Input file with pair-wise distances (shoreline populations) to test for isolation-by-distance
DOI: 10.5061/dryad.pp0q1/11
title: Summary file for CERVUS analyses

description: Parentage assignment of the pond mating experiment
DOI: 10.5061/dryad.pp0q1/12
title: Microsatellite genotypes of F1 and parental fish (pond 1)

description: Microsatellite genotypes used for parentage assignment in pond 1
DOI: 10.5061/dryad.pp0q1/3
title: Body shape data of wild populations

description: tps input file with landmark coordinates for body shape analyses of 20 populations
DOI: 10.5061/dryad.pp0q1/4
title: Body shape data of individuals from the pond experiment

description: tps input file with landmark coordinates for body shape analyses of 20 populations
DOI: 10.5061/dryad.pp0q1/5
title: Gill raker data of wild populations

description: Metric measurements on specimens used to compare gill raker morphology in wild populations
DOI: 10.5061/dryad.pp0q1/6
title: Gill raker data of F1 individuals

description: Metric measurements on F1individuals used to compare gill raker morphology
DOI: 10.5061/dryad.pp0q1/7
title: Lower pharyngeal jaw morphology data of wild populations

description: tps input file with landmark coordinates used for geometric morphometric on lower pharyngeal jaws
DOI: 10.5061/dryad.pp0q1/8
title: Data on stomach contents

description: Stomach content components of wild populations
DOI: 10.5061/dryad.pp0q1/9
title: Input file for partial mantel tests and MRM

description: Input file with pair-wise distances (lake-stream populations) to test for associations between genetic differentiation, morphometric traits and environment
DOI: 10.5061/dryad.pr577/1
title: Experiment I

description: Experiment I (male mate choice for experienced and naive males in absence and presence of females)
DOI: 10.5061/dryad.vb120/1
title: Iannone_et_al_JAE_Woodland_Invasion_and_Soils

description: Data used to construct severity index, to calculate differences between invaded and uninvaded point of pairs pairs in below-ground soil parameters, and to model these below-ground differences in response to invasion severity.
DOI: 10.5061/dryad.13272/1
title: Fungus_Alignment_7loci_125individual_4326nt

description: Alignmnet file of 125 Ophiocordyceps sinensis individuals on seven nuclear loci: nrDNA ITS, MAT1-2-1, csp1, OSRC14, OSRC17, OSRC27, and OSRC32. See ReadMe file for dataset partition.
DOI: 10.5061/dryad.13272/2
title: Insect_Alignment_3loci_125individual_1404nt

description: Alignment of 125 ghost moth individuals on three loci:COI, cytb, and wg. See ReadMe file for dataset partition.
DOI: 10.5061/dryad.13272/3
title: Fungus_MP_BestOutputTree

description: Best MP tree of Ophiocordyceps sinensis based on 6 loci (nrDNA ITS, MAT1-2-1, csp1, OSRC14, OSRC17, and OSRC27)
DOI: 10.5061/dryad.13272/4
title: Fungus_Bayes_OutputTree.con

description: BI tree of Ophiocordyceps sinensis based on 6 loci (nrDNA ITS, MAT1-2-1, csp1, OSRC14, OSRC17, and OSRC27)
DOI: 10.5061/dryad.25696/2
title: Table2_rattusVneo_allprobes
DOI: 10.5061/dryad.2hr77/1
title: Cell volume

description: Volume of individual cells from 7-227d of evolution.
DOI: 10.5061/dryad.304dn/3
title: A. pulchellus and A. krugi nuclear DNAH3 sequences

description: Alligned and phased nuclear DNAH3 sequences for A. pulchellus, A. krugi and outgroups
DOI: 10.5061/dryad.313dq/1
title: Supplementary Table 1

description: Monte Carlo calculation mean differences on richness (S), Simpson (1-D) and Shannon (H’) diversity indices and associated p-values comparing LAs (living assemblages) and DAs (dead assemblages) and open water and littoral environments from Las Mostazas (LM), Los Carpinchos (LC) and Nahuel Rucá (NR). Significant values at α = 0.05 are in boldface.
DOI: 10.5061/dryad.313dq/2
title: Supplementary Table 2

description: List of diatom species mentioned in the text, their authorities and life form, salinity and nutrient classifications (according to de Wolf, 1982; Denys, 1991/1992 and Van Dam, 1994). E: epiphyte; B: benthic; Aer: aerophilous; P: plankton; Tp: tychoplankton; H: halophobous; OI: oligohalobous indifferent; OH: oligohalobous halophilous; M: mesohalobous; PO: polyhalobous; Dys: dystrophic; Eu: eutrophic; Mt: mesotrophic; Ot: oligotrophic; I: indifferent.
DOI: 10.5061/dryad.313dq/3
title: Supplementary Table 3

description: Results of HMD (Homogeneity in Multivariate Dispersions) tests comparing live and dead diatom assemblages in total (littoral+open waters), littoral and open waters datasets showing: ratio (premortem variation/total LD variation), the estimates of premortem and postmortem variation, the significance values of modified test of multivariate dispersions, which indicates whether variation among DAs and the centroid of LAs is larger (overdispersion) or smaller (underdispersion) than variation among LAs and their centroid. NS= not significant at α = 0.05.
DOI: 10.5061/dryad.313dq/4
title: Supplementary Table 4

description: Results of HMD ((Homogeneity in Multivariate Dispersions) tests comparing littoral and open waters dispersions. Significant values at α = 0.05 are in boldface
DOI: 10.5061/dryad.34dt1/1
title: Sequence data for Mixornis gularis

description: Illumina MiSeq Fastq files, including index read sequences
DOI: 10.5061/dryad.34dt1/2
title: wasmannia.tar

description: Alignment files for ant data
DOI: 10.5061/dryad.34dt1/3
title: yeast.tar

description: Yeast alignment files
DOI: 10.5061/dryad.3pf37/2
title: chrna1

description: Nexus file containing sequences obtained for CHRNA1 (cholinergic receptor nicotinic alpha-polypeptide 1) from Delphinus delphis, Delphinus capensis and Delphinus tropicalis. Samples were collected from stranded or live animals using biopsies in the Atlantic, Pacific and Indian Oceans.
DOI: 10.5061/dryad.3vc1b/1
title: 4_areas

description: Deer genotypes for 17 microsatellite loci. The first two letters in the sample name denote the locations used in the analysis.
DOI: 10.5061/dryad.43mg3/1
title: 01_ML_phylogeny.zip

description: This file contains all the data necessary to re-run our ML tree using the full alignmentcontaining all 564 species. There are 5 files. 'burleigh_concat.phy' is the alignment file in phylip format. 'commandline' is the commandline we used to run RAxML version 7. 'partitions' describes how we partitioned our data (RAxML uses that file). 'RAxML_result.burleigh_concat.raxml.out' has the tree file that results from our analysis. 'raxmlHPC' is the raxml executable we used to run our analyses, on a Mac desktop computer.
DOI: 10.5061/dryad.43mg3/2
title: 02_sister_pairs.zip

description: This file contains data and R code for the sister pairs analyses. There are 2 files. 'raw_data_sister_pairs.csv' is a comma separated values file that contains all of the branch length and life history data we used in the sister pairs analyses. There is one row per sister pair in the analysis, which has data on: the two families in the sister pair, the proportion of genera we had height data for in each family, the number of species in each family, the average height of each family (log transformed value in mm), nuclear branch length for each family (in units of substitutions/site), chloroplast dN branch length for each family (also in substitutions/site), chloroplast dS branch length for each family (also in substitutions/site), Latitude for each family (in distance from the equator), UV for each family (measured as in Davies et al 2004), and Temperature for each family (in Kelvins). 'sister_pairs_analyses.r' contains all R code used for the sister pairs analyses. To use it, you will need to download R (it's free), install the relevant packages (at the top of the .r file), and then change the line at the top which starts 'setwd' to point to the folder on your computer that contains the raw_data_sister_pairs.csv file. As you go through the R code, it will print out all of the results in the paper that used sister pairs analyses.
DOI: 10.5061/dryad.43mg3/3
title: 03_R8S

description: This file contains input files and the results files from running R8S on the ML tree, and on 1000 bootstraps of the ML tree. There are 3 files and 2 folders. 'base_files' is just a holder for some basic R8S input files, that the python script uses(see below). This folder contains: the r8s executable we used (compiled for macs), the basic r8s.txt input file we used for each r8s analysis (which has data on our fossil  calibrations), and a .txt file that contains the ML tree, and 1000 boostrapped trees estimated in RAxML as described in the paper. 'bootstrap_rates.txt' contains the results of the R8S analyses, each family is listed on its own row, and each row has 1001 associated columns. The first column contains the ML rate, subsequent columns contain bootstrap rates (in substitutions/site/myr). This is the main output file produced by the python script (see next). 'run_BS_r8s.py' is a python script that will run r8s on the ML tree and the 1000 bootstrap trees. Before running it, create an empty directory in the same folder as the script  called "bootstrap_results", then change the "start_dir" and "tree_file" variables at the top of the script to point to the directory the script is in, and the tree file in the'base_files' folder respectively. Then run the script using python. Briefly, the script takes each tree from the tree file, makes a r8s input file, runs r8s, then parses the output to extract the rates for each family. It then outputs these to the 'bootstrap_rates.txt' file. Be aware that the script stores all r8s results, which can take a lot of space (about 1GB) when the analyses are all complete.
DOI: 10.5061/dryad.43mg3/4
title: 04_PGLS

description: This file contains 5 files, sufficient to re-do all of our PGLS analyses. 'bootstrap_rates.txt' contains the results of the ML r8s analysis and all 1000 subsequent bootstrap analyses. 'growth_forms.csv' contains information on the growth forms of species in each family. 'PGLS_analyses.r' is an R script which you can use to re-run all of our PGLS analyses. To use it you will need to change the line at the top that starts 'setwd' to point to the folder on your computer that contains all of the input files here. You'll also need to download R, and the packages listed at the top of the file. 'R8S_trees.txt' is a file of the 1001 trees from R8S. These are used in the PGLS analyses to correct for nonindepdence. The first tree is the ML tree, the rest are bootstrap trees. 'raw_data_sister_pairs.csv' is a csv file of the raw data. It's included here so that the R script will run without additional hassle. But it's identical to the file described in the '02_sister_pairs' section above.
DOI: 10.5061/dryad.4v178/1
title: Kim_et_al_2013_JEB
DOI: 10.5061/dryad.5kh00/1
title: Human treadmill walking position data, 3 markers

description: Compressed file contains text files with human walking position data for 3 markers, 10 subjects, 3 trials. See readme.txt and original article for more details.
DOI: 10.5061/dryad.6mb78/1
title: Lattin et al. 2013 data

description: Data from radioligand binding assays on House Sparrow spleen, belly skin and back skin collected at six different times of year in 2011-12 in Somerville and Medford MA. Samples were run in triplicate and standardized per mg protein using Bradford assays.
DOI: 10.5061/dryad.6n890/1
title: Pleistocene Data (Raw)

description: The Pleistocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.
DOI: 10.5061/dryad.6n890/2
title: Pliocene Data (Raw)

description: The Pliocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.
DOI: 10.5061/dryad.6n890/3
title: Miocene Data (Raw)

description: The Pleistocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.
DOI: 10.5061/dryad.6n890/4
title: Oligocene Data (Raw)

description: The Oligocene data from the Paleobiology Database (www.paleobiodb.org), downloaded 10-09-2013. Please note that this is raw data, un-culled. See the manuscript for a discussion of the culled elements.
DOI: 10.5061/dryad.7785h/3
title: aeb3 phylogenies

description: Methods of inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009).  Aeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.
DOI: 10.5061/dryad.7m6kg/74
title: Fig. 11d: ROM 61496 — Large morph of Nectocaris from the Burgess Shale

description: Full size, high-resolution images as displayed in Fig. 11d, plus original (pre-interference) images.
DOI: 10.5061/dryad.82c67/1
title: Melanin cline dataset

description: Data on the hindwing melanin across Estonia and up through Finland.
DOI: 10.5061/dryad.b911r/2
title: individual microsatellite markers and spatial coordinates HM 2007

description: Individual genotypes and spatial coordinates for all individuals sampled in the patch network HM in 2007.
DOI: 10.5061/dryad.dg85v/1
title: Traits of herbaceous crop species and their wild progenitors

description: data on functional traits of 30 herbaceous crop species and their wild progenitors
DOI: 10.5061/dryad.f0g7v/1
title: Kawahara_et_al_2013_Manduca

description: Nexus file for Kawahara et al. (2013) study
DOI: 10.5061/dryad.f5q32/1
title: Data on geographic locations, sex, microsatellites, CHD markers, sequences and bioclimatic variables
DOI: 10.5061/dryad.j015n/7
title: fish-nexus-files-from-uce-alignment.tar.gz

description: NEXUS alignment files for all taxa across UCE loci, lacking entries for taxa with missing data.
DOI: 10.5061/dryad.kq72k/1
title: Physiological Measurement Data

description: This file contains complete physiological data for fat mass, food intake, VO, VCO, and 9 month body weight for all mice in the study.
DOI: 10.5061/dryad.kq72k/2
title: Weekly Weights Data

description: This file contains weekly weight data (g) for mice used in this study.
DOI: 10.5061/dryad.kq72k/3
title: Glucose Tolerance Test Data

description: This file contains data from the glucose tolerance test, with measures for glucose and insulin at 0, 15, 30, 60, and 120 minutes as well as area under the curve (AUC) measurements for all mice in this study.
DOI: 10.5061/dryad.n5d15/3
title: Grasshopper mortality 2011-2012

description: Spider predator consumption rates of grasshopper prey during behavioral observations in terraria. Includes mortality rates collected during summer 2011 and 2012.
DOI: 10.5061/dryad.nd2mb/10
title: Supplementary Appendix 10

description: Check of claimed errors in Neptune by Lloyd et al (2011).
DOI: 10.5061/dryad.nd2mb/9
title: Supplementary Code 9

description: R script: Subsampling Neptune.
DOI: 10.5061/dryad.nf757/5
title: Flow Cytometery Data for Figure S4
DOI: 10.5061/dryad.nf757/6
title: Flow Cytometery Data for Figure S5
DOI: 10.5061/dryad.nf757/7
title: Flow Cytometery Data for Figure S8

description: Starting ratios for these competitions were X/6, where X is the number in the second slot of the filename (strain_X_time.zzz)
DOI: 10.5061/dryad.nf757/8
title: Flow Cytometery Data for Figure S10
DOI: 10.5061/dryad.nf757/9
title: Flow Cytometery Data for Figure S12
DOI: 10.5061/dryad.pp0q1/13
title: Microsatellite genotypes of F1 and parental fish (pond 2)

description: Microsatellite genotypes used for parentage assignment in pond 2
DOI: 10.5061/dryad.pp0q1/14
title: Microsatellite genotypes of F1 and parental fish (pond 3)

description: Microsatellite genotypes used for parentage assignment in pond 3
DOI: 10.5061/dryad.pp0q1/15
title: Microsatellite genotypes of F1 and parental fish (pond 4)

description: Microsatellite genotypes used for parentage assignment in pond 4
DOI: 10.5061/dryad.pp0q1/16
title: Microsatellite genotypes of F1 and parental fish (pond 5)

description: Microsatellite genotypes used for parentage assignment in pond 5
DOI: 10.5061/dryad.pr577/2
title: Experiment II

description: Experiment II (male mate choice in presence of females only and with stimulus males hidden)
DOI: 10.5061/dryad.pr577/3
title: Experiment III

description: Experiment III (male coloration and aggressive behaviour)
DOI: 10.5061/dryad.q32td/1
title: Sharick_OXSTRESS_FE

description: Oxidative stress markers in breeding northern elephant seals.
DOI: 10.5061/dryad.q8r53/1
title: Appendix B - Iacarella et al

description: Raw data (experimental results) for Figures 2 & 3 in Iacarella et al. Ecol Appl.
DOI: 10.5061/dryad.qc297/1
title: DATA TABLE 1 Reproductive performance and body weight

description: Measurements of reproductive performance and body weight of inbred and outbred snails assessed under controlled laboratory conditions. For column abbreviations see data sheet 'DATA TABLE 1 Legend'.
DOI: 10.5061/dryad.qp47h/1
title: dataset_exclosures_def

description: Data on the vegetation in the exclosures placed in riparian vegetation in Dutch fen wetland and the vegetation development over two growing seasons.
DOI: 10.5061/dryad.r0t1q/1
title: ExpressionData

description: The expression data from Tribolium castaneum whole body and reproductive tracts samples provided here is the output of ArrayStar gene expression software that was used to processes and normalize NimbleGen-generated raw expression data (Prince, Kirkland and Demuth 2010, Genome Biol Evol 2:336-346).
DOI: 10.5061/dryad.s903c/2
title: Giese et al 2013_suppl_meteorological data IMGERS 2004-2006

description: daily meteorological data of the experimental years 2004 -2006
DOI: 10.5061/dryad.t9f50/1
title: MAIN DATA FILE

description: Sheet 1: Potential of frequency of 2 types of notes for signalling. Sheet 2: Responses of males to natural soft calls. Sheet 3: Responses of males to soft calls when the cost of assessment was decreased. Column headings in the comments of headlines.
DOI: 10.5061/dryad.0q13g/1
title: Economy_Releases

description: Release and recapture data for juvenile Atlantic salmon released in all streams in the Economy River. See Excel file for a description of column headers.
DOI: 10.5061/dryad.0q13g/2
title: Stewiacke_Releases

description: Release and recapture data for juvenile Atlantic salmon released in streams in the Stewiacke River. See Excel file for details on column headings.
DOI: 10.5061/dryad.0q13g/3
title: GreatVillage_Releases

description: Release and recapture data for all juvenile Atlantic salmon released into streams in the Great Village River. See Excel file for a description of column headers.
DOI: 10.5061/dryad.13272/10
title: raw data of density survey
DOI: 10.5061/dryad.13272/5
title: Fungus_Garli_OutputTree

description: ML tree of Ophiocordyceps sinensis based on 6 loci (nrDNA ITS, MAT1-2-1, csp1, OSRC14, OSRC17, and OSRC27)
DOI: 10.5061/dryad.13272/6
title: Insect_MP_BestOutputTree

description: Best MP tree of ghost moths based on 2 loci (COI and wg)
DOI: 10.5061/dryad.13272/7
title: Insect_Bayes_OutputTree.con

description: BI tree of ghost moths based on 2 loci (COI and wg)
DOI: 10.5061/dryad.13272/8
title: Insect_Garli_OutputTree

description: ML tree of ghost moths based on 2 loci (COI and wg)
DOI: 10.5061/dryad.13272/9
title: raw data of infection trial
DOI: 10.5061/dryad.16v7n/7
title: HandlingTimes

description: Flower handling times recorded during the flower visitation observations described above (and reported in Visitation.csv). See ReadMe file associated with Visitation.csv for further information.
DOI: 10.5061/dryad.16v7n/8
title: SearchSpeeds

description: Search speeds calculated from flight times and estimated distances between flowerheads, in 2009 (the summer before the rest of the data in this dataset were collected), for the main visitors to H. virgata. See ReadMe file associated with Visitation.csv for further information.