cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2598k/2
title: Data_seed traits_experiment 1

description: Data on seed traits following experimental crosses at floral developmental stage 1-4 in Collinsia heterophylla. Recipients and pollen donor were grown in either high or low levels of soil resources. Seed traits = number of seeds per capsule, capsule seed weight, maturity time from cross till harvest.
DOI: 10.5061/dryad.2598k/3
title: Data_plant traits_experiment 1

description: Data on traits for plants grown in either high or low levels of soil resources in Collinsia heterophylla. Traits = flower start estimated as day from the first plant started flowering, plant height, number of branches, number of flowers on the main branch.
DOI: 10.5061/dryad.2598k/4
title: Data_anther-stigma contact_experiment 1

description: Data on anther-stigma contact estimated at floral developmental stage 1-4 of flowers for plants grown in either high or low levels of soil resources in Collinsia heterophylla. S = stigma shorter than anther, C = stigma-anther contact, L = stigma longer than anther
DOI: 10.5061/dryad.2598k/5
title: Data_plant height_experiment 2

description: Data on plant height for plants grown in either high or low levels of soil resources in supplementary experiment in Collinsia heterophylla.
DOI: 10.5061/dryad.2598k/6
title: Data_pollen traits_experiment 2

description: Data on pollen traits assessed in vitro for plants grown in either high or low levels of soil resources in supplementary experiment in Collinsia heterophylla. Pollen traits = germination rate (germinated vs. ungerminated) after 15 min, germination rate (germinated vs. ungerminated) after 1h, 45 min, pollen tube growth rate estimated for ten replicate pollen tubes after 1h, 45 min.
DOI: 10.5061/dryad.26f7v/1
title: Microsatellite marker data of Boswellia papyrifera populations in Ethiopia

description: The file "Data fine-scale structure of Boswellia papyrifera TGGE paper.xlsx" contains the microsatellite data used in the study "Fine-scale spatial genetic structure in the frankincense tree Boswellia papyrifera (Del.) Hochst. and implications for conservation", by A. B. Addisalem, J. Duminil, D. Wouters, F. Bongers, M. J. M. Smulders, published in Tree Genetics & Genomes (2016) DOI 10.1007/s11295-016-1039-2.The data are given both as a list (sheet ‘Genotype and GPS’) and as input files for SpaGeDi (sheets ‘Input for SPAGEDI’). Microsatellite marker data are given as allele size in bp, two columns per genotype/marker, 0 = null allele
DOI: 10.5061/dryad.2dc34/1
title: Bacterial densities

description: Densities of bacteria during 66-day experiment
DOI: 10.5061/dryad.2dq68/1
title: Halliwell_et_al_2016_Behav_Ecol_DATA

description: .csv file containing all data necessary to reproduce the analyses presented in this article
DOI: 10.5061/dryad.3372n/1
title: langwig_batloads_by_class

description: Attached is the bats in each load class for model fitting. Count is the number of individuals sampled in each class. Frac is the number in each class divided by the total sampled. N is the count of bats at the site, and cases is the estimated number of total individuals infected, based on the sample. se is the standard error of the fraction, and Nse is the standard error of the cases. The column header "time" is the month and decimal day of sampling, with 12 added to the months of Jan - Apr (e.g. Jan is month 13). The columns "class" and "class character" are the load classes used in the modelling.
DOI: 10.5061/dryad.3vk01/1
title: Supplementary material and data
DOI: 10.5061/dryad.422jp/1
title: Data: Altered feeding behavior in mosquitoes and associated fitness parameters

description: Data includes life history data for a total of 921 individual mosquitoes, each numbered with a unique id number given in the first column. Feed.D4-Feed.D16 describe feeding compliance with -1 meaning offered a blood meal but not taken, 1 meaning offered and fed, and 0 meaning not offered a blood meal and, thus not fed. DOD represents day of death and is the day a mosquito was observed to die, counting day 0 as the first day of the experiment and 24 as the last day of the experiment. Natural.LH indicates whether a mosquito died naturally (1) or not (0). Dying unnaturally include deaths by experimental handling or escape from container. Wing length is the length of the right wing in mm. Immune and Feeding treatments indicate which experimental group the mosquito was placed in. Replicate indicates which of two experimental replicates the mosquito was in, with "5" taking place in Spring 2015, and "6" taking place in Summer/Fall 2015. Replicate.end indicates the number of adult days over which experimental observations took place. Fitness is the estimate of individual intrinsic rate of increase, r, based on the survival and reproduction data for that individual (methods for modeling r described in Ohm 2016). Clutch1-Clutch5 are the sums of eggs produced for each individual after each blood meal, for example Clutch 1 is the sum of eggs an individual produced after the first blood meal Clutch 2, after the second, etc. d0-d23 list the number of eggs each individual laid for that day, from d0 (the start of the experiment) to d23 (last day of the experiment). Age is the final age of the mosquito on it's death day, adding the average length of time spent in the juvenile stage to it's observed death day. tot_r is a slightly different calculation of r that used different assumptions in its calculation not discussed in Ohm et al 2016.
DOI: 10.5061/dryad.4mv7h/1
title: AMF function
DOI: 10.5061/dryad.4nt0f/1
title: Supplemental Dataset 1

description: Computational Analysis of Transcriptome-Wide AS.
DOI: 10.5061/dryad.5934k/1
title: Hemodynamic monitoring and Physiologic Parameters
DOI: 10.5061/dryad.5934k/2
title: S1 Fig

description: figure
DOI: 10.5061/dryad.5vv5v/1
title: Plant and insect microbial symbionts alter the outcome of plant-herbivore-parasitoid interactions

description: Data from two experiments describing interactions between arbuscular mycorrhizal fungi, Solanum sp. (potato plants), aphids, and parasitoids.
DOI: 10.5061/dryad.67136/3
title: Late-season data

description: Late-season data used in analyses of end of season variation in ectoparasites, endoparasites, male mobility, badge size, and CORT.
DOI: 10.5061/dryad.6fb43/1
title: Epistasis data CM and MM for dryad
DOI: 10.5061/dryad.6kc60/1
title: ESF REPTILES BONNET X

description: Raw data used for the main analyses. Note that additional details (e.g. parturition date, total body size) and explanations about each variable (e.g. measurements, exclusion of several data) can be provided. Contact X Bonnet in this case.
DOI: 10.5061/dryad.76jr5/4
title: Detection_Corrected_Abundance&Landscape_Variables

description: Detection corrected small mammal abundance data and landscape variables used in community analyses.
DOI: 10.5061/dryad.88fh0/1
title: Selaginella_alignment

description: Alignment of the combined three-region dataset (rbcL, pgiC, and SQD1). Sequences from "the sanguinolenta group" excluded. Data partitions and excluded characters are listed.
DOI: 10.5061/dryad.88fh0/2
title: Selaginella_BI_con_MrBayes

description: The Bayesian tree (50% majority consensus) inferred from "Selaginella_alignment.nexus" using MrBayes. Figure 2 in article.
DOI: 10.5061/dryad.8q8p7/1
title: DRYAD_selection gradients DATA
DOI: 10.5061/dryad.c261c/1
title: Electrophysiological data from Pérez-Escobar et al. 2016

description: This file contains the spike times, position data, electrode location, and light conditions for the recordings on the circular arena and the linear track.
DOI: 10.5061/dryad.d3m1j/1
title: Individual frog measurement data

description: This file contains measurement data for individual frogs, along with information on population origin and disease status for populations and individuals. Museum registration details refer to specimen I.D. for the Museum Victoria, Australia.
DOI: 10.5061/dryad.fd11f/1
title: Holzschuh_etal_2016_EcolLett

description: The file contains all data used in the analyses of this paper.
DOI: 10.5061/dryad.gs0gv/1
title: Haponskietal_partula_pyRADparameter_files

description: .zip archive contains all pyRAD parameter files used to generate the 85, 90, 95% similarity threshold datasets across 4, 16, and 20 taxa as presented in Haponski et al.
DOI: 10.5061/dryad.h846r/2
title: Ostrich Overground Gait Data

description: File containing bird ID, hip height, body mass, time of each step, position, gait ID, relative speed (vel_norm), relative step frequency (stepFreq_Norm), relative step length (stepLength_Norm) and energy phase for all recorded steady steps,  walk to run transitions and run to walk transitions. (Note the 'gait_ID' column is only in the steady data, not the gait transitions. 1=walk and 2 = run, based on the gait metric described and used in the manuscript).
DOI: 10.5061/dryad.m37gc/1
title: badger habitat use observed and expected

description: This excel file contains, for each GPS-collared badger, the proportions of locations falling into each land use type. These data were used to perform compositional analyses of badger habitat selection. Raw badger GPS-collar data are available on MoveBank.
DOI: 10.5061/dryad.m37gc/2
title: simultaneous badger cattle location pairs

description: Simultaneous GPS-collar locations of badgers, and cattle within those badgers' home ranges, used to explore proximity between the two species. The expected distributions of separation distances were generated from these data by permutation. Raw GPS-collar data are available on MoveBank.
DOI: 10.5061/dryad.mp8rt/11
title: temperature_dependent_phenotypic_data

description: Wing length, thorax length, and wing length to thorax length ratio for two lines from a range of developmental temperatures.
DOI: 10.5061/dryad.n70c7/1
title: Andrew's toad pooled RAD-seq data

description: The file includes reference sequences used for alignment, SNPs identified with PoPoolation2 and their FST values of all population pairs, and genepop format data of SNPs identified with PoPoolation2. The command line used for SNP calling with PoPoolation2 could be found in README.txt.
DOI: 10.5061/dryad.nh7pg/1
title: MrBayes files

description: This is a ZIP file consisting of 10 separate input files for the program MrBayes version 3.2.2 (Ronquist et al. 2012), which creates phylogenetic trees. Each file is for a separate one, two or three gene dataset.  See Table 2 of paper for details of datasets and analyses, Table 1 for site codes and Table S1 for full details of specimen numbers.
DOI: 10.5061/dryad.nh7pg/2
title: TCS files

description: This is a ZIP file consisting of 4 separate input files for the program TCS version 1.21 (Clement et al. 2000), which creates haplotype networks. Each file is for a separate analysis.  See Table 2 of paper for details of datasets and analyses, Table 1 for site codes and Table S1 for full details of specimen numbers.
DOI: 10.5061/dryad.nh7pg/3
title: Mega files

description: This is a ZIP file consisting of 4 separate input files for the program Mega6 (Tamura et al. 2013), which creates phylogenetic trees. Each file is for a separate single gene dataset.  See Table 2 of paper for details of datasets and analyses, Table 1 for site codes and Table S1 for full details of specimen numbers.  “Aus” = Australia, “BI” = “Barrow Island”, “Can” = Canary Islands, “CRE” = “Cape Range East, “PH” = Pilbara High, “PL” = Pilbara Low, “Okin” = Okinawa, “TULKI” = Halosbaena tulki, “Xmas” = Christmas Island.
DOI: 10.5061/dryad.nh7pg/4
title: BEAST file

description: This is an input file for the program BEAST 2 version 2.1.3 (Bouckaert et al. 2014), which creates phylogenetic trees and time-trees using a 4 gene dataset. See Table 2 of paper for details of datasets and analyses, Table 1 for site codes and Table S1 for full details of specimen numbers.
DOI: 10.5061/dryad.r82jg/1
title: Meliphagidae ecology

description: Field measurements of Australian Meliphagidae foraging behavior. Contains species-averaged measurements for 74 of 75 species that occur in Australia. Conopophila whitei is not included here. FD is an abbreviation for foliage density. Third refers to distance from trunk, where larger values refer to larger distances from trunk.
DOI: 10.5061/dryad.r82jg/2
title: Meliphagidae morphology

description: Museum-collected measures of Meliphagidae morphology. Contains measurements for 74 of 75 Australian species. Dataset does not included Eungella Honeyeater (Bolemoreus hindwoodi).
DOI: 10.5061/dryad.rb075/1
title: DRYAD_apparent.survival_movement
DOI: 10.5061/dryad.rb075/2
title: DRYAD_nest.abundance.activity_season.length
DOI: 10.5061/dryad.rb075/3
title: DRYAD_nest.DSR
DOI: 10.5061/dryad.rb075/4
title: DRYAD_young.fledged
DOI: 10.5061/dryad.rb075/5
title: Metadata for DRYAD files
DOI: 10.5061/dryad.rk398/1
title: ECOG_02551_Microclimate_Data

description: Daily summaries for microclimate data from Dane county, WI. during the winter of 2013-2014. Data includes minimum daily (min.day), minimum average daily (min.av.day), maximum daily (max.day), maximum average daily (max.av.day), and minimum and maximum daily PRISM data for each location as well (minT.prism; maxT.prism).
DOI: 10.5061/dryad.sh0h0/3
title: Afrobatrachia_Sequence_Alignment

description: A nexus format sequence alignment of the five nuclear markers (FICD, KIAA2013, POMC, RAG1, TYR) and 16S data, along with relevant MrBayes style partitions and models defined. The alignment contains 186 taxa and 3700 bp.
DOI: 10.5061/dryad.sh0h0/4
title: Power_Analyses_1_Data&Code

description: Directory contains the character codings and tree used by the accompanying R script to simulate discrete character data. The script will simulate each of the four characters independently and combine these results in an output file, with 500 replicates, for a total of 500 output files.
DOI: 10.5061/dryad.sh0h0/5
title: Power_Analyses_2_SimulationResults

description: The resulting output files from the previous step. The directory contains 500 files, each with independent simulations for characters 1-4 (note number of states varies across characters) across all taxa included.
DOI: 10.5061/dryad.sh0h0/6
title: Power_Analyses_3_ConvertToBayesTraits&Inputs

description: Includes python script to convert simulation output files to BayesTraits binary input format (Simulation_Outputs_processing_for_BayesTraits.py). Instructions for usage and details of conversion are annotated at the top of the script. The results of this conversion process are in the directory "3_BayesTraits_inputs", which contains subdirectories of the relevant character comparisons, each with 500 input files. These subdirectories contain a tree file, and will need the "BayesTraitsV2" executable placed within. These subdirectories are the focus of the next bundle of scripts.
DOI: 10.5061/dryad.sh0h0/7
title: Power_Analyses_4_BayesTraitsScripts&Results

description: There are two python scripts used to execute BayesTraits on the subdirectories in the previous bundle, "BayesTraits_wrapper_ML.py" and "BayesTraits_wrapper_Bayesian.py". Each will automatically generate the independent and dependent model files required to run BayesTraits, and automatically access the tree file and BayesTraits executable in the subdirectory. It will run serial analyses across all the input files in a subdirectory, using the maximum likelihood version or Bayesian version with stepping stone sampling. Instructions and details are annotated at the top of those scripts. The results can be summarized using the relevant python script, bayesian ("Summary_bf_testing.py") or ml ("Summary_lr_testing.py") version. These will open the output files from each of the 500 analyses in a subdirectory and perform either likelihood ratio tests or bayes factors to compare the independent and dependent models for each input file. The output of these scripts for our set of analyses is provided in the directory "4_Results".
DOI: 10.5061/dryad.sm454/1
title: Experimental Data

description: Behavioural Data from Experiments 1 and 2.
DOI: 10.5061/dryad.v540q/1
title: Phenotypic and genetic correlations between parent and offspring traits

description: The data describing phenotypic and genetic correlations between parent and offspring traits in the burying beetle Nicrophorus vespilloides. The data derive from a full sib, paternal half-sib breeding design.
DOI: 10.5061/dryad.vb957/4
title: MN_Walleye_data_Honsey_et_al_Ecol_Apps

description: These data describe age (yrs), total length (mm), sex (see Metadata tab), and maturity (see Metadata tab) of walleye collected in a variety of Minnesota water bodies from 1993-2011. The data also include information on water body name (with a unique ID for each water body) and sampling gear type. These data are copyright 2016, Minnesota Department of Natural Resources.
DOI: 10.6084/m9.figshare.3564570
title: Appendix B. Data assimilation approach.

description: Data assimilation approach.
DOI: 10.5061/dryad.1pj16/1
title: Fitness data

description: Juvenile survival and adult reproductive success for isofemale lines of C. maculatus in 5 different environments.
DOI: 10.5061/dryad.20c5c/13
title: Cv_VMN_Injection_12hCirculation

description: VMN particle injection, 12 hours circulation time, particle concentration map
DOI: 10.5061/dryad.20c5c/14
title: Psi_VMN_Injection_12hCirculation

description: VMN particle injection, 12 hours circulation time, map of the particles adhering to the capillary walls
DOI: 10.5061/dryad.20c5c/15
title: Tt_VMN_Injection_24hCirculation

description: VMN particle injection, 24 hours circulation time, temperature map
DOI: 10.5061/dryad.20c5c/16
title: Cv_VMN_Injection_24hCirculation

description: VMN particle injection, 24 hours circulation time, particle concentration map
DOI: 10.5061/dryad.20c5c/17
title: Psi_VMN_Injection_24hCirculation

description: VMN particle injection, 24 hours circulation time, map of the particles adhering to the capillary walls
DOI: 10.5061/dryad.20c5c/18
title: Tt_VMN_Injection_48hCirculation

description: VMN particle injection, 48 hours circulation time, temperature map
DOI: 10.5061/dryad.20c5c/19
title: Cv_VMN_Injection_48hCirculation

description: VMN particle injection, 48 hours circulation time, particle concentration map
DOI: 10.5061/dryad.20c5c/20
title: Psi_VMN_Injection_48hCirculation

description: VMN particle injection, 48 hours circulation time, map of the particles adhering to the capillary walls
DOI: 10.5061/dryad.29tj3/1
title: microplitis 2016-10-28

description: Data for Figure 1 and 2
DOI: 10.5061/dryad.2dc34/2
title: Phage densities

description: Phage densities during 66-day experiment
DOI: 10.5061/dryad.2dc34/3
title: Phage resistance

description: Phage resistance data for 66-day experiment
DOI: 10.5061/dryad.2dc34/4
title: 12-day experiment

description: Data from 12-day experiment
DOI: 10.5061/dryad.2r504/1
title: Bird data

description: Data used for the worked example of the paper. For each of 135 birds species, data on telencephalon mass (lntele), body mass (lnbody), and biparental care (Care) are provided. Continuous measurements (telencephalon and body mass) are log-transformed (Ln). The dataset was originally developed by Shultz & Dunbar (2010: Biol J Linn Soc); see linked paper for reference.
DOI: 10.5061/dryad.2r504/2
title: Bird phylogeny

description: Tree calibrated to time for 135 species of birds used in the worked example (branch lengths in units of time: Mya). It corresponds to a pruned tree from Hedges et al. (2015: MBE); see linked paper for reference and further details about the phylogeny.
DOI: 10.5061/dryad.2tp56/1
title: drive-download-20161008T232841Z

description: August - December 2014
DOI: 10.5061/dryad.2tp56/2
title: drive-download-20161008T233312Z

description: January - April 2015
DOI: 10.5061/dryad.3c769/1
title: 2010 Common Garden Phenotypes

description: This is an excel spreadsheet that with two tabs: one with the data and one with an explanation of the column headers in the data sheet. This file includes all data for all individuals that were grown and measured in my 2010 field experiment at the University of British Columbia farm in Vancouver, BC, Canada. Please note that these individuals were filtered in various ways for different analyses (e.g. only those planted in the replicated family design, or excluding individuals with putative hybrid ancestry). Please contact me if you need further details or would like a filtered dataset.
DOI: 10.5061/dryad.3c769/2
title: SNP genotype data

description: This is an excel spreadsheet that with two tabs: one with the data and one with an explanation of the column headers in the data sheet. This file includes all data for all individuals that were genotyped using the Sequenom iPLEX Gold technology for this study, including individuals from species other than Helianthus argophyllus which were not included in the manuscript. Please note that these individuals were filtered in various ways for different analyses (e.g. only those planted in the replicated family design, or excluding individuals with putative hybrid ancestry). Please contact me if you need further details or would like a filtered dataset.
DOI: 10.5061/dryad.3c769/3
title: Sequenom SNP marker metadata

description: This is an excel spreadsheet that with two tabs: one with the data and one with an explanation of the column headers in the data sheet. This file includes data for all markers that were included in two panels of 40 by the Sequenom iPLEX Gold technology for this study. Please note that these markers were filtered for reliability and genotype call rate in the final analyses. Please contact me if you need further details or would like a filtered dataset.
DOI: 10.5061/dryad.3h9k4/1
title: GIS-Vegetation data

description: This is a .zip file containing the raw observations of eelgrass occurrence at each location.  Each are is included as a separate .csv file.  Site abbreviations are present in each file title and are described fully in the main text of the paper.  Included in the .zip file is a file titled "Shapefile attribute table descriptions.xlsx" which has a description of the fields and how they connect to other files.
DOI: 10.5061/dryad.3h9k4/2
title: reorderd segments

description: This is a file with reordered segments for each of the eelgrass areas.  See ReadMe file for details.
DOI: 10.5061/dryad.3h9k4/3
title: shore_midpoints_with_attributes_utm_nad83_pat-pub

description: Shoreline attribute file for 100m segments of Puget Sound, WA shoreline. Description of the columns can be found in the readme file accompanying the GIS-Vegetation data.
DOI: 10.5061/dryad.3h9k4/4
title: Example estimation code and control files
DOI: 10.5061/dryad.4nt0f/2
title: Supplemental Data Set 2

description: Computational Analysis of Transcriptome-Wide Differential Gene Expression.
DOI: 10.5061/dryad.4nt0f/3
title: Supplemental Data Set 3

description: Splicing Index Analysis.
DOI: 10.5061/dryad.4nt0f/4
title: Supplemental Data Set 4

description: Analysis of NMD Target Features and Overlap between NMD- and Light-Regulated AS.
DOI: 10.5061/dryad.4nt0f/5
title: Supplemental Data Set 5

description: Categorization of Light-Regulated and Reference Gene Sets into Functional Subgroups.
DOI: 10.5061/dryad.4nt0f/6
title: Supplemental Data Set 6

description: Expressed Intergenic Regions.
DOI: 10.5061/dryad.4nt0f/7
title: Supplemental Data Set 7

description: Computational Analysis of Transcriptome-Wide AS Changes in Response to Red Light Based on the Data from Shikata et al. (2014).
DOI: 10.5061/dryad.5242j/1
title: Model version and URL
DOI: 10.5061/dryad.5242j/2
title: Inputs, settings, and state variables for RHESSys simulations

description: This includes all files necessary to run RHESSys simulations with the file structure already set up.
DOI: 10.5061/dryad.68s67/1
title: Supplementary isotope and radiocarbon data on subfossil hippos and tortoises of Madagascar

description: Raw and corrected d13C data and 14C and calibrated radiocarbon ages before present, and data sources for now-extinct Hippopotamus and Aldabrachelys on Madagascar