cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.50p47/5
title: Supplemental Dataset 10: Insertion list for the dataset used for Figure 5, 5' side, raw.
DOI: 10.5061/dryad.50p47/6
title: Supplemental Dataset 11: Insertion list for the dataset used for Figure 5, 3' side, raw.
DOI: 10.5061/dryad.50p47/7
title: README file for Supplemental Datasets 7-11
DOI: 10.5061/dryad.5tp6r/1
title: Twin and Family Longitudinal Measures of Cortical Thickness

description: .RData file containing demographic information and vertex-level longitudinal measures of cortical thickness. Users will need to install the free software package R at http://http://cran.us.r-project.org. The readme object within the .RData file contains descriptions of individual variables. Vectors of vertex-level results can be visualized using brain-view2; see https://wiki.mouseimaging.ca/display/MICePub/brain-view to access information on how to download brainview. Further details on cortical thickness measures and zygosity determination can be found in the original manuscript.
DOI: 10.5061/dryad.68mj4/1
title: Climate

description: This file contains data on the timing of snowmelt from 1935-2012, average April-May temperatures from 1973-2011, and minimum April-May temperatures from 1973-2011.  The timing of snowmelt was observed from 1975-2012, and estimated from 1935-1974 based on correlations with river runoff.  Temperature data come from the NOAA station in Crested Butte, Colorado.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/2
title: Long-term flowering_year

description: This file contains data on flowering time (first flowering and peak flowering) from 1973-2011 averaged across all plots, as well as snowmelt data and average April-May temperature data for these years.  Timing of flowering was collected by David Inouye and collaborators.  Snowmelt data was collected by billy Barr.  Temperature data come from the Crested Butte (CO) NOAA station.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/3
title: Long-term flowering time at the plot level

description: These are data on flowering time (first flowering time and peak flowering time) for all plots from 1973-2011.  Data were collected by David Inouye and collaborators.  Temperature data are from the Crested Butte, CO NOAA station, and snowmelt data were collected by billy barr.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/4
title: Individual level data for RILs (Recombinant Inbred Lines)

description: This file contains the individual level data for selection analyses and estimates of response to selection in the recombinant inbred lines (RILs) planted in the Montana and Colorado parental environments.  Included are data on planting site, family identification, timing of first flowering, plant size at flowering, absolute and relative fitness, and covariates.  These data were collected by Jill Anderson and Tom Mitchell-Olds in the field.  Text Wrangler was used to create the data file.
DOI: 10.5061/dryad.68mj4/5
title: Family level averages for the Recombinant Inbred Lines (Colorado)

description: This file contains family-level average trait values for the recombinant inbred lines (RILs) in the Colorado garden.  Columns include: family, leaf number at flowering (standardized to a mean of 0 and standard deviation of 1), height at flowering (standardized to a mean of 0 and standard deviation of 1), relative fitness (=absolute fitness/maximum fitness of individuals), and flowering time (both standardized to a mean of 0 and SD of 1, and unstandardized).  Standardizations were made on the individual level data prior to calculating the average values.  Jill Anderson collected these data at the Colorado field garden.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/6
title: Carpenter_Meadow_transect_2010

description: This file contains phenotypic and fitness data on naturally-recruiting Boechera stricta plants in 5 transects.  Jill Anderson collected these data at the Carpenter Meadow site in 2010.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/7
title: Carpenter_Meadow_transect_2011

description: This file contains phenotypic and fitness data on naturally-recruiting Boechera stricta plants in 5 transects.  Jill Anderson collected these data at the Carpenter Meadow site in 2011.  The data file was created in Text Wrangler.
DOI: 10.5061/dryad.68mj4/8
title: Carpenter_Meadow_experiment

description: This file contains data from the experiment at Carpenter Meadow to assess natural selection on flowering in local genotypes. Jill Anderson collected data  in the field in 2010. Analyses included size at planting (number of leaves) and cohort as fixed effects, and row nested within block as random effects. The data file was created in Text Wrangler.
DOI: 10.5061/dryad.75nv22qj/20
title: turtles-genetrees-no-snake-from-cloudforest.tar.bz2

description: STAR & STEAC Genetrees generated from the data in turtles-individual-nexus-files-for-loci.tar.bz2, dropping snake, using Cloudforest (map-reduce Phybase).
DOI: 10.5061/dryad.7d2g2/2
title: Dataset2

description: Nexus file for Dataset 2, 38-taxon dataset.
DOI: 10.5061/dryad.7h9f4/3
title: SteepSelection_CDPOP

description: 3) Steep spatial selection gradient (‘steep’): For this scenario, stronger spatial selection gradients were assigned to each genotype, with the relative fitness coefficients for AA of 1.0, 0.6, and 0.2 for black, mixed, and white waters, respectively. An opposite spatial selection gradient was implemented for aa (0.2, 0.6, and 1.0 for black, mixed, and white waters, respectively). Aa received a uniform selection gradient of 0.2 in all three scenarios.
DOI: 10.5061/dryad.7h9f4/4
title: BarrierRemove_HighMigration_CDPOP

description: Simulating Secondary Contact 1) We initially placed complete barriers on the riverscape to restrict movement of individuals to and from the three subgroups (Negro, Maderia, and Amazon). We then conducted an isolation-by-riverine distance simulation modeling experiment within each subgroup using a movement distance that considered the maximum extent of the riverscape (i.e., mimicking the spatial selection simulation parameters or high migration).
DOI: 10.5061/dryad.7h9f4/5
title: BarrierRemove_LowMigration_CDPOP

description: Simulating Secondary Contact 1) We initially placed complete barriers on the riverscape to restrict movement of individuals to and from the three subgroups (Negro, Maderia, and Amazon). We then conducted an isolation-by-riverine distance simulation modeling experiment within each subgroup using a movement distance that considered nearest neighbor extent of the riverscape (i.e., low migration). For the low migration scenario, offspring dispersed to locations nearer to their birth location with probability based on the inverse-square of distance and a restricted threshold of 200 km, which reduced the occasional long-range dispersers as in the high migration scenarios.
DOI: 10.5061/dryad.82181/1
title: Dataset Nabholz Glémin Galtier 2008

description: This is the dataset used in :Nabholz B, Glémin S, Galtier N. 2008. Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis. Mol. Biol. Evol 25:120–130.0 or NA indicates missing data.Life-history traits are from AnAge database (http://genomics.senescence.info/species/)De Magalhães JP, Costa J. 2009. A database of vertebrate longevity records and their relation to other life-history traits. J. Evol. Biol. 22:1770–1774.mass : body mass in gramlongevity : maximum longevity in Yearsmetabolism : Basal metabolic rate in Wmaturity_F : Female sexual maturity in daymaturity_M : Male sexual maturity in daygestation : Gestation in dayRate : Substitution rate (subst/site/MA) estimated with Cytochrome b third codon position.
DOI: 10.5061/dryad.88qf4/1
title: Angiosperm trees used for simulations, based on estimate of Bell et al. 2010.

description: Phylogenetic estimate of flowering plants and phylogenies used in simulations.  Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Bell, C. D., D. E. Soltis, and P. S. Soltis. 2010. The age and diversification of the angiosperms re-revisited. Am. J. Bot. 97:1296-1303.
DOI: 10.5061/dryad.88qf4/3
title: Harpaline beetle trees used for simulations, based on estimate of Ober and Heider 2010.

description: Phylogenetic estimate of harpaline beetles and phylogenies used in simulations.  Original tree is in 'Original Tree' tree block. 'Trees for simulation' tree block contains 100 trees with (i) branch lengths scaled to generation time and (ii) branch widths scaled to effective population size as described in Oliver (2013). Dated phylogenetic estimate was originally published in: Ober, K.A. and T. N. Heider. 2010. Phylogenetic diversification patterns and divergence times in ground beetles (Coleoptera: Carabidae: Harpalinae). BMC Evol. Biol. 10:262.
DOI: 10.5061/dryad.b2d29/1
title: Tadpole morphology

description: Morphological measurements of Agalychnis callidryas tadpoles reared in one of 5 predator treatments in Gamboa, Panama. Column headings are: Block of experiment, Tank tadpoles came from, Predator treatment, Hatching age treatment, Individual tadpole from each tank, Body length, Total tadpole length, Tail muscle height, Tail fin height, Body height, Max body height, and Body area.
DOI: 10.5061/dryad.b2d29/2
title: Tadpole swimming

description: Agalychnis callidryas swimming performance after being raised with different predators in Gamboa, Panama. Column headings are: Distance tadpole swam (cm), Number of tadpole, Number of swims (values may be averages of multiple swims), Number of frames swam, Number of tailbeats used, Rate of tailbeats per second, Speed of tadpoles (cm traveled/second), Total amount of time swimming, Number of tailbeats used per cm traveled, Predator treatment, Hatching age treatment, Block of experiment, Tank of experiment.
DOI: 10.5061/dryad.b835k/1
title: Sankar_et_al_data_file_1

description: Archive of tables (tab-delimited) combining raw data for all features of all cells in all sections obtained from Col-0.
DOI: 10.5061/dryad.b835k/2
title: Sankar_et_al_data_file_2

description: Archive of tables (tab-delimited) combining raw data for all features of all cells in all sections obtained from Ler.
DOI: 10.5061/dryad.b835k/3
title: Sankar_et_al_data_file_3

description: Archive of tables (tab-delimited) of the normalized data used in machine learning for the Col-0 sections from data file 1, combined with the cell type assignment.
DOI: 10.5061/dryad.b835k/4
title: Sankar_et_al_data_file_4

description: Archive of tables (tab-delimited) of the normalized data used in machine learning for the Ler sections from data file 2, combined with the cell type assignment.
DOI: 10.5061/dryad.cr3g5v4f/1
title: Mimulus_msats

description: This is a zipped file that contains two fastq files. They represent the data for microsatellite loci developed for Mimulus ringens from using Illumina paired-end reads. The paired-end reads are in separate files and for each sequence the locus name is in the title with the prefix "Miri" for Mimulus ringens.
DOI: 10.5061/dryad.ft48k/2
title: Admixed anadromous

description: This file contains multilocus data (15 microsatellite loci) for anadromous hybrid alewife and blueback herring (n=92) used in analysis of genomic clines.
DOI: 10.5061/dryad.ft48k/3
title: Admixed Kerr

description: This file contains multilocus data (15 microsatellite loci) for landlocked (Kerr Reservoir) hybrid alewife and blueback herring (n=119) used in analysis of genomic clines.
DOI: 10.5061/dryad.ft48k/4
title: Parental ALE

description: This file contains multilocus data (15 microsatellite loci) for 100 purebred alewife specimens used in the simulation of hybrids (HYBRIDLAB v.1.0) and in the analysis of genomic clines by Hasselman et al. (2014).
DOI: 10.5061/dryad.g2r32/1
title: Normal Bee data - spss output

description: Real text file containing touch test data in blocks of 5 trials
DOI: 10.5061/dryad.g2r32/2
title: Quinine versus water 1

description: graph of quinine vs. H2O as aversive stimulus for differential conditioning.
DOI: 10.5061/dryad.g2r32/3
title: graph pad Q versus water

description: Graphpad file containing intermediate and comparison data used to generate acquisition curves for differential conditioning procedure.
DOI: 10.5061/dryad.g924s/1
title: Mating outcomes from controlled crosses of side-blotched lizards (Uta stansburiana)

description: This data set was created from a controlled laboratory breeding study of wild-caught side blotched lizards (Uta stansburiana), conducted in 2004 and 2006. Each dam is mated to a single sire, and data on their throat colors and mating outcomes are provided.
DOI: 10.5061/dryad.gt178/1
title: CJ_geno_1026SNP

description: The genotype data of 1026 SNPs in 14 populations with 186 individuals.
DOI: 10.5061/dryad.k4m41/1
title: All individual clone sequences

description: This file lists all the clone sequences that were confirmed as arbuscular mycorrhizal fungi and therefore were used in sequence analysis. The file is in FASTA format.
DOI: 10.5061/dryad.n5n37/1
title: integration

description: Program to integrate numerically the selection gradient on a sex modifier locus over a linear genetic map (C++ program)
DOI: 10.5061/dryad.n5n37/2
title: simulation program

description: Haploid sex modifier simulation program (C++ program)
DOI: 10.5061/dryad.q4r60/4
title: fielddata_Egea-Serranoetal21Jan14

description: Larval trait divergence  in the wild (Supplementary material)
DOI: 10.5061/dryad.q4r60/5
title: distancesEgea-SerranoetalJan14

description: MRM data for among population trait divergence – survival difference associations (Supplementary material)
DOI: 10.5061/dryad.qt48h/11
title: Marjanovic_&_Laurin_App_11

description: Model parameters chosen by Modeltest 3.7 using a neighbor joining (NJ) and the most parsimonious (MP) guide trees, compared to the model used by Zhang et al. (2005; pers. comm.) which was selected by Modeltest 3.06.
DOI: 10.5061/dryad.qt48h/12
title: Marjanovic_&_Laurin_App_12

description: Quartets used for quartet-dating in QDate 1.11 (see Table 5).
DOI: 10.5061/dryad.qt48h/13
title: Marjanovic_&_Laurin_App_13

description: Molecular divergence dates (rounded to Ma ago) calculated by quartet dating using QDate 1.11 using the evolution models from the three right columns of Appendix 11, compared to those reported (with confidence intervals) by Zhang et al. (2005) and to those from our supertree (Figs. 3–7).
DOI: 10.5061/dryad.qt48h/6
title: Marjanovic_&_Laurin_App_6

description: Biological nomenclature.
DOI: 10.5061/dryad.qt48h/7
title: Marjanovic_&_Laurin_App_7

description: List of localities that have yielded lissamphibian fossils.
DOI: 10.5061/dryad.rc628/3
title: Appendix 1 cytb 1050bp 080612

description: Haplotype Table whole cytochrome b sequences
DOI: 10.5061/dryad.rc628/4
title: Appendix 2 cytb 450bp 080612

description: Haplotype table partial cytochrome b
DOI: 10.5061/dryad.s42n1/1
title: Lagator et al. Effects of sex and migration in adaptation to sink environments dataset

description: Experimental data: Optical density measurements of growth of experimentally selected populations of Chlamydomonas reinhardtii
DOI: 10.5061/dryad.s5c8k/4
title: Needle N, 15N and Photosynthesis

description: Measurements of needle nitrogen concentration, needle 15N and needle net photosynthesis on the final sampling date in each of the habitats during late August of 2010 and 2011.
DOI: 10.5061/dryad.s5c8k/5
title: Seasonal Needle N and 13C

description: Measurements of needle N concentration and needle 13C made on approximately weekly intervals on 8 supplementary trees in each habitat during the 2011 growing season.
DOI: 10.5061/dryad.s5c8k/6
title: Fertilizer Branch Extension Growth

description: Measurements of annual branch extension growth made in 2007 and 2008 on 15 control trees and 15 trees that were fertilized with N, P and K adjacent to the treeline site in September of 2006, 2007 and 2008.
DOI: 10.5061/dryad.sn878/1
title: hh

description: spss file
DOI: 10.5061/dryad.tt0tq/1
title: Species descriptions of Namibimydas and Nothomydas in SDD format

description: Natural language species descriptions of Namibimydas and Nothomydas as exported from Lucid Builder 3.5 in SDD format.
DOI: 10.5061/dryad.vj7nr/1
title: AGT_Alignment
DOI: 10.5061/dryad.vj7nr/2
title: DBE_Alignment
DOI: 10.5061/dryad.vj7nr/3
title: GBSS&SS_Alignment
DOI: 10.5061/dryad.vj7nr/4
title: PGM_Alignment
DOI: 10.6084/m9.figshare.12980738
title: R0225_20180605a_videos

description: Rat 0225, skilled reaching data collected in Leventhal laboratory by Alexandra Bova
DOI: 10.5061/dryad.23g44/1
title: USYB-2012-210 Supp Data
DOI: 10.5061/dryad.23g44/11
title: DP35

description: alignment
DOI: 10.5061/dryad.23g44/2
title: *Dermo_paleo

description: xml file
DOI: 10.5061/dryad.23g44/5
title: *Hemir_taxonomy

description: xml file
DOI: 10.5061/dryad.23g44/7
title: ControlRegion

description: alignment
DOI: 10.5061/dryad.23g44/8
title: DP5

description: alignment
DOI: 10.5061/dryad.23g44/9
title: DP14

description: alignment
DOI: 10.5061/dryad.25d04/1
title: HeskethEtAL_2012_Data
DOI: 10.5061/dryad.3768m/1
title: R script for glmm analyses

description: Annotated code necessary to run the GLMM analyses. Also need the three data files: rodents.csv, annuals.csv, precip.csv.
DOI: 10.5061/dryad.3mt58823/1
title: Individual Gene Trees

description: Bayesian majority-rule consensus trees reconstructed for the 12 individual nuclear loci and the concatenated mitochondrial loci. Trees are presented as phylograms with branch lengths representing the average number of substitutions per site. Numbers on branches represent posterior probabilities.
DOI: 10.5061/dryad.40nk2/1
title: Brain microarray data

description: mRNA from whole brain without pituitary glands were analyzed with Agilent microarray.
DOI: 10.5061/dryad.40nk2/2
title: Testis microarray

description: mRNA from testis were analyzed with Agilent microarray.
DOI: 10.5061/dryad.40nk2/3
title: Expression_design

description: Probe sequences for expression microarray.
DOI: 10.5061/dryad.4dg60/1
title: Coverdale et al 2014 Data

description: This file contains raw data described in Coverdale et al. (2014) "Indirect human impacts reverse centuries of carbon sequestration and salt marsh accretion". Please contact the authors with any questions.
DOI: 10.5061/dryad.4g96s/1
title: 14lociDRYAD

description: The datafile is in GENEPOP format. It comprises genotype scores for 14 Crassostrea gigas-specific microsatellite loci. Locus names are listed at the beginning of the file under the title line, the first 7 loci are EST linked loci, the last 7 are anonymous loci. The first column under the loci names indicates the 6 population (WONE, WTWO, WTHR, AQON, AQTW, BONE) and their individuals. The genotypes for each individual and loci are in the columns 2 – 15. Missing genotypes are coded as "000". Allele scores for each locus are concatenated into six digits, with the first three letters representing allele "A", and the second three letters representing allele "B".
DOI: 10.5061/dryad.4v0c5/4
title: SNP_genotypes_160

description: This tab-separated file contains the genotype data for samples from 4T, 3Ps, 3NO and 4VsW analyzed with the 160 SNP panel.
DOI: 10.5061/dryad.5bd5r/2
title: Supplementary information

description: Supplementary material; tables S1, S2 and S3
DOI: 10.5061/dryad.5d6p6/5
title: LSU Salgado

description: Partial large nuclear ribosomal subunit sequence alignment
DOI: 10.5061/dryad.6354b/2
title: KingClonalityData1

description: Copy number log-ratio data for the 31 samples in the manuscript. It is a gzipped text file. This is part 1. Use cat to concatenate all 6 parts.
DOI: 10.5061/dryad.6kp30/2
title: body mass and fat score

description: Dataset used for the analysis of variation in body mass and fat score during the experiment
DOI: 10.5061/dryad.7d2g2/3
title: Supplementary Table 1

description: Supplementary Table 1
DOI: 10.5061/dryad.8271f/1
title: ITS1 reads after quality trimming

description: Fasta file containing all of the trimmed sequences (n=188,300) used in this study.  Poor quality sequences, mycobiont sequences, and chimeric sequences have been removed.  Singleton and doubleton OTU sequences are still present.
DOI: 10.5061/dryad.8271f/2
title: ITS1 read after quality trimming-group membership

description: This file contains a list of all 188,300 sequences used in the study and their associated group membership.  For example, samples in the study came from 3 host species (Pine, Pelt, Moss) x 3 individuals for each host (1,2,3) x 3 tissue storage methods (Fresh, CTAB, Silica).  So the name Pine3CTAB denotes Pinus host # 3, tissue stored in CTAB buffer prior to DNA extraction.
DOI: 10.5061/dryad.8271f/3
title: OTU abundance matrix by host/microsite/treatment

description: This file is the output from the mothur command make.shared for all 188,300 sequences in the study.  It is an abundance matrix with the number of sequences for each sample at every level of sequence divergence (e.g., unique, 0.00, 0.01, 0.05).  Level of 0.05 was used for the analyses for this study.  This file contains all OTU.
DOI: 10.5061/dryad.853t3/1
title: Lpictus con 2OG

description: Fasta file of all the mtDNA sequences used to run phylogeographic analyses on JModeltest, Bayes Phylogenies, TCS, Mega and DNAsp.
DOI: 10.5061/dryad.853t3/2
title: Geneland

description: Data used to run Geneland. The file includes coordinates and sequences. Nucleobases were changed by numbers (1-4) in order to be able to run Geneland.
DOI: 10.5061/dryad.8f73k/1
title: all_switchgrass_SNPs_filtered.txt

description: SNPs identified within the switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Trailblazer, Carthage and Shelter.
DOI: 10.5061/dryad.8f73k/2
title: all_switchgrass_SNPs_with_context_sequence.txt

description: This file contains context sequence surrounding SNPs identified within the switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Trailblazer, Carthage and Shelter.
DOI: 10.5061/dryad.8f73k/3
title: Alamo_transcript_assemblies_all_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Alamo.  This file includes all transcript isoforms.
DOI: 10.5061/dryad.8gh7p/1
title: DNA quantity and RNA quality and quantity for preservation of rat tissues under field simulated conditions and change in DNA concentration for different postmortem times.

description: The file has the quality (RIN value in Bioanalyzer) and quantity data (NanoDrop) of RNA extractions and DNA quantity data (NanoDrop) from different rat tissues preserved for a combination of times and conditions. We also include DNA concentration from extractions done on muscle rat tissue after a series of time intervals 0 hours-2 weeks.
DOI: 10.5061/dryad.8ht80/1
title: Package_Microviridae

description: This package contains the sequences of the Microviridae genomes assembled in the associated study, as well as an annotation file for each genome in genbank format.
DOI: 10.5061/dryad.c316t/2
title: Dryad 2 - microsatellites - Dmuliebre

description: D. muliebre microsatellite allele scores
DOI: 10.5061/dryad.c316t/3
title: Dryad 3 - microsatellites - Dferrugineum

description: Microsatellite allele scores for D. ferrugineum
DOI: 10.5061/dryad.c8qn1/1
title: carbohydrate storage data

description: Column 1: growth category, as in Table 2 of paper, Column 2: treatment (c= control, t1= one defoliation, t2= two defoliations), Column 3: harvest (harvests 1-6), Column 4: carbohydrate concentration (mass spectrometry counts), Column 5: total taproot carbohydrates (mass spectrometer counts)