cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2m22/1
title: Data_For_Kovachetal2013_EvolApps

description: This file contains the data used in "Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing".  The data are organized based on the methods used to analyze them and year.  The first three sheets are the data used for estimating the effective population size - the files are in ONeSAMP format.  The next three files are the data sets used to test for autocorrelation (GENALEX) and population structure (STRUCTURE) - the files are in GENALEX format.  The next sheet "Allozymes" contains the raw allele frequency data that were used to calculate G"st between early and late migrating fish in 1979-1983.  Each row is a different locus, the first column is the number of genotypes for each locus, and the next several columns are the observed allele frequencies at that locus.  The next three sheets are the data files used to calculate G"st for the microsatellite data from 1993, 2001, 2009.  The final file contain the data that were used to test for genetic homogeneity between the different quartiles of the migration timing distribution.
DOI: 10.5061/dryad.q164g/1
title: ColbeckAl_RSPB-2012-2552_DataDryad.xlsx

description: Excel file containing information for 1524 belugas, namely: Code, Location of capture, code of location of capture, Day (if available), month(if available), and year of capture, age (if available), sex (if available), and multilocus genotype at 13 microsatellite loci (in pb, one allele per column)
DOI: 10.5061/dryad.r4c7r/1
title: Oppenheim phenotypes and genotypes

description: File includes phenotypes and marker genotypes of all assayed insects.
DOI: 10.5061/dryad.sg45t/1
title: Density of caterpillars and percentage of caterpillars that were parasitized

description: The density of caterpillars was estimated each March from 1987 to 2013 on 10 lupine bushes (cats/lup) and in 5 transects dominated by poison hemlock (cats/hem).  SE refers to the standard error of each estimate.  The time series in this data file extends that used in the paper.
DOI: 10.5061/dryad.sj168561/1
title: Microsatellites

description: Microsatellite data included in this study, formatted for input into GenAlex
DOI: 10.5061/dryad.sk32d/1
title: Maternal exposure to predators
DOI: 10.5061/dryad.sp0ts0hc/2
title: Swift_etal_2012_AgeComp_Grip_DataExcel

description: Data in Microsoft Excel format
DOI: 10.5061/dryad.sp0ts0hc/3
title: Swift_etal_2012_AgeComp_Grip_DataASCII

description: Data in ASCII text format
DOI: 10.5061/dryad.t4n0g/1
title: Viburnum_Common_Garden

description: The number of non-herbivorous mites collected on leaves of Viburnum plants in a common garden in Ithaca, NY. Column headings: "EFN/Domatia type" = the location and presence/absence of extrafloral nectaries (EFN) and domatia ("absent" = no EFN or domatia, "lamina" = laminar EFN and tuft domatia, "petiole" = petiolier EFN and tuft domatia, "marginal" = marginal EFN and tuft domatia) ; "Species" = the species name of the Viburnum plant, "N Mites" = the number of non-herbivorous mites on the plant leaf.
DOI: 10.5061/dryad.t4n0g/2
title: Viburnum_acerifolum_mites

description: The number of non-herbivorous mites collected on experimentally manipulated leaves of Viburnum acerifolium. Field experiment conducted at near Ithaca, NY, USA (42 30 2.34N, 76 26 8.49W). Column headings: "TREMNT" = experimental treatment/manipulation applied to plant ("ALL OPEN" = control tar placed near, but not covering, extrafloral nectaries (EFN) and domatia, "BOTHX" = tar blocking/covering both EFN and domatia, "DOMX" = tar blocking/covering domatia and tar control near EFN, "EFNX" tar blocking/covering EFN and tar control near domatia); "Mites" = the number of non-herbivorous mites.
DOI: 10.5061/dryad.tf767/1
title: Schuett et al_Biol Letts_PO regressions data
DOI: 10.5061/dryad.tr16k/4
title: Tomato_Vac

description: This file contains data on CMV viral accumulation (µg virus/g tissue fresh weight) on tomato plants infected by CMV with or without satRNAs (semicolon delimited format). Data was used to estimate CMV transmissibility and transmission parameters according to Escriu et al. 2003 (Evolution 57, 755-765) and Escriu et al. 2000 (Phytopathology 90, 1068-1072).
DOI: 10.5061/dryad.vt84k/1
title: Dataset

description: There are three spreadsheets with data. The spreadsheet "Soil_dataset" contains the raw soil data, as well as the values of the RS index derived from them. The spreadsheet "IEMs_dataset" contains the raw amonium and nitrate values obtained from ion-exchange membranes, as well as the values of the RS index derived from them. The spreadsheet "SEM_dataset" contains the data used in the SEM models. After each data spreadsheet there is a spreadshet with the associated metadata, where a description of all the variables and units can be found.
DOI: 10.5061/dryad.13d31/1
title: DIFFERENT STENT

description: Included here is baseline data Logistic regression analyses
DOI: 10.5061/dryad.13d31/2
title: Baseline data Logistic regression analyses

description: Included here is baselinebaseline data Logistic regression analyses
DOI: 10.5061/dryad.1q88j/12
title: Cover_Herb_Residual

description: Plot-level values of total (summed) cover over the study period (1979 to 2008) of residual herbaceous species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are % (values can exceed 100%).
DOI: 10.5061/dryad.1q88j/2
title: Biomass_Herb_Colonist

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for colonizing herbaceous species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.1q88j/22
title: Richness_Herb_Total

description: Richness over the study period (1979 to 2008) of all herbaceous species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are number of species/plot.
DOI: 10.5061/dryad.1q88j/7
title: Biomass_Shrub_Total

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for all shrub species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.1qp42/1
title: Haloferax volcanii reference genome

description: The Hfx. volcanii genome that we used to align reads
DOI: 10.5061/dryad.27q72/1
title: BEAST infile for Iguania ND1 data

description: XML formatted infile for fossil calibrated analysis of Iguania ND1 data in BEAST
DOI: 10.5061/dryad.27q72/2
title: *BEAST infile for Species Tree Estimation of Subset A

description: XML formated infile for species tree estimation of subset A dataset in *BEAST. Includes ND1, ND1 flanking regions, PRLR, and UBN1 sequences.
DOI: 10.5061/dryad.27q72/3
title: *BEAST infile for Species Tree Estimation of Subset B

description: XML formated infile for species tree estimation of subset B dataset in *BEAST. Includes ND1, ND1 flanking regions, PRLR, and UBN1 sequences.
DOI: 10.5061/dryad.27q72/6
title: BEAST infile for Oplurus cyclurus, constant pop size

description: XML formated infile for estimation of Oplurus cyclurus gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes constant growth model.
DOI: 10.5061/dryad.2n545/7
title: M1044
DOI: 10.5061/dryad.2n545/8
title: M1366
DOI: 10.5061/dryad.2n545/9
title: M1510
DOI: 10.5061/dryad.3m5fc/10
title: Matlab function for two age four stage class model 1

description: Matlab function that is called by the small_neutral.m file and comp_smallmats.m file
DOI: 10.5061/dryad.3m5fc/11
title: Matlab function for two age four stage class model

description: A matlab function that is called by small_neutral.m and comp_smallmats.m file for the two age and four stage class example.
DOI: 10.5061/dryad.3m5fc/12
title: Matlab code for generating Fig. 2-4

description: Matlab code for generating Fig. 2-4 using Output files: killer_out, patches1_out, small_neutral, and smallouts
DOI: 10.5061/dryad.3m5fc/13
title: Soay Sheep IPM matrices used for Appendix

description: Data base that has been used for the Soay Sheep example including the matrices (Age-stage structured with dimensions of 900x900).
DOI: 10.5061/dryad.3m5fc/5
title: Matlab output file for two patch model

description: This is the Matlab output generated from the patches_analysis file
DOI: 10.5061/dryad.3m5fc/6
title: Matlab code for two age class four size class example: matices

description: Matlab code that generates the data for the two age class four size class model. It generates an output file called small_neutral
DOI: 10.5061/dryad.3m5fc/7
title: Matlab output file small_neutral

description: Matlab output file for two stage four age class model: small_neutral output file. Generated from small_neutral.m file
DOI: 10.5061/dryad.3m5fc/8
title: Matlab code two age four stage class example run second

description: Matlab code for the two age four stage class example that generates the data for Fig. 3
DOI: 10.5061/dryad.3m5fc/9
title: Matlab output two age four stage class example

description: Matlab output for the two age class four stage class example generated by comp_smallmats.m file
DOI: 10.5061/dryad.7137r/11
title: bird1386_pair4_son1_all_songs
DOI: 10.5061/dryad.7137r/12
title: bird1385_pair4_son2_all_songs
DOI: 10.5061/dryad.7137r/13
title: bird1162_pair5_tutor_all_songs
DOI: 10.5061/dryad.7137r/14
title: bird1398_pair5_son1_all_songs

description: sound file
DOI: 10.5061/dryad.7785h/1
title: aeb1 phylogenies

description: The Aeb1 phylogenies include representatives of all major phyla/supergroups for the three domains of life (when available).  Archaea, Eukarya, and Bacteria protein sequences were aligned at once (no profile alignment) and protein alignments were trimmed individually and then concatenated into a supermatrix (resulting in 13432 positions).  Aeb1 contains no “Archezoan” sequences (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) but has some fast evolving eukaryotes, including Euglenozoa.  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).
DOI: 10.5061/dryad.78b2h/1
title: Dryad_Evolution_12-0587.R1
DOI: 10.5061/dryad.79364/1
title: Barnes et al Data files for ECE-2014-06-0295

description: Excel spreadsheet containing the fragment lengths or allele sizes of 12 microsatellite loci amplified for 459 isolates of Dothistroma septosporum collected from 15 different countries. The mating type of each isolate is also indicated.
DOI: 10.5061/dryad.7c425/1
title: Prunus lannesiana var. speciosa data

description: 2cohorts_data.xls ...Genotype data in the GenAlEx format (for 2 cohorts data). | 8poplations_data.xls ...Genotype data in the GenAlEx format (for 8 populations data). | 3subpopulations_data.xls ...Genotype data in the GenAlEx format (for 3 subpopulations data). | PlotA_adults_seeds.csv ...Genotype data of parentage analysis in the Cervus format (for plot A). | PlotB_adults_seeds.csv ...Genotype data of parentage analysis in the Cervus format (for plot B). | plotA_2001.xls ...Data of various factors on mating success (plot A in 2001). | plotA_2002.xls ...Data of various factors on mating success (plot A in 2002). | plotB_2001.xls ...Data of various factors on mating success (plot B in 2001). | plotB_2002.xls ...Data of various factors on mating success (plot B in 2002). | plotA_sgs.txt ...SPAGeDi formatted data for spatial genetic structure analysis (for plot A). | plotB_sgs.txt ...SPAGeDi formatted data for spatial genetic structure analysis (for plot B).
DOI: 10.5061/dryad.7kd74/4
title: Genbank Accession Numbers of cyt b and CR for SIlver pheasant and Kalij pheasant in China
DOI: 10.5061/dryad.7m6kg/44
title: Fig. 7c: ROM 60100 — Nectocaris pteryx mouthparts from the Burgess Shale

description: Direct illumination
DOI: 10.5061/dryad.7m6kg/60
title: Fig. 10g: ROM 59656 – Nectocaris pteryx from the Burgess Shale

description: Posterior region. Stripes represent a taphonomic feature produced by the bars
DOI: 10.5061/dryad.7m6kg/61
title: Fig. 10i: Reconstruction of nectocaridid internal anatomy

description: Model showing relationship between bars (brown, interpreted as being associated with muscle), gills (mauve), fins (cream), and axial cavity (blue).  Model generated in Blender.
DOI: 10.5061/dryad.7m6kg/63
title: Fig. 11a: HK-MF-00002 — Nectocaris ?pteryx, large morph from Chengjiang

description: Infill of funnel canal appears braided; axial cavity reworked by burrowing
DOI: 10.5061/dryad.7sd19/1
title: Colonizing macroinvertebrate community data
DOI: 10.5061/dryad.7sd19/2
title: Biofilm function and structure data
DOI: 10.5061/dryad.9qt14/6
title: Geneland

description: Input files and R script for Geneland v4.0.3.
DOI: 10.5061/dryad.9qt14/7
title: IM and IMa

description: Input and output files for IM and IMa.
DOI: 10.5061/dryad.9qt14/8
title: Coalescent Simulations

description: Tree files simulated with Mesquite v2.75 and chi-square test.
DOI: 10.5061/dryad.9qt14/9
title: BEAST

description: Input and output from the Extended Bayesian Skyline Plot implemented in BEAST v1.7.5.
DOI: 10.5061/dryad.b1q2n/14
title: figure3.zip

description: Files: figure3.zip (contains files well.XXX (XXX are numbers from 001 - 096, from 101 to 196, and from 201 to 204))Format: ZIP archive (contains flow cytometry data file FCS 2.0)Contents: Flow cytometry analyses of bacterial cultures. Samples were excited at a wavelength of 488 nm, while emission was detected at 510 nm (GFP) and 560 nm (DsRed).
DOI: 10.5061/dryad.b8h1n/1
title: NEXUS alignment Calligrapha CPS data
DOI: 10.5061/dryad.bv432/1
title: 2358_1_supp_1_n0l8hh

description: Table with distribution of crinoid taxa at each locality considered
DOI: 10.5061/dryad.c08b5/2
title: IM_cyano_vs_melano

description: IM input for cyanocinctus versus melanocephalus comparison
DOI: 10.5061/dryad.c8jg8/1
title: PE3
DOI: 10.5061/dryad.c8jg8/2
title: PE4
DOI: 10.5061/dryad.c8jg8/3
title: PE_PGRS26
DOI: 10.5061/dryad.c8jg8/5
title: PE_PGRS51
DOI: 10.5061/dryad.dj342/2
title: Measurement data

description: Measurements (in millimeters) of specimens used in morphometric analyses.
DOI: 10.5061/dryad.ff52k/1
title: longitudinal

description: longitudinal data on female yearly reproductive success and ornament expression
DOI: 10.5061/dryad.g0b20/3
title: ITS

description: Alignment of ITS region (partial 18S - ITS1 - 5.8S - ITS2- partial 28S)  of Zanclea sp. associated with different Acropora species
DOI: 10.5061/dryad.g0b20/4
title: ITS1

description: Alignment of ITS of Zanclea sp. associated with different Scleractinia species
DOI: 10.5061/dryad.h016k/1
title: 2012BASECOPSIAD ingles (2)

description: The files that we submit do not contain any personally identifiable human subject information
DOI: 10.5061/dryad.h0228/3
title: DarwinTunes-medley-at-250-generations

description: A medley of audio loops selected manually from a particular point in the evolution of experimental population 1 (EP1).
DOI: 10.5061/dryad.j57c0/2
title: 2_ITS_complete_rooted

description: ITS alignment in Nexus format
DOI: 10.5061/dryad.j57c0/3
title: 2_GPD_complete_rooted

description: GPD alignment in nexus format
DOI: 10.5061/dryad.j57c0/4
title: 3_mtlsu_complete_rooted

description: mtLSU alignment in nexus format
DOI: 10.5061/dryad.kg007/1
title: Carotenoid plasma and trait data used for comparative analyses

description: Carotenoid plasma levels and coding for carotenoid-dependent traits per bird species included in the comparative analyses. The file also includes the appropriate references from which the carotenoid plasma levels were extracted.
DOI: 10.5061/dryad.kg521/1
title: Genotype information for Agrostis chloroplast SSR, matK, and Agrostis nuclear SSR markers.

description: The excel file shows the genotype information for each individual plant for matK and all Agrostis chloroplast SSR (AcpSSR) markers on the first tab, and the genotype information for each individual plant for all the Agrostis nuclear SSR (AnuSSR) markers in the second tab. For the AcpSSR tab, the first column corresponds to the plant name and each of the following columns corresponds to one marker. In the AnuSSR tab, the first column corresponds to the plant name and each of the following columns represents an allele for each of the AnuSSR markers used. In both cases, “na” indicates no information is available for that plant-marker combination.
DOI: 10.5061/dryad.nc6bs/1
title: Morandin et al. Vg sequences

description: This file contains Vitellogenin and Vitellogenin-like sequences (amino acid and predicted protein) used for the phylogenetic tree (Figure 1), annotated in insect species for Morandin et al. 2014.
DOI: 10.5061/dryad.nc6bs/2
title: Morandin et al. Vg alignment

description: This file contains the alignment of Vitellogenin and Vitellogenin-like sequences used for the phylogenetic tree (figure 1) presented in Morandin et al. 2014.
DOI: 10.5061/dryad.nc6bs/3
title: Morandin et al. FexsVgs alignment

description: This file contains alignment generated via ClustalX of Vitellogenin and Vitellogenin-like sequences of Formica exsecta.
DOI: 10.5061/dryad.q03g2/4
title: Geographic Distance Matrix

description: Distance in kilometers between the edges of the elephant sampling polygons
DOI: 10.5061/dryad.r4c7r/2
title: Oppenheim permutation results

description: File contains results of permutation tests of marker-phenotype association for all traits discussed in the manuscript. Empirical significance thresholds are given in the file.
DOI: 10.5061/dryad.s6n57/1
title: Medicago Fecundity

description: Fecundity values for each plant
DOI: 10.5061/dryad.st020/1
title: Phenotype and molecular data for each F2 population

description: This file contains phenotype and molecular marker data from three F2 populations. Each spreadsheet corresponds to one population. 09S95, F2 T1693 x YP. 09S96, F2 GBL  x YP. 09S97, F2 SM x GBL. Abbreviations: YP, cv Yellow Pear. GBL, cv Gold Ball Livingston.  SM,  cv San Marzano. T1693, cv T1693.
DOI: 10.5061/dryad.st020/2
title: Raw genotype data extracted from Genome studio Software

description: This file contains the genotype scores for 7720 SNPs generated with the SolCAP Illumina Infinium Assay for 40 samples. The samples are the parental genotypes: YP, cv Yellow Pear. GBL, cv Gold Ball Livingston.  SM,  cv San Marzano. T1693, cv T1693. B95A, bulk with the 15 most round genotypes in 09S95 population. B95B, bulk with the 15 most elongated genotypes in 09S95 population. B96A, bulk with the 15 most round genotypes in 09S96 population. B96B, bulk with the 15 most elongated genotypes in 09S96 population. B97A, bulk with the 15 most round genotypes in 09S97 population. B97B, bulk with the 15 most elongated genotypes in 09S97 population. Also the 15 most round and 15 most elongated genotypes in the F2 GBL x YP (09S96) are shown.
DOI: 10.5061/dryad.st020/3
title: T-test result of each recombinant F2-F3 family

description: This file contains phenotype and molecular marker data used for progeny test in F2-F3 recombinant families. The t-test result for fruit shape index in each recombinant family also is shown.
DOI: 10.5061/dryad.tm80k/1
title: Supplementary_Material_Search_bias

description: C code and Windows executables, to calculate bias for wagner trees and branch-swapping starting from random trees.
DOI: 10.5061/dryad.16h8j/1
title: analysisdata_140628

description: This data is SPSS.
DOI: 10.5061/dryad.1q88j/25
title: Richness_Shrub_Total

description: Richness over the study period (1979 to 2008) of all shrub species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are number of species/plot.
DOI: 10.5061/dryad.25131/10
title: plot_propDur - 09-16-12

description: R script for plotting figure 8 from the main text.
DOI: 10.5061/dryad.25131/7
title: ratesVresolved_08-16-12

description: An R workspace file containing all simulation data needed for plotting the results of the simulations comparing sampling and differentiation rates (i.e. Fig. 7). Can be read into R with function load().
DOI: 10.5061/dryad.25131/8
title: plotting_script

description: R plotting script for all supplemental figures and figures 3-6 of the main text.
DOI: 10.5061/dryad.2637g/5
title: genbank accession data

description: table of genbank accession numbers and sequence authorship
DOI: 10.5061/dryad.269gp/1
title: Kim_et_al_(Heredity)
DOI: 10.5061/dryad.26qn0/1
title: Y-STR haplotypes and haplogroups in Partecipanza and S. Giovanni in Persiceto samples
DOI: 10.5061/dryad.27q72/10
title: BEAST infile for Oplurus cyclurus, Watershed Model Zone E

description: XML formated infile for extended Bayesian skyline plot analysis of Oplurus cyclurus from watershed model (Wilme et al. 2006) Zone E in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.
DOI: 10.5061/dryad.27q72/12
title: PRLR alignment

description: Alignment of sequence data for PRLR from all oplurine taxa included in this study. Alleles were determined either through TA cloning or computationally using the program PHASE.
DOI: 10.5061/dryad.27q72/13
title: UBN1 alignment

description: Alignment of sequence data for UBN1 from all oplurine taxa included in this study. Alleles were determined either through TA cloning or computationally using the program PHASE.
DOI: 10.5061/dryad.27q72/4
title: BEAST infile for Oplurus cuvieri, constant pop size

description: XML formated infile for estimation of Oplurus cuvieri gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes constant population size model.
DOI: 10.5061/dryad.27q72/5
title: BEAST infile for Oplurus cuvieri, exponential growth

description: XML formated infile for estimation of Oplurus cuvieri gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes exponential growth model.
DOI: 10.5061/dryad.27q72/7
title: BEAST infile for Oplurus cyclurus, exponential growth

description: XML formated infile for estimation of Oplurus cyclurus gene tree and divergence times in BEAST 1.6.2. Includes sequence data for ND1 and ND1 flanking regions and assumes exponential growth model.
DOI: 10.5061/dryad.27q72/8
title: BEAST infile for Oplurus cuvieri, Watershed Model Zone 8

description: XML formated infile for extended Bayesian skyline plot analysis of Oplurus cuvieri from watershed model (Wilme et al. 2006) Zone 8 in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.
DOI: 10.5061/dryad.27q72/9
title: BEAST infile for Oplurus cyclurus, Watershed Model Zone 6

description: XML formated infile for extended Bayesian skyline plot analysis of Oplurus cyclurus from watershed model (Wilme et al. 2006) Zone 6 in BEAST 1.6.2. Includes sequence data for ND1, ND1 flanking regions, PRLR, and UBN1.
DOI: 10.5061/dryad.2ds7p/1
title: BodyWeights_data

description: Body weights of mice used in this study, across time post-injury
DOI: 10.5061/dryad.2ds7p/2
title: 3chamber_test_data

description: Mice injured at adolescence (postnatal day 35) and tested in the three-chamber social approach task at adulthood. Percentage time spent in each chamber was quantified.