cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sp4t0/12
title: Supplemental Appendix 2

description: Legend for models and analyses in Supplemental Appendices 3 and 4.
DOI: 10.5061/dryad.sp4t0/13
title: Supplemental Appendix 3

description: Reclassified GARP models. Each figure shows the reclassified GARP models for each genus in each time-slice of each sequence. Note that GARP values indicate suitability and range from 0 to 100. See Supplemental Appendix 2 for explanation of the color values.
DOI: 10.5061/dryad.sp4t0/14
title: Supplemental Appendix 4

description: Original Maxent Models, Reclassified Maxent Models, and Geographic overlap analyses. Each figure shows the original Maxent model outputs in the left column, and the reclassification of that model to the right. The far right images are the final reclassified overlap analysis of the forward projected model and the original model of the next consecutive time slice. Model output values range from 0.0 to 1.0 and indicate probability. Final overlap calculation values indicate agreement, and range from 1 to 4. See Supplemental Appendix 2 for explanation of symbology.
DOI: 10.5061/dryad.sp4t0/7
title: Supplemental Table 5

description: Weighted percent of geographic overlap between models generated byGARP and Maxent per time slice.
DOI: 10.5061/dryad.sp4t0/8
title: Supplemental Table 6

description: Overlap calculations for percent geographic overlap between Maxent models. The weighting scheme and percent overlap calculations are described in Supplemental Text.
DOI: 10.5061/dryad.sp4t0/9
title: Supplemental Table 7

description: ENMtools I and D values relative to the 95% confidence interval. Both of these metrics are measured from 0 (complete dissimilarity) to 1 (identity). I/D values that fall within the 95% C.I. (“in”) indicate models that are no more/less similar than random and are interpreted as evidence of niche conservatism. I/D values that fall above the 95% C.I. (“out, high”) and indicate statistical niche conservatism. I/D values that fall below the 95% C.I. (“out, low”) are interpreted as evidence of niche evolution.
DOI: 10.5061/dryad.147r0/1
title: genotypes
DOI: 10.5061/dryad.147r0/2
title: geneflow_landscape_variables

description: The table contains landscape variables measured within the corridors between the study populations of Lychnis flos-cuculi in Oberaargau region, Switzerland. The corridors had different widths, which have been indicated in variable names: 50, 100, 300, 500 and 1000 meters. Columns include the proportion of the following landscape variables measured within corridors: forests (indicated as "forest" in the column name), settlements ("settlement"), the verges of ditches, streams and rivers ("water") and agricultural land ("agri"). Landscape variables were measured using VECTOR25 data by Swisstopo. In addition to landscape variables, the table includes cumulative elevation change between the study populations (in meters) as well as Euclidean distance between populations (in meters). The table also includes the measure of gene flow used in the study - genetic differentiation Fst.
DOI: 10.5061/dryad.1v02q/1
title: Shapefile of county-level bagworm occupancy

description: Shapefile of county-level bagworm occupancy constructed from Wollerman, E. H. 1971. Bagworm. United States Department of Agriculture Forest Pest Leaflet 97.
DOI: 10.5061/dryad.1v02q/2
title: Adult bagworm longevity

description: Data on adult bagworm longevity (in hours) by sex
DOI: 10.5061/dryad.221t6.1
title: Data from: A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species
DOI: 10.5061/dryad.221t6.2
title: Data from: A century-long genetic record reveals that protist effective population sizes are comparable to those of macroscopic species
DOI: 10.5061/dryad.221t6.2/1.1
title: Pdalei_Msat_Genotypes

description: Microsatellite genotypes (at six loci) for strains of the marine dinoflagellate P.dalei.  Each sample represents the strains that could be revived from a slice of sediment core taken from Koljo Fjord, Sweden.
DOI: 10.5061/dryad.36p54/1
title: Parr survey data and associated spawner densities
DOI: 10.5061/dryad.36p54/2
title: Res09-06Copeland2009 Idaho Natural Production Monitoring and Evaluation

description: This document describes the sampling design for this data set.
DOI: 10.5061/dryad.420h7/3
title: Online Appendix 2

description: This is online Appendix 2 that includes all GenBank numbers for all samples with data already available on GenBank.
DOI: 10.5061/dryad.420h7/4
title: DATASET_Lampropeltis

description: This is the dataset consisting of phased sequences in nexus format. It includes a full cytb dataset (329 taxa) and a smaller cytb dataset that only includes samples that were also used for the nuclear datasets (124 taxa).
DOI: 10.5061/dryad.420h7/5
title: Online Appendix 1

description: This appendix includes all information for the samples used in the study.
DOI: 10.5061/dryad.450qq/1
title: Streptophytina_by_genus_alignment.phy

description: A phylip-format alignment file for use with the program RAxML, containing nucleotide sequence data extracted from GenBank for all available land plant genera. The partition file "Streptophytina_by_genus_partitions.part.reduced" should be used in conjunction with this one.
DOI: 10.5061/dryad.450qq/2
title: Streptophytina_by_genus_partitions.part

description: A RAxML partition file to be used with the alignment file "Streptophytina_by_genus_partitions.alignment.reduced".
DOI: 10.5061/dryad.450qq/3
title: RAxML_bestTree.generic_tree

description: The maximum likelihood tree topology found using the alignment file "Streptophytina_by_genus_partitions.alignment.reduced" and the partition file "Streptophytina_by_genus_partitions.part.reduced" using the parameters described in the PLoS One publication. The tree has been rooted manually.
DOI: 10.5061/dryad.450qq/4
title: generic.ultrametric

description: An ultrametric chronogram generated using the program treePL and the maximum likelihood topology, as described in the PLoS One manuscript text.
DOI: 10.5061/dryad.450qq/5
title: scripts

description: Python (and some other) scripts used to create figures, automate analyses, and perform other tasks related to the generation of the results as well as the manuscript itself. These are explained further internally using comments, and also discussed in the PLoS One publication.
DOI: 10.5061/dryad.450qq/6
title: generic_tree_dated

description: A configuration file for treePL used to generate the "generic.ultrametric.tre" file.
DOI: 10.5061/dryad.45hh0/1
title: 131021 Genomics assisted ancestry deconvolution in grape

description: Genome-wide SNP data for grapevine samples (Vitis) used for ancestry estimation. Sample IDs for individuals used as ancestral populations and interspecific hybrids. Scripts used for simulating interspecific hybrids using the genotype data.
DOI: 10.5061/dryad.4gb6n541/1
title: Raeymaekers et al-MolEcol-2012 D vs Gst

description: Sheet 1: microsatellite data (6 loci) of 28 lowland and upland samples collected in 2004. Sheet 2: microsatellite data (14 loci) of 18 lowland and upland samples collected in 2004. Sheet 3: microsatellite data (6 loci) of 21 upland samples collected in 2002.
DOI: 10.5061/dryad.4hp5n/1
title: Covert_et_al_2013_PNAS_data

description: Data from the paper includes fitness values from all main experiments, all replay experiments, and lines of descent for reconstructing the analysis of sign-epistasis.
DOI: 10.5061/dryad.4md5s/2
title: Daughters daily reproduction

description: Reproductive output of aphid daughters assessed every other day.
DOI: 10.5061/dryad.4md5s/3
title: Daughter weight

description: Weight of aphid daughters.
DOI: 10.5061/dryad.51b94/1
title: Richardson 2012_MolEcol_AMMA genotype file

description: Genepop formatted genotype file for the spotted salamander (Ambystoma maculatum) dataset. File consists of a title line followed by the 14 microsatellite loci names and then full genotypes for each individual within each population (coded corresponding to Supplementary Table 1 from the manuscript).
DOI: 10.5061/dryad.5418t/2
title: Time since MRCA for pairs of species

description: Raw data used for analyses of "geographical ranges of species" described in Material and Methods of the main text. This data file includes information regarding age since most recent common ancestor for pairs of species. Remaining data used for the analyses are given in data file "Dataset Fig 5 part1".
DOI: 10.5061/dryad.5418t/3
title: Data Fig 5 part 1

description: Raw data used for the analyses of "Geographical ranges of species", described in Material and Methods section of the main text. This file includes information regarding species center of distribution (centroids), altitudinal distribution and body size (mm). infromation regarding the age since most recent common ancestor for pairs of species is given in a separate data file ("Time since MRCA for pairs of species").
DOI: 10.5061/dryad.5418t/4
title: Alignment_4genes

description: Sequence alignment of 4 genes (COI, CAD, TPO and 28S) for all species. This alignment was used for the inference of  Maximum Likelihood and Bayesian Inference trees.
DOI: 10.5061/dryad.5418t/5
title: Medusa_richness_file

description: Richness file used for MEDUSA analyses to detect changes in diversification rate in the collapsed MCC tree.
DOI: 10.5061/dryad.5418t/6
title: MCC1 tree

description: Time calibrated Maximum Clade Credibility tree resulted from BEAST analyses using published rates of COI. This tree was used for diversification rate analyses.
DOI: 10.5061/dryad.5418t/7
title: MCC2 tree

description: Maximum Clade Credibility tree uncalibrated to absolute time.
DOI: 10.5061/dryad.5418t/8
title: MEDUSA_MCC1_Collapsed_tree

description: MCC1 tree collapsed to 23 tips. This tree was used in MEDUSA analyses.
DOI: 10.5061/dryad.5418t/9
title: MEDUSA_MCC2_Collapsed_Tree

description: Maximum Clade Credibility Tree uncalibrated to absolute time and collapsed to 23 tips. this tree was used for MEDUSA analyses.
DOI: 10.5061/dryad.555hd/5
title: Isotopic analysis

description: δ15N of environmental nitrate and ammonia, as well as long-skinny and short-fat Ridgeia tubeworms
DOI: 10.5061/dryad.57n57/1
title: nodI_seq_larger_data_set
DOI: 10.5061/dryad.57n57/2
title: nodI_seq_smaller_data_set
DOI: 10.5061/dryad.57n57/3
title: nodJ_seq_larger_data_set
DOI: 10.5061/dryad.57n57/4
title: nodJ_seq_smaller_data_set
DOI: 10.5061/dryad.57n57/6
title: nodIJ_tree_larger_data_set_LogDet_NJ
DOI: 10.5061/dryad.5f0h8/1
title: Data from: Calculating structural complexity in phylogenies using ancestral ontologies

description: See README.txt
DOI: 10.5061/dryad.5km28/1
title: Alternative_life_history_strategies_in_an annual_fish_Polacik_et_al
DOI: 10.5061/dryad.6356f/11
title: CO2 Dataset (CSV format)

description: The dataset of elevated CO2 effects on the concentration of chemical elements in foliar and edible tissues of crops and wild plants. This file is in CSV format and made-ready for analysis with statistical package such as R. The same data can also be found in XLSX format for easy viewing (decreases are blue, increases are red) as another file posted here.
DOI: 10.5061/dryad.6356f/12
title: CO2 Dataset (XLSX format)

description: The dataset of elevated CO2 effects on the concentration of chemical elements in foliar and edible tissues of crops and wild plants. This file is in XLSX format for easy viewing (decreases are blue, increases are red). The same data can also be found in CSV format made-ready for analysis with statistical package such as R.
DOI: 10.5061/dryad.6356f/16
title: Table S1

description: This table provides supportive data for Figures 1-8 and contains the outcomes of statistical analyses of various data subsets. It consists of two sheets: Results and ReadMe.
DOI: 10.5061/dryad.7b79m/1
title: Raw data (plant and aphid variables)

description: Data was collected in a controlled glasshouse experiment as described in the associated paper. The data file was created using Microsoft Excel (2010)
DOI: 10.5061/dryad.7d039/1
title: Streptococcus genome phylogeny

description: Whole genome phylogeny of the Streptococcus genus. The phylogenetic tree was constructed using the EDGAR tool based on complete genome sequences of streptococci. The branch of the members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) is delimited by a bracket.
DOI: 10.5061/dryad.7vv50/9
title: hap_G100.A1.O_X

description: Phased haplotypes present in a outbred population. Used for simulation of inbreeding. This are the chromosome X haplotypes of a androdioecious population, replicate nº1, from generation G100.
DOI: 10.5061/dryad.81p60/1
title: Plant species distribution, seed dispersal traits, and environmental data for southwest Australia

description: Plant distribution data from the Western Australia Herbarium. Environmental data from worldclim (climate) and the Australian Natural Resources Data Library (soils). See publication for details.
DOI: 10.5061/dryad.81p60/2
title: Plant species distribution, seed dispersal traits, and environmental data for northern Europe

description: Plant distribution data from Atlas Florae Europaeae. Environmental data from worldclim (climate) and, for soils, Batjes, N. H. 1997 A world dataset of derived soil properties by FAO–UNESCO soil unit for global modelling. Soil Use and Management 13, 9–16. See publication for details.
DOI: 10.5061/dryad.81p60/3
title: R scripts used to perform analyses described in journal article.

description: Annotated R scripts required to run GDM on plant distribution data.
DOI: 10.5061/dryad.82ms3/1
title: Pflex_structure

description: Data file with alleles for 4 microsatellite markers used to run analyses in the program STRUCTURE for Plexaura flexuosa.
DOI: 10.5061/dryad.82ms3/2
title: singlehaps_structure

description: Data file with alleles for 5 haploid microsatellite markers used to run analyses in the program STRUCTURE for Symbiodinium.
DOI: 10.5061/dryad.82ms3/3
title: totalmatrix_structure

description: Data file with presence/absence matrix for multiple alleles in Symbiodinium.  Used for analyses with the program STRUCTURE.
DOI: 10.5061/dryad.82ms3/4
title: Pflex_create

description: File used to generate program-specific input files for Plexaura flexuosa dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2).  Example files created include those for Genepop, Arlequin, and Bayesass.
DOI: 10.5061/dryad.82ms3/5
title: singlehaps_create

description: File used to generate program-specific input files for Symbiodinium "singlehaps" dataset using CREATE (https://bcrc.bio.umass.edu/pedigreesoftware/node/2).  Example files created include those for Genepop and Arlequin.
DOI: 10.5061/dryad.85078/1
title: manacus_snpcnt

description: This file contains information on the number of reads representing each of two SNP states in each individual manakin across 59,100 loci. The file is organized by locus. For further details on how this file was generated, see the manuscript.
DOI: 10.5061/dryad.85078/2
title: manacus_assembly.bam

description: This file contains the entire assembly for the reference based assembly described in the manuscript.
DOI: 10.5061/dryad.85078/3
title: Mvitellinus_draft_genome

description: This file contains the first draft assembly of the M. vitellinus genome. This file will be embargoed until a paper containing a full description of this and 49 other avian genomes is published, most likely in early 2013.
DOI: 10.5061/dryad.855kh/1
title: BlueHoleCombinedData_Dryad
DOI: 10.5061/dryad.855kh/2
title: lab males_Dryad
DOI: 10.5061/dryad.b8d60/1
title: Raw Data Mastersheet

description: Mastersheet of all raw data for greenhouse, field, germination, and fluorometer studies on separate excel sheets.  A key to all data labels is also added on the fifth sheet.
DOI: 10.5061/dryad.bm676/17
title: SPECIES_LOCATIONS_twenty_demography_sites

description: Locations of Clarkia xantiana ssp. xantiana populations that were the subjects of detailed demographic sampling and experiments. Easting is eastward position (longitude) in meters, UTM NAD 27 zone 11 North, and northing is northward position (latitude) in meters, UTM NAD 27 zone 11 North.
DOI: 10.5061/dryad.c03c2/2
title: Jaffe et al-Interspecific sims Sall

description: Sampling protocol and simulations used to construct the null hypothesis under random paternity allocation. Interspecific simulations based on the entire data set (Sall, n = 72 species),  performed accross all species.
DOI: 10.5061/dryad.c03c2/3
title: Jaffe et al-Interspecific sims Ssig by superfamily

description: Sampling protocol and simulations used to construct the null hypothesis under random paternity allocation. Interspecific simulations based on the species with skew values differing from the random skew expectation (Ssig, n = 56 species), performed within ants, bees and wasps.
DOI: 10.5061/dryad.c03c2/4
title: Jaffe et al-Interspecific sims Ssig

description: Sampling protocol and simulations used to construct the null hypothesis under random paternity allocation. Interspecific simulations based on the species with skew values differing from the random skew expectation (Ssig, n = 56 species), performed across all species.
DOI: 10.5061/dryad.cc2sk/1
title: Alignments and Supplement.tar
DOI: 10.5061/dryad.f2g14/1
title: On-line data support_monitoring and modelling forest expansion
DOI: 10.5061/dryad.g4g11/1
title: Lendemer_Harris_datapacket

description: This zipped folder contains the input files for molecular phylogenetic analyses performed on sequences of Porpidia albocaerulescens s.l. This includes the following: 1) inputs for maximum parsimony, maximum likelihood and Bayesian inference analyses of an nrITS dataset, 2) inputs for maximum parsimony, maximum likelihood and Bayesian inference analyses of an mtSSU dataset, and 3) inputs for supplemental analyses of the same dataset with an additional sequence from GenBank that was added after the initial submission of the manuscript.
DOI: 10.5061/dryad.h1v63/1
title: Data from Campagna et al 2013 Ecology and Evolution

description: Microsatellite data set and all Structure, Geneland, Arlequin and IMa2 input files.
DOI: 10.5061/dryad.j16p2/1
title: Extant carnivore indices

description: Extant carnivore dietary and postcranial indices used in this study.
DOI: 10.5061/dryad.j16p2/2
title: Fossil carnivore indices

description: Fossil carnivore dietary and locomotor indices used in this study.
DOI: 10.5061/dryad.j9704/2
title: ForBebberScript

description: Data for calculation of millipede species diversity following the methods of Bebber et al., 2007
DOI: 10.5061/dryad.j9704/3
title: SpAccumulation

description: Millipede species accumulation data.
DOI: 10.5061/dryad.k501d/1
title: Moura et al supplementary file 14Jul13

description: online supplement
DOI: 10.5061/dryad.mn0d5/1
title: Genotypes

description: The file contains the genotypes of 188 pure Merino and 188 pure Poll Dorset. En each row of the file appears the individual Id followed by the genotypes of the 48599 SNP coded as allele content (0,1,2).
DOI: 10.5061/dryad.mn0d5/2
title: Breeds

description: The file contains the codification used in the GBLUP experiment for the pure individuals. The file contains per row the individual Id and the code for breed trait (1=Merino, 0=Poll Dorset)
DOI: 10.5061/dryad.p78p5/1
title: TauDataTable

description: Parameters and results from simulation runs that allowed the threshold, tau, to evolve. The file lists: 'Run#' - internal designation of run based on researchers' simulations; 'SDM' - whether the system was initiated as XX/XY or ZZ/ZW; 'rho' - the relative survival of an atypical genotype (WW or YY) compared to other genotypes; Tau_start - the single value of tau that all individuals in the population had at the beginning of the simulation; Tau_end_mean - the mean value of tau across individuals in the population after 10,000 iterations of the simulation; Tau_end_min - the minimum value of tau across individuals in the population after 10,000 iterations of the simulation; Tau_end_max - the maximum value of tau across individuals in the population after 10,000 iterations of the simulation; Tau_end_SD - the standard deviation  of tau across individuals in the population after 10,000 iterations of the simulation.
DOI: 10.5061/dryad.r95c6/3
title: Environmental parameters

description: pH, conductivity (μS), total dissolved solids (ppm) and dissolved oxygen content (mg/l) measurements by site.
DOI: 10.5061/dryad.r95c6/4
title: Phenotypic trait data

description: For each individual: Mountain of origin (Mountain), Site abbreviation (Population), Altitude (low or high), Egg mass of origin (Family), Treatment (temperature; oC), Basket (within Treatment), Weight at metamorphosis (Weight; g), Snout-vent length change from start to end of experiment (SVL; mm), Larval Period (days), Growth rate (Rate; g/day), Egg diameter (Egg, mm), Survival
DOI: 10.5061/dryad.r95c6/5
title: R-script for QST model

description: For QST model using lme4 package
DOI: 10.5061/dryad.r95c6/6
title: ReadMe

description: ReadMe file for all data
DOI: 10.5061/dryad.17b18/1
title: Genotypes

description: Genotyping data at 8 loci for each individual
DOI: 10.5061/dryad.17b18/2
title: FST

description: Pairwise Fst values between the different laboratory lineages and field populations
DOI: 10.5061/dryad.17b18/3
title: Titers_Wolbachia_Bacteria

description: Quantitative PCR data for all tissue samples
DOI: 10.5061/dryad.1k571/1
title: landmarks

description: raw-Landmarks of fish considered in the geometric morphometrics analysis. Metadata is contained in the ReadMe Document and the ID and the name of the picture of the tps file link both tables.
DOI: 10.5061/dryad.1k571/2
title: metadata

description: Metadata for the raw-Landmarks of fish considered in the geometric morphometrics analysis. The ID and the name of the picture of the tps file link both tables.
DOI: 10.5061/dryad.1v02q/3
title: Bagworm emergence phenology

description: Summary data for bagworm emergence phenology
DOI: 10.5061/dryad.1v02q/4
title: Bagworm larval survival

description: Bagworm larval survivorship as a function of latitude
DOI: 10.5061/dryad.1v02q/5
title: Bagworm female mating success

description: Data on the proportion of females mated as a function of latitude
DOI: 10.5061/dryad.1v02q/6
title: Bagworm pupal survival

description: Bagworm pupal survivorship as a function of latitude
DOI: 10.5061/dryad.26n2q/1
title: White-tailed Deer Case Study

description: Very-high frequency (VHF) collar and reward-tag data for a case study on white-tailed deer in Pennsylvania from 2009-2011. The data is in the format required by program SURVIV, and the additional code to run the integrated Brownie tag-recovery and known-fate model is included.
DOI: 10.5061/dryad.26n2q/2
title: Turkey Case Study

description: Very-high frequency (VHF) collar and reward-tag data for a case study on wild turkey in Pennsylvania from 2010-2012. The data is in the format required by program SURVIV, and the additional code to run the integrated Brownie tag-recovery and known-fate model is included.
DOI: 10.5061/dryad.3f0v5/1
title: Cross-breed experiment results and 454 microsatellite tests

description: In this file are two sheets.The first sheet is labelled 'cross breed' and contains the genotyping results from the cross-breeding experiments in this study - females, eggs, larvae and males. The allele/s for each locus are given, as well as the area under the allele peak (used to estimate relative paternal contribution, as described in the paper). The second sheet provides the alleles found for each microsatellite locus identified from the 454 sequencing analysis, tested on 95 samples. Only those loci that showed any polymorphism are included here. All alleles were identified by sequencing, with identification and allele peak area estimation done using the software PeakScanner (see paper for more details).
DOI: 10.5061/dryad.41hk5/1
title: Marmoset_data_csv

description: Raw data of each session
DOI: 10.5061/dryad.41hk5/2
title: Schematic_Representation_Exchange

description: Schematic illustration of the exchange