cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hb2bt/1
title: Heterospecific pollen tolerance_Clarkia 2014 pollen tube data
DOI: 10.5061/dryad.kp11q/11
title: phenotypic_data_new

description: Description of the lateral plate morphology in danish threespine populations. The morph is determined by the number of lateral plates : low plated (10 or fewer plates), partially plated (between 10 and 21 plates) and full plated (more than 21 plates) (Le Rouzic et al. 2011). See the manuscript for more details. Note: For HAL population, the HAL phenotypes are from individuals from the locality HAL reported in the manuscript but not those that were sequenced (due to technical issues)
DOI: 10.5061/dryad.kp11q/5
title: sticklebacks_DK

description: sticklebacks_DK.log, Plink input file for running Faststructure on the nine threespine stickleback populations
DOI: 10.5061/dryad.kp11q/6
title: sticklebacks_DK

description: sticklebacks_DK.nosex, Plink input file for running Faststructure on the nine threespine stickleback populations
DOI: 10.5061/dryad.kp11q/7
title: Danish_sticklebacks_genepop

description: input file for running Genepop on the nine danish threespine stickleback populations
DOI: 10.5061/dryad.kp11q/8
title: sticklebacks_Danish

description: vcf from Stacks version 1.13 for the nine danish threespine stickleback populations
DOI: 10.5061/dryad.kp11q/9
title: amova_Fst_outlier_test_sorted_by_chromosome_used_for_Fig_5

description: Results of the FST-based outlier test by Beaumont & Nichols (1996) as implemented in Arlequin 3.5 (Excoffier & Lischer 2010) sorted by chromosome. The analysis encompasses all samples and p-values are plotted for each SNP across all 21 chromosomes.This file was used to make the figure 5 in the manuscript. SNPs that show significantly high FST (p ≤ 0.001) are candidates for marking genomic regions under diversifying selection, whereas  SNPs showing significantly low FST (p ≤ 0.001), potentially reflecte balancing selection.
DOI: 10.5061/dryad.pd6mn/1
title: demographic, parasitologic, and biomarker data

description: The data set includes the demographic, parasitologic, and biomarker variable values from 182 participants from an O. viverrini endemic area of Khon Kean Province in Thailand.
DOI: 10.5061/dryad.qn765/1
title: Cator and Pietri et al. 2015_ Master Data

description: Data sheet containing raw data for Fig 1, 2, 3, and S1.
DOI: 10.5061/dryad.r8d10/1
title: Data_Morante-Filho_etal_JAE

description: Bird communities and environmental data sampled in 36 forest sites in two landscapes in Brazilian Atlantic Forest.
DOI: 10.5061/dryad.rg0s0/1
title: Data

description: This file contains the data that was used in the analyses. The data was collected in the field in the Centre d'Études Biologiques de Chizé, France, between 2005 and 2007.
DOI: 10.5061/dryad.rg0s0/2
title: Analysis script

description: This file contains the R code for the analyses.
DOI: 10.5061/dryad.199k8/1
title: Sharing Analysis 2013-14

description: Data on the sharing metric for whole song sharing and introductory phrase sharing. For each male (identified by color band combination) the sharing metric is averaged across his adjacent neighbors. Also given are song repertoire sizes and number of songs recorded.
DOI: 10.5061/dryad.199k8/2
title: Song sharing per dyad of adjacent male song sparrows

description: For each pair of adjacent territorial male song sparrows, the file gives the number of whole song types shared and the number of introductory phrases shared.
DOI: 10.5061/dryad.199k8/3
title: PARTIAL MATCHING ANALYSIS

description: For each focal male, whether he did (YES) or did not (NO) repertoire match playback of an unshared neighbor song and whether he sang the same target song(s) for playback of an unshared stranger song, counting partially shared songs as a repertoire match.
DOI: 10.5061/dryad.199k8/4
title: WHOLE SONG MATCHING ANALYSIS

description: For each focal male, whether he did (YES) or did not (NO) repertoire match playback of an unshared neighbor song and whether he sang the same target song(s) for playback of an unshared stranger song, counting only wholly shared songs as a repertoire match.
DOI: 10.5061/dryad.199k8/5
title: neighbor:stranger

description: Number of songs given by subjects in response to playback of neighbor song and to playback of stranger song.
DOI: 10.5061/dryad.238b2/1
title: Exploitation rates by humans and natural predators on marine and terrestrial prey species

description: A data file used in the majority of the figures and analyses that appear in the paper. It contains estimates of exploitation rate (n=2125) by humans and natural predators on prey species from marine and terrestrial ecosystems globally. Exploitation rates are expressed as proportion of the biomass removed from marine systems and as proportion of individuals removed from terrestrial systems. Please see the ReadMe file for more information.
DOI: 10.5061/dryad.244b8/1
title: M_zapota_Data_GenAlEx

description: This is the microsatellite allele information in GenAlEx format for all populations and individuals for Manilkara zapota.
DOI: 10.5061/dryad.244b8/2
title: geographic coordinates for GenAlex

description: This is an Excel file formatting for GenAlEx that contains all the geographic coordinate information for each individual represented in the microsatellite file.
DOI: 10.5061/dryad.387cc/1
title: ORRE-ORPA_MicrosatDataset_11loci_636individuals

description: Microsatellite loci data for 636 individuals of Oreocarya paradoxa and O. revealii from 21 populations in the Colorado Plateau
DOI: 10.5061/dryad.3m342/1
title: Fruit availability, forest structure, visits of frugivore birds and seed rain

description: The following file includes data of vegetation structure, fruit availability, frugivore activity and dispersed seeds measured in a Mediterranean pineland of Southeastern Spain (Natural Park Sierra de Baza) for 4 consecutive years (2009-2012).
DOI: 10.5061/dryad.3m342/2
title: mistletoe seed rain and mistletoe seeds stuck on branches

description: mistletoe seed rain and mistletoe seeds stuck on branches
DOI: 10.5061/dryad.4b3h7/10
title: Otago_var_rates

description: BEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Otago including the use of penguin (Lambert et al. 2002) fixed/prior and BayesSSC estimates, and the optimised dataset (from BayeSSC).
DOI: 10.5061/dryad.4b3h7/11
title: SIS aDNA Otago alignment

description: DNA sequence alignment of L. chalconotus Otago.
DOI: 10.5061/dryad.4b3h7/12
title: SIS aDNA Foveaux alignment

description: DNA sequence alignment of L. chalconotus Foveaux Strait.
DOI: 10.5061/dryad.4b3h7/7
title: Randomisation Tests

description: BEAST .xml files for randomisation tests of estimated substitution rate for L. chalconotus Foveaux Strait (x20) and Otago (x20).
DOI: 10.5061/dryad.4b3h7/8
title: BEAST 33 htype

description: BEAST .xml file for the phylogenetic analysis of the 33 haplotype (including out-group sequences) dataset.
DOI: 10.5061/dryad.4b3h7/9
title: Foveaux_var_rates

description: BEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Foveaux Strait including the use of penguin (Lambert et al. 2002) fixed/prior, Otago fixed/prior, and BayesSSC estimates, and the optimised dataset (from BayeSSC).
DOI: 10.5061/dryad.5mr0s/1
title: Thakur et al 2015 Cascading effects of belowground predators on plant communities are density dependent
DOI: 10.5061/dryad.6t6gp/1
title: Field measurement data

description: The file contains field measurements of trees, including site (1 to 48), coordinates (x,y,z, in meters), tree diameter and height, species, crown centroid location (x, y, in meters), and crown vector length (in meters) and direction (degrees).
DOI: 10.5061/dryad.78m34/1
title: C. gouldii mark-recapture data set

description: Mark-recapture data file needed to run Bayesian survival analysis for Chalinolobus gouldii example, as detailed in Supplement 4, page 8.
DOI: 10.5061/dryad.81fv1/1
title: C_rotundicauda_chelicerate_transcriptome

description: C_rotundicauda chelicerate transcriptome assembled using Trinity as described in accompanying manuscript. .fasta.gz file, needs unpacking using gzip or similar before use
DOI: 10.5061/dryad.81fv1/2
title: T_tridentatus_chelicerate_transcriptome

description: T. tridentatus chelicerate transcriptome assembled using Trinity as described in accompanying manuscript. .fasta.gz file, needs unzipping using gzip or similar before use.
DOI: 10.5061/dryad.8f230/1
title: 16SrRNA+PhyloPhlAn

description: This is a zip file that contains three folders. One folder includes all raw data from the 16S amplicons used to create figure 1. Another folder includes the aligned 16S for creating figure S2. The last folder includes the whole tree data, protein alignments and taxa code for creating figure 2.
DOI: 10.5061/dryad.b1g80/1
title: Aldabra_Giant_Tortoise_Transect_Data_1998_2012

description: Aldabra Giant Tortoise Data from 12 Monitored Transects (1998-2012) across Aldabra Atoll, Seychelles.  Please refer to Readme File for abbreviations used in the dataset.
DOI: 10.5061/dryad.dd34q/2
title: Data_ScoringDay1_Hatchlings
DOI: 10.5061/dryad.fp1k7/10
title: resistance matrix
DOI: 10.5061/dryad.fp1k7/7
title: cGD_matrix
DOI: 10.5061/dryad.fp1k7/8
title: Linearized FST matrix
DOI: 10.5061/dryad.fp1k7/9
title: Log_Euclidean Distance
DOI: 10.5061/dryad.gm2v0/10
title: Linear Models - Central California

description: R script used to perform linear model selection for Central California populations
DOI: 10.5061/dryad.gm2v0/2
title: Allelic Richness Code_standarich

description: R script for calculating standardized allelic richness using R package "standarich"
DOI: 10.5061/dryad.gm2v0/3
title: Allelic Richness Data

description: Data file for calculating standardized allelic richness using R package "standarich"
DOI: 10.5061/dryad.gm2v0/4
title: CCA Script

description: R script for performing canonical correspondence analysis for environmental data and Structure cluster membership
DOI: 10.5061/dryad.gm2v0/5
title: CCA Data

description: Data file for use with the CCA script for performing canonical correspondence analysis for environmental data and Structure cluster membership in R
DOI: 10.5061/dryad.gm2v0/6
title: Habitat Network Script

description: R script for performing network analysis for summer transport time using R package "igraph"
DOI: 10.5061/dryad.gm2v0/7
title: Habitat Network_OceanDistanceMatrices

description: Matrix of ocean transport distances for use with the Habitat Network Script
DOI: 10.5061/dryad.gm2v0/8
title: Habitat Network_site_centers

description: Location data for use with the Habitat Network Script
DOI: 10.5061/dryad.ht357/1
title: B4SC Visual screening - Data

description: Data analysed from B4 School Check vision screening referrals  1 March 2010 to 28 February 2011
DOI: 10.5061/dryad.j1c4t/1
title: Data associated with Dowling et al, The Trojan Female Technique for pest control:

description: All the column headers are self explanatory. mtDNA is the mtDNA haplotype, and paternal line is the strain to which females of each mtDNA line were crossed. In the competitive assays, the response variable is a binomial vector comprising the number of offspring sired by the focal male, and the number sired by the tester male. The column 'wild type offspring' denotes those offspring sired by the focal males, and the column 'brown eye offspring' denotes those offspring sired by the tester males. In the non-competitive assays, the column "total offspring" denotes the reproductive success of the focal males.
DOI: 10.5061/dryad.j25t0/1
title: Garden Tree Survey

description: Location of gardens surveyed, and details of trees identified including size (circumference, diameter and height).
DOI: 10.5061/dryad.j25t0/2
title: Existing and Modelled Above-ground Carbon

description: Zip file contains comma-delimited data files of existing above-ground carbon stored in the existing tree stock, modelled biomass carbon resulting from tree planting in domestic, public and mixed ownership land over 25 years, and modelled live and harvested biomass carbon resulting from short-rotation coppice over 25 years
DOI: 10.5061/dryad.j25t0/3
title: Carbon assimilated over 25 years

description: Quantities of biomass carbon assimilated over 25 years through modelling tree planting and short-rotation coppice
DOI: 10.5061/dryad.mb1d0/1
title: Khaya_MeanMatrices_2004_2007

description: This file includes mean matrices for 12 populations of Khaya senegalensis surveyed in Benin (West Africa) from 2004 to 2007. For each population, I averaged three yearly transition matrices (2004-2005, 2005-2006, 2006-2007). These matrices were built using demographic data was collected from the 12 populations using 1-ha plots for each population (two adjacent subplots of 0.5 ha, separated by the river bed when the population was in a gallery forest.
DOI: 10.5061/dryad.pm37b/1
title: Read Me Raw Data

description: Read me file describing the data files
DOI: 10.5061/dryad.pm37b/2
title: Call Duration Raw Data

description: Raw data for female responses to the call duration stimuli
DOI: 10.5061/dryad.pm37b/3
title: Call Period Raw Data

description: Raw data for female responses to the call period stimuli
DOI: 10.5061/dryad.r4553/1
title: random_sample_raxml

description: Python script for generating randomized nucleotide datasets of different lengths for analysis in RAxML. These were used to generate the rarefaction curves shown in the study. Requires docopt.py, which is not included.
DOI: 10.5061/dryad.r4553/2
title: Eytan-etal2015_AssemblyCode

description: Java code used for processing sequencing runs before phylogenetic analyses.
DOI: 10.5061/dryad.r4553/3
title: Ovalentaria_Alignments

description: Alignments used for phylogenetic analyses
DOI: 10.5061/dryad.sm6n2/1
title: Data experiment 1

description: Data set of the experiment 1
DOI: 10.5061/dryad.sm6n2/3
title: Data experiment 2

description: Data set of experiment 2, only including relevant information
DOI: 10.5061/dryad.238b2/2
title: Proportion of mortality data for terrestrial systems

description: A data file with proportion of mortality data for terrestrial systems, used for generating Fig 1B. All cases include paired mortality estimates of humans and non-human predators on shared prey. This dataset includes a total of 99 cases, including cases from the larger predrate file (n=51) that have proportion of biomass estimates as well as cases (n=48) with only proportion of mortality estimates. This dataset is formatted for paired comparisons (wide format) and is included as a separate data file for convenience. Please see the ReadMe file for more information.
DOI: 10.5061/dryad.238b2/3
title: R Code for human predator data analyses

description: An R file that includes code for generating the figures and analyses in the manuscript
DOI: 10.5061/dryad.45kd1/1
title: Kuemmerli_etal_JEvolBiol_all_data

description: This file contains all data presented in Kuemmerli et al. Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa.
DOI: 10.5061/dryad.4hg2p/1
title: KS1-alignment

description: Aligned sequences of KS1 gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/2
title: LHS1-alignment

description: Aligned sequences of LHS1 gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/3
title: SSII1-alignment

description: Aligned sequences of SSII1 gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/4
title: WAXY-alignment

description: Aligned sequences of WAXY gene fragment from 307 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/5
title: HD3A-alignment

description: Aligned sequences of HD3A gene fragment from 296 individuals of Oryza nivara and O. rufipogon and one individual of O.barthii used as outgroup.
DOI: 10.5061/dryad.5hq6r/1
title: Simulation data

description: This file contains the output of 100 replicate simulations for each parameter setting of our study (both of the results presented in the main text and in the SI). The folders are named as follows: game_mutationrate_payoffconfiguration_behaviouralimplementation_mutationregime. The abbreviations stand for the following: IPD = Iterated Prioner's Dilemma game, ISD = Iterated Snowdrift game, NN = neural network, TM = 1:1 mapping, GM = entire-genome muation, LM  = per-locus mutation. Each folder contains 100 .txt files with simulation output. Time is on the rows (top row is the first generation), the frequencies of the different strategies (in the same order as in table 2 of the main text) are on the columns.
DOI: 10.5061/dryad.81fv1/3
title: L_polyphemus_genome_contigs.fa

description: L polyphemus genome contigs assembled as described in accompanying manuscript. NB .fasta.gz file, needs to be unpacked using gzip or similar before use
DOI: 10.5061/dryad.81fv1/4
title: T_tridentatus_genome_contigs.fa

description: T_tridentatus genome contigs assembled as described in accompanying manuscript. NB .fasta.gz file, needs to be unpacked using gzip or similar before use
DOI: 10.5061/dryad.81fv1/5
title: C_rotundicauda_genome_contigs.fa

description: C_rotundicauda genome contigs assembled as described in accompanying manuscript. NB fasta.gz file, requires unpacking using gzip or similar before use
DOI: 10.5061/dryad.b29k1/1
title: Complete transisthmian date values

description: The spreadsheet contains all data from publications cited in Bacon et al. 2015, showing data that were omitted, data that were corrected, and data that were correct, as well as summary statistics.
DOI: 10.5061/dryad.c3g80/1
title: AFLPmatrix_original_B_nana

description: Binary AFLP matrix with 119 markers, 570 individuals of Betula nana and B. glandulosa generated by 3 primer combinations
DOI: 10.5061/dryad.c3g80/2
title: AFLPmatrix_orginal_Betula_pub_alle_332_155

description: Binary AFLP matrix with 155 markers, 332 individuals of mainly Betula pubescens, but also including reference species and hybrids generated by 3 primer combinations
DOI: 10.5061/dryad.c3g80/3
title: AFLPmatrix_Betula_all_901ind_104_markers_1primer

description: AFLP matrix based on the combined scoring of on primer in common among the original data sets for B. nana and B. pubescens and reference species
DOI: 10.5061/dryad.c3g80/4
title: AFLPmatrix_Betula_nana_only_528_115

description: Subset of the original AFLP matrix (3primers)nwithout populations of B. glandulosa, 115 polymorphic markers and 528 ind
DOI: 10.5061/dryad.c3g80/5
title: AFLP_matrix_Betula_pub_only_303_132

description: Subset of the original aflp matrix of B. pubescens, without reference populations-only including 303 individuals  of B. pubescens, 3 primer combinations, 132 markers
DOI: 10.5061/dryad.c3g80/6
title: Betula_901_104structure-input

description: Input-file to STRUCTURE software based on the combined AFLP matrix with 901 individuals, 104 markers (one primer combination)
DOI: 10.5061/dryad.d4g4n/1
title: KMZ file defining border of the California Floristic Province

description: This data file describes the border of the California Floristic Province in western North America. It is openable in Google Earth or other GIS applications.
DOI: 10.5061/dryad.d4g4n/2
title: Occurrence data for native land plants of the California Floristic Province

description: This data file contains information on the occurrence of native land plants (bryophytes and vascular plants) within major sub-regions of the California Floristic Province, including Baja California (Mexico), Oregon, California, and Nevada.
DOI: 10.5061/dryad.d4g4n/3
title: GIS file for CFP (DBF)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.d4g4n/4
title: GIS file for CFP (PRJ)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.d4g4n/5
title: GIS file for CFP (SBN)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.fn7gv/1
title: Morphology, microsatellite markers and stomach contents

description: Columns from left to right: individual code, location where individual was collected, year of collection, haplotype group individual belongs to, PCs1, 2, 3 and 4 of body shape, PCs 1 and 2 for LPJ shape, microsatellite data, stomach content data. Absence of data marked as N/A
DOI: 10.5061/dryad.gm2v0/11
title: Linear Models - Santa Barbara Channel

description: R script used to perform linear model selection for Santa Barbara Channel mainland populations
DOI: 10.5061/dryad.gm2v0/12
title: Linear Models - Southern California

description: R script used to perform linear model selection for Southern California populations
DOI: 10.5061/dryad.gm2v0/13
title: Genetic Network Script - gtx2network

description: R script to construct a network based on Cavalli-Sforza chord distance between populations
DOI: 10.5061/dryad.gm2v0/9
title: Linear Models Data

description: Pairwise data for use with Linear Model R scripts. Includes comparison pair, Population In ID, Population Out ID, Groups to which Populations belong (SCA=Southern California, SBC=Santa Barbara Channel Mainland, CCA=Central California), Pairwise linearized FST (FST/1-FST), Distance between sites, Area of habitat between sites, Habitat area per km between sites, Summer and Winter mean temperature difference between sites, Summer and Winter mean maximum significant wave height, transport time (5km model), Annual, Seasonal, and Monthly minimum mean transport time between sites, and biomass correlation between sites using a 500m, 1000m, and 2000m buffer area around each site.
DOI: 10.5061/dryad.h75rk/1
title: Hunt_et_al_2015_Dryad_data_sheets

description: Raw data collected from laboratory experiments used for the following analyses: sheet 1.  Age-specific fecundity, sheet 2. In vivo fungal growth, sheet 3. Tolerance (Mortality vs. CFUs), sheet 4. Intrinsic rate of increase, sheet 5. Lifetime reproductive success, sheet 6. Survival (individual vials), sheet7. Mortality (population cages), sheet 8. Temperature preference. Key: NT - no treatment, HT - heat-killed fungal treatment, MR - Live fungal treatment.