cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j7n42/3
title: Female Specimen Data

description: This file contains the corresponding information for the specimens in the TPS file including lot number, locality, collection date, predation pressure, habitat type, centroid size, and relative caudal peduncle area.
DOI: 10.5061/dryad.j7n42/4
title: Male Specimen Data

description: This file contains the corresponding information for the specimens in the TPS file including lot number, locality, collection date, predation pressure, habitat type, centroid size, and relative caudal peduncle area.
DOI: 10.5061/dryad.m5v49/1
title: Neotropical Miliuseae Clade (Annonaceae)

description: This Nexus file is a concatenated aligment containing plastid (rbcL,matK,ndhF, trnLF, psbA-trnH, ycf1, rps16-trnQ) and nuclear r(ITS) sequences of the Neotropical Miliuseae Clade (Annonaceae) used in this study.
DOI: 10.5061/dryad.m5v49/2
title: OrtizRodriguez et al_Subclade_A

description: The MAXENT input files used in the analysis of the climatic preferences of the three subclades (A–C) of the Desmopsis Stenanona clade (Annonacea) are available. 
1. Subclade A_MAXENT_File: coordinates longitude and latitude of subclade A
DOI: 10.5061/dryad.m5v49/3
title: OrtizRodriguez et al_subclade_B

description: The MAXENT input files used in the analysis of the climatic preferences of the three subclades (A–C) of the Desmopsis-Stenanona clade (Annonacea) are available. 
1. Subclade A_MAXENT_File: coordinates longitude and latitude of subclade B
DOI: 10.5061/dryad.m5v49/4
title: OrtizRodriguez et al_subclade_C

description: The MAXENT input files used in the analysis of the climatic preferences of the three subclades (A–C) of the Desmopsis-Stenanona clade (Annonacea) are available. 
1. Subclade A_MAXENT_File: coordinates longitude and latitude of subclade C
DOI: 10.5061/dryad.q104g/1
title: R-code

description: The file contains: The R-code: (1) To generate a small random interaction matrix. (2) To generare the  parameterization of intrinsic growth rates corresponding to the random interaction matrix. This vector of intrinsic growth rates can be generated either randomly with no other constraints, all elements with the same value, randomly inside the feasibility domain, or the vector that corresponds to the geometric centroid of the feasibility domain. (3) To check whether the community with the given random interaction matrix and chosen parameterization is feasible and stable.
DOI: 10.5061/dryad.qc3m7/2
title: final data summary for dryad

description: This is the summary data for the paper contact the authors for explanation of the treatments codes.
DOI: 10.5061/dryad.rr3667m/10
title: Table A4

description: Model fit and parameter estimation for analyses of continuous traits. Phylogenetic signal was assessed using Blomberg’s K (2003) and Pagel’s λ (Pagel 1999). Statistical significance for these indices was based on comparison to a non-phylogenetic model (K = 0, λ = 0), with a significant P-value indicating rejection of the non-phylogenetic model.
DOI: 10.5061/dryad.rr3667m/11
title: Table A5

description: Correlations between internal fertilization and anisogamy and oogamy using Pagel’s test (1994)
DOI: 10.5061/dryad.rr3667m/12
title: Table 1

description: Phylogenetic t-test for sexual traits, using three continuous metrics of multicellular complexity (rounds of cell division, percent somatic cells, natural logarithm-transformed body length). A phylogenetic t-test comparing natural logarithm-transformed zygote diameter of isogamous and anisogamous algae is included. When multiple metrics were used, p-values were adjusted for multiple comparisons following Benjamini and Hochberg (1995).
DOI: 10.5061/dryad.rr3667m/6
title: Dataset 2

description: Continuous multicellularity metrics and discrete character states for sexual traits and associated references for volvocine taxa. For heterothallic species, only one strain of a mating pair has been given.
DOI: 10.5061/dryad.rr3667m/7
title: Table A1

description: PCR primers used in this study. *indicates a reverse primer
DOI: 10.5061/dryad.rr3667m/8
title: Table A2

description: The best partition and nucleotide substitution scheme as determined by PartitionFinder version 2.1.1 (Lanfear et al. 2016). “Position” refers to codon position.
DOI: 10.5061/dryad.rr3667m/9
title: Table A3

description: Model fit and parameter estimates for analyses of discrete traits. For phylogenetic signal, the D value was calculated (D &lt; 0 indicates stronger phylogenetic signal than a Brownian motion model; D = 0 indicates Brownian motion; D = 1 indicates random, non-phylogenetic distribution of states among taxa). Significant P-values associated with a given model indicate that the model is rejected. For discrete traits, the first state listed in the column header is state 0, and subsequent states are state 1 or state 2. The value q is the transition rate between the two states (ancestral state on the left, derived state on the right). Bayes factors (BF), taking phylogenetic uncertainty into account, were estimated based on twice the difference between the highest harmonic mean log likelihood for each model (ER, equal rates; SYM, symmetric rates; ARD, all rates different), calculated from nine independent MCMC runs for each model. Interpretation of Bayes factors is as follows: 0 to 2 barely worth mentioning, 2 to 6 positive, 6 to 10 strong, &gt;10 very strong (Kass and Raftery 1995).
DOI: 10.5061/dryad.s5f28/1
title: Suplplementary materials for Magnolia mercedesiarum (subsect. Talauma, Magnoliaceae): a new Andean species from northern Ecuador with insights to its potential distribution

description: Supplementary materials cover detailed methods and results for species distribution modelling (SDM) of modern Magnolia mercedesiarum distribution
DOI: 10.5061/dryad.v1q13/1
title: Desiccation experiment

description: This compressed directory contains two files. 'dessication_trials_2017.csv' provides the data for the desiccation experiment. This includes the morph type (green vs. grey or red = melanic), weights, and time to death. The second file 'commands_melExp.R' provides the R code used to analyse the data. This presents some initial exploratory analyses and the final analysis used for the paper.
DOI: 10.5061/dryad.v1q13/2
title: Stripe freq. dependence experiment

description: This compressed directory contains three files related to the experimental test for frequency-dependent selection of stripe (versus no stripe). 'recapture_data.txt' provides the raw data, which includes the number of striped vs. green (unstriped) insects re-captured and the treatment ID (2 = 20% stripe, 8 = 80% stripe). The directory also includes the R code ('commands_freqDep.R') used to fit the Bayesian model (the model itself is in another text file, 'binmod', which is also included).
DOI: 10.5061/dryad.1cf2p/1
title: Neutral SNP's

description: Genotype data in STRUCTURE format for 8,786 neutral SNPs
DOI: 10.5061/dryad.1cf2p/2
title: Outlier SNP's

description: Genotype data in STRUCTURE format for 323 outlier SNPs
DOI: 10.5061/dryad.1cf2p/3
title: Sequence outlier SNPs

description: Reference sequence of outlier SNPs
DOI: 10.5061/dryad.1pj2600/1
title: Extinct canid dataset

description: Taxonomic, trait, duration, and locality coverage data for 131 species of North American fossil canids.
DOI: 10.5061/dryad.1pj2600/2
title: Slater (2015) canid tree - pruned

description: Topology of canid tree from Slater (2015), pruned to the species included in Balisi et al.
DOI: 10.5061/dryad.1pj2600/3
title: Statistical analyses

description: Scripts for principal component analysis, linear regressions, quantile regressions, and the associated plots.
DOI: 10.5061/dryad.1pj2600/4
title: Code for Figure S3

description: Figure S3 is a time-scaled canid tree using the pruned Slater (2015) phylogeny, with black bars representing stratigraphic ranges as calculated using PyRate.
DOI: 10.5061/dryad.1pj2600/5
title: Results of principal component analysis

description: Only PC1 is needed for trait analysis.
DOI: 10.5061/dryad.1pj2600/6
title: Trait evolution model scripts

description: R code for trait evolution model-fitting.
DOI: 10.5061/dryad.5ff8194/2
title: Theta Fig. 4

description: This file includes the data of lateral inclination (theta) during stance phase in Fig. 4 in the manuscript.
DOI: 10.5061/dryad.5ff8194/3
title: Data Fig. 5 and Fig. 6

description: It contains all the data of  Theta_td and Theta_lo of all the trials from NONE, SR, and SR-CIR cases. The detailed data for Fig .6, including the average value and standard deviation is also contained.
DOI: 10.5061/dryad.5vn76/5
title: Simulation Modeling
DOI: 10.5061/dryad.5vn76/6
title: Metadata_for_specimens
DOI: 10.5061/dryad.5vn76/7
title: README
DOI: 10.5061/dryad.6b55m22/1
title: GPS, accelerometer and environmental data for individually tracked brent geese

description: GPS and accelerometer tracking data of individual dark-bellied Brent geese, linked to metadata on bathymetry and tidal information.
DOI: 10.5061/dryad.6b55m22/2
title: Field observations of defecations and antagonistic interactions

description: Field observations of defecations and antagonistic interactions of dark-bellied brent geese on Terschelling island
DOI: 10.5061/dryad.6b55m22/3
title: Biometry and resightings of dark-bellied brent geese

description: Biometry and resightings of dark-bellied brent geese captured on Terschelling island in 2005, 2010, 2011, 2013, 2014 (i.e. successful breeding years in the arctic when birds returned with juveniles) as obtained from the geese.org database (accessed 24 Feb 2016).
DOI: 10.5061/dryad.6b55m22/4
title: sampling locations

description: locations of exclosures and locations of 4 m^2 circles in which geese droppings were collected
DOI: 10.5061/dryad.6b55m22/5
title: grass and brent goose excreta sampling

description: Pasture grass and excreta sampling and chemical analysis, goose excreta densities and vegetation height
DOI: 10.5061/dryad.6b55m22/6
title: weight of individual brent goose excreta

description: Dry weights of individual brent goose excreta
DOI: 10.5061/dryad.6b55m22/7
title: energy and ash content of grass and excreta

description: bom calory measurements and ash content of pasture grass and brent goose excreta
DOI: 10.5061/dryad.6b70g11/1
title: GOCC-beluga whale genetic data

description: contains detailed genetic data on beluga whales, including GenBank accession numbers, mtDNA haplotype frequencies and microsatellite locus allele frequencies
DOI: 10.5061/dryad.6t536/2
title: Study1_raw

description: Raw data from study 1
DOI: 10.5061/dryad.6t536/3
title: Study2_raw

description: Raw data from study 2
DOI: 10.5061/dryad.6t536/4
title: Study3_raw

description: Raw data from study 3
DOI: 10.5061/dryad.70d46/1
title: YardSurvey

description: Survey given only to homes where we collected tree data. See table 3 for details and appendix S2 for questions.
DOI: 10.5061/dryad.70d46/2
title: NeighborhoodSurvey

description: Survey on tree attributes sent to 100 homes in each neighborhood. See Table 3 for more details and appendix S2 for survey questions.
DOI: 10.5061/dryad.70d46/3
title: TreeData

description: Tree species data including both street and residential trees and their traits. See tables 2 and 3 for more details.
DOI: 10.5061/dryad.72p93h1/1
title: Data

description: File containing all non-pedigree data. Columns are as follows:

pnum – anonymous identifier for individual woman;

IDc – identity of the woman’s childhood family;

byear – the woman’s year of birth;

cregcode – the parish in which the woman was born;

afr – Age at First Reproduction (in the manuscript, we refer to this as Age at First Birth [AFB]);

coparent.of.firstborn – identity of the recorded father of the woman’s eldest child;

natal.family.of.coparent.of.firstborn – identity of the recorded father’s childhood family;

status – the HISCAM score for the recorded father, based on his recorded occupation(s). See paper for details and further references.
DOI: 10.5061/dryad.72p93h1/2
title: Pedigree

description: The pedigree file
DOI: 10.5061/dryad.72p93h1/3
title: R script

description: An R script to repeat our analyses
DOI: 10.5061/dryad.77bn3/1
title: Transmucosal impedance change following TNBS infection

description: Data file "Gut impedance studies" describes data presented in Figure 1.
DOI: 10.5061/dryad.b32q9/1
title: Forage quality and quantity per plot and year

description: Data file contains 4 measurements of forage quality - In vitro dry matter digestibility (IVDMD), acid detergent fiber (ADF), neutral detergent fiber (NDF), and nitrogen concentration (%N) and a measure of per plot peak biomass for each of 3 grass species in the study.
DOI: 10.5061/dryad.cs133/1
title: genotype and phenotype of 1092 cows
DOI: 10.5061/dryad.g34gs/1
title: Smith-Ramesh Dryad Archive

description: This zip archive includes the raw model output presented in Smith-Ramesh 2018, Ecology Letters, entitled "Predators in the plant-soil feedback loop: Aboveground plant-associated predators may alter the outcome of plant-soil interactions", as well as the code files used to generate the data.  The data were generated using a cellular automaton model.
DOI: 10.5061/dryad.k3b6sv7/1
title: Sexual Selection Data S.thoracica FINAL BehEcol00445

description: Data on sexual selection as a function of size and coloration of the sexually selected male forelegs of the dimorphic dung fly Sepsis thoracica
DOI: 10.5061/dryad.p563h62/1
title: Predation experiment S.thoracica Data BehEcol00463

description: Arthropod predation data as a function of size and coloration of the sexually selected forelegs of European populations of the dimorphic dung fly Sepsis thoracica
DOI: 10.5061/dryad.r31js91/1
title: Draft Genome CDS

description: Sequences extracted from various draft genomes used in the selection analyses.
DOI: 10.5061/dryad.r31js91/2
title: FDR Control Results

description: Results of analyses to control the false discovery rate (FDR).
DOI: 10.5061/dryad.r31js91/3
title: PAML Files

description: Alignment and tree files needed to run the PAML analyses.
DOI: 10.5061/dryad.r31js91/4
title: PAML Results Tables

description: Detailed results and summary tables of each of the PAML analyses.
DOI: 10.5061/dryad.sc41rn3/1
title: Net Ecoystem Exchange and C in harvest
DOI: 10.5061/dryad.t34k1/1
title: Model 1

description: Probability of a male group member siring extra-pair young based on relatedness to male breeder, group member size, and sex ratio of group members.
DOI: 10.5061/dryad.t34k1/2
title: Model 2

description: Probability of a male group member siring extra-pair young based on relatedness to female breeder, group member size, and sex ratio of group members
DOI: 10.5061/dryad.t34k1/3
title: Model 3

description: Fisher's exact test: testing whether extra-pair young in a brood is independent of presence of related male group member to male breeder
DOI: 10.5061/dryad.v1q13/10
title: R workspace for mel-stripe selection inference in FHA

description: This R workspace contains the results from fhaAbcMel.R, which runs the selection inference for the FHA between 2011 and 2013. It is required by fhaEcolSmel.R.
DOI: 10.5061/dryad.v1q13/3
title: VCF filtering scripts

description: This compressed directory contains two perl scripts that we used to filter the VCF files with the genetic variant data for the FHA population (2011 vs. 2013) and for the between-generation experiment.
DOI: 10.5061/dryad.v1q13/4
title: Genomic change in FHA (2011-2013)

description: This compressed directory contains the allele frequency data ('pEM_fha2011.txt' and 'pEM_fha2013.txt') and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the FHA population between 2011 and 2013. The R script used for the analysis is 'FHA_genomicChangeMelStripy.R'.
DOI: 10.5061/dryad.v1q13/5
title: Between-generation experiment genomic change

description: This compressed directory contains the allele frequency data ('p*') and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the between-generation experiment (the source population for this was OGA). The R script used for the analysis is 'OGAgenomicChangeMelStripy.R'.
DOI: 10.5061/dryad.v1q13/6
title: Within-generation experiment genomic change

description: This compressed directory contains the allele frequency data ('in_p_ecol*', column three gives the maximum likelihood allele frequency estimates) and associated scripts for the analyses of genomic change (allele frequency change across the genome) for the within-generation experiment (the source population for this was FHA). The R script used for the analysis is 'exp_genomicChangeMelStripy.R'.
DOI: 10.5061/dryad.v1q13/7
title: Scripts for mel-stripe selection analysis

description: This compressed directory contains two R scripts used to estimate selection coefficients for FHA (between 2011 and 2013 = 'fhaAbcMel.R') and during a within-generation release-recapture experiment (also at FHA = 'fhaEcolSmel.R'). Additional data (text) files required by these scripts are included ('ecolGbsHost.txt', 'snpids_fha', 'SurvivalGbs.txt', and 'fha2013pheno.txt'). Larger R data workspaces and genetic data files referenced in the scripts have been uploaded individually ('pntest_fha2011.txt', 'pntest_fha2013.txt', 'fhaAbcMel.rdat', 'fhaAbcEcolSMel.rdat').
DOI: 10.5061/dryad.v1q13/8
title: Genotype estimates for FHA 2011

description: Matrix of genotype estimates (mean of the posterior with genetoypes coded as 0, 1 or 2, but the mean being non-integer valued) for FHA in 2011. Rows denote SNPs and columns denote individuals. See scripts in melstripeSelectionFHA.tar.gz for details.
DOI: 10.5061/dryad.v5374/1
title: ed1a

description: Sequence reference of Escherichia coli ed1a for breseq analysis
DOI: 10.5061/dryad.70d46/4
title: NurseryData

description: Species inventory for visited nurseries. See text for more details.
DOI: 10.5061/dryad.77bn3/2
title: Histological score of inflammaed tissue

description: File contains histological score data used in Figure 3E, F.
DOI: 10.5061/dryad.77bn3/3
title: Histological analysis of leukocyte infiltration

description: Files contains data used to generate Figures 4-6.
DOI: 10.5061/dryad.7r1j0d6/1
title: Candolin et al Funct Ecol 2018

description: The three data sets of the paper
DOI: 10.5061/dryad.8hn63/1
title: Protohertzina compressa holotype

description: Holotype specimen of Protohertzina compressa. Scale bar = 400 µm. Slide number: NRM-PZ X 7032.
DOI: 10.5061/dryad.8hn63/2
title: Retiranus balticus holotype

description: Holotype specimen of Retiranus balticus. Scale bar = 400 µm. Slide number: NRM-PZ X 7062.
DOI: 10.5061/dryad.8hn63/3
title: Lontohystrichosphaera grandis holotype

description: Holotype specimen of Lontohystrichosphaera grandis. Scale bar = 500 µm. Slide number: NRM-PZ X 7023.
DOI: 10.5061/dryad.95486/1
title: Tits_Females_dataset

description: Phenotypic data on tits
DOI: 10.5061/dryad.95486/2
title: Climatic_data

description: Climatic data, South France (Monthly temperature 1970-2015)
DOI: 10.5061/dryad.97d83g0/1
title: cp.ambigua.final.nex

description: chloroplast alignment
DOI: 10.5061/dryad.97d83g0/2
title: nuc.ambigua.final.nex

description: nuclear alignment
DOI: 10.5061/dryad.97d83g0/3
title: cp.ambigua.mb.con.tre

description: the bayesian reconstruction of the chloroplast phylogeny - the chloroplast bayesian gene tree
DOI: 10.5061/dryad.97d83g0/4
title: nuc.ambigua.mb.con.tre

description: the bayesian reconstruction of the nuclear phylogeny - the nuclear bayesian gene tree
DOI: 10.5061/dryad.97d83g0/5
title: chl.ML.boot.tre

description: the maximum likelihood reconstruction of chloroplast phylogeny - the chloroplast ML tree
DOI: 10.5061/dryad.97d83g0/6
title: nuc.ML.boot.tre

description: the maximum likelihood reconstruction of nuclear phylogeny - the nuclear ML tree
DOI: 10.5061/dryad.97d83g0/7
title: amb.starbeast.species.tre

description: species tree based from *BEAST using cp and nuclear data
DOI: 10.5061/dryad.bm4f9n0/1
title: Inputs, settings, and state variables for RHESSys simulations

description: This includes all files necessary to run RHESSys simulations with the file structure already set up.
DOI: 10.5061/dryad.f9s4424/1
title: raw_data

description: Contains six tab-delimited files with all data used in this analysis. See README file for details.
DOI: 10.5061/dryad.f9s4424/2
title: GSplasticity_code

description: R code to generate all figures and reproduce all analyses
DOI: 10.5061/dryad.gm367.1
title: Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
DOI: 10.5061/dryad.gm367.1/2.1
title: Baltic_Cfit_Input

description: Input file for Cfit software. Includes populations geographic distances along the Baltic-Atlantic continuum (see paper) and allele counts for each populations.
DOI: 10.5061/dryad.gm367.1/3.1
title: Barents_Cfit_Input

description: Input file for Cfit software. Includes geographic distances for populations along the Barents-Atlantic continuum (see paper) as well as allele counts for each populations.
DOI: 10.5061/dryad.gm367.2
title: Data from: SNP-array reveals genome wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar)
DOI: 10.5061/dryad.gm367.2/1.2
title: Genotypes_Dryad

description: 6176 SNP genotypes for 1295 samples used in submitted analysis (all but Foyle River population). For access to genotypes from Foyle River samples, please contact Dr. Dennis Ensing at Agri-Food & Biosciences Institute, Fisheries &  Aquatic Ecosystems Branch . See paper for information on genotyping and SNP discovery.
DOI: 10.5061/dryad.gm367.2/2.2
title: Baltic_Cfit_Input

description: Input file for Cfit software. Includes populations geographic distances along the Baltic-Atlantic continuum (see paper) and allele counts for each populations.
DOI: 10.5061/dryad.gm367.2/3.2
title: Barents_Cfit_Input

description: Input file for Cfit software. Includes geographic distances for populations along the Barents-Atlantic continuum (see paper) as well as allele counts for each populations.
DOI: 10.5061/dryad.jq5g627/1
title: Table S1 - Full data set.

description: Data was collected by reading papers associated with environmental association analyses. Data includes location, species, methods used, genetic parameters of data sets reviewed, and analytical parameters of the analyses.
DOI: 10.5061/dryad.jq5g627/2
title: R code for mixed-effects linear models

description: The R code used to create the figures and estimate regressions of the data set.
DOI: 10.5061/dryad.m4g1601/1
title: EmpiricalSppComposition
DOI: 10.5061/dryad.m4g1601/2
title: EmpiricalDivGradients

description: Empirical diversity gradients across grid cells calculated from species composition data
DOI: 10.5061/dryad.r31js91/5
title: Sequence Alignments

description: Multiple sequence alignments for each gene.
DOI: 10.5061/dryad.r31js91/6
title: Transcriptome Assemblies

description: De novo Trinity assemblies of the colubrid snake eye transcriptomes.
DOI: 10.5061/dryad.tm617/1
title: NZ Mouse Plink .bim file
DOI: 10.5061/dryad.tm617/2
title: NZ Mouse Plink .bed file
DOI: 10.5061/dryad.tm617/3
title: NZ Mouse Plink .fam file
DOI: 10.5061/dryad.v1q13/11
title: Genetic variant data for mapping color

description: This BCF file (binary version of VCF) contains the genetic variant data used for mapping color in Timema cristinae.
DOI: 10.5061/dryad.v1q13/12
title: Genetic variant data for mapping stipre (pattern)

description: This BCF file (binary version of VCF) contains the genetic variant data used for mapping stripe (pattern) in Timema cristinae.
DOI: 10.5061/dryad.v1q13/13
title: Traiting mapping

description: This compressed directory contains the input files (see input) and scripts (see scripts) used for genome-wide association mapping of stripe and color. README files are included in the input and scripts sub-directories.