cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.27kk4/2
title: Eye diameter and body length measures on lab-reared Daphnia obtusa for broad-sense heritability estimation

description: Eye diameter (um) and body length (um) measurements from a common garden experiment on a number of clones of Daphnia obtusa isolated from ponds in Congaree National Park, South Carolina. Each row corresponds to associated identifiers and measurements for a single individual Daphnia. Pond of origin indicates the name of the pond that the original clone was isolated from. D. obtusa clone refers to the name of the clone (pond abbreviation and a number for specific identity). Daphnia size class was determined as small (≤900 μm), medium (901 μm -1399 μm), and adult (≥1400 μm). These size classes reflect ontogenetic growth from juveniles to adults.
DOI: 10.5061/dryad.3023m/10
title: Extra_Figure5_Sequences

description: Sequences of the RAD tags used to produce trees in Figure 5 of the paper (FASTA format)
DOI: 10.5061/dryad.3023m/2
title: 2_Unique_RAD_Tags

description: Sequences of the unique RAD tags
DOI: 10.5061/dryad.3023m/3
title: 3a_BSP_pipeline_log

description: Parameters used to generate BAM/SAM files
DOI: 10.5061/dryad.3023m/5
title: 5_VCF_extract_files

description: Data extracted from Variant Call Format files
DOI: 10.5061/dryad.3023m/6
title: 6_R_code_count_PCA

description: Data and R code for principal component analysis (PCA) of the count data from the ‘Core Dataset’
DOI: 10.5061/dryad.3023m/7
title: 7_MtDNA_sequences

description: MtDNA sequence data for 142 krill. Two fragments were sequenced: 655 bp Cytochrome c Oxidase subunit I (COI) and 569 bp NADH Dehydrogenase subunit 1 (ND1).
DOI: 10.5061/dryad.3023m/9
title: 4 Variant call format files V2

description: Variant call format files  derived from the RAD sequencing
DOI: 10.5061/dryad.3b77f/10
title: File 10_Morphology_Loadings for 45 craniodental measurements

description: Loadings for 45 craniodental measurements included in PCA analysis.
DOI: 10.5061/dryad.3b77f/2
title: File 2_Primers for 20 nuclear gene segments

description: Gene symbol and name, primer sequences, and description of the 20 nuclear gene segments used in the study.
DOI: 10.5061/dryad.3b77f/3
title: File 3 Best-fitting models for nuclear gene segments
DOI: 10.5061/dryad.3b77f/4
title: File 4 Sequence characteristics

description: Length (bp = base pairs), number of variable sites, number of parsimony-informative sites and mean empirical base frequency of the mitochondrial (CYTB and mitochondrial genome) and nuclear (20 individual loci and concatenated) data sets used in the phylogenetic analyses.
DOI: 10.5061/dryad.3b77f/5
title: File 5 Microsatellite results_genetic diversity_populations

description: Mean genetic diversity indices for 38 autosomal microsatellite loci in four golden jackal populations plus gray wolves and dogs (n=128). Standard errors are given in parenthesis. N = number of individuals; Na = number of alleles; He = expected heterozygosity.
DOI: 10.5061/dryad.3b77f/6
title: File 6 Microsatellite results_genetic diversity_38 loci

description: Number of alleles (Na), observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (Fis) computed as in Weir and Cockerham [S67] for each of the 38 microsatellites genotyped at four golden jackal populations, gray wolves and dogs. Deviations from Hardy-Weinberg expectations in each population are indicated with * (p&lt;0.05).
DOI: 10.5061/dryad.3b77f/7
title: File 7 Microsatellite results_Likelihoods for genetic clusters
DOI: 10.5061/dryad.3b77f/8
title: File 8 Microsatellite results_Neighbor-joining genetic distance network
DOI: 10.5061/dryad.3b77f/9
title: File 9_D-statistics_plot

description: D-statistic results for each D-statistic comparison done in the study.
DOI: 10.5061/dryad.3d22k/1
title: Expert uncertainty estimates for all 60 questions in the SEJ protocol document

description: This tab-delimited text file contains raw values provided by all 10 experts for all 60 questions in the structured expert judgment (SEJ) protocol document (Appendix S3).  The six columns are defined as follows: “Expert” refers to the expert identification codes used in the article; “Qnum” refers to the number of each question in the SEJ protocol document (Appendix S3); “Qid” is a brief coded description of the key variables in each question (codes are arranged as watershed location – storm event number – site description – influent/effluent load – pre/post restoration condition; see Appendix S3 for the full details of each question); “Percentile.05” is the 5th percentile of the probability distribution envisioned by each expert to describe the total nitrogen load for each question (units are kg total nitrogen); “Percentile.50” and “Percentile.95” refer to the 50th and 95th percentiles of the distribution, respectively (units are kg total nitrogen).  Note that expert names are not associated with their estimates; the ordering of expert names in Appendix S2 is different than the ordering of their estimates in the data.
DOI: 10.5061/dryad.53d34/1
title: NewHybrids_v.1_input_file

description: This is the input file for NewHybrids v1 (Anderson & Thompson 2002; Anderson 2008)  analyses, used to identify pure species and hybrids and to classify hybrids into categories (i.e., F1, F2, backcross with M. galloprovincialis, or backcross with M. trossulus). This file includes only diagnostic SNPs. We used Jeffreys-type priors and a burn in of 10,000 sweeps followed by 50,000 sweeps in five separate runs. Convergence of Q across runs were again checked.
DOI: 10.5061/dryad.53d34/2
title: INTROGRESS_v.1.22_input_file_(locus_data)

description: This is file 1 (locus data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
DOI: 10.5061/dryad.53d34/3
title: INTROGRESS_v.1.22_input_file_(parent_1_data)

description: This is file 2 (parent 1 data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
DOI: 10.5061/dryad.53d34/4
title: INTROGRESS_v.1.22_input_file_(parent_2_data)

description: This is file 3 (parental 2 data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
DOI: 10.5061/dryad.53d34/5
title: INTROGRESS_v.1.22_input_file_(admix_data)

description: This is file 4 (admix data) of 4 input files needed for running the R package INTROGRESS v1.22 (Gompert & Berkle 2010). These files together allow maximum-likelihood estimate of the ancestry (multilocus hybrid score) of each individual, and genomic cline analysis, which compares admixture at a single locus to average admixture across the rest of the genome. We used the parametric approach, first estimating a multilocus hybrid index and then fitting clines in genotype frequencies at individual SNPs as a function of the neutral expectation derived from the genome-wide hybrid index.
DOI: 10.5061/dryad.53d34/6
title: STRUCTURE_v.2.3.4_input_file

description: This is the input file needed to run STRUCTURE v2.3.4 (Pritchard et al 2000; Falush et al 2003; Falush et al 2007), which we used to identify pure species and hybrids. STRUCTURE jointly assigns individuals probabilistically to the two parental classes without prior input. STRUCTURE analyses used all 1,337 SNPs that passed our primary filters. We used a burn in of 50,000 sweeps and then ran 100,000 sweeps in five separate runs checking for convergence of the estimated membership coefficient (Q) across runs.
DOI: 10.5061/dryad.53d34/7
title: adegenet_package_v.1.4-2_input_file

description: This is the input file needed to performed a principle components analysis with the "adegenet" package version 1.4-2 (Jombart et al 2008) in the R version 3.1.0 environment (R Core Team, 2013). The results from this analysis were used to inform definitions of parental genotypes.
DOI: 10.5061/dryad.53d34/8
title: tags_from_STACKS_populations.pl_script

description: This was an output of the populations.pl script from the Stacks pipeline, used to filter SNPs scored in at least 75% of samples (parameter -r 0.75). This yielded a total of 1,337 SNPs. The original file name was "batch.8.catalog.tags.tsv". More information on the file format can be found at http://catchenlab.life.illinois.edu/stacks/comp/populations.php.
DOI: 10.5061/dryad.579kj/1
title: Stacks analysis of common bottlenose dolphin RAD sequences

description: Results of Stacks analysis of RAD sequencing data generated from pooled genomic DNA from common bottlenose dolphins sampled along the Florida Gulf of Mexico coastline.  Sample pools include live coastal dolphins from the Florida Panhandle (PLC, N=17) and central-west Florida (CWLC, N=26) and live estuarine dolphins from St. Joseph Bay in the Panhandle (PLE, N=12) and Sarasota Bay in central-west Florida (CWLE, N=25). Additional sample pools include samples from bottlenose dolphin strandings (dead samples) during unusual mortality events (UMEs) associated with harmful algal blooms (HABs) in the Panhandle in 1999 (PU99, N=16) and 2004 (PU04, N=35) and during HABs between 1992 and 2006, including a UME in 2005-2006, in central-west Florida (CWU, N=25).  Two groups of samples (PLC and CWU) were divided for sequencing into pools of excellent and good quality genomic DNA.  PL represents samples from the Florida Panhandle that cannot be definitively attributed to either coastal or estuarine dolphin populations. Stacks parameters are described in the Methods section of Cammen et al. (2015).  Chromosome accession numbers refer to scaffolds in the bottlenose dolphin genome: Ttru_1.4/turTru2 (GCA_000151865.2).  The spreadsheet includes both the alleles detected at each RAD locus as well as the depth of read coverage within the sample pool for the given alleles.  Analyses described in the manuscript were conducted on a subset of these RAD loci that passed additional filters: 1 SNP with a sample-wide minor allele frequency greater than 0.10; present in at least 2 sample pools.
DOI: 10.5061/dryad.65tt7/1
title: Donihue et al. 2015 Feed or Fight Data

description: All data archived here were used for analyses in Donihue et al. "Feed or Fight: Testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard." Data is in five worksheets. Please see ReadMe file for additional information.
DOI: 10.5061/dryad.84d4j/1
title: M13 sequencing run, part 1
DOI: 10.5061/dryad.c85gk/6
title: DGGE

description: Presence and absence of bands comprising the fingerprint patterns generated by PCR-DGGE. MA- Massachusetts; NY-New York; NC-North Carolina; (F)-Forest; (O)-Oldfield; IN- Invaded soil;OU-Non-invaded soil
DOI: 10.5061/dryad.c85gk/7
title: Degradation of phenolics

description: Percent of initially added phenolics recovered at various sampling times. IN-  inoculum from invaded soil; OUT- inoculum from non-invaded soil.
DOI: 10.5061/dryad.gv506/1
title: SG_Nested_Data

description: Historic dataset of Scottish coastal grasslands, derived from the Scottish Coastal Survey (1975–1977); For details see: Shaw, M.W., Hewett, D.G. & Pizzey, J.M. (1983). Scottish coastal survey. Institute of Terrestrial Ecology. Bangor Research Station, Bangor, Gwynedd. The dataset is nested: i.e. records of plant species with taken following a hierarchical sampling design, measuring nested community compositions at 4m2 and 200m2. The uploaded dataset comprises species information (recorded as octets) on 3033 nested samples.
DOI: 10.5061/dryad.kp11q/1
title: Danish_sticklebacks
DOI: 10.5061/dryad.kp11q/2
title: sticklebacks_DK

description: sticklebacks_DK.bed, Plink input file for running Faststructure on the nine threespine stickleback populations
DOI: 10.5061/dryad.kp11q/3
title: sticklebacks_DK

description: sticklebacks_DK.bim, Plink input file for running Faststructure on the nine threespine stickleback populations
DOI: 10.5061/dryad.kp11q/4
title: sticklebacks_DK

description: sticklebacks_DK.fam, Plink input file for running Faststructure on the nine threespine stickleback populations
DOI: 10.5061/dryad.p834j/1
title: conditional_logit_data for Dryad_FINAL
DOI: 10.5061/dryad.p834j/2
title: modularity_data for Dryad_FINAL

description: data to assess drivers of modularity
DOI: 10.5061/dryad.p834j/3
title: nests_success_data for Dryad

description: data to compare nest success between individuals who nest in habitat types similar to natal habitat type versus those that don't
DOI: 10.5061/dryad.p834j/4
title: nest_fledge_data for Dryad_FINAL

description: maladaptive habitat selection and explains geographic structure of a highly mobile bird
DOI: 10.5061/dryad.pj56m/1
title: urogallus microsatellite genotypes
DOI: 10.5061/dryad.1g347/1
title: data on mating rate in water striders

description: These data were used to analyze the determinants of mating rate in water striders. The data set is constituted of all the possible pairs of males and females available for mating within each pool (see methods and readme file). Males and females were considered available if they were single and on the water. We then recorded whether each pair was mating (1) or not during the next scan observation (0, see 'mating' variable below). Each row corresponds to a single observation on a particular pair at a given time. Each column lists the values for a given variable. The description of each variable is given in the readme file. The data files are in a comma separated format.
DOI: 10.5061/dryad.1g347/2
title: data on mating duration in water striders

description: These data were used to analyze the determinants of mating duration. The data set includes all observations in which a given male and female were observed mating. For each of these observations, we then determined whether they pursued (1) or ceased mating (0) at the next scan observation. Each row corresponds to a single observation on a given pair at a given time. Each column lists the values for a given variable. The description of each variable is given in the readme file. The data files are in a comma separated format.
DOI: 10.5061/dryad.1g347/3
title: read me first!

description: This file provides contact information, an overview of the methods, and details each variable presented in the data files.
DOI: 10.5061/dryad.2j4vj/1
title: Dryad data Harborne et al Oikos OIK-02602

description: The spreadsheet contains three worksheets. The first two sheets provide the raw field data that was input into the linear mixed-effects models to generate Table 1 and 2 and Figs 2 and 3. Variables are separated into explanatory and response variables, and the labels are self-explanatory. Collection methods are described in the paper. The third sheet provides the outputs of the simulation model that was plotted to create Fig 4. Model design and parameterisation are described in the paper.
DOI: 10.5061/dryad.3b77f/11
title: File 11_Morphology_Loadings for craniodental ratios

description: Loadings for nine arcsine-transformed craniodental ratios included in PCA analysis
DOI: 10.5061/dryad.3d22k/2
title: Realizations for the 11 calibration variables in the SEJ protocol document

description: This tab-delimited text file contains empirically measured values for the 11 calibration variables in the structured expert judgment (SEJ) protocol document (Appendix S3).  The three columns are defined as follows: “Qnum” refers to the number of each question in the SEJ protocol document that corresponds to a calibration variable (Appendix S3); “Qid” is a brief coded description of the key variables in each question (codes are arranged as watershed location – storm event number – site description – influent/effluent load – pre/post restoration condition; see Appendix S3 for the full details of each question); “TN.load.kg” is the empirically measured total nitrogen load (units are kg total nitrogen).
DOI: 10.5061/dryad.46r30/1
title: DryadData

description: This data file contains five sheets. "Wild Data" and "Wild Data Individual Offspring" contains the lengths of offspring and their mothers after collecting pregnant females from the wild. "Lab Data" and "Lab Data Individual Offspring" contain data from a laboratory breeding experiment, whereby the daughters of wild-caught mothers were raised in different environments to produce four groups of females (Old/Large, Old/Small, Young/Large, Young/Small) to measure the effect of maternal size and age on offspring size and number. The final sheet - "Meta-data" - contains descriptions of the headers used in the four sheets of data.
DOI: 10.5061/dryad.4b3h7/1
title: Translation Table

description: This table contains the internal laboratory codes used to identify mtDNA control region sequences (in the uploaded sequence alignments), and their corresponding GenBank numbers. Asterisked (*) sequences indicate exemplar sequences used in the 33 haplotype dataset.
DOI: 10.5061/dryad.4b3h7/2
title: aDNA optomisation code

description: Code for implementing the optimisation of ancient-DNA datasets for analysis in BayeSSC.
DOI: 10.5061/dryad.4b3h7/3
title: SISaDNA1perHap33

description: Nexus file containing one sequence of each haplotype (including out-group sequences) for the 33 haplotype dataset.
DOI: 10.5061/dryad.4b3h7/4
title: OtagoBSPr2

description: BEAST .xml file for Bayesian Skyline analysis of L. chalconotus Otago.
DOI: 10.5061/dryad.4b3h7/5
title: FoveauxBSPr1

description: BEAST .xml file for the Bayesian Skyline analysis of L. chalconotus Foveaux Strait.
DOI: 10.5061/dryad.4b3h7/6
title: BayeSSC par files

description: BayeSSC .par files for joint (Otago and Foveaux Strait) Models 1-6, and Otago only Models 1-3.
DOI: 10.5061/dryad.53d34/9
title: SNPs_from_STACKS_populations.pl_script.tsv

description: This is the output of the populations.pl script from the Stacks pipeline, used to filter SNPs scored in at least 75% of samples (parameter -r 0.75). This yielded a total of 1,337 SNPs. The original file name was "batch.8.catalog.snps.tsv". More information on the file format can be found at http://catchenlab.life.illinois.edu/stacks/comp/populations.php. We compressed the file for convenience.
DOI: 10.5061/dryad.579kj/2
title: RAD locus allele frequencies

description: Allele frequencies for 7,431 polymorphic (single SNP) RAD loci that were assessed for an association with bottlenose dolphin survival following exposure to harmful algal blooms.  Allele frequencies for each sample pool were calculated based on the proportion of reads sequenced for each SNP variant (see “Stacks analysis of RAD data” Dryad file).  Depth indicates the total number of reads per locus and sample pool; sample size indicates the number of individuals sequenced in the sample pool (note this varies for PLC and CWU because individuals of good and excellent quality DNA were separated during library preparation).
DOI: 10.5061/dryad.579kj/3
title: Fisher’s Exact Test for differences in allele frequency between live and dead bottlenose dolphins

description: Results (p values) of Fisher’s Exact Test for differences in allele frequency between pools of live and dead dolphins. Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.”  Fisher’s exact tests, which were implemented in R, use a contingency table approach to assess deviations from a null hypothesis of no association between genotype and phenotype for each locus independently.
DOI: 10.5061/dryad.579kj/4
title: BayeScan analyses of comparisons of live and dead bottlenose dolphins

description: Results of BayeScan analyses of comparisons of RADseq allele frequencies between live and dead dolphins. Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.”  BayeScan (v2.1) implements a Bayesian approach to assess evidence for selection at a given locus by comparing population- and locus-specific components of FST across multiple loci (Foll and Gaggioti 2008).
DOI: 10.5061/dryad.579kj/5
title: Smoothed pairwise genetic differentiation (FST) and overall nucleotide diversity (pi)

description: Smoothed pairwise genetic differentiation (FST) and overall nucleotide diversity (pi) across bottlenose dolphin RAD loci.  Sample pool abbreviations as in description for “Stacks analysis of common bottlenose dolphin RAD sequences.”  FST was calculated from nucleotide diversity at each population and across the pooled populations, where nucleotide diversity was calculated using allele counts (see equation 2 in Hohenlohe et al. 2010). Accession numbers refer to scaffolds in the killer whale genome (Oorc_1.1, GCA_000331955.2). Smoothed average FST was calculated using a Gaussian function with theta of 150kb and windows truncated at 3σ from centre in both directions
DOI: 10.5061/dryad.6kp2n/1
title: JEcol-Midgley et al.

description: Litter quality and decomposition rates
DOI: 10.5061/dryad.7f4v1/1
title: Phylogenetic trees and sexual system classifications

description: Provided are: (1) Trees - a directory with phylogenetic trees for all genera in the study. (2) Sexual_systems - a directory with sexual system assignments for all species. (3) sexual.system.classifications.csv - a file with the classifications of sexual system (per species) into "broad" and "strict" definitions.
DOI: 10.5061/dryad.84d4j/2
title: M13 sequencing run, part 2
DOI: 10.5061/dryad.84d4j/3
title: Lambda sequencing run, part 1
DOI: 10.5061/dryad.84d4j/4
title: Lambda sequencing run, part 2
DOI: 10.5061/dryad.84d4j/5
title: DNA_CS sequencing run
DOI: 10.5061/dryad.84d4j/6
title: Original submission code
DOI: 10.5061/dryad.dd34q/1
title: Data_ScoringDay1
DOI: 10.5061/dryad.dd34q/3
title: Data_ScoringDay2
DOI: 10.5061/dryad.fp1k7/1
title: BioClim 30s clipped

description: BioClim 19 climate variables plus altitude clipped to United States and Canada.
DOI: 10.5061/dryad.fp1k7/2
title: BioClim 2.5 clipped

description: Bioclim 2.5 arc minute WorlClim layers clipped to the United States and Canada.
DOI: 10.5061/dryad.fp1k7/3
title: Paleo 2.5 clipped

description: Paleo-climate layers from WorldClim clipped to the United States and Canada.
DOI: 10.5061/dryad.fp1k7/4
title: Genotype_data

description: Microsatellite genotypes
DOI: 10.5061/dryad.fp1k7/5
title: eastclade_locality

description: 484 occurrence points downloaded from public databases, HerpNet and GBIF
DOI: 10.5061/dryad.fp1k7/6
title: Locality_East&West Clade

description: Occurrence data for wood frogs downloaded from public databases, HerpNet and GBIF.
DOI: 10.5061/dryad.gm2v0/1
title: Genotype Data_Structure format

description: Complete genotype data in Structure program format. Row 1 lists the microsatellite markers. Microsatellite data are presented in two-column per marker format. Missing data are indicated with -9. Column 1 gives the population and sample identifier, column 2 gives the population number, remaining columns are microsatellite data.