cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s4sh6/2
title: Dcopei_landscape_distances

description: These data are landscape distances between study sites calculated using least cost path (LCP) analysis (columns B-JJ) and Circuitscape resistance analysis (columns JL-KB). LCP data represent the weighted averages of all landscape layers along a particular LCP (indicated in the row below the region name), and all LCPs were corrected for topography. Landscape cost surfaces were developed using the following GIS datasets downloaded from online databases (including abbreviations and source of data citations from Trumbo et al. 2012): stream networks (USGS 2001) (str10 = 10:1 cost of movement outside streams, str100 = 100:1 cost of movement outside streams), canopy cover (cc) (Homer et al. 2004), frost-free periods (ffp) (Rehfeldt 2006), growing season precipitation (gsp) (Rehfeldt 2006), landcover (lc) (Homer et al. 2004), and heat load index (hli) (McCune and Keon 2002). For streams, a "no" following abbreviation means that large rivers were excluded from the stream network. For all continuous variables, a "1" following the abbreviation means an exponentially increasing non-linear response, such that the transformed surface T1 = 100^ (original cost surface). A "2" following the abbreviation means an exponentially decreasing non-linear response such that the transformed surface T2 = 100 - 100^(1- original cost surface). The "strghtline" data are null models of isolation by Euclidean distance alone.
DOI: 10.5061/dryad.t0q94/1
title: Electronic Supplementary Material

description: Electronic Supplementary Material (ESM) accompanying the paper.
DOI: 10.5061/dryad.t0q94/2
title: Dataset

description: Please refer to ReadMe file.
DOI: 10.5061/dryad.1117q/1
title: 2012-SystBiol-Adams-Final-SuppMaterial

description: Supplementary Material containing results from additional computer simulations that assess the Type I error rate and statistical power of the proposed likelihood method.
DOI: 10.5061/dryad.1117q/2
title: Adams2012-SystBiolData

description: Average linear measurements for three traits from each of 44 Plethodon species used in this study.
DOI: 10.5061/dryad.1c1m4qc6/3
title: Relaxed clock MCMC analysis, trees subsample

description: This file contains 200 trees subsampled from a relaxed-clock MCMC analysis conducted in BEAST (see XML file in this submission for details on how analysis was conducted). Comparative analyses conducted in the paper were conducted over this set of tree and summarized as the mean +/- the 95% phylogenetic uncertainty interval.
DOI: 10.5061/dryad.1c1m4qc6/4
title: Individual flow cytometry data points, Carex subgenus Vignea

description: Flow cytometry data were analyzed in FlowJo software to estimate genome sizes, following protocols described in the publication associated with this dataset. This Excel spreadsheet contains the individual flow cytometry data points used to estimate genome size for all species in the publication.
DOI: 10.5061/dryad.218p2/1
title: Davey2012_MolEcol_Dryad_Submission.tar

description: Scripts and data files required to replicate figures and calculations for associated paper. Details in DESCRIPTION.md file, included in archive.
DOI: 10.5061/dryad.320kb06t/1
title: DRYAD genotypic data for two focal species

description: File 1 Genotypic data for two focal species: Excel spreadsheet of genotypic data for 50 individuals each of two focal sparid species for the developed microsatellite markers in these species. There are nine microsatellite markers for Pachymetopon blochii and nine for Lithognathus lithognathus. The program GeneMarker was used to score the alleles.
DOI: 10.5061/dryad.320kb06t/2
title: DRYAD location information of species

description: File 2 Location information of species: Excel spreadsheet of specimens used and locations sampled for the microsatellite marker development and cross-species amplification study.
DOI: 10.5061/dryad.320kb06t/3
title: DRYAD primers and 454 sequences for additional sparid loci

description: File 3 Primers and 454 sequences for additional sparid loci: Excel spreadsheet of additional microsatellite markers identified in two focal sparid species from two repeat enrich libraries (using the FIASCO protocol) and a fraction of 454 sequencing. The table includes repeat type, primers, fragment size and the 454 sequences in FASTA format.
DOI: 10.5061/dryad.3s36r118/1
title: norwood
DOI: 10.5061/dryad.62hk145k/1
title: raw data Waldner & Traugott MER-12-0024

description: Original screening and biomass data
DOI: 10.5061/dryad.c0f2n3mj/1
title: *BEAST and Skyride xml files

description: This .zip file contains the xml input files of the best model for the *BEAST analysis and GMRF Skyride.
DOI: 10.5061/dryad.c0f2n3mj/2
title: IMa input and nested models files

description: The IMa.zip contains two files: The input file for IMa and the nested models files needed to test competing hypotheses of gene flow patterns
DOI: 10.5061/dryad.c0f2n3mj/3
title: Silva2012_alignments

description: This zip files contain the alignments of the six nuclear markers in NEXUS leave format.
DOI: 10.5061/dryad.jk87h/1
title: Copy of Sleepy Lizard Salmonella Genotype Data (2)

description: The salmonella genotypes from each of 20 subsamples from each of the 60 lizards sampled in the survey
DOI: 10.5061/dryad.jk87h/2
title: Copy of T rugosa social network matrix 2010 for Mol Ecol

description: A matrix of the network strengths among each pair of lizards within the 60 lizards sampled in the study
DOI: 10.5061/dryad.jr56h/1
title: SequenceData

description: Raw sequence data and pileups
DOI: 10.5061/dryad.jr56h/2
title: SNP matrix

description: SNP matrix produced from the .vcf genotype calling file by VCFTOOLS
DOI: 10.5061/dryad.jr56h/3
title: allSNP

description: SNP data (5985 SNPs in total) discovered from both herring populations in vcf 4.1 format
DOI: 10.5061/dryad.jr56h/4
title: fixed_loci_index

description: Fixed loci (1567 in total) on distinct alleles in the two sample locations. Each element in this file is an index of a SNP in "allSNP.vcf".
DOI: 10.5061/dryad.jr56h/5
title: herring_details

description: Office 2010 excel format table of details concerning the BLAST analysis for the study "High degree of cryptic population differentiation in the Baltic Sea herring Clupea harengus". The table columns include "RAD_id", "Reference", "E-value", "Similarity" and "Sample sequence in FASTA". The calculated values are collected with Blast2GO program. For additional descriptions, see README.txt.
DOI: 10.5061/dryad.qk770/1
title: AFLPdataVandepitteetal2012

description: Genotype data based on Amplified fragment length Polymorphism (AFLP) of the ms entitled "Recolonization after habitat restoration leads to decreased genetic variation in populations of a terrestrial orchid" by Vandepitte et al. accepted in 2012 by Molecular Ecology. Rows 2-272: each line is the AFLP genotype of a separate Dactylorhiza incarnata plant, individuals are labeled according to the number of their population (=sampling location) of origin Table 1 in the publication. Column 1: Population ID; Column 2-92: AFLP loci, 1 decodes the presence of a band, 0 the absence.
DOI: 10.5061/dryad.sr14q/1
title: MbipiaPundamilia_M2
DOI: 10.5061/dryad.sr14q/2
title: MbipiaPundamilia_M1
DOI: 10.5061/dryad.sr14q/3
title: MbipiaPundamilia_M4
DOI: 10.5061/dryad.v0t0d/1
title: Figure 1 xml file

description: xml file used in the BEAST analyses of Drosophila using 218 ingroup species and 9 calibration points.
DOI: 10.5061/dryad.v0t0d/2
title: Figure 1 tree

description: Figure 1. Summarized chronogram for the subgenus Drosophila obtained with BEAST using 218 species and 9 calibration points. It corresponds to the analysis run with the Figure 1 xml file.
DOI: 10.5061/dryad.v0t0d/3
title: Figure 2 xml file

description: xml file used to run the BEAST analysis of Figure 2, using 153 species for which there was sequence data for 2 or 3 genes and 9 calibration points.
DOI: 10.5061/dryad.0hd1s/1
title: 29_aeb

description: Concatenation of 29 genes conserved in Bacteria, Archaea and eukaryotes.
DOI: 10.5061/dryad.292q34fp/1
title: Mixed mating outcrossing rate database

description: This Excel file contains data on outcrossing rates and the inbreeding coefficient for plants species collected from published literature. Column headings in the file are described in the associated ReadMe file.
DOI: 10.5061/dryad.6q81t4m4/1
title: PredationNZ_Dryad_DATA
DOI: 10.5061/dryad.7dn526gq/1
title: TABLE - SSR marker data

description: This Table provides a complete list of the 144 SSR markers used to screen the single-plant progeny lines selected from the soybean cultivars Benning, Cook, and Haskell and information about the markers, being polymorphic or not.
DOI: 10.5061/dryad.7dp3126p/1
title: Lateral plate counts and EDA STN382 allel number

description: Individual based data providing the name of the lake sampled (Lake), an identifier for each individual (Individual), the number of later plates counted on the left side on the keel (Keel), the number of STN382 C alleles (STNallele), the total number of lateral plates counted on the left side (Total_Plates) and the assigned phenotypic morph (Morph). Plate morph abbreviations are as follow: LP - low plated with 10 or less anterior plates, LPK - as LP but with plates on the keel, PPNK - partial plated, i.e. having &gt; 10 plates but no plates on the keel, PPK - as PPNK but with plates on the keel, FP - fully plated with plates continuously along the left side
DOI: 10.5061/dryad.j7q8p/1
title: RAD_cydmelhec_data.geno

description: Space delimited tabular file giving the genotype calls used this paper. They were filtered from the .vcf files (generated by GATK unified genotyper) and represent all bases that were called with a genotype quality &gt;=30 in multiple individuals. Individuals are in columns and genome positions in rows. Missing data are given as "N". This file was filtered for the relevant individuals and all sites with missing data removed prior to running analyses with any of the given scripts.
DOI: 10.5061/dryad.j7q8p/2
title: clumpy

description: Python script used to split the single calls file(s) into individual RAD loci. The output consists of multiple files - one for each locus found - all in the same format as the original calls input file, and a comma separated values file with the start and end positions in the genome and length of each RAD locus.
DOI: 10.5061/dryad.j7q8p/3
title: population_matrix_taxon

description: A file giving taxonomic groupings for each population for the AMOVA analysis
DOI: 10.5061/dryad.j7q8p/4
title: population_matrix_CP

description: A file giving colour pattern groupings for each population for the AMOVA analysis
DOI: 10.5061/dryad.j7q8p/5
title: Hmel_chromosomes_dec_2011_OLD_HOX_no_header_filtered

description: A file relating the scaffolds to chromosomes (inferred from RAD mapping from The Heliconius Genome Consortium 2012). This was used to generate genome-wide plots.
DOI: 10.5061/dryad.j7q8p/6
title: Fst2

description: R script used to calculate Fst between all pairs of populations. Inputs are as Fst.r.
DOI: 10.5061/dryad.j7q8p/7
title: population_matrix_geo

description: A file giving geographic groupings for each population for the AMOVA analysis
DOI: 10.5061/dryad.j7q8p/8
title: geno_to_haplo_54

description: Perl script used to go from genotype calls to haplotype calls (not phased). This was done before running the Fst scripts but not AMOVAs.
DOI: 10.5061/dryad.j7q8p/9
title: Fst

description: R script used to calculate the Fst values for the major race and species comparisons discussed in the paper. Inputs are the indidividual RAD locus haplotpe files and the summary statistics file generated by clump.py
DOI: 10.5061/dryad.kn8b72m5/1
title: SUPPLEMENTARY DATABASE F0R Ausich & Roerser

description: Ontogey figures
DOI: 10.5061/dryad.n6661sh1/1
title: Cardiac Rehab in HF Stage 1 Survey

description: Stage 1 of the national survey included all centres that provided phase 3 rehabilitation in England, Wales, and Northern Ireland registered on the National Audit of Cardiac Rehabilitation (NACR) database funded by the British Heart Foundation. Each centre was sent a 17 item, one page postal questionnaire that asked respondents to indicate whether they routinely provided a cardiac rehabilitation service for patients with heart failure and to identify and give brief details about barriers to provision of such a service. The stage 1 questionnaire was mailed out by the NACR office in York (A copy of the stage 1 questionnaire is included as an appendix to the main paper ).
DOI: 10.5061/dryad.n6661sh1/2
title: Cardiac Rehab in HF Stage 2 Survey

description: Stage 2 of the survey was sent from the Royal Cornwall Hospitals Trust and included all centres that confirmed in stage 1 that they provided a separate cardiac rehabilitation service for patients with heart failure. These centres were sent a 44 item, five page questionnaire designed to find out more about the nature (patient demographics and staffing) and content of their cardiac rehabilitation service (see appendix of the main paper for a copy of the stage 2 questionnaire). In the first instance, the stage 2 questionnaire was sent by email, with a letter explaining why more detailed information was being requested from the centres. To optimise response rates, non-responders were sent personalised letters with stamped addressed envelopes, and these were followed by reminder emails and telephone calls
DOI: 10.5061/dryad.n6661sh1/3
title: NACR Database Stage 1 ComparisonData

description: To validate the data, responses from stage 1 in terms of the demographic and activity features of the centres were compared with information from the NACR (the methods and measures used by the NACR are described on and available for download from www.cardiacrehabilitation.org.uk/nacr).
DOI: 10.5061/dryad.p0d83/1
title: dataHeredity
DOI: 10.5061/dryad.sr2hd7md/1
title: Cellinese_Appendix1

description: This document represents the proposal for changes to the PhyloCode, with respect to species. It was submitted on October 5, 2011 to the Committee of Phylogenetic Nomenclature, International Society for Phylogenetic Nomenclature.
DOI: 10.5061/dryad.v0t0d/10
title: Fig5B

description: Figure 5. Backbone topology used in the MEDUSA analyses. Phylogeny backbone from analysis with 218 species and 5 calibration points. Tip names refer to the species groups (those polyphyletic were clustered into a single clade) and numbers in brackets refer to the species richness of the tip. Numbers on nodes indicate divergence times.
DOI: 10.5061/dryad.v0t0d/4
title: Figure 2 tree

description: Summarized chronogram for the subgenus Drosophila obtained with BEAST using 153 species and 9 calibration points, corresponding to the Figure 2 xml file analysis.
DOI: 10.5061/dryad.v0t0d/5
title: Figure 3 xml file

description: File used to run the BEAST analyses of the subgenus Drosophila obtained with BEAST using all 218 species and 5 calibration points. Corresponding to the Figure 3.
DOI: 10.5061/dryad.v0t0d/6
title: Figure 3 tree

description: Figure 3. Summarized chronogram for the subgenus Drosophila obtained with BEAST using 218 species and 5 calibration points. It corresponds to the Figure 3 xml file.
DOI: 10.5061/dryad.v0t0d/7
title: Fig4A

description: Ancestral reconstruction of geographic distribution. Tree showing the main dispersal events inferred to have occurred during the evolution of the Drosophila subgenus.
DOI: 10.5061/dryad.v0t0d/8
title: Fig4B

description: Ancestral reconstruction of ecological niche. Trees showing the main ecological shifts inferred to have occurred during the evolution of the Drosophila subgenus.
DOI: 10.5061/dryad.v0t0d/9
title: Fig5A

description: Figure 5. Backbone topology used in the MEDUSA analyses. A) phylogeny backbone from analysis with 218 species and 9 calibration points. Tip names refer to the species groups (those polyphyletic were clustered into a single clade) and numbers in brackets refer to the species richness of the tip. Numbers on nodes indicate divergence times.
DOI: 10.5061/dryad.0hd1s/2
title: aeb_fasta_files.tar

description: Single genes conserved between Bacteria, Archaea and eukaryotes. These are the "raw" fasta files, before alignment editing.
DOI: 10.5061/dryad.0hd1s/3
title: arch_euk_fasta.tar

description: Single genes conserved between Archaea and eukaryotes. These are the raw sequence files before editing.
DOI: 10.5061/dryad.0hd1s/4
title: 63_genes

description: 63AE dataset (described in article)
DOI: 10.5061/dryad.0hd1s/5
title: 64_genes

description: 64AE dataset (described in article)
DOI: 10.5061/dryad.0hd1s/6
title: 64_singles.tar

description: The genes used to make the 64AE dataset, after masking of poorly-aligning and uninformative sites.
DOI: 10.5061/dryad.0hd1s/7
title: 29_alns_cut.tar

description: The genes used to make the 29BAE dataset, after masking of poorly-aligning and uninformative sites.
DOI: 10.5061/dryad.0hd1s/8
title: rrna.tar

description: LSU and SSU rRNA sequence files (FASTA format) and alignment (PHYLIP format). Used to produce Figure 1 of the article.
DOI: 10.5061/dryad.0hd1s/9
title: newick_trees.tar

description: Newick tree files corresponding to Figures 1 and 2 of the article.
DOI: 10.5061/dryad.11vq033v/1
title: DryadEukaryoteData.tar
DOI: 10.5061/dryad.83p1130j/1
title: Master Alignment

description: Master alingment of mitochondrial genome and nuclear rag1 data in nexus format. The matrix includes a tree block with the maximum likelihood tree obtained with RAxML v7.2.6. This data file has also been deposited in TreeBASE under accession number S11625.
DOI: 10.5061/dryad.83p1130j/2
title: Supplementary Material

description: Distinct structural features of the mitochondrial genome of Crotaphatrema lamottei.
DOI: 10.5061/dryad.98s363k3/1
title: Microsatellite allele sizes of Pacific lamprey from 20 locations along the west coast of North America

description: Microsatellite allele sizes determined using Genemapper, formatted for Genepop.
DOI: 10.5061/dryad.98s363k3/2
title: List of haplotypes and composite haplotypes for Pacific lamprey collected from 20 locations along the west coast of North America

description: RFLP haplotypes determined by gel electrophoresis
DOI: 10.5061/dryad.bq4pp7f9/1
title: Lalic and Elena Heredity raw data

description: Page 1 contains the raw TEV accumulation data generated by qPCR. Page 2 contains the average malthusian parameter estimated for each double mutant (with SEM) and the corresponding pair of single mutants. Page 3 contains the fitness (W) values for each genotype and the computation of epistasis coefficients. Page 4 evaluates the inequalities for sign and reciprocal sign epistases.
DOI: 10.5061/dryad.h4j28d1n/1
title: Data for archive

description: Full description of sources provided in the article
DOI: 10.5061/dryad.j7q8p/10
title: amova1

description: R script used to perform AMOVA analyses. Generates a distance matrix based to genotype calls and used the ade4 package to run Amovas. Inputs are the indidividual RAD locus genotype files and the summary statistics file generated by clump.py and character matrix files (see below).
DOI: 10.5061/dryad.j7q8p/11
title: Fst_spcorr

description: R script used to calculate correlations between Fst values at increasing genomic distances. Input is the output from Fst.r.
DOI: 10.5061/dryad.j7q8p/12
title: genotype_matrix

description: A starting genotype matrix assuming sepatare genotypes for each individual that is modified by the AMOVA script.
DOI: 10.5061/dryad.j7th2/1
title: Fundulus notatus raw data

description: Excel file containing the raw data (morphometric measurements as well as data on population, drainage, habitat, age, and sex).
DOI: 10.5061/dryad.q41jr576/1
title: HDY-11-OR0388R dryad
DOI: 10.5061/dryad.qf488/1
title: Microsatellites data

description: The 23 microsatellites used for the Bayesian clustering analyses. The populations, refere to Méthot Lake (MET), Petit Saint-Bernard Lake (BER), Lac des Écorces aquaculture facility (LDE), Bourassa Lake (BOU) and Jacques Cartier aquaculture facility (JC).
DOI: 10.5061/dryad.tb40v/1
title: Conchoecissa sequence data

description: Assembled 454 transcriptome data, otherwise unpublished. Only sequences used in MBE-published phylogenetic analysis are provided here. Collection information:  Trawl Lower Sur Canyon on R/V Western Flyer Trawl on Western Flyer 36.06° N 122.29 W December 10th, 2009
DOI: 10.5061/dryad.tb40v/2
title: Morphological matrix for phylogenetics

description: Morhpological data matrix, including extant and fossil taxa. Stored in Morphobank, project ID 689
DOI: 10.5061/dryad.tb40v/3
title: Raw 454: Vestalenula_sp

description: Raw Transcriptome sequence from full bodies. Adapter sequences included. Pooled together multiple individuals. Adapter = AAGCAGTGGTATCAACGCAGAGTACTTTTTTCTTTTTT. Collection Information: Freshwater Puddle, Isla Colon, Bocas del Toro, Panama. Net collecting 9º21.17'N 82º15.45'W July 29th, 2009 10cm
DOI: 10.5061/dryad.tb40v/4
title: Raw 454: Vestalenula_sp quality file

description: Quality associated with fasta file.
DOI: 10.5061/dryad.vk7sr8tr/1
title: Mountain pine beetle colonization and reproductive success measurements within fire-injured lodgepole pine of the Greater Yellowstone Ecosystem
DOI: 10.5061/dryad.08507r35/1
title: Larix_decidua_sample_info

description: This data file contains information about sampling location individual genotype information for 18 Larix decidua populations from across the natural distribution range. Columns 1-3: Population ID and corresponding geographical coordinates. Columns 4-30: 413 Individual genotypes of 18 populations, each composed of 13 loci. Missing data value: 0
DOI: 10.5061/dryad.0h887/1
title: Raw data Dryad

description: Growth rate data in mm/day for all temperatures, populations, isolates and replicates.
DOI: 10.5061/dryad.1q3b6/1
title: ES_1_morph_Matrix

description: Electronic supplement (ES) 1 Morphological data matrix of head characters (complete dataset) used for the initial tree reconstructions with clique affiliation indicated in columns 2-4.
DOI: 10.5061/dryad.1q3b6/2
title: ES_2_initial_morph_trees

description: Electronic supplement (ES) 2 Initial tree inference of the complete morphological data set with detailed support values for each node. A RaxML bootstrap supports; B Bremer supports; C Posterior probabilities; D Parsimony bootstrap supports.
DOI: 10.5061/dryad.1q3b6/3
title: ES_3_initial_mol_trees

description: Electronic supplement (ES) 3 Tree inference of the molecular data set with detailed support values for each node. A RaxML bootstrap supports; B Posterior probabilities.
DOI: 10.5061/dryad.20617h5g/1
title: ALG11 DNA alignment

description: DNA sequence alignment of the ALG11 gene in Nexus format
DOI: 10.5061/dryad.20617h5g/2
title: COI DNA alignment

description: DNA sequence alignment of the COI gene in Nexus format