cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v134j/5
title: tpc118794Supplemental

description: Supplemental Figures and Tables
DOI: 10.5061/dryad.17bn1/4
title: ASU_Acar_v2.1.exon.fa -- A fasta file of each exon of each of the transcripts in ASU_Acar_v2.1

description: Exons are duplicated if they are shared between transcripts.
DOI: 10.5061/dryad.1mt1h/1
title: EST-SSR genotypes

description: EST-SSR genotypes of 724 individuals of Shorea leprosula used in the publication. Samples were collected in the natural populations of Malay Peninsula, Sumatra and Borneo and a plantation forest in Java. The data are in a format suitable for the program GenAlEx (Peakall and Smouse 2006).
DOI: 10.5061/dryad.1mt1h/2
title: chloroplast DNA sequences

description: Final DNA sequence assembly for the four noncoding chloroplast DNA regions of 177 individuals of Shorea leprosula used in the publication. Samples were collected in the natural populations of Malay Peninsula, Sumatra and Borneo and a plantation forest in Java.
DOI: 10.5061/dryad.1mt1h/3
title: Sample locations

description: Locations of the 27 populations of Shorea leprosula and numbers of samples analyzed in the publication. The three populations in Sarawak has been excluded from our EST-SSR analysis due to their small sample sizes.
DOI: 10.5061/dryad.1mt1h/4
title: IM input file

description: An input file for the analysis of an Isolation-with-migration model between the Malay/Sumatra and the Borneo population groups of Shorea leprosula, based on the polymorphisms in the four noncoding chloroplast DNA regions.
DOI: 10.5061/dryad.1mt1h/5
title: IM setting file

description: Parameter setting for the analysis of an Isolation-with-migration model between the Malay/Sumatra and the Borneo population groups of Shorea leprosula, based on the polymorphisms in the four noncoding chloroplast DNA regions.
DOI: 10.5061/dryad.1qp42/2
title: Haloferax nucleosome centre positions

description: Archaeal browser track with 1-based nucleosome centre positions, bed file
DOI: 10.5061/dryad.23g44/23
title: debruyntableS1

description: TABLE S1.  Sampling locations and sample information for this study.
DOI: 10.5061/dryad.23g44/24
title: debruyntableS2

description: TABLE S2. Genbank accession numbers for this study.
DOI: 10.5061/dryad.23g44/25
title: debruyntableS3

description: Table S3. mtDNA Control region: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/26
title: debruyntableS4

description: Table S4. mtDNA COI: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/27
title: debruyntableS5

description: Table S5. DP5: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/28
title: debruyntableS6

description: Table S6 DP14: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/29
title: debruyntableS7

description: Table S7. DP21: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/30
title: debruyntableS8

description: Table S8. DP35: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.2s22q/1
title: Activity, preimaginal mortality and resistance data

description: Original data of activity, preimaginal mortality and resistance of homozygotes for single copies and two duplicated alleles of the ace-1 gene and their hybrids. For each variable the indiduals data are provided.
DOI: 10.5061/dryad.3768m/3
title: Rodent energy requirements 1978-2008

description: See manuscript for a description of rodent data collection methodology and equations used to convert rodent abundances into energy requirements.
DOI: 10.5061/dryad.3df32/1
title: Phylogenetic data matrix

description: The full, aligned phylogenetic data matrix, including definitions of character partitions and exclusion sets, in Nexus format.
DOI: 10.5061/dryad.3df32/2
title: Tree files

description: This file contains phylogenetic tree files for all reported phylogenetic analyses.  See the attached ReadMe file for more information.
DOI: 10.5061/dryad.3nh92/1
title: MER_Nichols2012_figure1_amplifiability

description: This data corresponds to Figure 1 within the publication entitled, 'Browsed twig eDNA: diagnostic PCR to identify ungulate species' published in Molecular Ecology Resources. Figure 1 is a model of how browsed twig environmental DNA degrades over time, represented by the total proportion of samples from moose, red deer and roe deer combined that amplified under our final PCR protocol. The data is separated into species. Samples were initially browsed by the above three species and then put on a fence to simulate natural conditions in the field and sampled at approximately 2 week intervals.
DOI: 10.5061/dryad.47hc8/2
title: Etosha lion observational data

description: This file contains field data collection sheets received from Olivia Forge. Data includes lion pride constituencies with dates and notes based on field observations.
DOI: 10.5061/dryad.55qg0/1
title: Population genetic dataset Anopheles sundaicus CO1 alignment

description: DNA alignment of a fragment of mitochondrial CO1/cox1 gene from Anopheles sundaicus s.l. Individual haplotypes are submitted to GenBank accession numbers GQ395814-GQ395927 and details for each specimen are given in publication Supplementary table S1.
DOI: 10.5061/dryad.55qg0/2
title: Population genetic dataset Anopheles sundaicus ITS2 alignment

description: DNA alignment of a fragment of ITS2 (ribosomal internal transcribed spacer 2) from Anopheles sundaicus s.l. used for biogeographical study. Individual haplotypes are submitted to GenBank Popset number 261599508 and details for each specimen are given in publication Supplementary table S1.
DOI: 10.5061/dryad.55qg0/3
title: Population genetic dataset Anopheles sundaicus Mpi alignment

description: DNA alignment of a fragment of Mpi (mannose phosphatase isomerase) gene from Anopheles sundaicus s.l. used for biogeographical study. Individual haplotypes are submitted to GenBank Popset number 262386140 and details for each specimen are given in publication Supplementary table S1.
DOI: 10.5061/dryad.55qg0/4
title: Population genetic dataset Anopheles sundaicus Mpi long alignment

description: DNA alignment of a fragment of  Mpi (mannose phosphatase isomerase) gene from Anopheles sundaicus s.l. used for ecological study. Individual haplotypes are submitted to GenBank Popset number 261599516 and details for each specimen are given in publication Supplementary table S1.
DOI: 10.5061/dryad.566n8/2
title: Ima2 parameter prior file for 3 P. densata groups

description: Parameter prior file of Ima2 used in multipopulation analyses for 3 P.densata groups
DOI: 10.5061/dryad.74tg7/1
title: Hough et al. (2013). SupMat - Jan14
DOI: 10.5061/dryad.7j564/2
title: PDDDModel_V2.R

description: PDDDModel_V2.R contains the actual code for the model. The model is contained inside a function called RunModel, which is called upon in ExecuteCode.R.
DOI: 10.5061/dryad.7j564/3
title: SetupModel.R

description: SetupModel.R contains code to define all the default parameters, vectors, and matrices used in the main code.
DOI: 10.5061/dryad.7j564/4
title: Functions.R

description: Functions.R contains the customized functions used throughout.
DOI: 10.5061/dryad.7j564/5
title: output.Rdat

description: output.Rdat is the output file used to create Figure 2, S1, and S2.
DOI: 10.5061/dryad.7s5p5/1
title: Simulation Code for Multiple Environmental Variables Scenario

description: Run using R
DOI: 10.5061/dryad.7s5p5/2
title: Simulation Code for Delay between Development and Selection Scenario

description: Run in R
DOI: 10.5061/dryad.7t7d9/1
title: SSU phylogeny of amicronucleate Tetrahymena
DOI: 10.5061/dryad.7t7d9/2
title: SSU amicronucleate tree Newick format

description: SSU amicronucleate tree in Newick format
DOI: 10.5061/dryad.83kd1/2
title: 1471-2229-10-112-s2

description: Details about significant quantitative trait loci from the ColxKas mapping population.
DOI: 10.5061/dryad.83kd1/3
title: 1471-2229-10-112-s3

description: Details about significant quantitative trait loci from the LerxCol mapping population.
DOI: 10.5061/dryad.83kd1/4
title: 1471-2229-10-112-s4

description: Details about significant quantitative trait loci from the LerxCvi mapping population.
DOI: 10.5061/dryad.83kd1/5
title: Copy of 1471-2229-10-112-s5

description: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/6
title: Copy of 1471-2229-10-112-s6

description: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.8f73k/12
title: Shelter_transcript_assemblies_representative_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Shelter.  This file includes only representative transcript.
DOI: 10.5061/dryad.8f73k/13
title: Trailblazer_transcript_assemblies_all_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Trailblazer.  This file includes all transcript isoforms.
DOI: 10.5061/dryad.8f73k/14
title: Trailblazer_transcript_assemblies_representative_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Trailblazer.  This file includes only representative transcript.
DOI: 10.5061/dryad.8f73k/15
title: Wabasso_transcript_assemblies_all_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso.  This file includes all transcript isoforms.
DOI: 10.5061/dryad.8f73k/16
title: Wabasso_transcript_assemblies_representative_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso.  This file includes only representative transcript.
DOI: 10.5061/dryad.8f73k/17
title: combined_switchgrass_transcript_assemblies_all_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases using seven switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Shelter, Trailblazer and Carthage.  This file includes all transcript isoforms.
DOI: 10.5061/dryad.8f73k/18
title: combined_switchgrass_transcript_assemblies_representative_isoforms.fasta

description: RNA-seq transcript assemblies created with Velvet/Oases using seven switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Shelter, Trailblazer and Carthage.  This file includes only representative transcript.
DOI: 10.5061/dryad.8fn8j/1
title: ymerge.fastq

description: Raw sequence data generated by Ion Torrent.
DOI: 10.5061/dryad.8fn8j/2
title: otus

description: Representative sequences of 97% similarity OTUs
DOI: 10.5061/dryad.8fn8j/3
title: OTU_matrix_presence-absence

description: OTU / site distribution matrix
DOI: 10.5061/dryad.9ht88/1
title: Data: Spore carriage by flies

description: Data for experiment on spore carriage by flies after exposure to fruiting bodies. Formatted as tab-delimited text file for use with R. Columns and values described in comments (lines beginning with #).
DOI: 10.5061/dryad.b3h4q/10
title: Fecal cortisol metrabolite levels in playback experiment

description: Fecal cortisol metabolite levels in female squirrels prior to being exposed to the playback treatments (Fig. S3). All data collected in Kluane, Yukon, Canada.
DOI: 10.5061/dryad.b3h4q/11
title: Table S4 - playback fecal cortisol metabolite data

description: Contains data for Table 4 about how the playback experiment affected fecal cortisol metabolite levels. Data collected in Kluane, Yukon, Canada.
DOI: 10.5061/dryad.b3h4q/9
title: Effects of GC manipulation on fecal cortisol metabolites

description: Effects of GC manipulation on fecal cortisol metabolite levels in pregnant females (Fig. S1). All data collected in Kluane, Yukon, Canada.
DOI: 10.5061/dryad.cr17v/2
title: Microsatellite, AFLP and Hybrid index data

description: -Table with individual genotypification for 3 Color pattern (Sb,Kw,Yb) loci and 14 Microsatellite Loci. For a total 14 populations and 478 individuals.-Table with individual genotypification for 562 AFLP loci. For a total of 14 populations and 169 individuals. -Genoypic and Phenotypic Hybrid Index. For 107 individualas from the contact zone.
DOI: 10.5061/dryad.cv240/2
title: Capture_location_dataset

description: Capture location dataset. Description in the enclosed readme file.
DOI: 10.5061/dryad.d1nd3/1
title: Growth curve data

description: Metadata used for Figure 1, Figure 2 and supplementary Figure 1.                                                                               # The variables in the file include                                        temp = rearing temperature of flies                                      age = hours from hatching                                                              stage = developmental stage                                                    weight = weight of individuals in mg
DOI: 10.5061/dryad.d1nd3/3
title: Critical size breakpoint R script

description: R script for calculating using the breakpoint method. The file includes scripts for finding the breakpoint in the plot of ttp vs. larval weight at starvation, bootstrapping data and permutation test.
DOI: 10.5061/dryad.d5c67/2
title: Second invasion experiment
DOI: 10.5061/dryad.hc967/2
title: LukasCluttonBrock_MonogamyinPrimates_SupplementforPNAS_Letter

description: Supplementary file describing the data collection and analyses. Please note that this file is not stored directly with the online publication at PNAS.
DOI: 10.5061/dryad.hm74t/2
title: GOsannotatedallattemptedSNPs

description: File summarizing the annotation (A. thaliana chromosome position, gene Tair ID and  associated Gene Ontology terms) and ensemble results of all 300 SNP attempted in Sisymbrium austriacum.
DOI: 10.5061/dryad.hm74t/3
title: coordinates

description: Latitude and longitude data of the 23 analyzed Sisymbrium populations
DOI: 10.5061/dryad.jc402/1
title: Evolution_sequencing_data

description: This file contains 454 amplicon sequencing data for the ancestral strains and the evolved lines (EvoS and EvoD lines). The file includes raw sequencing data as well as alignment files.
DOI: 10.5061/dryad.m42s5/1
title: Read Me. Codes and Comments
DOI: 10.5061/dryad.q0v43/1
title: NBA data

description: These are the data used for the modeling of overall points scored by sex and age (NBA all) and of point type by sex and age (NBA points)
DOI: 10.5061/dryad.rk13d/1
title: alignment_CO2_CO1_coenagrion_scitulum

description: Alignment in fasta format of CO2 and CO1 sequences of Coenagrion scitulum
DOI: 10.5061/dryad.s3937/1
title: for Dryad

description: Pulse rates for male courtship song and female acoustic preference in Laupala cerasina, L. eukolea, F1 interspecific hybrids and F2 interspecific hybrids.
DOI: 10.5061/dryad.sj862/1
title: Raw molecular evolutionary parameters used for statistics

description: Measures of intron pi and Tajima's D from various genes in Drosophila pseudoobscura, used to test for associations with coding region Ka/Ks (relative to D. miranda), coding region dxy (relative to D. miranda), and recombination rate (measured empirically within D. pseudoobscura)
DOI: 10.5061/dryad.sj862/2
title: Regression statistics from study

description: Table indicating regression coefficients, r(2) value, p-value, and sample size for all associations tested in study
DOI: 10.5061/dryad.sp70n/1
title: vanBreugel_Suver_Dickinson_JEB_2014_Octopamine_Acceleration

description: This dataset, a text file, contains all of the trajectories used in the following paper: van Breugel, F; Suver, M; and Dickinson, M (2014). Octopaminergic modulation of the visual flight speed regulator of Drosophila. J Exp Biol 217, 1-8. Each row describes one frame of data, trajectories can be parsed by selecting rows with the same object id number (the first column). The column values are described in the second line of the data file. The data was collected using an automated 10-camera 3D tracking system, and smoothed with a constant velocity kalman smoother. See the Methods section of the paper for more details.
DOI: 10.5061/dryad.ts98d/6
title: H_desmarestianus_transcriptome

description: Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
DOI: 10.5061/dryad.ts98d/7
title: Guide Tree for PAML analysis

description: This is the tree that was used in codeml as a guide tree for the branch and branch-site tests (see text of methods).  The tree is unrooted to as is required for these tests.  The two desert lineages, Dipodomys spectabilis and Chaetodipus baileyi have been marked with #1 to indicate them as foreground branches to be assigned a different rate than the rest of the tree.  D_spec = Dipodomys spectabilis, C_bail = Chaetodipus baileyi, H_desm = Heteromys desmarestianus, M_musc = Mus musculus.
DOI: 10.5061/dryad.05510/1
title: Time spent in dark compartment during gas exposure

description: This data was collected in the UBC Centre for Disease Modelling from 2010-2011. Three experiments were carried out separately, with each tab in the excel file representing one experiment. There are two abbreviations: "ISO" represents isoflurane and "CO2" represents carbon dioxide.
DOI: 10.5061/dryad.07551/1
title: Dispersing hemipteran vectors have reduced arbovirus prevalence

description: Excel file for data collected from the field and analyzed in the laboratory.  For key, see, ReadMe file.
DOI: 10.5061/dryad.0dg5h/1
title: Poecilia butleri cytochrome b data for all individuals in nexus format
DOI: 10.5061/dryad.1bt11/1
title: Summaryofdata for Cloaking (version 1)

description: summary from published data and several unpublished experiments.
DOI: 10.5061/dryad.1mn40/1
title: MHCIIB alignments by group

description: Sanger sequence data, obtained by PCR, cloning and sequencing. Sequences sorted in alignments based on higher taxonomic groups (family/order). Each sequence name includes species abreviation (first two letters of the genus name and first two letters of species name), gene name and sequence ID.
DOI: 10.5061/dryad.23g44/31
title: debruyntableS9

description: Table S9. DP37: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/32
title: debruyntableS10

description: Table S10. HP5: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/33
title: debruyntableS11

description: Table S11. HP54: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/34
title: debruyntableS12

description: Table S12. HP56: Maximum Likelihood fits of 24 different nucleotide substitution models
DOI: 10.5061/dryad.23g44/35
title: debruyntableS13

description: TABLE S13.  Dermogenys+Nomorhamphus geographic range evolution.
DOI: 10.5061/dryad.23g44/36
title: debruyntableS14

description: TABLE S14.  Hemirhamphodon geographic range evolution.
DOI: 10.5061/dryad.23g44/37
title: debruyntableS15

description: TABLE S15. Bayes Factors (BF) of mtDNA Bayesian phylogeographic analyses of diffusion rates in Southeast Asian halfbeaks (Dermogenys+Nomorhamphus).
DOI: 10.5061/dryad.23g44/38
title: debruyntableS16

description: TABLE S16.  Bayes Factors (BF) of mtDNA Bayesian phylogeographic analyses of diffusion rates in Southeast Asian halfbeaks (Hemirhamphodon).
DOI: 10.5061/dryad.370nq/2
title: PCR2
DOI: 10.5061/dryad.3768m/4
title: Annual winter precipitation 1978-2008

description: Total precipitation from October of the previous year through March of the year noted.
DOI: 10.5061/dryad.3mt25/1
title: Supplemental Data for Microsatellite and Sperm analyses
DOI: 10.5061/dryad.4n3d1/1
title: FASTA alignment of assembled mtDNA genome sequences used in ML analysis (excluding reference genomes Ia,Ib, IIa and IIb)

description: FASTA alignment of whole mitogenome sequences for Phytophthora infestans samples considered in our ML analysis
DOI: 10.5061/dryad.4tf74/2
title: Mallard_HA NA alignments Text_MEC-12-0355.R1
DOI: 10.5061/dryad.50dc6/2
title: Individual of Crella elegans with spermatic cysts

description: Individual collected by SCUBA on April'10 and fixed in RNAlater. Assembled with CLC Genomics Workbench 4.6.1 (CLC bio, Aarhus, Denmark).
DOI: 10.5061/dryad.50dc6/4
title: Reference transcriptome obtained by pooling reads from three different life stages of Crella elegans (individual with larvae, individual with spematic cysts and non-reproductive individual)

description: Individuals collected by SCUBA on October'09, March'10 and April'10 and fixed in RNAlater. Each sample was sequenced independently and afterwards reads from all three samples were pooled together and assembled with CLC Genomics Workbench 4.6.1 (CLC bio, Aarhus, Denmark).
DOI: 10.5061/dryad.55qg0/5
title: CO1_MSN

description: Minimum spanning network created using Arlequin.
DOI: 10.5061/dryad.55qg0/6
title: Arl_MSN

description: Minimum spanning network created using the software Arlequin.
DOI: 10.5061/dryad.55qg0/7
title: Arlequin input file of the Mpi dataset

description: Arlequin input file of the Mpi dataset. Haplotypes for all individual reported separately.
DOI: 10.5061/dryad.55qg0/8
title: Arlequin input file of the CO1 dataset.

description: Arlequin input file of the CO1 dataset. Haplotypes for all individual reported separately.
DOI: 10.5061/dryad.7j564/7
title: ReadMe
DOI: 10.5061/dryad.83kd1/10
title: Copy of 1471-2229-10-112-s10

description: Additional File 10: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/11
title: Copy of 1471-2229-10-112-s11

description: Additional File 11: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/12
title: Copy of 1471-2229-10-112-s12

description: Additional File 12: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/13
title: 1471-2229-10-112-s13

description: Additional File 13: UV Spectra. Additional description and a figure showing the spectral output of the UV313 bulbs and the irradiance under the Mylar-D and cellulose di-acetate filters used for -UV-B and +UV-B treatment of cotyledons.
DOI: 10.5061/dryad.83kd1/7
title: Copy of 1471-2229-10-112-s7

description: Additional File 7: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/8
title: Copy of 1471-2229-10-112-s8

description: Additional File 8: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).
DOI: 10.5061/dryad.83kd1/9
title: Copy of 1471-2229-10-112-s9

description: Additional File 9: All measured cotyledon-opening angles, arranged by experimental round and RIL population in excel spreadsheet format (xls). Each file contains angles for with both +UV-B (cellulose di-acetate) and -UV-B (Mylar).