cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18b29/3
title: H2O2 production in Col0 after aphid moult exposure

description: Production of ROS in Col-0. Confocal JPEG files and 8 bits ImageJ converted images. Col-0 leaves after exposure to aphid skin of Myzus persicae (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and  collected after 24 hours. .
DOI: 10.5061/dryad.314b5/1
title: resistance landscape for snow leopard

description: Floating point raster resistance landscape model for snow leopard range in Central Asia
DOI: 10.5061/dryad.3k8c0/1
title: Electronic supplementary files for Plaistow et al. - Offspring provisioning explains clone specific maternal age effects on life history and lifespan in the water flea, Daphnia pulex

description: 1. Table S1 - details of the 57 models fitted to the PMRN data in experiment 2. 2. Data used in the multivariate analyses in experiment 1. 3. Data used for the age-specific reproduction analysis used in experiment 1. 4. Data used for comparing age-specific mortality rates in experiment 1. 5. Data used for the growth analysis in experiment 2. 6. Data used for the PMRN analysis in experiment 2.
DOI: 10.5061/dryad.3n216/1
title: SupplemntalData01

description: Locality Register
DOI: 10.5061/dryad.54r4n/1
title: Brain region and total brain volume data

description: "Data file Noreikiene et al.xls" contains information on brain region(bulbus olfactorius, telencephalon, tectum opticum, cerebellum and hypothalamus) volumes andtotal brain volume, which were estimated using the ellipsoid model in three-spined sticklebacks as described in the paper. Also, the data file provides information on the sex and body size of individuals used in the study,their pedigree information and treatments they were exposed to.More details are provided as comments in the file.
DOI: 10.5061/dryad.54r4n/2
title: Genotype data

description: "Genotypes Noreikiene et al.xlsx" contains genotype information (10 polymorphic microsatellite markers)for individuals analyzed in the study and their parents (30 dams and 15 sires).Genotype information was used to assign offspring to their parents and construct a pedigree,which is also given in the file. More details are provided as comments in the file.
DOI: 10.5061/dryad.65th6/12
title: 41515_sanger_all_tree_ML

description: Newick tree file for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/13
title: 41515_sanger_all_tree

description: Fasta alignment for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/14
title: 44107_sanger_tree_ML

description: Newick tree file for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/15
title: 44107_sanger_tree

description: Fasta alignment for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/16
title: Association_SNPfiles_Plink

description: Plink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for GWAS in T52 (T52v2maf01gr09), B34 (B34v2maf01gr09) and BT68 (BT68v2maf01gr09new)
DOI: 10.5061/dryad.65th6/17
title: Admixture_inputfiles

description: Plink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for Admixture analysis in T52 (T52v2maf01gr1_LDprunned_thin01), B34 (B34v2maf01gr1_LDprunned) and BT68 (BT68v2POPSTnew)
DOI: 10.5061/dryad.7652s/1
title: PCR_DNA_test_results
DOI: 10.5061/dryad.7gg25/1
title: raw_reads

description: Raw reads divided by primers of 454 pyrosequencing of gokushovirus degenerate PCR products from Saanich Inlet (raw_reads.zip).
DOI: 10.5061/dryad.7gg25/2
title: OTUs

description: OTUs at 97% for each of the primer bins (OTUs.zip).
DOI: 10.5061/dryad.7gg25/3
title: alignments_and_trees

description: Alignment and tree of the major capsid protein phylogeny (alignments_and_trees.zip).
DOI: 10.5061/dryad.bb75p/1
title: RSOSdata_final
DOI: 10.5061/dryad.db6kg/1
title: funct_eco_2015_orientation

description: Matlab code and data for replicating Figures 2-7, Figures S1-S5 and modelling.
DOI: 10.5061/dryad.gc371/1
title: inbreeding coefficients

description: Inbreeding coefficients calculated from a 9-generation deep pedigree of a wild population of banded mongooses
DOI: 10.5061/dryad.gc371/2
title: mate_guarding

description: Behavioural data file. Males ('guard') observed guarding females ('indiv') during morning or afternoon ('time') observation periods. Strength of association: 0 = no association; 1 = strong association; 2 = medium strength association; 3 = weak association. Confidence of observation: 1 = strong; 2 = medium; 3 = weak.
DOI: 10.5061/dryad.gc371/3
title: pedigree

description: Pedigree inferred from MasterBayes and Colony assignments including year individual was born.
DOI: 10.5061/dryad.jk34r/1
title: 454 OTU RAW data files

description: OTU data from 454 sequencing 4 samples per treatment. H = healthy WS = controls showing signs of white syndrome MET = treated corals with Metronidazole, AMP = treated coral with Ampicillin, PARA = treatment with Paromomycin sulfate
DOI: 10.5061/dryad.mh67v/1
title: Zip file containing datasets and results

description: See the README file.
DOI: 10.5061/dryad.n5s02/1
title: BEAST Divergence Dating Tree Files

description: Tree files resulting from analysis of (1) CYTB alone in BEAST, (2) 26 genes in BEAST, and (3) 16 genes in *BEAST.
DOI: 10.5061/dryad.n5s02/2
title: BEAST Divergence Dating XML Files

description: Input XML files for (1) CYTB alone in BEAST, (2) 26 genes in BEAST, and (3) 16 genes in *BEAST.
DOI: 10.5061/dryad.n5s02/3
title: BEAST EBSP XML Files

description: BEAST Extended Bayesian Skyline Plot XML input files for all six Thylamys lineages.
DOI: 10.5061/dryad.p1p29/4
title: Roitberg_et_al_geographic_distances

description: Geographic distances among study samples (in km) used in our Mantel tests: See Fig. 1 in Roitberg et al. (2015) for geographic map and Table 1 for the phenotypic characteristics of the study samples.The distances were calculated using the geographic coordinates.  Note that for most study samples, values for the longitude and the latitude are average values for several sites from which the study animals were collected; sites which provided relatively small amount of data were not considered for computing these average values.
DOI: 10.5061/dryad.pq6d7/1
title: Primary data on presence/absence of bird species in Oslo, Norway

description: The data file contains information on presence/absence of 90 bird species in 93 urban sites in Oslo and 176 rural sites in the surroundings of Oslo, together with information on location and size of each site.
DOI: 10.5061/dryad.qg823/1
title: data on male ornaments and MHC variation

description: see Read Me file for variable explanations
DOI: 10.5061/dryad.qg823/2
title: Whittingham Class I Sequences

description: MHC sequences and presence/absence for each male in Whittingham et al. Molecular Ecology 2015.
DOI: 10.5061/dryad.rt1kg/1
title: AMMA 10x10k loops

description: Matlab code for Ambystoma maculatum
DOI: 10.5061/dryad.rt1kg/2
title: AMTA 10x10k loops

description: Matlab code for Ambystoma talpoideum populations
DOI: 10.5061/dryad.rt1kg/3
title: RASY 10x10km loops

description: Matlab code for Lithobates sylvaticus populations
DOI: 10.5061/dryad.rt1kg/4
title: AMOP 10x10k loops

description: Matlab code for Ambystoma opacum populations
DOI: 10.5061/dryad.s6f0p/1
title: Dehnhard_2015_PLoS_ONE_data

description: Body mass, body condition and egg mass data of individually marked male and female southern rockhopper penguins breeding on New Island, Falkland / Malvinas Islands. Analyses in Dehnhard et al. 2015 PLoS ONE were based on this dataset.
DOI: 10.5061/dryad.s8m97/1
title: Data_of_Figure_1_2.Number_of_offspring_of_pollen_carried_and_pollen-free_foundresses_according_to_different_foundress_numbers.xls

description: Number of offspring of pollen carried and pollen-free foundresses according to different foundress numbers
DOI: 10.5061/dryad.sp048/1
title: phylip_input_27libraries

description: Phylip input file for neighbour joining tree
DOI: 10.5061/dryad.th441/3
title: Flower visitor observations

description: Observations of flower visitors on _Rhododendron calendulaceum_ and flower parts contacted; taken June 2014.
DOI: 10.5061/dryad.th441/4
title: Papilio glaucus v. Speyeria cybele on flame azalea

description: Field observations of contact between a butterfly and anthers versus stigmas during visits to _Rhododendron calendulaceum_ flowers by the butterflies _Papilio glaucus_ and _Speyeria cybele_. Contact with flower part during a flower visit = 1, absence of contact with a flower part = 0.
DOI: 10.5061/dryad.th441/5
title: Pollen & wing scale load on stigmas from naturally visited flowers

description: After observing a visit by a butterfly in the field, stigmas from R. calendulaceum flowers were clipped and attached to a microscope slide in the field. Data show presence/absence (=Y/N) of pollen and butterfly wing scales on stigmas as scored after examining stigmas under the microscope.
DOI: 10.5061/dryad.th441/6
title: Pollinator exclusion experiment data

description: Data from experimental exclusion of flower visitors to _Rhododendron calendulaceum_. Treatments applied 6/12/14 - 6/13/14 and fruit set scored 8/4/14-8/7/14. Treatments defined as follows: A = flowers open to all visitors; B = mesh + cage (all visitors excluded); C = cage (only large visitors, e.g. big butterflies, excluded); D = maximum fruit set (unopened flwrs covered with ziplock until open, then pollinated by hand with outcrossed pollen).
DOI: 10.5061/dryad.th441/7
title: Stigma load from single butterfly visits on emasculated flowers

description: _Rhododendron calendulaceum_ twigs bearing budding inflorescences were cut in the field and kept in water in the lab. Flowers were emasculated upon anthesis, and emasculated inflorescences were attached to the end of a pole and presented to foraging _Papilio glaucus_ butterflies near flowering _R. calendulaceum_ plants in the field. Stigmas of emasculated flowers were removed and attached to a microscope slide in the field following a visit, and scored for the presence/absence (=Y/N) of pollen grains and butterfly wing scales upon inspection under the microscope.
DOI: 10.5061/dryad.22sf3/1
title: Dense supermatrix

description: This phylip format supermatrix alignment was generated using agalma 0.3.5 and orthologous genes were identified by pair wise BLASTp followed by clustering using MCL. The dense supermatrix has all 30 taxa and 70% matrix occupancy, with 1,125 peptide sequences and 101,652 amino acid sites.
DOI: 10.5061/dryad.22sf3/2
title: Sparse supermatrix

description: This phylip format supermatrix alignment was generated using agalma 0.3.5 and orthologous genes were identified by pair wise BLASTp followed by clustering using MCL. The sparse supermatrix has all 30 taxa and 34% matrix occupancy, with 4,645 peptide sequences and 630,945 amino acid sites.
DOI: 10.5061/dryad.22sf3/3
title: Species tree from PhyloBayes analysis on dense supermatrix

description: Baysian phylogenetic analyses were done with PhyloBayes 1.3b-mpi on the dense supermatrix using the CAT-GTR model with the following command: “pb_mpi -S -d supermatrix.dense.phylip -cat -gtr outputFile”. A total of 31,623 generations were run over three chains.
DOI: 10.5061/dryad.22sf3/4
title: Species tree from RAxML analysis on dense supermatrix

description: Maximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the dense supermatrix using the GAMMAWAG model with 1,000 boot strap iterations.
DOI: 10.5061/dryad.22sf3/5
title: Species tree from RAxML analysis on sparse supermatrix

description: Maximum likelihood phylogenetic analyses were done with RAxML 7.7.6 on the sparse supermatrix using the GAMMAWAG model with 100 boot strap iterations.
DOI: 10.5061/dryad.31f77/1
title: CoralliumRubrum_Contigs
DOI: 10.5061/dryad.31f77/2
title: CoralliumRubrum_SNP
DOI: 10.5061/dryad.31f77/3
title: CoralliumRubrum_AnnotationFile
DOI: 10.5061/dryad.4rr39/1
title: Reference library for arctic and boreal bryphytes

description: Arctic and boreal bryophyte reference library, chloroplast P6-loop trnL (UAA) intron, c-h primers.
DOI: 10.5061/dryad.4vn13/1
title: List of newborns measured at birth

description: A list of all newborns measured at birth including those scored for their behavior. The data include maternal identity, birth date, sex at birth, morphology data and identity of the release population as well as density treatment.
DOI: 10.5061/dryad.4vn13/2
title: Activity behavior at birth

description: Recordings of activity behavior in all newborns at birth with code of each newborn, date and time of recordings, recorded data.
DOI: 10.5061/dryad.4vn13/3
title: Antipredator behavior at birth

description: Recordings of boldness behavior (response to a simulated predator attack) in all newborns at birth with code of each newborn, date and time of recordings, recorded data.
DOI: 10.5061/dryad.4vn13/4
title: Sociability behavior at birth

description: Recordings of sociability behavior (response to odor cues of adult male conspecifics) in all newborns at birth with code of each newborn, date and time of recordings, recorded data.
DOI: 10.5061/dryad.4vn13/5
title: Recapture data of newborns

description: Recaptures data of newborns at the end of the experiment. A list of all surviving newborns with their id, capture date, morphology and mass at capture.
DOI: 10.5061/dryad.4vn13/6
title: Reproduction data

description: Data on reproductive females with id of each female and including mass before and mass after parturition, parturition date and fecundity (sum of yellow unfertilized eggs, eggs with aborted embryos, newborns dead at birth and live newborns).
DOI: 10.5061/dryad.8112f/8
title: Scripts

description: Scripts used for assembly, base calling, and orthology assessment of the Anchored Phylogenomics loci (script by ARL).
DOI: 10.5061/dryad.928fj/1
title: Genomic scaffold sequences with MHC class I sequences from Atlantic salmon

description: Sequences are from a final assembly using Sanger (~4X) and Illumina (~202X) data assembled with MaSuRCA {Zimin, 2013}
DOI: 10.5061/dryad.9b65b/1
title: Input data file for QTL mapping
DOI: 10.5061/dryad.9r9m3/1
title: Eopsaltria australis mitogenomes IonTorrent reads

description: Ion Torrent reads from Long-Range PCR's of complete mitochondrial genomes of Eastern Yellow Robin (Eopsaltria australis), sister species (E. griseogularis) and outgroups. Morales et al. Purifying and positive selection of a widespread passerine with mitonuclear discordance. Molecular Ecology.Samples are already demultiplex and in fastq format. reference genome can be found in NCBI: JX901073 - http://www.ncbi.nlm.nih.gov/pubmed/23125406 -
DOI: 10.5061/dryad.gc371/4
title: relatedness

description: Pairwise relatedness coefficients calculated from a 9-generation deep pedigree.
DOI: 10.5061/dryad.gc371/5
title: BMRP_Genotype_data_Dec_2014

description: Raw microsatellite genotype data
DOI: 10.5061/dryad.kg017/1
title: Saarinen et al_oikos

description: Field data collected for the paper 10.1111/oik.02233. For details, see ReadMe.txt.
DOI: 10.5061/dryad.n5s02/4
title: BEAST PS SS Model Comparisons XML Files

description: BEAST input XML files for Path Sampling/Stepping Stone Sampling coalescent model comparisons (constant size versus exponential change) for all six Thylamys lineages.
DOI: 10.5061/dryad.n5s02/5
title: BPP Input Files

description: All input files used in BPP for the estimation of divergence times between A and B lineages.
DOI: 10.5061/dryad.n5s02/6
title: Geographic Information

description: Excel file containing specimen museum voucher numbers, detailed locality information, and geographic coordinates for individuals sequenced in Giarla et al. (2014).
DOI: 10.5061/dryad.n5s02/7
title: 16 Nexus Files from Giarla et al 2014

description: DNA alignments of 14 anonymous loci, one X-linked intron, and the mitochondrial gene CYTB. Densely sampled among the six focal Andean lineages. Data originally from Giarla et al. (2014).
DOI: 10.5061/dryad.n5s02/8
title: 26 Nexus Files from Giarla and Jansa 2014

description: Alignments of 26 loci used to estimate divergence times in BEAST. Loci are sampled across 50 different marsupial taxa. Originally from Giarla and Jansa (2014).
DOI: 10.5061/dryad.n715n/10
title: Figure 2a - Results of sim. 1 - subst. rate s2

description: Complete file set of data set 1 that was simulated under the multispecies coalescent model and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2a.
DOI: 10.5061/dryad.n715n/11
title: Figure 2b - Results of sim. 1 - subst. rate s1

description: Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s1. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s1 of Figure 2b.
DOI: 10.5061/dryad.n715n/12
title: Figure 2b - Results of sim. 1 - subst. rate s2

description: Complete file set of data set 1 that was simulated in the presence of migration between species and under substitution rate s2. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s2 of Figure 2b.
DOI: 10.5061/dryad.n715n/13
title: Simulated Data behind Figure 2a - subst. rate s1

description: Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
DOI: 10.5061/dryad.n715n/14
title: Simulated Data behind Figure 2a - subst. rate s2

description: Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated under the multispecies coalescent model and substitution rate s2. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
DOI: 10.5061/dryad.n715n/15
title: Simulated Data behind Figure 2b - subst. rate s1

description: Complete set of nucleotide sequence data alignments simulated on genealogies that were themselves simulated in the presence of migration between species and under substitution rate s1. The individual files constitute the input for the Python script BEAUTiAutomator.py to generate the XML-formatted input files for *BEAST.
DOI: 10.5061/dryad.n715n/9
title: Figure 2a - Results of sim. 1 - subst. rate s1

description: Complete file set of data set 1 that was simulated under the multispecies coalescent model and under substitution rate s1. The uncompressed folder constitutes the input for the R package P2C2M to generate the first column of columnspace s1 of Figure 2a.
DOI: 10.5061/dryad.nq070/1
title: MTBC_SNP_align_200.phy_phyml_tree
DOI: 10.5061/dryad.nq070/2
title: H37Rv_SNP_align_200.phy_phyml_tree
DOI: 10.5061/dryad.nq070/3
title: whole_genome_phyml
DOI: 10.5061/dryad.nq070/4
title: whole_genome_Bayes
DOI: 10.5061/dryad.qg823/3
title: Whittingham Class II Sequences

description: MHC sequences and presence/absence for each male in Whittingham et al. Molecular Ecology 2015.
DOI: 10.5061/dryad.s8m97/2
title: Data_of_Figure_3_4.Number_of_the_offspring_of_pollen_and_pollen-free_foundresses_across_different_species

description: Number of the offspring of pollen and pollen-free foundresses across different species
DOI: 10.5061/dryad.s8m97/3
title: Data_of_Figure_4.Number_of_the_foundress_and_the_fruit diameter_across_different_species

description: Number of the foundress and the fruit diameter across different species
DOI: 10.5061/dryad.s8m97/4
title: Notes

description: Notes about the abbreviation of fig scientific name
DOI: 10.5061/dryad.sp048/2
title: phylip_outtree_27libraries

description: Phylip tree file
DOI: 10.5061/dryad.sp048/3
title: phylip_outfile_27libraries

description: Phylip output file for neighbour joining tree
DOI: 10.5061/dryad.sp048/4
title: MA-7.bam

description: Alignment file for sample MA7: male adults, colony 7
DOI: 10.5061/dryad.sp048/5
title: MA-9.bam

description: Alignment file for sample MA9: male adults, colony 9
DOI: 10.5061/dryad.sp048/6
title: MA-11.bam

description: Alignment file for sample MA11: male adults, colony 11
DOI: 10.5061/dryad.sp048/7
title: ML-7.bam

description: Alignment file for sample ML7: male larvae, colony 7
DOI: 10.5061/dryad.sp048/8
title: ML-9.bam

description: Alignment file for sample ML9: male larvae, colony 9
DOI: 10.5061/dryad.07nj3/1
title: The microsatellite genotypes and mitochondrial DNA sequences

description: The file contains tables of the microsatellite genotypes, mitochondrial DNA sequences and their references, and information about the localities of the samples used in this study.
DOI: 10.5061/dryad.22sf3/6
title: SOWHAT constraint tree - Asteroidea and Echinozoa

description: The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test if Asteroidea was a sister group to Echinozoa.
DOI: 10.5061/dryad.22sf3/7
title: SOWHAT constraint tree - Crytosynirgid hypothesis

description: The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test the Cryptosynirgid hypothesis.
DOI: 10.5061/dryad.22sf3/8
title: SOWHAT constraint tree - Ophiuroidea and echinoderms

description: The SOWH test was implemented using the sowhat software package, with the following command: “perl sowhat --constraint=Alternate.hypo.tre --aln=supermatrix.dense.phylip --model=PROTGAMMAWAG --dir=outDir --name=outFile --rax='raxmlHPC-PTHREADS-SSE3 -T 16' --seqgen=seq-gen --reps=500 --stop &gt;output.txt”. This constraint tree was constructed to test if Ophiuroidea was a sister group to the rest of echinoderms.
DOI: 10.5061/dryad.4rr39/2
title: lemming diet data

description: DNA metabarcoding diet data on lemming feces samples from Bylot Island. Dataset includes sequence data, environmental variables and validation data for lemming species identification.
DOI: 10.5061/dryad.5c1g6/1
title: phyloeny matching dataset

description: Based on the published DaPhNe plant phylogeny (Durka & Michalski 2012 Ecology), trimmed to plants within present food web dataset (2587 taxa). Missing taxa added (113) as described in manuscript. Phylogeny is in newick format.
DOI: 10.5061/dryad.5c1g6/2
title: Pearse_Altermatt2015-R code for Dryad

description: R code with general functions for host use models and predictions.  Appended at the end of the file is specific code for the manuscript.
DOI: 10.5061/dryad.8r6m4/1
title: SacconeVirtanen-Oikos-02399-Plant-Composition

description: Table of 300 observations and 109 variables. Variables (columns) 1 to 4 = Year, treatment, replicate number, soil moisture. variables 5 to 104 = species abundances. variables 105 to 109 = accumulated plant functional type abundances
DOI: 10.5061/dryad.fd862/1
title: 5112_fasta_in_silico_SNPs.tar

description: Fasta alignment files from which putative in silico SNPs have been extracted.
DOI: 10.5061/dryad.j8r8q/3
title: UCD2014_Chr27_Critical_Interval_CanFam3.1
DOI: 10.5061/dryad.j8r8q/4
title: UCD_2014.tfam

description: PLINK GWAS file
DOI: 10.5061/dryad.j8r8q/5
title: UCD_2014.tped

description: PLINK tped format GWAS file