cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9tt2t/4
title: Toxodon_MLP 86-III-25-15
DOI: 10.5061/dryad.9tt2t/5
title: Blank
DOI: 10.5061/dryad.cc3jg/2
title: Development.time_Pupal.mass_Audusseau_et_al

description: Data on pupal time (day) and pupal mass (mg) according to species (A. urticae, A. io, P. c-album), family (or clutch), and plant fertilization treatment.
DOI: 10.5061/dryad.cc3jg/3
title: Plant_nutrient_content_Audusseau_et_al

description: Leaf content of nitrogen and phosphorus (% dry mass) of plants in the four fertilization treatments and plants collected in nature. Time corresponds to the number of day from the beginning of the experiment.
DOI: 10.5061/dryad.cc3jg/4
title: survival_Audusseau_et_al

description: Number of individuals that failed to reach emergence and number of individuals that reached adulthood according to species (A. urticae, A. io, P. c-album), family (or clutch), and plant fertilization treatment.
DOI: 10.5061/dryad.f0nf4/1
title: Lau_2006_Experiment_reciprocal_transplant.csv

description: Please see associated README file. These data were originally presented in J. A. Lau.  2006.  Evolutionary responses of native plants to novel community members.  Evolution 60:56-63. They are fitness data from a reciprocal transplant experiment in which Acmispon wrangelianus genotypes collected from populations invaded or uninvaded by Medicago polymorpha were transplanted into a full 2 x 2 factorial experiment manipulating the presence of the exotic plant Medicago polymorpha and insect herbivores in invaded sites and into insecticided/non-insecticided plots in uninvaded sites. The README file also describes a related dataset (see Lau_2006_Field_reciprocal_transplant).
DOI: 10.5061/dryad.f0nf4/2
title: Lau 2006 Field reciprocal transplant

description: Please see associated README file. These data were originally presented in J. A. Lau. 2006. Evolutionary responses of native plants to novel community members. Evolution 60:56-63. They are fitness data from a reciprocal transplant experiment in which Acmispon wrangelianus genotypes collected from populations invaded or uninvaded by Medicago polymorpha were transplanted into invaded and uninvaded sites. The README file also describes a related dataset (see Lau_2006_Experiment_reciprocal_transplant).
DOI: 10.5061/dryad.f0nf4/3
title: Lau_and_Strauss_ 2005_Year_2_data

description: Please see associated README file. These data were originally presented in J. A. Lau and S. Y. Strauss.  2005.  Insect herbivores drive important indirect effects of exotic plants on native communities.  Ecology 86:2990-2997.	The data characterize phenotypic traits (flowering time, size, herbivory) of naturally occurring Acmispon wrangelianus individuals growing in a 2 x 2 factorial experiment where the presence of the invasive plant Medicago polymorpha and insect herbivores were experimentally manipulated. The README file also describes a related dataset (see Lau_and_Strauss_2005_Year_1_data).
DOI: 10.5061/dryad.f0nf4/4
title: Lau_and_Strauss_2005_Year_1_data

description: Please see associated README file. These data were originally presented in J. A. Lau and S. Y. Strauss. 2005. Insect herbivores drive important indirect effects of exotic plants on native communities. Ecology 86:2990-2997. The data characterize phenotypic traits (flowering time, size, herbivory) of naturally occurring Acmispon wrangelianus individuals growing in a 2 x 2 factorial experiment where the presence of the invasive plant Medicago polymorpha and insect herbivores were experimentally manipulated. The README file also describes a related dataset (see Lau_and_Strauss_2005_Year_2_data).
DOI: 10.5061/dryad.n69t3/1
title: hemidactylus_frenatus.4.2

description: RADtools output for Hemidactylus frenatus data
DOI: 10.5061/dryad.n69t3/2
title: hemidactylus_turcicus.4.2

description: RADtools output for Hemidactylus turcicus data
DOI: 10.5061/dryad.n69t3/3
title: thecadactylus.4.2

description: RADtools output for Thecadactylus rapicauda data
DOI: 10.5061/dryad.n69t3/4
title: aristelliger_expectatus_1.4.2

description: RADtools output for Aristelliger expectatus data
DOI: 10.5061/dryad.n69t3/5
title: hemidactylus_mabouia_TT.4.2

description: RADtools output for Hemidactylus mabouia data
DOI: 10.5061/dryad.n69t3/6
title: heteronotia_1.4.2

description: RADtools output for Heteronotia binoei data
DOI: 10.5061/dryad.n69t3/7
title: sphaero_nicholsi.4.2

description: RADtools output for Sphaerodactylus nicholsi data
DOI: 10.5061/dryad.n69t3/8
title: sphaero_mac_vc.4.2

description: RADtools output for Sphaerodactylus macrolepis data
DOI: 10.5061/dryad.pb830/1
title: GD1_Lactobacillus_QH_data

description: Overall average of two samples from each patient for GD1 PCR, quantitative histology for Lactobacillus, and quantitative histology of the small airways
DOI: 10.5061/dryad.r31sg/1
title: VCF file

description: This is the raw VCF file containing all 32,978 variant genetic sites initially identified from assembled reads.
DOI: 10.5061/dryad.vr176/1
title: Population means for traits

description: population means for all traits reported in this study
DOI: 10.5061/dryad.0qr3g/1
title: Haddeland et al._genotypes_and_metadata

description: the excel file contains 2 sheets: sheet1 contains a description of the data in sheet2, sheet2 contains the microsatellite genotypes, length and sex information for 994 individuals of Thymallus thymallus
DOI: 10.5061/dryad.1366f/1
title: DATA for WORKFORCE EFFECTS IN MOLE-RAT SOCIETIES

description: The data file contains three data sheets, corresponding to each of the three major analyses in the paper. The column headings describe the contents of each field and should be self-explanatory.
DOI: 10.5061/dryad.9tt2t/10
title: Parsimony tree created in Phylip

description: Parsimony tree created in Phylip from sequences found in both specimens for each taxa.
DOI: 10.5061/dryad.9tt2t/6
title: Bayesian Analysis
DOI: 10.5061/dryad.9tt2t/7
title: Maximum Likelihood tree

description: Maximum Likelihood tree from sequences found in both specimens for each taxa above highest false positive match.
DOI: 10.5061/dryad.9tt2t/8
title: PMF tree

description: Maximum Likelihood tree from sequences observed in PMF
DOI: 10.5061/dryad.9tt2t/9
title: Cropped ML tree

description: Maximum Likelihood tree from sequences when cropped to match only sequences present in specimens analysed.
DOI: 10.5061/dryad.b59qj/1
title: Microsatellite genotype data for all individuals

description: This file contains microsatellite genotype data for the 1334 individuals used in the study. The columns contain: 1) the individual's ID, 2) the population ID, and 3) microsatellite loci split into two alleles per locus.
DOI: 10.5061/dryad.b59qj/3
title: Ecological Niche Model Presence Points

description: These are latitudes / longitudes of all presence points used in the ecological niche model.
DOI: 10.5061/dryad.b59qj/4
title: MaxENT Environmental Layers

description: This file contains all environmental layers (100m resolution) originally tested in the ecological niche model in .asc format.
DOI: 10.5061/dryad.b59qj/5
title: Pairwise Fst & Dps tables

description: Pairwise Fst and Dps values for all 3 transects.
DOI: 10.5061/dryad.b59qj/6
title: NEW gps

description: GPS coordinates for all collection localities
DOI: 10.5061/dryad.d1d1m/1
title: Data used in the paper -Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology-

description: In this folder, their are the data used in the paper "Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom".
DOI: 10.5061/dryad.gt524/1
title: genotype and spatial data for Antechinus agilis

description: Column 1 = Unique Individual ID, Column 2 = the sex of the  individuals, Column 3 = the region that each individual was assigned to for the spatial genetic analysis, Columns 4-29 = microsatellite genotype with the alleles for each loci listed in adjacent columns, Columns 30-31 geographic coordinates of the individuals averaged over tapping locations
DOI: 10.5061/dryad.gt524/2
title: genotype and spatial data for Trichosurus cunninghami

description: Column 1 = Unique Individual ID, Column 2 = the sex of the  individuals, Column 3 = year of capture, Columns 4-33 = microsatellite genotype with the alleles for each loci listed in adjacent columns, Columns 34-35 geographic coordinates of the individuals averaged across all trap locations recorded during a two year window (centred on the year in question)
DOI: 10.5061/dryad.kb699/1
title: harvest_and_quotas

description: Includes data of harvest quotas and number of harvested moose.
DOI: 10.5061/dryad.kt0s8/1
title: 1_Fig3_concatenated_Kodama.nex

description: Concatenated sequences of the seven nuclear genes used for the building the Neighbor Net network shown in Fig. 3A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/2
title: 2_Fanca

description: The Fanca sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.n69t3/10
title: correlophus_rev14.4.2

description: RADtools output for Correlophus ciliatus data
DOI: 10.5061/dryad.n69t3/11
title: lialis.4.2.ALL

description: RADtools output for Lialis burtonis data
DOI: 10.5061/dryad.n69t3/12
title: christinus.4.2

description: RADtools output for Christinus marmoratus data
DOI: 10.5061/dryad.n69t3/13
title: rsw.py

description: Python script to identify sex-specific markers from RADtools output
DOI: 10.5061/dryad.n69t3/14
title: squamates_TSD_skinks

description: Pruned squamate phylogeny that includes skink species with putative TSD
DOI: 10.5061/dryad.n69t3/15
title: squamates_NoTSD_skinks

description: Pruned squamate phylogeny that excludes skink species with putative TSD
DOI: 10.5061/dryad.n69t3/16
title: squamates_TSD_skinks_data

description: Squamate sex determination data that includes skink species with putative TSD
DOI: 10.5061/dryad.n69t3/17
title: squamates_NoTSD_skinks_data

description: Squamate sex determination data that excludes skink species with putative TSD
DOI: 10.5061/dryad.n69t3/9
title: gehyra_mutilata.4.2

description: RADtools output for Gehyra mutilata data
DOI: 10.5061/dryad.15f51/1
title: COIhaplotypes

description: COI Haplotypes among the Peripatopsis overbergiensis
DOI: 10.5061/dryad.15f51/2
title: 18S partial sequence

description: 18S haplotypes
DOI: 10.5061/dryad.67dn4/1
title: Alignments of Sanger sequences per locus (nexus format)

description: Locus-specific alignments of Sanger sequences in nexus format. For information about loci, refer to Supplementary Table 2; for information about individuals/samples, refer to Supplementary Table 1 in the original publication.
DOI: 10.5061/dryad.67dn4/2
title: Super-matrices of concatenated RADseq loci (phylip format)

description: Super-matrices STRICT and RELAXED consisting of concatenated RAD sequencing loci, in phylip format. Key for the sample codes are given in separate text files.
DOI: 10.5061/dryad.67dn4/3
title: SNP matrix from RAD sequences (nexus format)

description: Matrix of effectively non-linked and non-automorphic Single Nucleotide Polymorphisms (SNP's) of Cyanistes samples, based on RAD sequences, in nexus format. Key for the sample codes are given in a separate text file.
DOI: 10.5061/dryad.67dn4/4
title: *BEAST species tree 18nc + 2mt DNA Sanger markers (Fig 2a)

description: Tree file for Figure 2a, 18 nuclear and 2 mitochondrial Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript.
DOI: 10.5061/dryad.67dn4/5
title: *BEAST marker-specific trees 18nc + 2mt DNA Sanger markers

description: The compressed tarball contains 20 marker specific (18 nuclear and 2 mitochondrial) tree files (nexus format) from the *BEAST analysis of Sanger sequence markers. The tree files are in nexus format. Markers are named according to Supplementary Table 2, samples according to Supplementary Table 1.
DOI: 10.5061/dryad.67dn4/6
title: *BEAST species tree 18 ncDNA Sanger markers (Suppl Fig 2)

description: Tree file for Supplementary Figure 2, 18 nuclear (but no mitochondrial) Sanger sequence markers. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure is found in the readme file. For further details, see the manuscript.
DOI: 10.5061/dryad.67dn4/7
title: SNAPP species tree, based on RADseq SNP's (nexus format)

description: Species tree file for Figure 2b, RADseq SNP matrix analysed with SNAPP. The tree is in nexus format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
DOI: 10.5061/dryad.85569/1
title: long_realign

description: The DNA data file of the four partial loci sequenced during the present study
DOI: 10.5061/dryad.9gk52/1
title: Tuber_melanosporum_442326SNPs_resource

description: This file in gff format corresponds to the list of the 442,326 SNPs produced comparing seven Tuber melanosporum geographic accessions.  The SNP calling was performed with the BWA/SAMTools and CLC Genome Workbench programs and only SNPs called by both methods were retained.
DOI: 10.5061/dryad.9gk52/2
title: Tuber_melanosporum_60507SNPs_resource

description: This file in gff format corresponds to the list of the 60,507 SNPs in genomic region putatively free of selection. These SNPs were used for BEAST and maximum likelihood phylogenies. These SNPs originated from the initial 442,326 SNPs resource. SNPs in repeated sequences, gene models and genomic regions putatively under selection were not included in this file.
DOI: 10.5061/dryad.9gk52/3
title: Tuber_melanosporum_Tree_Beast

description: This file in newick format corresponds to the BEAST bayesian reconstruction realized with the 60,507 SNPs in region free of selection. The time estimation were obtained using a most recent common ancestor for this tree of 131,128 ± 23,098 years. This tree is presented in figure 4 of the manuscript.
DOI: 10.5061/dryad.9gk52/4
title: Tuber_melanosporum_Tree_Beast

description: This file in xml format has been used as input for BEAST. Bayesian phylogenetic analysis was conducted with 5,000,000 generations, a sampling for each 1,000 generations, and a burn-in value of 1,250 with BEAST version v1.7.5  using the Hasegawa-Kishino-Yano (HKY) DNA substitution model.
DOI: 10.5061/dryad.9gk52/5
title: Tuber_melanosporum_ML

description: This file in newick format corresponds to the maximum likelihood phylogeny realized using the default parameters of PhyML with 100 bootstrap replicates. This tree was produced using the 60,507 SNPs in genomic regions putatively free of selection. This tree is presented in figure S1 and S6.
DOI: 10.5061/dryad.9gk52/6
title: Tuber_melanosporum_genes_v1_2

description: This file in gff format correspond to the 9,952 gene models of Tuber melanosporum considered in this analyse.  Details are provided in the manuscript concerning this gene catalogue realization.
DOI: 10.5061/dryad.h3690/1
title: Morphometric data from antler flies when raised on different diets

description: See ReadMe file.
DOI: 10.5061/dryad.kt0s8/10
title: 11_BEAST_input_Kodama

description: Concatenated sequences of the seven nuclear genes used for the BEAST analysis shown in Fig. 4 (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/3
title: 3_Spire2

description: The Spire2 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/4
title: 4_Tcf25

description: The Tcf25 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/5
title: 5_Mc1r_409bp

description: The Mc1r sequence (409 bp) data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/6
title: 6_Def8

description: The Def8 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/7
title: 7_Afg3l1_all

description: The Afg3lI sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/8
title: 8_Dbndd1

description: The Dbndd1 sequence data used for the construction of the Neighbor Net network shown in Fig. 2A (Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/9
title: 9_Mc1r948bp_Arlequin

description: The Mc1r sequence (948 bp) data used for population genetic analyses using Arlequin ver 3.5 (Kodama et al., 2015).
DOI: 10.5061/dryad.tg0nq/1
title: Data from field experiments

description: Data collected during field experiments (relates to ‘Step 1’ in the published paper), to assess how signal strength is affected by inter-tag distance, as well as by a set of nuisance parameters (habitat type, tag height above ground, and relative antenna orientation).
DOI: 10.5061/dryad.67dn4/10
title: Brief log of RADseq data processing, including custom scripts

description: Brief work log for analyses of RADseq data. I have used little snippets of custom scripts (which you are free to use and modify), but this log also makes use of plenty of neat little scripts made by other people. One script, by Shannon Hedtke, was modified to fit the purposes in this workflow, and that modified script is provided separately.
DOI: 10.5061/dryad.67dn4/11
title: concatenatenexus_edMSR

description: This program is written by Shannon Hedtke, and takes all nexus files in a directory and concatenates them. I have modified the original script, which splits sequence names on "_" and removes all duplicates of the left hand side - something that is good for cleaning up among GenBank versions of the same sequence, but bad for removing allelles.
DOI: 10.5061/dryad.67dn4/8
title: Best ML tree for RAD sequence super-matrix RELAXED (Fig 4; newick format)

description: Best ML tree computed in RAxML for RAD sequence matrix RELAXED, corresponding to Figure 4. The tree is in newick format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
DOI: 10.5061/dryad.67dn4/9
title: Best ML tree for RAD sequence super-matrix STRICT (Suppl Fig 5; newick format)

description: Best ML tree computed in RAxML for RAD sequence matrix STRICT, corresponding to Supplementary Figure 5. The tree is in newick format. A translation table between taxon names used in the file, and taxon names used in the figure, is found in the readme file. For further details, see the manuscript.
DOI: 10.5061/dryad.6m68b/1
title: Tables for statistical analyses

description: The title for each table is self-explanatory. Data were collected in the field and several statistical analyses were conducted. Each table corresponds to one or more analysis. Abbreviations for variables are as follow:  LDATE=laying date, CS=clutch size, HDATE=hatching date. The breeding season is specified as 2012 or 2013 as appropriate.
DOI: 10.5061/dryad.742qf/1
title: Morphometric analysis of the studied sample
DOI: 10.5061/dryad.742qf/2
title: Autozooecial diameter in the studied sample
DOI: 10.5061/dryad.85569/2
title: FIGURE S1

description: Comparison of selected node ages based on different calibration schemes.
DOI: 10.5061/dryad.85569/3
title: Supplementary material

description: DNA substitution models for each of the four loci
DOI: 10.5061/dryad.85569/4
title: Table S1

description: Testing between different models for the divergence time estimation using external rates and one fossil point.
DOI: 10.5061/dryad.85569/5
title: Table S2

description: Testing of different biogeographic scenarios using BioGeoBears.
DOI: 10.5061/dryad.85569/6
title: Table S3

description: Results of the test correlating the biogeographic areas.
DOI: 10.5061/dryad.ds68k/1
title: Timelapse images showing transfer of GFP between cells

description: Co-cultures of cross-feeding genotypes of E.coli and A.baylyi were observed after 9 hours of growth in liquid media. Images of this co-culture were taken every 2 minutes to visualize the transfer of GFP between cells connected by nanotubes. The zip file contains unprocessed images in tiff format of three different channels- bright-field, green and red. Each folder contains 18 images, the file name indicates the time point.
DOI: 10.5061/dryad.f76f2/1
title: ShizukaMcDonald_data

description: Compressed file containing 172 data matrices. The cell values represent the number of times the row individual 'beat' the column individual.
DOI: 10.5061/dryad.f76f2/2
title: Metadata

description: This .csv file includes citation information and some basic data for each data matrix.
DOI: 10.5061/dryad.j631f/1
title: Catharus_ustulatus_draft_assembly_annotation_Feb13_2015.tar

description: Folder containing draft genome assembly and annotation. Assembly generated using a reference-based approach and three paired-end 100bp Illumina libraries (one fragment, two mate pair). Annotation generated using the MAKER pipeline.
DOI: 10.5061/dryad.j897m/1
title: Plate01-malaise-BR_S13_L001_R1_001.fastq
DOI: 10.5061/dryad.j897m/2
title: Plate01-malaise-BR_S13_L001_R2_001.fastq
DOI: 10.5061/dryad.kt0s8/11
title: 12_STRUCTURE_Kodama

description: Concatenated sequence data used for assessment of population genetic structure using the dataset of the seven nuclear genes from 98 Mus musculus and the software STRUCTURE, version 2.3 (Fig. 3B, Kodama et al., 2015).
DOI: 10.5061/dryad.kt0s8/12
title: 10_Mc1r_upstream_Noncoding

description: The non-coding region immediately upstream of the Mc1r exon 1 region. The data were used for construction of the median joining network shown in Fig 5A (Kodama et al., 2015).
DOI: 10.5061/dryad.q428q/1
title: Plant parameters

description: The data were collected in the field. Excel was used to create the data. SE-standard error, Treatment: C- control,DU-dung and urine return; M-mowing; T-trampling; DU+M-mowing combined with the addition of dung and urine; M+T-mowing combined with trampling; DU+T-trampling combined with the addition of dung and urine; DU+M+T-mowing combined with trampling and the addition of dung and urine
DOI: 10.5061/dryad.q428q/2
title: Soil parameters

description: The data were collected in the field. Excel was used to create the data. SE-standard error, MBC-soil microbial biomass carbon, MBN- soil microbial biomass nitrogen. Treatment: C- control,DU-dung and urine return; M-mowing; T-trampling; DU+M-mowing combined with the addition of dung and urine; M+T-mowing combined with trampling; DU+T-trampling combined with the addition of dung and urine; DU+M+T-mowing combined with trampling and the addition of dung and urine
DOI: 10.5061/dryad.q428q/3
title: Soil microbes' parameters

description: The data were collected in the field. Excel was used to create the data. SE-standard error, Gram+-gram positive bacteria, Gram--gram negative bacteria, AMF- arbuscular mycorrhizal fungi, B/F-bacteria to fungi ratio. Treatment: C- control,DU-dung and urine return; M-mowing; T-trampling; DU+M-mowing combined with the addition of dung and urine; M+T-mowing combined with trampling; DU+T-trampling combined with the addition of dung and urine; DU+M+T-mowing combined with trampling and the addition of dung and urine
DOI: 10.5061/dryad.s5c90/1
title: Supplemental file

description: Morphometric analysis of selected species
DOI: 10.5061/dryad.4767v/1
title: Data_ThiffaultEtAl_EcoEvo
DOI: 10.5061/dryad.50rb3/1
title: Stickleback Female Preference Data

description: Each row represents a single behavioral trial and the preference measures associated with that trial.  Each female was tested twice so there are two rows per female.  See Readme file for column descriptions.
DOI: 10.5061/dryad.60c8b/1
title: Data from virus bioassays - both generations

description: These are data from two bioassays reported in the paper
DOI: 10.5061/dryad.b91t7/1
title: montana weather data

description: This is the precipitation data used in the paper
DOI: 10.5061/dryad.b91t7/2
title: veg

description: This file contains the plant and rock cover data used in the paper.