cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gg8fg/1
title: Appendix S1

description: Appendix S1: Compendium of all German beetle species used in this study including information on their geographical  distribution, specimen count, BIN, Mean and Max ISD, Nearest-Neighbor(NN) species and Distance to NN.
DOI: 10.5061/dryad.gg8fg/2
title: Appendix S2

description: Appendix S2: Accession numbers, BOLD Sample-IDs and species names for all specimens used in this study.
DOI: 10.5061/dryad.gg8fg/3
title: Appendix S3
DOI: 10.5061/dryad.vk966/1
title: Behavioral Data and Subject Information

description: This file contains the handedness and tool use performance data as well as information on the subject ID, sex, rearing history and colony membership.
DOI: 10.5061/dryad.vk966/2
title: Pedigree file

description: This is the pedigree file and contains the subject, sire and dam information.
DOI: 10.5061/dryad.gg8fg/10
title: CO1-5P Alignments

description: 15 files of 1000 aligned CO1 sequences
DOI: 10.5061/dryad.28v87/1
title: Data base Dynamics seedling/sapling community

description: This database contains data from survival and recruitment of seedling/sapling community, collected from 2008 to 2013 in southern Mexico.
DOI: 10.5061/dryad.23k27/1
title: DepositionAnalysis

description: R Script for generalized linear model and contrast analysis for scat accumulation samples collected from September 2012 to July 2012 at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.23k27/2
title: dep.data

description: Raw data for scat accumulation surveys used in the generalized linear model and contrast analyses. Data collected from September 2012 to July 2012 at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.23k27/3
title: kitfoxes

description: Raw DNA degradation data for kit fox faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah. (Coding: 1 indicates successful PCR amplification, presence of ADO, or presence of FA; 0 indicates failed PCR amplification, no detection of ADO, or no detection of FA)
DOI: 10.5061/dryad.23k27/4
title: coyotes

description: Raw DNA degradation data for coyote faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah. (Coding: 1 indicates successful PCR amplification, presence of ADO, or presence of FA; 0 indicates failed PCR amplification, no detection of ADO, or no detection of FA)
DOI: 10.5061/dryad.23k27/5
title: loci

description: Data on average locus lengths for kit fox and coyote faecal DNA samples used in the mixed-effects logistic regression models for PCR success, allelic dropout (ADO) and false alleles (FA). Faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.23k27/6
title: pcr

description: SAS script for the mixed-effects logistic regression models of PCR success for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.23k27/7
title: ado

description: SAS script for the mixed-effects logistic regression models of allelic dropout for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.23k27/8
title: fa

description: SAS script for the mixed-effects logistic regression models of false alleles for coyote and kit fox faecal DNA samples collected in 2012 during winter and summer at Dugway Proving Ground, Utah.
DOI: 10.5061/dryad.cq2kh/1
title: Proc B Dryad_mesocosm dispersal data

description: The number of dispersed seeds in mesocosms for four plant species under different ant treatments: (AR = single colony of native ant, MR = single colony of invasive ant, ARAR and MRMR double colonies of either species, NOANTS controls.
DOI: 10.5061/dryad.cq2kh/2
title: Proc B Dryad_mesocosm recruitment

description: Plant recruitment of four plant species in mesocosms with different ant treatments.
DOI: 10.5061/dryad.rp30d/2
title: Common eider data for Harms et al MS: Feather corticosterone reveals effect of moulting conditions in an Arctic migratory bird

description: These data were collected from the field from 2007-2011. Column headings are as follows: ID (year plus bird band number); Band (bird band number); year (year eider was captured); CORTf (feather corticosterone in pg/mm); arrival (eider arrival date on breeding colony in Julian days); relArrival (relative arrival date); mass (eider mass in grams); Lay (date first egg was laid); relLay (relative lay date); nest (at least one egg was successfully hatched); Survival (1=eider found dead by end of breeding season, 0= eider that was not found dead during breeding season)
DOI: 10.5061/dryad.760v9/1
title: Supplementary Table 1
DOI: 10.5061/dryad.ff4fs/1
title: GTseq_Data

description: Compressed folder (.zip) containing sequencing data and input files necessary for genotyping using the GTseq method described in the manuscript.
DOI: 10.5061/dryad.pk045/1
title: tables and scripts

description: This contains all tables we generated from RNAseq libraries as read counts as well as statistic results. It also contains the r scripts used in this study
DOI: 10.5061/dryad.pk045/2
title: downsampling_tables

description: It contains read counts tables as results of down-sampling as well as the expression of last 500bp at 3'end genes
DOI: 10.5061/dryad.4c2bj/1
title: Risk of bias meta-analysis data

description: Risk of bias data extracted from publications identified through systematic review and included in a meta-analysis of preclinical thiazolidinedione animal studies. A user guide describing the data and abbreviations is included in the Excel file.
DOI: 10.5061/dryad.6490g/1
title: anakeestiicola_data_packet

description: This is a zipped folder that contains two files. 1) The mtSSU alignment used for this study to illustrate the phylogenetic placement of Lecanora anakeestiicola, and 2) The nrITS alignment used to examine genetic distance between populations/vouchers of the same species.
DOI: 10.5061/dryad.8g55g/1
title: changes_MACP_datapacket

description: This is a zipped folder containing the following items: 1) alignments of Cladonia nrITS sequences used in Bayesian Inference (BI), maximum likelihood (ML), and maximum parsimony (MP) analyses in this study; 2) alignment of nrITS sequences of Lecanora cinereofusca s.l. used for examination of genetic distance; 3) alignments of mtSSU sequences of Lecanoraceae illustrating the monophyly and phylogenetic placement of Lecanora cinereofusca s.l. used in in Bayesian Inference (BI) and maximum likelihood (ML) analyses in this study.
DOI: 10.5061/dryad.k4227/1
title: Magallon_etal_data

description: Nucleotide sequence data.
DOI: 10.5061/dryad.36vq2/1
title: Bicknell et al. data

description: Detection rates of birds, bats, and large mammals at each site before and after logging, as well as site details and metrics. Each table includes a description to interpret the data.
DOI: 10.5061/dryad.k4227/2
title: Magallon_etal_PL_100bs

description: 100 bootstrap trees obtained with maximum likelihood in RAxML, dated with Penalized Likelihood.
DOI: 10.5061/dryad.k4227/3
title: Magallon_etal_PL_ML

description: Maximum likelihood tree obtained with RAxML and dated with Penalized Likelihood.
DOI: 10.5061/dryad.k4227/4
title: Magallon_etal_UCLN

description: Dated tree obtained with the uncorrelated lognormal (UCLN) method in BEAST.
DOI: 10.5061/dryad.n2q7f/1
title: Sceloporus GFF3 annotation files

description: Annotation, gene ontology, and genomic sequences in GFF3 format
DOI: 10.5061/dryad.n2q7f/2
title: Orthologous groups

description: Orthologous groups predicted by OrthoMCL. Datasets included: 35 Sceloporus species, plus the Anolis carolinensis, Gallus gallus, and human proteins.
DOI: 10.5061/dryad.3jm3n/1
title: Rhinella marina transcriptome non redundant assembly
DOI: 10.5061/dryad.3jm3n/2
title: Rhinella marina transcriptome full assembly
DOI: 10.5061/dryad.3jm3n/3
title: Rhinella schneideri transcriptome non redundant assembly
DOI: 10.5061/dryad.3jm3n/4
title: Rhinella schneideri transcriptome full assembly
DOI: 10.5061/dryad.3jm3n/5
title: SNPs data for Rhinella marina and Rhinella schneideri
DOI: 10.5061/dryad.d702p/3
title: Marine particulate organic matter

description: The dataset includes information about latitude, longitude,depth and time of sampling of marine particulate organic phosphorus, nitrogen, and carbon
DOI: 10.5061/dryad.km38g/1
title: Trifolium_plastid_coding

description: A concatenated matrix of 59 protein coding plastid genes. Only coding regions were used, introns and intergenic regions were excluded in the alignment, due to plastome rearrangements (see manuscript of further description). The alignment was generated using Mafft v7.053b using -auto flag and trimmed using TrimAl with the -automated1 flag. This process was pipelined using Plast2Phy (https://github.com/saemi/plast2phy).
DOI: 10.5061/dryad.km38g/2
title: Trifolium_plastid_coding_ML

description: ML tree generated using GARLI (the config file is the ReadMe file). The model used GTR+G, based on a jModelTest search and an AIC test. 10 starts were prefromed and a 100 bootstrap replicates. Medicago truncatula is the outrgroup.
DOI: 10.5061/dryad.t74q4/1
title: Conus_miliaris_TRI_6_14.fa

description: Transcript assembly for Conus miliaris.  Assembly consists of 22 individuals collected from Easter Island, Guam and American Samoa.  Assembly was created from 100 bp paired-end reads.  Reads were first normalized then assembled with Trinity (version 20140413p1). Tissue source: venom ducts.
DOI: 10.5061/dryad.t74q4/2
title: American_samoa_TRI_6_14.fa

description: Transcript assembly for 6 individuals of Conus miliaris collected from American Samoa.  Assembly was created from 87,201,606 100 bp paired-end reads.  Transcripts were assembled with Trinity (version 20140413p1).  Tissue source: venom ducts.
DOI: 10.5061/dryad.t74q4/3
title: Easter_Island_TRI_6_14.fa

description: Transcript assembly for 8 individuals of Conus miliaris collected from Easter Island.  Assembly was created from 131,525,916 100-bp paired-end reads.  Transcripts were assembled with Trinity (version 20140413p1).  Tissue source: venom ducts.
DOI: 10.5061/dryad.t74q4/4
title: Guam_TRI_6_14.fa

description: Transcript assembly for 8 individuals of Conus miliaris collected from Guam.  Assembly was created from 130,566,380 100-bp paired-end reads.  Transcripts were assembled with Trinity (version 20140413p1).  Tissue source: venom ducts.
DOI: 10.5061/dryad.t74q4/5
title: American_Samoa_blastx_annotation

description: Parsed BLASTx report for C. miliaris from American Samoa.  Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database,  annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot  database.  Matches with an e-value &lt; 10-5 were retained.
DOI: 10.5061/dryad.t74q4/6
title: Conus_miliaris_blastx_annotation

description: Parsed BLASTx report for C. miliaris.  Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database,  annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot  database.  Matches with an e-value &lt; 10-5 were retained.
DOI: 10.5061/dryad.t74q4/7
title: Easter_Island_blastx_annotation

description: Parsed BLASTx report for C. miliaris from Easter Island.  Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database,  annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot  database.  Matches with an e-value &lt; 10-5 were retained.
DOI: 10.5061/dryad.t74q4/8
title: Guam_blastx_annotation

description: Parsed BLASTx report for C. miliaris from Guam.  Transcripts were seearched against local databases of non-redundant conotoxin and conotoxin signal sequences downloaded from the Conoserver database,  annotated proteins from two mollusc species available on the NCBI Unigene database (Aplysia californica and Lottia gigantea), all Conus related proteins downloaded from NCBI's nr database as well as the Swiss-Prot  database.  Matches with an e-value &lt; 10-5 were retained.
DOI: 10.5061/dryad.t74q4/10
title: Conus_miliaris_populations_expression_files.tar

description: Annotated tab-delimited expression count files (raw counts and FPKM values) with the number of reads mapping back to each transcript for all transcripts as well as toxin related only transcripts for all populations (Easter Island, Guam, and American Samoa) of Conus miliaris.
DOI: 10.5061/dryad.t74q4/11
title: Conus_miliaris_SNPs.tar

description: VCF file of 585,736 high-quality single nucleotide polymorphisms (SNPs) identified from 22 C. miliaris individuals from Easter Island, Guam and American Samoa.
DOI: 10.5061/dryad.t74q4/9
title: Conus_miliaris_individual_expression_files.tar

description: Annotated tab-delimited expression count files (raw counts and FPKM values) with the number of reads mapping back to each transcript for all transcripts as well as toxin related only transcripts for all Conus miliaris individuals.
DOI: 10.5061/dryad.1qh3k/1
title: popIIImap141023

description: Genetic map of Salix viminalis population S3
DOI: 10.5061/dryad.1qh3k/2
title: Genotypes+sex_141013

description: Genotypes of S3 mapping population in Joinmap infile format. Sex as morphological marker is included in this file too.
DOI: 10.5061/dryad.m77j0/1
title: MotionTest

description: Data used to testing background subtraction.
DOI: 10.5061/dryad.m77j0/2
title: Acctesting

description: R script for running performance analysis.
DOI: 10.5061/dryad.1qh3k/3
title: mapqtl-sex_141023

description: Phenotypic data on the sex of the individuals in the mapping population S3. Male = 1, Female = 2
DOI: 10.5061/dryad.38sn2/1
title: Longevity models in R

description: R code used to generate the results shown in figure 2.
DOI: 10.5061/dryad.38sn2/2
title: Simulations with Anther-smut data

description: R code showing the discrete, latent-period model used to generate the results shown in Figure 4 and supplemental Table S2
DOI: 10.5061/dryad.3g604/1
title: Blast sequences of 13 species in this study
DOI: 10.5061/dryad.3sh6d/1
title: Larracuente_Supplementary_file2

description: Maximum likelihood tree with bootstrap support of Rsp and Rsp-like repeats used in Figure 3.
DOI: 10.5061/dryad.f082m/1
title: raw_data_Fig1A

description: Height (mm) at which each individual larva (n=31) was found at time points t=0 hours post-infection (hpi) until 166 hpi. At each time point survival was monitored (alive/dead =A/D).
DOI: 10.5061/dryad.f082m/2
title: raw_data_Fig1B

description: Height at death (mm) was measured per individual. Three treatments: 1. Light from above only; 2. Light from below only; 3. Dark conditions only. Two replicate experiments performed for each of the treatments (column replicate #), combined data from these two replicates are used in graph  of Fig. 1B.
DOI: 10.5061/dryad.qc2qq/1
title: RAD "unitag" FASTA files for H. erectus

description: This FASTA file contains the RADseq "unitag" (unique RAD single end sequences) sequences for H. erectus.
DOI: 10.5061/dryad.qt071/1
title: Välimäki_et_al_2014_J_Anim_Ecol
DOI: 10.5061/dryad.2p51n/1
title: chip1_bp00x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 00x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.f082m/3
title: raw_data_Fig2

description: Height (mm) per individual larva measured at different time points after mock-infection, from 0 hours post mock-infection until 214 hpi (light/dark) or 184 hpi (only dark).Two treatments: 1. mock-infected larvae kept under normal light/dark conditions; 2. mock-infected larvae kept under dark conditions.
DOI: 10.5061/dryad.h95h0/1
title: External measurements_Nov 2014

description: Individual size, bite force and call frequency measurements for ten species of horseshoe bats (Rhinolophidae).
DOI: 10.5061/dryad.h95h0/2
title: Skull measurements_Nov 2014

description: Skull measurements for individuals from ten species of horseshoe bats (Rhinolophidae).
DOI: 10.5061/dryad.k14bq/1
title: TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.sort

description: Alignment of manuscript reference transcriptome sequence to reference genome with genetic map positions.bwa mem -t 6 -a -M \    HA412.v0.2.cabog.20111122.RHA280xRHA801.g    Map2.fasta \    TranscriptomeRef_mar30.fa \| samtools view -Sub - \| samtools sort -@ 2 -m 2G -l 9 - \    TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.    RHA280xRHA801.gMap2.sort
DOI: 10.5061/dryad.k14bq/2
title: TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.fasta

description: HA412 v0.2 scaffolds matching manuscript reference transcriptome.samtools view \    TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.sort.bam \| cut -f 3 \| sort \| uniq \&gt;TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.listgrepFasta \    TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.list \&lt; HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.fasta \&gt;TranscriptomeRef_mar30.TO.HA412.v0.2.cabog.20111122.RHA280xRHA801.gMap2.scaffolds.fasta
DOI: 10.5061/dryad.k1j51/1
title: NilssonOrtman2014_Headwidth_Data-1

description: Head widths (”hw”) of larvae of six species of damselflies (”spec”) reared in the laboratory at three or four temperatures ("temp"). Head widths are in the unit of millimeter. Head widths were measured at four different ages (”day”). These measurements were made immediately following hatching (day = 0),and at the age of 42, 84 and 126 days. Different species and populations were reared in three different years (”year”). Each species was sampled from populations at three different latitudes, namely near its southern range limit, at the core of its range and near the northern range limit (”lat”, coded as s, c and n, respectively). At each latitude, between two and four subpopulations were sampled (”pop”). The latitude (”lat”) and longitude (”long”) is given for each subpopulation. For a list of populations and abbreviations, please refer to Table S1 in the published paper. From each subpopulations, full-sib larvae were reared from several families (”fam”), i.e. they were hatched from eggs laid by a single female, and from each family we reared 5 individual larvae (”ind”) at each temperature.
DOI: 10.5061/dryad.2p51n/2
title: chip1_bp01x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 01x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/3
title: chip1_bp02x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1blocking  primer concentration = 02x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/4
title: chip1_bp05x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 05x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/5
title: chip1_bp10x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 10x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/6
title: chip1_bp20x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 20x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/10
title: chip2_bp00x_t45_c30

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 45PCR cycles = 30
DOI: 10.5061/dryad.2p51n/11
title: chip2_bp00x_t45_c35

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 45PCR cycles = 35
DOI: 10.5061/dryad.2p51n/12
title: chip2_bp00x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/13
title: chip2_bp00x_t50_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 50PCR cycles = 40
DOI: 10.5061/dryad.2p51n/14
title: chip2_bp00x_t55_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 55PCR cycles = 40
DOI: 10.5061/dryad.2p51n/15
title: Barcodes of the 11 species in the mock sample

description: Database with the COI barcodes of the eleven species obtained by Sanger sequencing (fasta file).
DOI: 10.5061/dryad.2p51n/7
title: chip1_bp40x_t45_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 1 blocking  primer concentration = 40x annealing temperature = 45PCR cycles = 40
DOI: 10.5061/dryad.2p51n/8
title: chip2_bp00x_t40_c40

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 40PCR cycles = 40
DOI: 10.5061/dryad.2p51n/9
title: chip2_bp00x_t45_c25

description: Raw data in fastq format from the sequencing of the mock sample using a 314 Ion Torrent chip. PCR conditions (see table 1 for details):chip = 2 blocking  primer concentration = 00x annealing temperature = 45PCR cycles = 25
DOI: 10.5061/dryad.0dq8s/1
title: RSOS_140386_alignment

description: Nexus alignment file of 26 opsin sequences (1005 nucleotides)
DOI: 10.5061/dryad.2p51n/16
title: Barcodes of 188 Entomobryidae from Genbank

description: Database with the COI barcodes of 188 species of Entomobryidae (Collembola) obtained from Genbank (fasta file). Search: Entomobryidae[Organism] AND COI[Gene Name] AND Barcode[Keyword] (accessed on July 30th, 2014)