cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf7g5.2/27.2
title: Breinholt_et_al_acrossLep_full_assemblies_all_loci

description: Fasta formatted sequence file containing sequences that pass pipeline step 1-6 for all loci and taxa in dataset 1-3. This file can be split using the split.py to separate into fasta files of individual loci.
DOI: 10.5061/dryad.rf7g5.2/3.2
title: final_soap_FG120036B

description: Assembly of Apatelodes pithala from Genbank SRA accession #SRR1794032, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5.2/39.2
title: contamination_filter

description: python script to process blast results of blasting sequences from each loci against themselves using usearch to identify contamination
DOI: 10.5061/dryad.rf7g5.2/41.2
title: Breinholt_et_al_RAW_DATA.tar.gz

description: compressed file containing the raw Illumina (2X100) AHE data
DOI: 10.5061/dryad.rf7g5/2
title: final_soap_GV120010B

description: Assembly of Urbanus proteus from Genbank SRA accession #SRR1794082 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5/3
title: final_soap_FG120036B

description: Assembly of Apatelodes pithala from Genbank SRA accession #SRR1794032, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5/4
title: Breinholt_et_al_Supplementary_File_1__S1-S11

description: Supplementary File 1: Microsoft excel document including Supplementary Table S1-S11 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5/5
title: Breinholt_et_al_Supplementary_Figure_S1

description: Supplementary Figure S1 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5/6
title: Breinholt_et_al_Supplementary_Figure_S2

description: Supplementary Figure S2 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5/7
title: Breinholt_et_al_Supplementary_Figure_S3

description: Supplementary Figure S3 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5/8
title: Breinholt_et_al_Supplementary_Figure_S4

description: Supplementary Figure S4 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5/9
title: Breinholt_et_al_Supplementary_Figure_S5

description: Supplementary Figure S5 from Breinholt et al. (2017)
DOI: 10.5061/dryad.s4g56/1
title: RAW_DATA
DOI: 10.5061/dryad.sq72d.2/21.2
title: BDFilterResults

description: BDFilterResults.csv data set includes information on 222 water filters that were analyzed for Bd (Batrachochytrium dendrobatidis), a chytrid fungus that can cause chytridiomycosis in amphibians. Samaples were analyzed by the U.S. Geological Survey using methods similar to those described in Kirshtein et al., 2007.
DOI: 10.5061/dryad.sq72d.2/22.2
title: WaterQualityBDFilters

description: “WaterQualityBDFilters.csv” – This table describes water quality information collected with a YSI sonde concurrent with sampling for Batrachochytrium dendrobaditis in water. See “Methods.txt” file for more information on field data collection methodology.
DOI: 10.5061/dryad.sq72d.2/23.2
title: Site Selection

description: This is a text file documenting the site selection procedures for the project. This information is also included with figures and tables in the "DataSummaryReport.pdf" document.
DOI: 10.5061/dryad.sq72d.2/24.2
title: Field methods

description: Text contained in this document is repeated with maps and other figures in the “DataSummaryReport.pdf” file included with this data submission. This file describes field methods in a .txt format to ensure readability in multiple computer formats.
DOI: 10.5061/dryad.sq72d.2/25.2
title: ListOfFiles

description: Contains a brief description of all files included in this data submission.
DOI: 10.5061/dryad.sq72d.2/26.2
title: Project Data Summary Report

description: This report provides background on the project, a full summary of site selection and field methods (with maps and figures), and a summary of the information contained in each data file included with this submission.
DOI: 10.5061/dryad.sq72d.2/27.2
title: 2010 Kenai Chemistry Analysis Pilot Year Summary

description: This document describes the results of preliminary analyses conducted after the 2010 pilot year of the study. These results were used to determine the sampling design for 36 sites in 2011 and 2012.
DOI: 10.5061/dryad.st621/25
title: Fig8_8B TTEST

description: Raw data and statistical analysis for Fig8B
DOI: 10.5061/dryad.st621/26
title: Fig8_8D TTEST

description: Raw data and statistical analysis for Fig8D.
DOI: 10.5061/dryad.st621/29
title: Fig8_8A Female Control averages

description: Raw data values and averages for control in Fig8A
DOI: 10.5061/dryad.st621/30
title: Fig8_8A Female P-L averages

description: Raw data values and averages for experimental genotype in Fig8A
DOI: 10.5061/dryad.st621/31
title: Fig9 Fig9A-B

description: Raw values and averages for Fig 9A-B
DOI: 10.5061/dryad.st621/32
title: Fig9_Binning

description: Averages for Fig 9 binned into 1-minute intervals
DOI: 10.5061/dryad.26bv4/1
title: Syssomonas multiformis predicted peptides (culture)

description: Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database). NOTE: although raw reads were subjected to several  cleaning steps, this file still contains a number of prey peptides (Spumella sp.)
DOI: 10.5061/dryad.26bv4/2
title: Syssomonas multiformis predicted peptides (sorted)

description: Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database).
DOI: 10.5061/dryad.26bv4/3
title: Pigoraptor vietnamica predicted peptides

description: Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database). NOTE: bacterial contamination present
DOI: 10.5061/dryad.26bv4/4
title: Pigoraptor chileana predicted peptides

description: Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database).
DOI: 10.5061/dryad.26bv4/5
title: Single gene alignments (trimmed) for phylogenomic analysis

description: Trimmed alignments for 255 genes and 38 taxa as used for the phylogenomic analysis (see Figure 2A and Table S1 of the manuscript) in fasta format.
DOI: 10.5061/dryad.2j0ks/1
title: Nutritional history and sex pheromone expression

description: Consumption and pheromone data for Nauphoeta cinerea males with different nutritional histories
DOI: 10.5061/dryad.3kh41/1
title: Schrader et al breeding data

description: Measures of breeding performance for all successful broods across the first 13 generations of experimental evolution.  The columns are as follow:  Carcass_mass_in_grams (the mass of the breeding carcass in grams), Environment (Control or No Care), Replicate (the replicate population, coded as A or B), Generation (the generation of experimental evolution), Pair (the unique breeding pair for a given Environment / Replicate / Generation), Brood_size (the number of larvae at dispersal), Brood_mass_in_grams (the total mass of all dispersing larvae in grams), Mean_larval_mass (the mean mass of dispersing larvae in grams, calculated as brood_mass_in grams/Brood_size).
DOI: 10.5061/dryad.4782m/1
title: Test crosses to determine mutant allele frequency in experimental populations

description: This file contains data from test crosses conducted to determine wildtype and mutant (gene disruption mutations) allele frequencies in replicate populations experimentally evolving in either a complex or simple mating environment. The data counts of are the inferred genotypes of males sampled at various time points (generations) over the course of the experiment. Each row corresponds to data from a single set of test crosses for a particular replicate population. Columns correspond to the following: generation: generation in which test cross was performed (note: no test crosses were performed at generation 0; rather replicates were established with individuals of known genotype); stock.number: corresponds to the stock number from the Bloomington Drosophila Stock Center (as of September 2014); experimental.code: corresponds to the experimental ID given to the mutant allele (also corresponds to the ID column in the supplemental materials); treatment: corresponds to the mating treatment (simple vs. complex); replicate: replicate population within treatment; heterozygote: number of heterozygote males sampled; wildtype: number of homozygous wildtype males sampled; mutant: number of homozygous mutant (gene-disruption mutation) males sampled.
DOI: 10.5061/dryad.4g8b7/1
title: .wav files used for playbacks

description: Here you find every .wav file that was used for the playback experiment in the two trials.
DOI: 10.5061/dryad.4g8b7/2
title: baseline vs. experiment comparison

description: File containing the proportion of 'stack' calls used as answer during the baseline recordings and both experimental trials.
DOI: 10.5061/dryad.4g8b7/3
title: Types of calls used as anwers

description: Each row contains numbers and proportion of answers for each call type by series. Each answer type, number and proportion has a dedicated column. When the number of answers wasn't higher than 5, NA was inserted (see methods).
DOI: 10.5061/dryad.4g8b7/4
title: Latency data

description: Here you find the data for: 1- the latency analysis for the complete playback series, 2- the supplementary analysis of the latency for the first 30 calls of the playback series and 3- the supplementary analysis of the latency for the last 30 calls of each playback series.
DOI: 10.5061/dryad.4g8b7/5
title: Number of answers data

description: Here you find the data for: 1 -  the total answers analysis for the complete playback series, 2- the supplementary analysis of the number of answers during the first 30 calls of the playback series and 3 -  the supplementary analysis of the number of answers during the last 30 calls of the playback series
DOI: 10.5061/dryad.559m9/1
title: Specimens examined of Xylodonta

description: Additional specimen data accompanying a review of the genus Xylodonta in Costa Rica.
DOI: 10.5061/dryad.6m20j/1
title: Quartet Sampling Results/Data: Cannon, et al. 2015

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Cannon et al 2015 study.
DOI: 10.5061/dryad.6m20j/2
title: Quartet Sampling Results/Data: Hinchliff and Smith 2014

description: A gzipped tar archive containing the input alignment and tree, and results the concatenated 200-replicate Quartet Sampling analyses for the Hinchliff and Smith 2014 study.
DOI: 10.5061/dryad.6m20j/3
title: Quartet Sampling Results/Data: Pryer, et al. 2016

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Pryer, et al. 2016
DOI: 10.5061/dryad.6m20j/4
title: Quartet Sampling Results/Data: Walker, et al. 2017

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Walker, et al. 2017 study.
DOI: 10.5061/dryad.6m20j/5
title: Quartet Sampling Results/Data: Xi, et al. 2014

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Xi, et al. 2014 study.
DOI: 10.5061/dryad.71pp6/2
title: Xenobiotic Metabolizing Enzme Specific Content

description: A comma separated format file containing individual enzyme specific content donor data
DOI: 10.5061/dryad.71pp6/3
title: Xenobiotic Metabolizing Enzyme Specific Activity

description: A comma separated file containing individual enzyme specific activity donor data
DOI: 10.5061/dryad.71pp6/4
title: Xenobiotic Metabolizing Enzyme Genotype

description: A comma separated format file containing individual genotype information for individual donors.
DOI: 10.5061/dryad.7k749/1
title: Microsatellite genotypes

description: Genotypes of 22 microsatellites from 837 northern elephant seals.
DOI: 10.5061/dryad.7kt3h/1
title: anticipating_emergence

description: All code used to simulate time series data, analyse data and create figures for the paper
DOI: 10.5061/dryad.9n2sm/1
title: Data on the effects of plant defenses and predators on herbivores

description: Data from manipulative laboratory and field experiments.
DOI: 10.5061/dryad.9pq6k/11
title: NIP51mRNA670_PP2AmRNA570_(1)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/12
title: NIP51mRNA670_PP2AmRNA570_(2)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/13
title: NIP51mRNA670_PP2AmRNA570_(3)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/14
title: NIP51mRNA670_PP2AmRNA570_(4)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/15
title: NIP51mRNA670_PP2AmRNA570_(5)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/16
title: NIP51mRNA670_PP2AmRNA570_(8)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/17
title: NIP51mRNA670_PP2AmRNA570_(6)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/18
title: NIP51mRNA670_PP2AmRNA570_(7)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/9
title: NIP51_Int1570_mRNA670_ (9)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), NIP5;1 Intron probes(Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.jk6rf/6
title: Jaguar Detection History

description: Data re: whether or not a jaguar or jaguar sign had been seen by the interviewee in the given sampling unit. Sampling units are rows, interview replicates are columns.
DOI: 10.5061/dryad.jk6rf/7
title: More Than Four

description: Data corresponding to whether or not &gt;4 interviews were conducted in the unit (1/0)
DOI: 10.5061/dryad.jk6rf/8
title: Site Covariates

description: All site covariates considered in the analysis. Summarized at sampling unit level.
DOI: 10.5061/dryad.k2v06/2
title: BMJOpen_SuppTable2

description: Educational strategies used in published studies describing pediatric surgery checklist implementation
DOI: 10.5061/dryad.k2v06/3
title: BMJOpen_SuppTable3

description: Attitudes across pediatric surgical teams in regards to the surgical safety checklist
DOI: 10.5061/dryad.k2v06/4
title: APPENDIX_I_CompleteSearchStrategy

description: Complete search strategy for pediatric surgical safety checklist systematic review
DOI: 10.5061/dryad.k2v06/5
title: APPENDIX III_Quality Assessment Tool

description: Diverse study quality assessment tool adapted from the NIH Quality Assessment Tool for Observational Cohorts and Cross-sectional Studies and The Newcastle-Ottawa Quality Assessment Scales and the Critical Appraisal Skills Programme (CASP) for both qualitative studies and cohorts
DOI: 10.5061/dryad.nc5dp/14
title: Kentrophoros sp. H sample 500-19 nuclei labels

description: Kentrophoros sp. H sample 500-19 - label file to mark cell nuclei. File in Amira format.
DOI: 10.5061/dryad.nc5dp/15
title: Kentrophoros sp. H sample 500-19 nuclei surface

description: Kentrophoros sp. H sample 500-19 - surface file for cell nuclei. File in Amira format.
DOI: 10.5061/dryad.np4hs/21
title: Exp2_S3_Session1b

description: This data file contains functional MRI data of subject 3 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 1, runs 5-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction. For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/22
title: Exp2_S3_Session2a

description: This data file contains functional MRI data of subject 3 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 1-3.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/23
title: Exp2_S3_Session2b

description: This data file contains functional MRI data of subject 3 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 4-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction.  For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/24
title: Exp2_S4_Session1a

description: This data file contains functional MRI data of subject 4 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 1, runs 1-4.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/25
title: Exp2_S4_Session1b

description: This data file contains functional MRI data of subject 4 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 1, runs 5-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction. For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/26
title: Exp2_S4_Session2a

description: This data file contains functional MRI data of subject 4 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 1-3.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/27
title: Exp2_S4_Session2b

description: This data file contains functional MRI data of subject 4 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 4-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction.  For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/28
title: Exp2_S5_Session1a

description: This data file contains functional MRI data of subject 5 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 1, runs 1-4.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/29
title: Exp2_S5_Session1b

description: This data file contains functional MRI data of subject 5 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 1, runs 5-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction. For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.rf7g5.2/28.2
title: Breinholt_et_al_shallow_full_assemblies_all_loci

description: Fasta formatted sequence file containing sequences that pass pipeline step 1-6 for all loci and taxa in dataset 4-6. This file can be split using the split.py to separate into fasta files of individual loci.
DOI: 10.5061/dryad.rf7g5.2/29.2
title: Breinholt_et_al_allcodonpostion123_acrossLep

description: Nexus file containing codon position 1 & 2  & 3 for 557 loci and 75 taxa used to make dataset 1-3. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5.2/30.2
title: Breinholt_et_al_aminoacid_DS1

description: Nexus file containing codon position 1 & 2 for 557 loci and 23 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5.2/33.2
title: Breinholt_et_al_DS4

description: Dataset 4 (shallow_probe+flanks). Nexus file containing 749 loci and 48 taxa. Alignments were trimmed with a density of 60% and entropy of 1.5 using alignment_DE_trim.py and flacking regions were processed with the flank_dropper.py to remove head or tail sequences using 2 standard deviations for both the head and tail. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5.2/34.2
title: Breinholt_et_al_degen12_DS3

description: Dataset 3 (acrossLEP_AHE+ALLtrans ). Nexus file consists of both AHE and the transcriptomic data of Kawahara and Breinholt 2015. The file contains codon position 1 & 2 for 2948 loci and 76 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5.2/35.2
title: Breinholt_et_al_aminoacid_DS2

description: Nexus file containing amino acid data for 557 loci and 75 taxa. See taxa_list.txt for species names of each taxon, this is an amino acid nexus file with a CHARSET that defines each loci. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.