cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m3p7d/13
title: Perl script for the extraction of the most abundant sequences for each OTU and each sample

description: This ZIP file contains a script called GOMS: Get OTU Main Sequence. GOMS is a Perl program based on mothur files. It thus requiers several files from mothur (http://www.mothur.org/wiki/454_SOP or http://www.mothur.org/wiki/MiSeq_SOP): .list file, .names file, .groups file and .fasta file. The user must also provide the number of the OTU and the treshold used to form the OTUs. GOMS generates a fasta file with, for each sample, the highly representative sequence of a given OTU, meaning the unique sequence which has the most important number of copies. Some information are also provided within the fasta file like the number of sequences and unique sequences assigned to the OTU and the number of copies of the main unique sequence.
DOI: 10.5061/dryad.m3p7d/4
title: MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 3 to 4)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m3p7d/5
title: MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 4 to 4)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m3p7d/6
title: MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 1 to 3)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m3p7d/7
title: MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 2 to 3)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m3p7d/8
title: MiSeq raw sequences (Run 2) of the V4 region 16S rRNA gene from the spleens of 348 murinae from Senegal and 26 positive and negative controls (part 3 to 3)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate using the MiSeq platform (Run 2). The 746 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 26 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2
DOI: 10.5061/dryad.m3p7d/9
title: Raw output files generated by the mothur program

description: This ZIP file contains seven output files (.groups, .names, .table, .taxonomy, .list, .fasta and .log) generated by the mothur program for the whole 16S rRNA dataset. The .log file contains all the mothur command lines used for the processing of the raw sequences.
DOI: 10.5061/dryad.n10d7/1
title: Madagascarophis Nexus Files

description: Three loci used in analyses (COI, RAG2, CMOS), including a file for the gene RAG2 that includes a heterozygous individual, denoted by allele "A" and "B."
DOI: 10.5061/dryad.n10d7/2
title: Madagascarophis_trees

description: The species tree from *BEAST and the three gene trees (COI, RAG2, CMOS) generated during the *BEAST run.
DOI: 10.5061/dryad.p1m52/1
title: Supplementary Figure S1

description: FIGURE S1. Example of a UCE alignment showing a short mismatch at one end. This portion of the alignment shows no variation with the exception of a stretch of 13 nucleotides with nine mismatches. Similar stretches are evident in 69 UCE alignments. The terminal gaps in three other taxa simply reflect the failure of those assemblies to extend all of the way to the end of the alignment.
DOI: 10.5061/dryad.p1m52/17
title: Supplementary Figure S3

description: FIGURE S3. Performance of the maximum parsimony (MP) criterion for phylogenetic estimation with UCE data. The topology of the single most parsimonious tree of 50929 steps recovered when UCE data were analyzed (A) was identical to the ML tree for those data. Minimum branch lengths for UCEs (i.e., the number of unambiguous synapomorphies) are shown above branches and bootstrap support is presented below branches. An MP analysis of combined UCEs+introns+mitochondrial data also yielded a single tree (of 59964 steps) with an identical topology. Bootstrap support for both analyses is reported as a percentage of 500 replicates. Full (100%) support is indicated using an asterisk (*). MP and ML branch lengths for the UCE data were strongly correlated (B), suggesting that the MP criterion is likely to have reconstructed character state transformations accurately. The graph was limited to internal branches.
DOI: 10.5061/dryad.pb68n/1
title: Figure S1

description: Raw Maximum Likelihood phylogenetic tree of the GCN5-related N-acetyltransferase (GNAT) superfamily and newly identified GNATs similar to Hoplolaimina homologs. Branches for each GNAT family are color-coded accordingly. Bootstrap support values are indicated at corresponding nodes, and those that support monophyly of each GNAT family are oversized in red font. Names and organisms found to contain each GNAT family are indicated to the right with brackets around the respective leaves. Sequence identifications are provided in parentheses at each leaf.
DOI: 10.5061/dryad.pb68n/2
title: Figure S2

description: Detailed Maximum Likelihood phylogenetic tree of the FAM7 GNATs including Hoplolaimina homologs. Branches for each phylogenetic group are color-coded according to their taxonomy. Bootstrap support values are indicated at corresponding nodes, and those that support possible horizontal gene transfer (HGT) events are oversized in red font. Organism names are indicated to the right with brackets around the respective leaves. Sequence identifications are provided in parentheses at each leaf.
DOI: 10.5061/dryad.pb68n/3
title: Figure S3

description: Detailed Maximum Likelihood phylogenetic tree of INVs similar to Hoplolaimina homologs. Branches for each phylogenetic group are color-coded according to their taxonomy. Bootstrap support values are indicated at corresponding nodes, and those that support possible horizontal gene transfer (HGT) events are oversized in red font. Organism names are indicated to the right with brackets around the respective leaves. Sequence identifications are provided in parentheses at each leaf.
DOI: 10.5061/dryad.pb68n/4
title: Figure S4

description: Detailed Maximum Likelihood phylogenetic tree of CMs similar to Hoplolaimina homologs. Branches for each phylogenetic group are color-coded according to their taxonomy. Bootstrap support values are indicated at corresponding nodes, and those that support possible horizontal gene transfer (HGT) events are oversized in red font. Organism names are indicated to the right with brackets around the respective leaves. Sequence identifications are provided in parentheses at each leaf. Note that the Nacobbus aberrans leaf is colored red to indicate its possible neofunctionalization from the other Hoplolaimina homologs (see supplementary text, Additional file 5).
DOI: 10.5061/dryad.pb68n/5
title: Figure S5

description: Detailed Maximum Likelihood phylogenetic tree of initially poorly clustered FAM7 GNATs. Branches for each phylogenetic group are color-coded according to their taxonomy. Bootstrap support values are indicated at corresponding nodes, and those that support possible horizontal gene transfer (HGT) events are oversized in red font. Organism names are indicated to the right with brackets around the respective leaves. Sequence identifications are provided in parentheses at each leaf.
DOI: 10.5061/dryad.tj4qg/10
title: tableS1.py

description: This is a Python 3 program tableS1.py. The input files are data2.txt and data4.txt. This program can be used to reproduce and replicate all results in S1 Table. Copy the files data2.txt, data4.txt and tableS1.py to the same directory. Give the command "python3 tableS1.py". The program asks three questions. Answer these questions and the results are displayed on the screen.
DOI: 10.5061/dryad.tj4qg/5
title: data2.txt

description: The selected word (SW) identified on day (D) of month (M) in CC. The daily prognosis (Prog) combinations are "GGG" (All lucky), "SSS" (All unlucky), "---" (All unknown) or "HET" (Heterogeneous). The same SW identifed at the same date by Leitz (1994) (Ltz="Yes" or "No") and Bakir (1966(Bkr="Yes" or "No").
DOI: 10.5061/dryad.tj4qg/6
title: data3.txt

description: The n = 6x564 time point t_i values of SSTP=1, 3, 5, 7, 9 and 11 of Table 3 in Jetsu et al. (2013).
DOI: 10.5061/dryad.tj4qg/7
title: data4.txt

description: The day (D) and month (M) values in CC used in computing the time points (t_i) for the days with the prognoses "GGG" and "SSS". These t_i are needed in computing the binomial distribution probabilities Q_B. There are N_G=177 and N_S=105 days with a "GGG" and "SSS" combination.
DOI: 10.5061/dryad.v8hk0/1
title: Data file_29thJan16

description: Experimental results from single photon avalanche photodiodes reported in the manuscript.
DOI: 10.5061/dryad.vn66m/1
title: Database primary productivity and metapopulation dynamics
DOI: 10.5061/dryad.2853k/2
title: Supplementary Table 1

description: Number of specimens, resting metabolic rate measured for extant species and osteohistological characters measured from all available femora in the sample.
DOI: 10.5061/dryad.2853k/3
title: Supplementary Table 2

description: Number of specimens, resting metabolic rate measured for extant species and osteohistological characters measured from all available humeri in the sample.
DOI: 10.5061/dryad.2853k/4
title: Supplementary Table 3

description: Resting metabolic rate measured for extant species and osteohistological characters measured from all available tibiae in the sample.
DOI: 10.5061/dryad.2853k/5
title: Supplementary phylogeny 1

description: Phylogenetic tree of all species in our sample, as a NEXUS file
DOI: 10.5061/dryad.2bm7d/1
title: Hopwood-Head-genitals_coevolve_2016

description: Full data associated with: "Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides". Description of data headings is included in Excel worksheets.
DOI: 10.5061/dryad.326fv/11
title: Fasta of Castoroides ohioensis collagen

description: Aligned fasta file of Castoroides ohioensis collagen I alpha 1 and alpha 2
DOI: 10.5061/dryad.326fv/2
title: Sample 2 - Injection 2 Orbitrap-Ion Trap

description: Sample 2 - Injection 2
DOI: 10.5061/dryad.326fv/3
title: Sample 1 - Injection 1 Orbitrap-Ion Trap

description: Sample 1 - Injection 2
DOI: 10.5061/dryad.326fv/4
title: Sample 1 - Injection 2 Orbitrap-Ion Trap

description: Sample 1 - Injection 2
DOI: 10.5061/dryad.326fv/5
title: Buffer control 2 - Injection 1 Orbitrap Ion Trap

description: Buffer control 2 - Injection 1
DOI: 10.5061/dryad.326fv/6
title: Buffer control 2 - Injection 2 Orbitrap Ion Trap

description: Buffer control 2 - Injection 2
DOI: 10.5061/dryad.326fv/7
title: Buffer control 1 - Injection 1 Orbitrap Ion Trap

description: Buffer control 1 - Injection 1
DOI: 10.5061/dryad.326fv/8
title: Buffer control 1 - Injection 2 Orbitrap Ion Trap

description: Buffer control 1 - Injection 2
DOI: 10.5061/dryad.326fv/9
title: PEAKS exports - Sample 1, Sample 2, Buffer control 1, Buffer control 2

description: CSV exports (peptide lists, protein lists, etc.) from PEAKS searching.
DOI: 10.5061/dryad.40494/22
title: Latrunculin replicate 1 prior to reagent
DOI: 10.5061/dryad.40494/23
title: Latrunculin replicate 1 after reagent
DOI: 10.5061/dryad.40494/24
title: Latrunculin replicate 1 recovery
DOI: 10.5061/dryad.40494/25
title: Latrunculin rep 2_fig 7_pt 1
DOI: 10.5061/dryad.40494/26
title: Latrunculin rep 2_fig 7_pt 2
DOI: 10.5061/dryad.40494/27
title: Latrunculin replicate 3 prior to reagent
DOI: 10.5061/dryad.40494/28
title: Latrunculin replicate 3 after reagent
DOI: 10.5061/dryad.40494/29
title: Latrunculin replicate 3 recovery
DOI: 10.5061/dryad.43b52/1
title: Evo_antioxidant defence_ data

description: Data file contains all measurements for antioxidant enzyme activities, oxidative damage and life-history parameters. Data presented are averaged values for each measurement.
DOI: 10.5061/dryad.4f1k5/1
title: Variation in Enchenopa male signal traits

description: Measurements of 7 Enchenopa male signal traits from two separate experiments. Each row corresponds to an individual male, and the first column denotes from which experiment each male belongs. Each signal trait is in its own column.
DOI: 10.5061/dryad.51j99/1
title: Genotyping_data_Hyperparasitoid_and_host_butterfly
DOI: 10.5061/dryad.61jq1/1
title: seed-add-data-output-file-descriptions

description: Description of remaining data files.  Additional publication associated with these data :  Brandt, Angela J., and Eric W. Seabloom. "Regional and decadal patterns of native and exotic plantcoexistence in California grasslands." Ecological Applications 21.3 (2011): 704-714.
DOI: 10.5061/dryad.61jq1/2
title: seed-add-data-output-biomass
DOI: 10.5061/dryad.61jq1/3
title: seed-add-data-output-block-soils

description: Contains data on soil chemistry of each block
DOI: 10.5061/dryad.61jq1/4
title: seed-add-data-output-full-plant-biomass-noseed
DOI: 10.5061/dryad.61jq1/5
title: seed-add-data-output-full-plant-cover
DOI: 10.5061/dryad.61jq1/6
title: seed-add-data-output-full-plant-cover-noseed
DOI: 10.5061/dryad.61jq1/7
title: seed-add-data-output-plot-utms
DOI: 10.5061/dryad.61jq1/8
title: seed-add-data-output-taxa-table-biomass

description: Contains data on each individual taxa in the biomass data set
DOI: 10.5061/dryad.6g6mj/1
title: HDY-15-OR0229RR

description: Archived data for Riquet F, Le Cam S, Fonteneau E, & Viard F, "Moderate genetic drift is driven by extreme recruitment events in the invasive mollusk Crepidula fornicata", Heredity.
The file HDY-15-OR0229RR is in Excel format containing microsatellite allele size data in sheet 1 entitled “microsatellite".
Columns are headed as follow: the sampling year and individual code followed by either the 15 microsatellite allele sizes (one column for one locus and each allele is coded in 3-digit).
DOI: 10.5061/dryad.6r40g/1
title: RedColobus_MHCI_fasta
DOI: 10.5061/dryad.7h3v1/1
title: reid_openscience_data

description: These cytokine data are based on total RNA samples taken from caecal tissue of commercial broilers, which were held under laboratory conditions. The birds were challenged with the pathogen Campylobacter jejuni. The results are expressed as fold changes in corrected target gene expression in infected birds relative to controls.
DOI: 10.5061/dryad.8ns67/1
title: Data_Kapun_JEB

description: Explanation of raw data: We measured development time (measured in h), egg-to-adult survival (proportion viability), chill coma recovery time (measured in h), oxidative stress resistance (age at death, measured in h), triglyceride content (measured in µg), wing size (measured in mm2), femur and tibia length (measured in mm), allometry differences (ratios of femur length to tibia length, (2) femur length versus wing area, and (3) tibia length versus wing area), Jacobian determinant values of wing shape differences (for males and females separately) for isochromosomal lines of D. melanogaster from Florida and Maine that were either homokaryotypic for the In(3R)Payne inverted arrangement or for the standard chromosomal arrangement. Our main goal was to analyze how traits covary with inversion karyotype (inverted versus standard arrangement) and geography (Florida versus Maine). Here we give the raw data for each trait as well as line means (see the worksheet "Summary"). For more details see our paper Kapun et al. (2016, "Parallel effects of the inversion In(3R)Payne on body size across the North American and Australian clines in Drosophila melanogaster", Journal of Evolutionary Biology). For additional details please contact the first author, Martin Kapun (martin.kapunl@unil.ch), or the corresponding author, Thomas Flatt (thomas.flatt@unil.ch).
DOI: 10.5061/dryad.9350r/1
title: Campitelli & Stinchcombe 2014 - Raw data all

description: Contains all of the raw data from this experiment. There are three separate data sheets: Sheet 1 contains raw quantitative phenotypic data (flowering time, growth rate, leaf damage, and fitness), which are described in the paper. Sheet 2 contains leaf temperature data. Sheet 3 contains data on Fv/Fm (photosynthetic efficiency), as well as the corresponding instantaneous leaf temperature measurements, both of which are described in the paper.
DOI: 10.5061/dryad.9bc55/1
title: Brown_Maternal body size influences offspring immune configuration defence in an oviparous snake

description: Family relationships, sex, body size, WBC profiles, WBC concentrations and WBC principal component #1
DOI: 10.5061/dryad.b754g/2
title: Land cover maps for Fagan et al. 2016

description: This contains the edited land cover maps used in Fagan et al. 2016, created from supervised classification of a 1986-2011 Landsat time series (a subset of path 15, row 53).  Please cite Fagan et al. 2013 and Fagan et al. 2016 when using these maps, and see the read me and those publications for further details.
DOI: 10.5061/dryad.c3s62/1
title: Southern right whale population model

description: This is the R script used to conduct the population assessments. Two example calls are also given.
DOI: 10.5061/dryad.c3s62/2
title: Southern right whale catch series for New Zealand and Southeast Pacific

description: Catch series data, as described in Carroll et al. 2014 (PLoS One 9:e93789), for input into population assessment model.
DOI: 10.5061/dryad.d7r4g/1
title: List of fossil hypodigms
DOI: 10.5061/dryad.d7r4g/2
title: Character matrix
DOI: 10.5061/dryad.ff051/4
title: Mitochondrial genome variant and non variant calls

description: This is a .vcf file of all variant and non-variant sites called across 10 or more of the 21 N. crassa strains.
DOI: 10.5061/dryad.fh3h6/1
title: Models and Motion Files Used to Generate Simulations

description: Please read the ReadMe file for detailed description of each file in the archive
DOI: 10.5061/dryad.hp8nv/1
title: Wasp choice assays in windtunnel data

description: The three data sheets show the data for the three types of comparisons that were made: (1) wasp choice when offered acaterpillar infested plant  and a caterpillar + pathogen infected plant (2) wasp choice when offered a healthy plant against a singleattacker infected/infected plant and (3) wasp choice when offered a caterpillar infested plant against a pathogen infected plant.
DOI: 10.5061/dryad.j7t92/1
title: Host selection behaviors of weevils_Lee et al

description: Relative abundance of T. compacta and T. mucorea adults found in Datura wrightii and Nicotiana attenuata populations. T. compacta and T. mucorea adult preference and larval performance.
DOI: 10.5061/dryad.m3p7d/14
title: Sequence alignment files of the V4 hypervariable region of the 16S rRNA used for the phylogenetic analysis

description: This ZIP file contains the FASTA files of the most abundant sequences from the 12 pathogenic OTUs (Bartonella, Borrelia, Ehrlichia, Orientia, Rickettsia, Streptobacillus  and Mycoplasma_OTU_1 to Mycoplasma_OTU_6) and reference sequences from Silva ribosomal database v119 for the same genera.
DOI: 10.5061/dryad.mt240/1
title: Data_all

description: Raw Data
DOI: 10.5061/dryad.p1m52/10
title: Supplementary File S7

description: pdf with Triplec (rooted triple consensus) trees for UCEs. UCE gene trees used to generate the Triplec trees have polytomies. The trees are the same as those used to generate the MRE consensus trees in file S4.
DOI: 10.5061/dryad.p1m52/18
title: Supplementary Figure S4

description: FIGURE S4. Estimates of gene trees for individual UCEs are poorly resolved. Box plot showing the number of resolved branches when those branches with &lt;50% support in ML bootstrap analyses (using the indicated programs) or posterior probabilities &lt;0.5 (using MrBayes). Similar data are shown for the optimal tree identified using GARLI with very short branches collapsed to form a polytomy (‘GARLI-opt’). Numbers of parsimony informative sites per UCE are used to define the sets of UCEs considered (‘all’ indicates that all UCEs with at least one parsimony informative site were included).
DOI: 10.5061/dryad.p1m52/2
title: Supplementary Figure S2

description: FIGURE S2. Number of variable (left) and parsimony informative (right) sites present in each UCE locus
DOI: 10.5061/dryad.p1m52/4
title: Supplementary File S1

description: Microsoft excel file including the unedited UCE locus lengths
DOI: 10.5061/dryad.p1m52/5
title: Supplementary File S2

description: Microsoft excel file including the model fit information for individual UCE loci (after editing)
DOI: 10.5061/dryad.p1m52/6
title: Supplementary File S3

description: Microsoft excel file including model fit information for traditional markers (introns and mitochondrial gene regions)
DOI: 10.5061/dryad.p1m52/7
title: Supplementary File S4

description: pdf with the MRE (‘greedy’) consensus trees of UCE gene tree estimates. UCE gene trees used to generate the MRE consensus have polytomies. The polytomies reflect branches with &lt;50% bootstrap support (RAxML, GARLI, and PhyML), posterior probability &lt;0.5 (MrBayes), or short branches (GARLI optimal trees).
DOI: 10.5061/dryad.p1m52/8
title: Supplementary File S5

description: pdf with MP-EST bootstrap trees for UCEs
DOI: 10.5061/dryad.p1m52/9
title: Supplementary File S6

description: pdf with ASTRAL bootstrap trees for UCEs
DOI: 10.5061/dryad.q8j43/1
title: beach_seine_BACI

description: beach_seine_BACI.csv is a comma-separated file containing data from beach seine surveys of juvenile fish populations from two sites on windward side of Oahu, Hawaii
DOI: 10.5061/dryad.qs626/1
title: PONE-D-14-48547R2_DATA

description: Excel workbook containing reported data for naive and chronic constriction injury (CCI) experimental groups.  Data are organized into 6 worksheets that correspond to manuscript Figures 2-5, S1, and S2.
DOI: 10.5061/dryad.r2250/1
title: Fenberg_et_al.

description: Sheet1: Male and Female wing length measurements and physical variables: mean, minimum, maximum temperature data and rainfall for March-September for the years of collection.  Sheet2: 10th percentile and median collection dates and physical variables: mean, minimum, maximum temperature data and rainfall for March-September for the years of collection.
DOI: 10.5061/dryad.rc2mp/1
title: Alignment of the sequences