cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5t0b8/2
title: Video_S1-Twotubes-Visible

description: Video S1: Two tubes condition—Visible baiting. In the experimental demonstration, E1 lifts up the two tubes, taps them against each other to show they are empty, and then places them in the v-shaped configuration on the ground in front of the occluder. She then picks up a fake fruit with her right hand and appears to place this fruit on the right distal side opening of one of the tubes (baiting hand and side was counterbalanced across monkeys). She then picks up the occluder and walks away so that the monkey can approach; in the real study she moved behind the camera person (E2). In the example response clip, the monkey approaches and looks in the right side. Note that orientation of video switches: in the demonstration it shows the monkey’s perspective, whereas in the example test clip E2 is behind E1 while she does the demonstration.
DOI: 10.5061/dryad.5t0b8/3
title: Video_S2-Twotubes-Hidden

description: Video S2: Two tubes condition—Hidden baiting. In the experimental demonstration, E1 lifts up the two tubes, taps them against each other to show they are empty, and then places them in the v-shaped configuration on the ground in front of the occluder. Before baiting the tubes, she moves the occluder in front of the tubes (from the monkey’s perspective). She then picks up a fake fruit with her left hand (hand counterbalanced across monkeys) and moved it down; the monkey’s view of the baiting event is then blocked by the occluder. She then picks up the occluder and walks away so that the monkey can approach; in the real study she moved behind the camera person (E2). In the example response clip, the monkey approaches and looks in the center opening of the tubes; in this example, the monkey visibly checks both tubes from this center position. Note that orientation of video switches: in the demonstration it shows the monkey’s perspective, whereas in the example test clip E2 is behind E1 while she does the demonstration.
DOI: 10.5061/dryad.5t0b8/4
title: Video_S3-Onetube-Visible

description: Video S3: One tube condition—Visible baiting. In the experimental demonstration, E1 lifts up the single tube and tapes it with her hand to show it is empty, and then places it on the ground with the openings perpendicular to the monkey’s perspective She then picks up a fake fruit with her left hand and appears to place this fruit on the side opening (baiting hand and side was counterbalanced across monkeys). She then picks up the occluder and walks away so that the monkey can approach; in the real study she moved behind the camera person (E2). In the example response clip, the monkey approaches and looks in the left side. Note that orientation of video switches: in the demonstration it shows the monkey’s perspective, whereas in the example test clip E2 is behind E1 while she does the demonstration.
DOI: 10.5061/dryad.5t0b8/5
title: Video_S4-Onetube-Hidden

description: Video S4: One tube condition—Hidden baiting. In the experimental demonstration, E1 lifts up the single tube and tapes it with her hand to show it is empty, and then places it on the ground with the openings perpendicular to the monkey’s perspective. She then picks up a fake fruit with her right hand (hand counterbalanced across monkeys) and moved it down; the monkey’s view of the baiting event is then blocked by the occluder. She then picks up the occluder and walks away so that the monkey can approach; in the real study she moved behind the camera person (E2). In the example response clip, the monkey approaches the center location and looks under the tube. Note that orientation of video switches: in the demonstration it shows the monkey’s perspective, whereas in the example test clip E2 is behind E1 while she does the demonstration.
DOI: 10.5061/dryad.5t0b8/6
title: Video_S5-Exclusion-Interference

description: Video S5: Example Exclusion—Interference. The target monkey is appropriately centered during the experimenter’s demonstration. E1 leaves so the subject can approach, but a larger male approached from the left side of the screen and displaces the target subject to the side before they can make a choice.
DOI: 10.5061/dryad.6d3v0/1
title: OG# to Protein List

description: An excel file listing the protein name, abbreviation, found KEGG function (if known), and the corresponding OG5 number of the alignment for all 58 presence/absence lateral gene transfers found. Each animo acid sequence alignment file is labeled with a unique OG5#.
DOI: 10.5061/dryad.6d3v0/2
title: Topologies with two LGT Events

description: Single gene trees in Newick format for the seven genes found with topologies consistent with two lateral gene transfers.
DOI: 10.5061/dryad.6d3v0/3
title: Presence/absence alignments

description: All 58 laterally transferred presence/absence animo acid sequence alignments found. Files are in text format.
DOI: 10.5061/dryad.701q8/1
title: raw data for meta-analysis of Gibert et al

description: Dataset reporting correlation coefficients between growth and traits from 103 articles published between 1983 and 2014. In total, 551 correlations relations linking growth rate to any of a list of 19 traits across a range of ontogenetic were reported here. Data are variable in multiple ways. Climate zones spanned from temperate regions to tropics. Different experiment types (laboratory, field, plantation or greenhouse), growth measurements and growth form (tree, woody or across growth form) were included. The number of species used for each correlation ranged from 2 to 300 species, with an average of 31.
DOI: 10.5061/dryad.82f5q/23
title: FISH experiments for line N02Y5117 Mace

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail
DOI: 10.5061/dryad.82f5q/24
title: FISH experiments for line N02Y5121

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail.
DOI: 10.5061/dryad.82f5q/25
title: FISH experiments for line N02Y5149

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail
DOI: 10.5061/dryad.82f5q/26
title: FISH experiments for line N02Y5154

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail.
DOI: 10.5061/dryad.82f5q/27
title: FISH experiments for line N02Y5156

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail.
DOI: 10.5061/dryad.82f5q/28
title: FISH experiments for line N02Y5163

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail
DOI: 10.5061/dryad.82f5q/29
title: FISH experiments for line N02Y2016

description: Zip file containing individual tif files of blue (DAPI) green (FITC) and red (Alexa594) fluorescence taken on Zeiss or Nikon epifluorescence microscope. File name give Slide code and probe combination, see FISH experiment file for list and FISH schedule files for more detail.
DOI: 10.5061/dryad.bj254/1
title: Malaria parasite data for Anopheles gambiae

description: This data file includes data on malaria infection in individual mosquitoes.  For each temperature treatment we dissected midguts (on day 7 post infection) or salivary glands (day 15 post infection) from 20 individual mosquitoes within each temperature treatment if numbers permitted.  The "Oocyst_data" tab includes data on whether or not a mosquito had oocysts on its midgut and overall oocyst burden.  The "Sporozoite_data" tab includes information on whether or not an individual mosquito had sporozoites in its salivary glands.  The "Data codes" tab includes information describing each column and how it is coded across both the "Oocyst_data" and "Sporozoite_data" tabs.
DOI: 10.5061/dryad.bj254/2
title: Malaria parasite data for Anopheles stephensi

description: This data file includes data on malaria infection in individual mosquitoes.  For each temperature treatment we dissected midguts (on day 7 post infection) or salivary glands (day 15 post infection) from 20 individual mosquitoes within each temperature treatment if numbers permitted.  The "Oocyst_data" tab includes data on whether or not a mosquito had oocysts on its midgut and overall oocyst burden.  The "Sporozoite_data" tab includes information on whether or not an individual mosquito had sporozoites in its salivary glands.  The "Data codes" tab includes information describing each column and how it is coded across both the "Oocyst_data" and "Sporozoite_data" tabs.
DOI: 10.5061/dryad.bn46h/1
title: Invertebrate drift

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.bq135/1
title: Raw timeseries data_annotated

description: This file contains the timeseries for eggs, juveniles, adult males and adult females mites from 60 replicate populations exposed to three environmental variation treatments (constant, randomly variable and periodically variable) and four harvesting treatments (unharvested, juvenile harvested (40%/week), adult harvested (40% week) or threshold harvested ( all above 60% pop size). Each treatment combination has six replicate population tubes. The details are in comment boxes in the attached excel file. Body size data for constant and period environment populations are also supplied in sheet 2 (i.e. data from Figure 4 in associated publication)
DOI: 10.5061/dryad.dj82k/1
title: PURCvsSanger_trees

description: Contains two files (a nexus alignment and a tree file) of the comparison of the alleles inferred by PURC versus those from cloning and Sanger sequencing. See figure S1 in the paper.
DOI: 10.5061/dryad.dj82k/2
title: all_regimes_trees

description: For each of the four loci, contains a tree that includes all the alleles inferred by each of the six analysis regimes.
DOI: 10.5061/dryad.dj82k/3
title: barcodes_pacbio

description: The 48 16-base barcodes designed by Pacific Biosciences.
DOI: 10.5061/dryad.dj82k/4
title: PURC_molecularlab_tracking

description: An example spreadsheet for sample tracking and library preparation (amplicon standardization, etc.)
DOI: 10.5061/dryad.dj82k/5
title: vouchertable_allruns

description: Voucher data for all three PacBio sequencing runs discussed in the manuscript.
DOI: 10.5061/dryad.dj82k/6
title: scripts_for_figures

description: Python and R scripts used to generate the figures.
DOI: 10.5061/dryad.dj82k/7
title: extract_specific_accessions

description: This script finds the "allele" sequences for a given set of accessions, from all regimes and runs provided. It can be useful to look at the effect of different analysis regimes -- less overwhelming than trying to look at huge trees of all accessions at once. Alternatively, use the merge_allRegimes_and_align.sh bash script to get all the sequences, from all the accessions.
DOI: 10.5061/dryad.dj82k/8
title: merge_allRegimes_and_align

description: Shell script to merge the inferred alleles from multiple analyses (ie, different analysis regimes) into a single alignment.
DOI: 10.5061/dryad.f4857/1
title: Data matrix: Acropyga_UCE-944-matrix
DOI: 10.5061/dryad.f4857/2
title: RAxML Besttree generated from Acropyga_UCE-944-matrix
DOI: 10.5061/dryad.f4857/3
title: Data matrix: Acropyga_UCE-100-best-matrix used for BEAST analyses
DOI: 10.5061/dryad.f4857/4
title: BEAST chronogram generated from Acropyga_UCE-100-matrix.
DOI: 10.5061/dryad.f4857/5
title: BEAST xml file used for analysis of Acropyga_UCE-100-matrix
DOI: 10.5061/dryad.fh0mc/1
title: Code for R simulations

description: These R scripts can be run to perform the power simulations that were used to generate Figures 2, 3, and 4 in the manuscript. NOTE: phylocurve version 2.0.0  or higher must be installed. To install the latest version of phylocurve, run the following code after loading the package 'devtools': install_github("ericgoolsby/phylocurve",dependencies =TRUE)
DOI: 10.5061/dryad.tm65d/1
title: Boa&Ophisaurus

description: Annotations of the coding sequences of three voltage-gated sodium channel genes (SCN4A, SCN8A, and SCN9A) from two species (Boa constrictor and Ophisaurus gracilis) in GenBank format.
DOI: 10.5061/dryad.tm65d/2
title: ReptileTimecal

description: Reptile phylogeny with time calibration in Newick format.
DOI: 10.5061/dryad.115m1/2
title: Dryad_BMC

description: This file contains : (i) information about the host range of each investigated/Eupelmus/ species including new records with regard to Al Khatib et al. - Systematic Entomology - 2014 ; (ii) information about the relationships between some morphological measurements and their ratios (two independent datasets).
DOI: 10.5061/dryad.1bv6n/1
title: Ring-width data

description: Yearly ring-width data (mm) for every studied tree
DOI: 10.5061/dryad.1bv6n/2
title: Metadata

description: Characteristics of every studied tree: code, site, species, reference article, contact person, status, age, dbh.
DOI: 10.5061/dryad.3936j/1
title: Eldridge_et_al_echidna_functionality_data

description: The file contains 60 rows of data used in the structural equation modelling. There are two worksheets in the file. The first (SEM) provides the raw data (as well as some log-transformed data used in the SEM) and the second file (SEM_metadata) a description of the data used.
DOI: 10.5061/dryad.3j0gg/1
title: Termite Community Data

description: In this file we present data of termite species per transect and per elevation. We also present the values of the environmental variables used in the study. In the last two spreadsheets we present data of functional distances and functional groups of the termite species found in our study.
DOI: 10.5061/dryad.4384p/1
title: scripts

description: This archive contains scripts that were used to analyze data presented in our manuscript. For phenotypic and genotypic data associated with these scripts please download the "data.zip" archive.
DOI: 10.5061/dryad.4384p/2
title: data - phenotype and genotype tables

description: Contains phenotypic and genotypic data used in our study. Example scripts containing information regarding analyses carried out on these data can be found in the "scripts.zip" archive.
DOI: 10.5061/dryad.5t0b8/7
title: Video_S6-Exclusion-Left

description: Video S6: Example Exclusion—Left. The target monkey watches the experimenter’s demonstration. E1 leaves so the subject can approach, but the subject runs away before approaching to make a choice.
DOI: 10.5061/dryad.5t0b8/8
title: Video_S7-Exclusion-NoApproach

description: Video S7: Example Exclusion—No Approach. The target monkey watches the experimenter’s demonstration. E1 leaves so the subject can approach, but the subject does not approach for more than 1 minute (timed with a stopwatch). Near the end of this time, the subject begins to groom another monkey who sat near them.
DOI: 10.5061/dryad.6p2v0/1
title: Microsatellite genotypes of Thaumeatopoea pityocampa (parental populations and hybrids) simulated from alleles frequencies estimated in STRUCTURE clusters SP and WP

description: The file is organized according to NEWHYBRID format. Individuals codes (first column) describe the genetic class of these simulated genotypes: parental SP (pSPsim), parental WP (pWPsim), F1sim, F2sim, back-cross SP (bcSPsim), back-cross WP (bcWPsim). 1000 genotypes were simulated for each genetic class.
DOI: 10.5061/dryad.6p2v0/2
title: Microsatellite genotypes of Thaumeatopoea pityocampa (parentalpopulations and hybrids) simulated from parental populationstaking intoaccount only SP and WP individuals assigned with STRUCTURE with aq-value &gt;0.9 in their respective cluster

description: The file is organized according to NEWHYBRID format. Individuals codes (first column) describe the genetic class of these simulated genotypes: parental SP (pSPsim), parental WP (pWPsim), F1sim, F2sim, back-cross SP (bcSPsim), back-cross WP (bcWPsim). 1000 genotypes were simulated for each genetic class
DOI: 10.5061/dryad.6qr6j/1
title: Archived data

description: Data used to create Figures 1 through 4. See file: Kline_EA_figure_dataTables_metadata.docx
DOI: 10.5061/dryad.6rn29/1
title: Raw data

description: The file contains raw data from the behavioural and fungal exposure experiments. Each worksheet is labelled with the corresponding experiment and more information about the raw data is given at the top of each worksheet.
DOI: 10.5061/dryad.768vg/1
title: Reflectance of mouth, rictal flange and body skin at the beginning of the treatment with cyproheptadine

description: Spectral reflectance (300nm to 700nm) of three begging-related traits of magpie nestlings: mouth (gape or palate), rictal flange and body skin at the beginning of the treatment with cyproheptadine (nestlings 2–4 days old). Values are means obtained from three replicates and corrected by a triangular smoothing (i.e. a floating mean with weights within a distance of 10nm).
DOI: 10.5061/dryad.768vg/2
title: Reflectance of mouth, rictal flange and body skin at the end of the treatment with cyproheptadine

description: Spectral reflectance (300nm to 700nm) of three begging-related traits of magpie nestlings: mouth (gape or palate), rictal flange and body skin at the end of the treatment with cyproheptadine (nestlings 10–12 days old). Values are means obtained from three replicates and corrected by a triangular smoothing (i.e. a floating mean with weights within a distance of 10nm).
DOI: 10.5061/dryad.768vg/3
title: Irradiance inside 10 active magpie nests

description: Irradiance measurements were performed in 10 active magpie nests between March and April of 2009, and between 09:00am and 11:00am in a magpie population in Guadix (Spain). It was done by placing the probe above the nest cup and pointing vertically toward the dome. Values are means per each nest from three replicates.
DOI: 10.5061/dryad.768vg/4
title: Nestling weights and colour measurements for the three begging-related traits before and after the treatment with cyproheptadine
DOI: 10.5061/dryad.76rd1/1
title: Weir et al. Anadromous body size

description: Average body sizes for male and female salmon across populations
DOI: 10.5061/dryad.76rd1/2
title: Weir et al. Parr maturity

description: Incidence of parr maturity in Atlantic salmon (Salmo salar) and masu salmon (Oncorhynchus masu)
DOI: 10.5061/dryad.bj254/3
title: Mosquito Survival Data

description: This data file includes in the "Survival Data" tab the daily mortality events for the associated infection experiments.  We have recorded number of mosquitoes alive vs. dead each day post-infection with human malaria.  We also followed a blood-fed, uninfected control group to determine if the effects of temperature and diurnal temperature range had a different impact on the daily probability of mosquito survival for P. falciparum infected mosquitoes.  Finally, we also recorded the number of mosquitoes that were dissected for midguts and salivary glands to assess parasite infection so that these cases could be censored in the downstream survival analysis.  The "Data Codes" tab has descriptors for the various column headings and data labels.
DOI: 10.5061/dryad.bn46h/2
title: Activity of individual fish

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.bn46h/3
title: Enclosure scans

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.bn46h/4
title: Substrate estimations

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.bn46h/5
title: Water current velocity measurements

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.bn46h/6
title: Water depth measurements

description: Data collected in the field in 2013. Please see ReadMe file for a description of column headings.
DOI: 10.5061/dryad.d2680/4
title: Data1

description: This file contains 5 columns (variables) x 23956 rows (excluding the first row, which contains the header with the variable names). The data were used to plot the development of DBH (diameter at breast height) inside bark with tree age classified by early growth and colored by lifespan (Figure 1 in Bigler 2016).
DOI: 10.5061/dryad.dj82k/9
title: batch_run_purc

description: Example shell script to run purc_recluster.py multiple times, with different analyses settings.
DOI: 10.5061/dryad.fq22f/1
title: PilakoutaHalfordRaczSmisethAMNAT2016

description: Raw data on the effects of contest experience and contest outcome on female reproductive investment and offspring fitness in the burying beetle Nicrophorus vespilloides.
DOI: 10.5061/dryad.h2m12/1
title: meadows_alldata

description: This file contains the number of field-collected thrips of each species and sex in the different experimental plots, as well as the cover of each Poaceae species.
DOI: 10.5061/dryad.h2m12/2
title: FitnessAssays_All_Data

description: This file contains the number of thrips counted in the experimental mesocosms. Sheets 1 and 4 contain fitness assays on different plant species that were used for Figure 1 of the manuscript. Sheets 2 and 3 contain adaptation assays, measured as numbers of offspring for a single, isolated female of asexual (sheet 2) or sexual (sheet 3) female. These data were used in Figure 3 of the manuscript.
DOI: 10.5061/dryad.h2m12/3
title: Mesocosms_elegans_rufus

description: This file contains the results of the competition experiment used in Figure 2 of the manuscript
DOI: 10.5061/dryad.jr6r5/1
title: Aquatic Ethanol (AE) Metagenome (Illumina reads)

description: Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.
DOI: 10.5061/dryad.jr6r5/2
title: Terrestrial Ethanol (TE) Metagenome (Illumina reads)

description: Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.
DOI: 10.5061/dryad.jr6r5/3
title: Terrestrial Voucher (TV) Metagenome (Illumina reads)

description: Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.
DOI: 10.5061/dryad.jr6r5/4
title: Aquatic Voucher PART 1 (AV) Metagenome (Illumina reads)

description: Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.# this archive was split in 2 files with the unix command$ gzip -c my_large_file | split -b 1024MiB - myfile_split.gz_# to uncompress, use$ cat myfile_split.gz_* | gunzip -c &gt; my_large_file# to uncompress in windows (ensure file parts are in correct order)$ copy /b file_aa + file_ab + file_ac + file_ad filetogether