cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fc384rk/2
title: - HDY-18-AO311  Back colour morph scores

description: Excel spreadsheet file containing back colour morph scores recorded for individual birds at the time they were first trapped and also for all subsequent field observations made on that individual. Each row represents data for an individual bird. Column 1 “territory_code” = code of social territory group to which individual bird was a member; Column 2 “ind_code” = code number of individual bird; Column 3 “Notes_when_trapped” = data on age, sex and back colour morph score recorded when bird was first trapped and banded (**see key below); “Average_back_score” = mean back colour morph score across all observations of an individual bird; “back_score_when_trapped” = back colour morph score recorded when bird was trapped and in the hand; “back_scores_when_sighted” = remaining values in row represent back colour morph scores recorded for subsequent field observations of that individual. Number of observation vary across individuals.

**key to “Notes when trapped”: This code contains information on age, sex and back colour morph score. The letter represents age and sex (if adult) i.e. C = chick; J = juvenile (sometimes recorded as “S” subadult); M = adult male; F = adult female. The number represents the back colour morph score recorded when bird was trapped and in the hand (see Supplementary File 1 for information on back colour morph score coding). For example, “C1” means a chick with back colour morph score of 1.
DOI: 10.5061/dryad.fc384rk/3
title: HDY-18-AO311 Back colour morph scores for genetically assigned family groups

description: Excel spreadsheet file containing back colour morph scores for family groups where chicks have a genetically assigned mother and father. Column 1 “territory_code” = code of social territory of family group; Column 2 “parent_midP” = mean back colour morph score of mother and father; Column 3 ”mom_BC” = back colour morph score of mother; Column 4 “dad_BC” = back colour morph score of father; Column 5 “#full_sibs” = number of full sib offspring assigned to mother and father combination; Column 6 “chick_BC” = back colour morph score of individual chick; Column 7 “mean_sibs_bc” = mean back colour morph score across full sibs assigned to mother and father combination; Column 8 “sibs_BC_SD” = standard deviation of back colour morph score across full sibs assigned to mother and father combination; Column 9 “unique_identifier” = unique identifier for family group.
DOI: 10.5061/dryad.fc384rk/4
title: HDY-18-AO311 animal model R script

description: Script containing R commands used for running animal models using R package MCMCglmm. Requires libraries: MCMCglmm, pedigree, MasterBayes. Associated input data required is in files “pedigreetxt.txt” (see File 5) and “phenotypestxt.txt” (see File 6).
DOI: 10.5061/dryad.fc384rk/5
title: pedigreetxt

description: Text file containing data on pedigree relationships among individual birds used for calculating heritability using animal models (see File 4 animal model R script). This file is required input data for running animal models.
DOI: 10.5061/dryad.fc384rk/6
title: phenotypestxt

description: Text file containing data for individual birds on back colour morph score “BC”,   year of birth i.e. cohort “YEAROFBIRTH”, and territory membership i.e. social group “TERRITORY”.  This file is required input data for running animal models (see File 4 animal model R script).
DOI: 10.5061/dryad.fk52454/1
title: Capture-recapture dataset

description: Data on date of birth, data of death, and lifetime recaptures in a wild population of the field cricket Gryllus campestris with sex and population sex ratio as covariates
DOI: 10.5061/dryad.fk52454/2
title: PhenotypicSenescence

description: Data on male calling activity with age for a wild population of Gryllus campestris with sex ratio as a covariate
DOI: 10.5061/dryad.j1st8p8/1
title: Peters et al. Data

description: Parasite data for Camarhynchus parvulus, Camarhynchus pauper and their hybrids.
Y (trait C) is the number of days the nestlings survived, Y (trait B) is the total number of Philornis downsi per nest. Ring number refers to the individual numbered aluminum rings the birds are banded with. Individual membership coefficient q(i) is the genetic membership coefficient derived from Bayesian clustering analysis of microsatellite data. Nest height is the height of the nest. Brood size is the maximum number of nestlings per nest. Total number of P. downsi/nest denotes the total number of P. downsi larvae, pupae and puparia per nest. Hybrid index refers to the degree of genetic admixture of the male and has been calculated using the individual membership coefficient. Nest ID is a unique number given to each nest for analyses purposes.
DOI: 10.5061/dryad.jq41758/1
title: Data-JEcol-2018-0401

description: Data from: Tree species diversity promotes litterfall productivity through crown complementarity in subtropical forests. Lists the variables used in structural equation models.
DOI: 10.5061/dryad.rb1bt3j/13
title: File S13. A fasta alignment of G2/Jockey-3 sequences from different contigs and outgroup species

description: We extracted the G2/Jockey-3 sequences based on Repeatmasker annotations and custom scripts. We then aligned and manually inspected G2/Jockey-3 sequences using Geneious v8.1.6.
DOI: 10.5061/dryad.rb1bt3j/14
title: File S14. The newick consensus tree of IGS sequences inferred using RAxML

description: We constructed maximum likelihood phylogenetic trees for IGS using RAxML v.8.2.11 with parameters “-m GTRGAMMA -T24 -d -p 12345 -# autoMRE -k -x 12345 -f a”.
DOI: 10.5061/dryad.rb1bt3j/15
title: File S15. The newick consensus tree of G2/Jockey-3 sequences inferred using RAxML

description: We constructed maximum likelihood phylogenetic trees for G2/Jockey-3 using RAxML v.8.2.11 with parameters “-m GTRGAMMA -T24 -d -p 12345 -# autoMRE -k -x 12345 -f a”.
DOI: 10.5061/dryad.rb8hr57/1
title: Predictive Model Data

description: Observation data collected from caribou calf mortality locations used in a generalized boosted tree model to predict the predator species.
DOI: 10.5061/dryad.rb8hr57/2
title: Cox Regression Model Data

description: Data from collared caribou calves used in a Cox proportional hazards model to identify differences in the intrinsic traits of calves killed by black bears versus coyotes.
DOI: 10.5061/dryad.s437221/1
title: night_and_day_activity_cage_change_III-Weekly

description: raw data in csv
DOI: 10.5061/dryad.s437221/2
title: night_and_day_activity_SOD_control_group_CNR

description: raw data in CSV
DOI: 10.5061/dryad.s437221/3
title: night_and_day_activity_SOD_control_group_JAX

description: raw data in CSV
DOI: 10.5061/dryad.sm76ms5/1
title: Experiment 1 recruitment data

description: Number of recruits recorded in each plot for Experiment 1. These data were used for Figures 3 - 5.
DOI: 10.5061/dryad.sm76ms5/2
title: Experiment 1 R script

description: R script used to analyse the data from Experiment 1 and produce Figures 3 - 5.
DOI: 10.5061/dryad.sm76ms5/3
title: Experiment 2 recruitment data

description: Number of recruits recorded in each plot for Experiment 2. These data were used for Figures 6 & 7.
DOI: 10.5061/dryad.sm76ms5/4
title: Experiment 2 R script

description: R script used to analyse the data from Experiment 2 and produce Figures 6 & 7.
DOI: 10.5061/dryad.t0p2f2c/10
title: paml_lws_alignment

description: Alignment of LWS opsin sequences used for paml analysis.
DOI: 10.5061/dryad.t0p2f2c/11
title: paml_rh1_alignment

description: Alignment of RH1 opsin sequences used for paml analysis.
DOI: 10.5061/dryad.t0p2f2c/12
title: paml_rh2a-1_alignment

description: Alignment of RH2A-1 opsin sequences used for paml analysis.
DOI: 10.5061/dryad.t0p2f2c/13
title: paml_rh2b-1_alignment

description: Alignment of RH2B-1 opsin sequences used for paml analysis.
DOI: 10.5061/dryad.t0p2f2c/5
title: Apogon_genediversity_RH2As

description: RH2A opsin gene alignments for amino acid by amino acid assessment of sequence diversity.
DOI: 10.5061/dryad.t0p2f2c/6
title: Apogon_genediversity_RH2Bs

description: RH2B opsin gene alignments for amino acid by amino acid assessment of sequence diversity.
DOI: 10.5061/dryad.t0p2f2c/7
title: Apogon_genediversity_SWS2As

description: SWS2A opsin gene alignments for amino acid by amino acid assessment of sequence diversity.
DOI: 10.5061/dryad.t0p2f2c/8
title: apogon_retinal_transcriptome_raw_reads

description: Total numbers of raw reads that mapped to the species specific opsin gene sequences for all used samples.
DOI: 10.5061/dryad.t0p2f2c/9
title: Apogon_opsin_expression

description: R-script used to convert read numbers to relative gene expression.
DOI: 10.5061/dryad.t50863s/1
title: Hydrology and vegetation
DOI: 10.5061/dryad.000mn47/3
title: Measurements_intervention_period_EMR

description: This dataset contains every measurement of vital sign(s) recorded in the electronic medical record during the intervention period.
DOI: 10.5061/dryad.000mn47/4
title: Measurements_intervention_period_EWS_system

description: This dataset contains every measurement of vital sign(s) recorded in automated EWS system during the intervention period.
DOI: 10.5061/dryad.07h0n14/1
title: 1_AHA_Genomic_datazip

description: 1. AHA Genomic Data for Pseudoxyrhophiinae and outgroups.
DOI: 10.5061/dryad.07h0n14/2
title: 2_Phylogenies_comparative_data

description: Includes the following files:
BAMM_control.txt
BioGeoBEARS
Code_Match_Nodes_Dates_Among_Methods.R
Comparative_Phylo_Table_AICc
Conversions_for_732_Tree_Tips.txt
Ecological_data_w_outgroups.txt
Locus_Models_372_individuals.txt
Partitions_models_732_IQ_Tree.txt
Tree_Astral_130_taxa
Tree_Astral_II_732
Tree_Beast_dated_130_not_Burned_in_R
Tree_CMOS_alignment.phy
Tree_CMOS_phy.tre
Tree_COI_alignment.phy
Tree_COI_phy.tre
Tree_concat_sanger_alignment.phy
Tree_concat_sanger_tree.tre
Tree_Dated_Point_PL_Astral_topology_130
Tree_Dated_Raxml_BootStrap_Point_tree_130
Tree_DatedPLTREE_Astral_Topology_Fitted_Raxml_732
Tree_IQ_Boot_SH_130.treefile
Tree_IQ_Tree_Concatenated_Partitioned_732_tips.treefile
Tree_IQTree_130_Conca_Partitionedt
Tree_MCMC_Dated_tree.txt
Tree_mcmc_rate_gram.txt
Tree_MG_ASTRAL_130_multi_individual_IQ_Trees
Tree_NAV5_alignment.phy
Tree_NAV5_phy.tre
Tree_PL_Dated_IQ_Bootstraps_130_root_edge
Tree_PLTree_Dated_1000_IQ_BS_130_Taxa_Tree_Annotator
Tree_RAG2_alignment.phy
Tree_RAG2_Phy.tre
Tree_RAxML_bestTree_732_with_partitions_raxml
Tree_RF_Comparisons.xlsx
        Tree_SVD_130_taxa.tre
DOI: 10.5061/dryad.07h0n14/3
title: 3_Code

description: Includes the following files:
Code_Add_Tips_Test_Diversification_TESS.R
Code_BPP_Dater.R
Code_BPP_Maker.R
Code_Character_Reconstruction.R
Code_Match_Nodes_Dates_Among_Methods.R
Code_Morlon_Model_Diversification.R
Code_Reprojection_species_points.R
Code_TESS_COMET_Modified.R
DOI: 10.5061/dryad.07h0n14/4
title: 4_Shapefiles_Species_Coordinates_EcoRegions

description: Includes the following files:
Madagascar terrestrial ecosystem shape files zip.zip
MG_ecoregion_attribute_summary.csv
species_coordinates.csv
Yoder & Nowak (2006) _shapefiles.zip
DOI: 10.5061/dryad.07h0n14/5
title: 5_BPP_by_Genus_Dates

description: 5. BPP Files with results organized by genus
DOI: 10.5061/dryad.07h0n14/6
title: 6_Sample_Data_Names_Sanger_AHA
DOI: 10.5061/dryad.07h0n14/7
title: Additional_Text_Methods
DOI: 10.5061/dryad.29p63mb/11
title: Permanova script

description: Script that uses PERMANOVA to test for differences in taxonomic composition of gut contents between pairs of species, at both order and OTU level of prey
DOI: 10.5061/dryad.29p63mb/12
title: Supplementary analyses script

description: Using datasets controlled for sampling year and elevation, this script calculates the Tukey HSD tests for each of the isotopic variables within each clade (web-builders and Spiny Leg spiders). Results appear in Supporting Information
DOI: 10.5061/dryad.29p63mb/13
title: Web photos 2013, 1 of 2

description: Field photos of webs measured for web architecture analysis
DOI: 10.5061/dryad.29p63mb/14
title: Web photos 2013, 2 of 2

description: Field photos of webs measured for web architecture analysis
DOI: 10.5061/dryad.29p63mb/15
title: Web photos 2014, 1 of 3

description: Field photos of webs measured for web architecture analysis
DOI: 10.5061/dryad.29p63mb/16
title: Web photos 2014, 2 of 3

description: Field photos of webs measured for web architecture analysis
DOI: 10.5061/dryad.29p63mb/17
title: Web photos 2014, 3 of 3

description: Field photos of webs measured for web architecture analysis
DOI: 10.5061/dryad.29p63mb/18
title: Gut content sequence reads

description: Sequence reads for prey DNA in individual spiders used for gut content analysis
DOI: 10.5061/dryad.45177sc/1
title: Flight data from ES -Gal4 x UAS-Kir2.1 flies

description: Data file contains raw flight data collected for fly genotype:Empty Split-Gal4 x UAS-Kir2.1. (Figure7- supplement ). See README for detaails on parsing file
DOI: 10.5061/dryad.45177sc/2
title: ss00096 x Kir data

description: Data contains flight data collected from ss00096  Split-Gal4 x UAS-Kir2.1 flies. Fig. 7 supplement. See README for details on how to parse.
DOI: 10.5061/dryad.45177sc/3
title: ss00096 x UAS-Toy-RNAi

description: Data from ss00096 Split-Gal4 x UAS Toy-RNAi flies. Figure 8b, Figure 8 Supplement. See README for details on how to parse.
DOI: 10.5061/dryad.5db0168/3
title: Nestling data

description: This file includes the data collected on nestlings that were included in the study. The statistical analysis of these data is reported in Table 4 and Table 5 of the published article.
DOI: 10.5061/dryad.5tf55rb/1
title: Get off my back_Biology Letters (all data uploaded to Dryad 2019-01-25)

description: All experimental data.
DOI: 10.5061/dryad.7jd76kq/4
title: S4_Data_xlsx

description: Published data (Fig 1A): Excel spreadsheet containing two separate sheets with data from literature: 1) data extracted from the publications and 2) the original  references.
DOI: 10.5061/dryad.7jd76kq/5
title: S8_Data.xlsx

description: Experimental data on zebra finches. The zebra finches data include five experiments.
DOI: 10.5061/dryad.7jd76kq/6
title: S6_Data_xlsx

description: Models for the unpublished data (Fig 1C): Excel spreadsheet contains 6 separate sheets; each sheet corresponds to a model to estimate the strength of assortative mating.
DOI: 10.5061/dryad.7jd76kq/7
title: S7_Data,xlsx

description: Data for Fig 2: Strength of assortative mating for body size in relation to sample size.
DOI: 10.5061/dryad.7jd76kq/8
title: S5_Data_xlsx

description: Data for Fig 1B: Strength of assortative mating for size as a function of data source.
DOI: 10.5061/dryad.7jd76kq/9
title: PRISMA_literature summary

description: The process of literature investigation.
DOI: 10.5061/dryad.7vf4004/10
title: Dimensionless Ulnar Cross-Sectional Data Species Means

description: Species means for ulnar cross-sectional traits. Values were rendered dimensionless using ulna lengths (see article). Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.7vf4004/11
title: Phylogeny of Sampled Mustelidae.

description: Phylogeny trimmed from Law, C.J., Slater, G.J., & Mehta, R.S. 2018. Lineage diversity and size disparity in 
Musteloidea: testing patterns of adaptive radiation using molecular and fossil-based methods. Syst. Biol. 67: 127-144.
DOI: 10.5061/dryad.7vf4004/12
title: R Code for Analysis of Cross-Sectional Traits

description: R code to run the analyses of our study, from rendering the original data dimensionless to fitting models of trait evolution and testing for allometry. The code uses humeral CSA as an example (this can of course be changed to other traits), being annotated for clarity.
DOI: 10.5061/dryad.7vf4004/13
title: Image Stacks BoneJ Analysis

description: TIFF (originally DICOM) image stacks analyzed with BoneJ for each sampled individual. Notes on institutional abbreviation, orientation of the cranio-caudal axis, and image stacks as increments of bone length included as a PDF document.
DOI: 10.5061/dryad.7vf4004/14
title: BoneJ Measurements

description: Output from image stacks analyzed with BoneJ for each sampled individual. Notes on institutional abbreviation, orientation of the cranio-caudal axis, and image stacks as increments of bone length included as a PDF document.
DOI: 10.5061/dryad.7vf4004/6
title: Dimensionless Humeral Cross-Sectional Data Species Means

description: Species means for humeral cross-sectional traits. Values were rendered dimensionless using humeral lengths (see article). Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.7vf4004/8
title: Dimensionless Radial Cross-Sectional Data Species Means

description: Species means for radial cross-sectional traits. Values were rendered dimensionless using ulna lengths (see article). Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.7vf4004/9
title: Ulnar Cross-Sectional Data All Individuals

description: Raw ulnar cross-sectional trait data for all individuals. Cross-sectional area (CSA), second moment of area (SMA), and section modulus (MOD) respectively have units of mm^2, mm^4, and mm^3. Column names denote increment of bone length (i.e., P5 indicates 5% of bone length, P10 indicates 10% of bone length, etc.).
DOI: 10.5061/dryad.8v0k1j3/1
title: Archive

description: Data files containing behavioral and electrophysiological data
DOI: 10.5061/dryad.bm517c8/1
title: Datasets and scripts used in the analyses of the article

description: This zipped folder contains the datasets, R scripts and command files of all analyses of the article. Some intermediate results are also included.
DOI: 10.5061/dryad.c89124p/1
title: Ewell et al 2019

description: Processed single unit data and LFP recordings from hippocampal area CA1 of control and epileptic Wistar rats. Matab code for detection of high frequency oscillations. See REAME file for detailed description.
DOI: 10.5061/dryad.ck6q52n/2
title: Dociostaurus_hispanicus

description: Genomic dataset (VCF format) obtained with STACKS for all genotyped populations and individuals.
DOI: 10.5061/dryad.ck6q52n/3
title: Dociostaurus_hispanicus_10000loci

description: Input file (STR format) with 10,000 unlinked SNPs used for performing Bayesian clustering (STRUCTURE) and principal component (ADEGENET) analyses.
DOI: 10.5061/dryad.ck6q52n/4
title: Dociostaurus_hispanicus_1250loci

description: Input file (STR format) with 1,250 unlinked SNPs used for obtaining observed summary statistics (ARLSUMSTAT) and performing Bayesian clustering (STRUCTURE) and principal component (ADEGENET) analyses.
DOI: 10.5061/dryad.ck6q52n/5
title: Dociostaurus_hispanicus_MIROC

description: Raster map (TIF format) obtained by projecting the environmental niche model (ENM) from MAXENT to the last glacial maximum (LGM, 21 ka) bioclimatic conditions derived from the MIROC-ESM general atmospheric circulation model.
DOI: 10.5061/dryad.ck6q52n/6
title: Dociostaurus_hispanicus_CCSM

description: Raster map (TIF format) obtained by projecting the environmental niche model (ENM) from MAXENT to the last glacial maximum (LGM, 21 ka) bioclimatic conditions derived from the CCSM4 general atmospheric circulation model.
DOI: 10.5061/dryad.ck6q52n/7
title: Dociostaurus_hispanicus_CURRENT

description: Raster map (TIF format) obtained by projecting the environmental niche model (ENM) from MAXENT to current bioclimatic conditions (WORLDCLIM).
DOI: 10.5061/dryad.ck6q52n/8
title: StairwayPlot

description: Genomic datasets (VCF format, exported from STACKS) and site frequency spectra (SFS) for each studied population and used for demographic reconstructions in STAIRWAY PLOT.
DOI: 10.5061/dryad.ck6q52n/9
title: LAYERS_Splatche2

description: Raster files (ASCII format) used for running demographic and genetic simulations in SPLATCHE2 under each tested model. For model description, see METHODS section and Table 2.
DOI: 10.5061/dryad.d5279d1/1
title: DataSharing_Dryad

description: Data from: One-shot dilation versus serial dilation technique for access in percutaneous nephrolithotomy: a systematic review and meta-analysis .
DOI: 10.5061/dryad.d6k0804/1
title: Ikin_DOI.10.1098.rspb.2019.0114_BirdData

description: Woodland bird presence absence data for site and year combinations.
DOI: 10.5061/dryad.d6k0804/2
title: Ikin_DOI.10.1098.rspb.2019.0114_TraitData

description: Ecological traits assigned to each bird species.
DOI: 10.5061/dryad.d6k0804/3
title: Ikin_DOI.10.1098.rspb.2019.0114_SiteData

description: Site attributes and species diversity data.
DOI: 10.5061/dryad.dj5f7kc/1
title: Effect sizes of 22 studies included in the quantitative analyses

description: This file presents effect size (i.e. difference between two levels of honey bee densities, as measured by colony densities or flower visitation rates) on the crop productivity variables for one crop. Productivity variable are represented by fruit set, seeds per fruit, yield per plant (Kg) and fruit weight (g).
When a study provided more than two levels of honey bee densities (which occurred in nine of the selected studies), we chose the two most extreme levels of these densities.
"Study details" give the complete references of all the selected studies used in the analyses.
DOI: 10.5061/dryad.fd4j10p/1
title: Martins et al. 2019 First experiment

description: Raw data from Experiment 1 in Martins et al. 2019.
DOI: 10.5061/dryad.g2t6204/1
title: A narrative description of all included studies_Appendix ST6

description: Here is meta data and information on all included studies summarised. Examples of available information are: experimental set-up, time elapsed since intervention, geopgraphical information, scale of study, focal species or relevant species Groups, change of dead Wood amounts and effetcs of intervention.
DOI: 10.5061/dryad.g2t6204/2
title: Extracted data_Appendix ST2
DOI: 10.5061/dryad.j3s5v66/1
title: Babbler Walk descriptive and duration JA

description: Babbler walk signal: descriptive statistic, duration of signalling and response type.
DOI: 10.5061/dryad.j3s5v66/2
title: BW use of gaze alternation

description: Babbler walk: use of gaze alternation
DOI: 10.5061/dryad.j3s5v66/3
title: OP use of gaze alternation

description: Object presentation: use of gaze alternation
DOI: 10.5061/dryad.jn95jm1/1
title: 18S CO1 Concatentated Alignment

description: DNA alignment in FASTA format. Includes 18S and CO1 sequences of all specimens used in the study as well as outgroups. Genbank numbers or specimen numbers are given after species name.
DOI: 10.5061/dryad.jn95jm1/2
title: CO1 Alignment

description: DNA alignment in FASTA format of Cytochrome Oxidase One (CO1) sequences. Data includes partial CO1 sequences from all Microstomidae in study as well as outgroups and was used, specifically, for bPTP analyses.
DOI: 10.5061/dryad.q15pc00/1
title: Scripts for primer design for SNP targets and filtering SNP data

description: This directory contains a folder with scripts to choose targets, and choose and design primers for multiplex PCR. These scripts were used to design primers for 192 SNPs from tigers (Panthera tigris). To begin with, a vcf file is required as input. The nextflow pipeline to LD-prune SNPs from the the input VCF and choose polymorphic and differentiating snps is the first step. These SNPs are submitted to the run_p3 pipeline to design primers. This pipeline selects 50,000 SNPs and outputs a bed file. These are used to design primers and as a final steps, the primers are written out in a format suitable for ordering. In addition to this folder, there is a text file with scripts for calling and filtering SNPs from raw fastq files of data generated by these primers and Illumina sequencing. The fastq files generated using these primers have been submitted to NCBI, accession number 
 PRJNA516037.