cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.28sm8.1/14.1
title: Morphological and genomic data for sample species, Excel format

description: Abbreviations: CP, cribriform plate; ORG, olfactory receptor gene.  Body mass estimates are species means. Where sexual dimorphism was present, we considered the sex of individuals when deriving the species body mass.  Individual dog breed body size estimates were averaged to calculate the mean body mass of the dog (Canis familiaris).  References for body mass and ORG data listed below the table.  For cribriform plate surface area data of individual specimens, see table S5.
DOI: 10.5061/dryad.28sm8.1/15.1
title: Morphological and genomic data for sample species, .csv format

description: Abbreviations: CP, cribriform plate; ORG, olfactory receptor gene.  Body mass estimates are species means. Where sexual dimorphism was present, we considered the sex of individuals when deriving the species body mass.  Individual dog breed body size estimates were averaged to calculate the mean body mass of the dog (Canis familiaris).  References for body mass and ORG data listed below the table.  For cribriform plate surface area data of individual specimens, see table S5.
DOI: 10.5061/dryad.28sm8.1/17.1
title: Assembly statistics for genome assemblies from which olfactory receptor gene counts were extracted; .csv format

description: Abbreviations, BGI: Beijing Genomics Institute; BCM: Baylor College of Medicine; Broad: Broad Institute; ICGSC: International Cat Genome Sequencing Consortium; WU: Washington University. Sources of data: NCBI Assembly, University of California Santa Cruz Genome Browser, Genome Reference Consortium.
DOI: 10.5061/dryad.28sm8.1/22.1
title: Sources and morphological data for felid species; Excel format

description: Museums and collections are as follows: FMNH: Field Museum of Natural History; LACM: Museum of Natural History of Los Angeles County; LACMRLP: Rancho La Brea Tar Pits; MMNH: James Ford Bell Museum University of Minnesota, Minneapolis; UCLAEEB: University of California Los Angeles Department of Ecology and Evolutionary Biology.  aEstimated body masses (in kg) are from [1] except for two species, Felis catus [9] and Smilodon fatalis [19] (see table S8 references).
DOI: 10.5061/dryad.28sm8.1/7.1
title: Key resource table, Excel format

description: Key resource table for sample specimens, CT scanning machines and facilities, and digital imaging software.
DOI: 10.5061/dryad.28sm8.1/9.1
title: Cribriform plate surface area data for individual specimens, Excel format

description: Identification, source, sex and morphological data for sample species.  Abbreviations, AMNH: American Museum of Natural History.  CMNH: Cleveland Museum of Natural History. DLC: Duke Lemur Center. DUPC: Duke University Primate Center. IZCAS: Institute of Zoology of the Chinese Academy of Sciences. LACM: Natural History Museum of Los Angeles County. LACMRLP: Rancho La Brea Tar Pits. MVZ: Museum of Vertebrate Zoology. SDSNH: San Diego Society of Natural History. UCLA: Dickey Collection at the University of California Los Angeles. UCLAEEB: UCLA Department of Ecology and Evolutionary Biology. USNM: National Museum of Natural History. UTO: University of Texas Austin. TMM: Texas Memorial Museum. *The presence of a cribriform plate in the ethmoid bone of the bottlenose dolphin (Tursiops truncatus) could not be established in this study.
DOI: 10.5061/dryad.33bf108/1
title: Trait data

description: Venation, trait, and climate data for tree species on an Andes-Amazon transect in southeastern Peru (CHAMBASA project).
DOI: 10.5061/dryad.3jj92rq/1
title: jae-f-database

description: A global database and ‘state of the field’ review of research into ecosystem engineering by land animals.
DOI: 10.5061/dryad.470pd/1
title: Dryad.tgz

description: You can untar and unzip with tar -xzvf Dryad.tgz. This will create one folder called Dryad. In that folder there are four separate folders. The first contains the 305 species tree and orthologs used to create the tree, seen in figure 3 of the publication. The Next is the Assemblies, these are in both PEP and CDS, they are associated with their keys but those can be changed using the NameKey.txt file. The next folder is FamilyAnalyses, this contains the orthologs, conflict analysis and species tree analyses for the five major families analyzed. The final folder is programs which contains a set of scripts used for the analysis.
DOI: 10.5061/dryad.4bm23/6
title: Leishmania naiffi LnCL223 bin contig annotation files

description: Leishmania naiffi LnCL223 bin contig annotation files
DOI: 10.5061/dryad.4bm23/7
title: Figure-1-high-resolution

description: Figure-1-high-resolution
DOI: 10.5061/dryad.4bm23/8
title: Supplementary-Tables

description: Supplementary-Tables
DOI: 10.5061/dryad.4bm23/9
title: Supplementary-Data

description: Supplementary-Data
DOI: 10.5061/dryad.4m281/6
title: tabulate_parsimony_shift_counts R script

description: script that uses pars.shift.counts (in character mapping R data file) to tabulate proportion of old vs. young splits associated with host shift or regional dispersal, and draw barchart as in Fig. 4A; can also tabulate by clade
DOI: 10.5061/dryad.4m281/7
title: mpr_shuffle R script

description: script that performs permutation to test whether observed difference between proportion of old vs. young splits associated with host shifts or regional dispersal is greater than expected under a null distribution of shuffled character states
DOI: 10.5061/dryad.4m281/8
title: summarize_simmap_results R script

description: script that summarizes host shift information from set of simmap reconstructions (used to create fig. 4B) using data in character mapping R data file
DOI: 10.5061/dryad.57h24/1
title: Predator Sample by OTU

description: Sequence counts in individual scat samples matching reference sequences of extant carnivores in the Santa Cruz Mountains. Scat samples were collected by citizen scientists on trails in seven Midpeninsula Open Space preserves and were all less than one week old.
DOI: 10.5061/dryad.57h24/2
title: Prey Sample by OTU

description: Sequence counts in individual scat samples matching reference sequences of extant vertebrates (potential prey species of mesocarnivores) in the Santa Cruz Mountains. Scat samples were collected by citizen scientists on trails in seven Midpeninsula Open Space preserves and were all less than one week old.
DOI: 10.5061/dryad.5bg1dt3/1
title: Link et al._2018

description: R.code for all analyses and graphics - code's data frames are linked to Github for ease of use.
DOI: 10.5061/dryad.5bg1dt3/2
title: Berberis.drymass.lm_Link et al. 2018

description: Dry mass and original (wet) mass of Berberis stems - 10 cm sections of varying stem diameters (1-25 cm).
DOI: 10.5061/dryad.5bg1dt3/3
title: Seedling.species.type_Link et al. 2018

description: Native tree seedlings densities observed and Berberis stem counts and predicted dry mass - 1 m^2 plot sizes.
DOI: 10.5061/dryad.5bg1dt3/4
title: Seedling.total_Link et al. 2018

description: Total tree seedling densities and Berberis stem counts and predicted dry mass - 1 m^2 plot sizes.
DOI: 10.5061/dryad.88ks4g5/1
title: Salamander Dataset

description: Salamander Dataset used for the real data analysis. It includes the field detection data, as well as the confirmatory data (from DNA analyses), for both species: P. cinereus and P. Shenandoah.
DOI: 10.5061/dryad.c76pf34/1
title: 2012-2016 MSAT Genotypes

description: Microsatellite genotypes of offspring and adult variegated fairy-wrens
DOI: 10.5061/dryad.c76pf34/2
title: 2012-2016 SNP Genotypes

description: SNP genotypes of offspring and adult variegated fairy-wrens
DOI: 10.5061/dryad.fh42m5f/1
title: Nomads

description: Demographic data for all nomads entering the study area, residents (1) and non-residents (0). File also includes environmental variables.
DOI: 10.5061/dryad.fh42m5f/2
title: Nomad Immigration

description: Per year immigration of male lions into the Serengeti study area
DOI: 10.5061/dryad.fh42m5f/3
title: Resident Takeovers

description: Per year turn over of resident male lion coalitions in the Serengeti
DOI: 10.5061/dryad.fh42m5f/4
title: CubRecruitment

description: Lion cub survival.
DOI: 10.5061/dryad.fn1q473/1
title: Number of fathers within a litter and CV of fetus mass

description: The first column corresponds to the estimated number of fathers within a litter. The second column corresponds to the coefficient of variation of fetus mass within a litter.
DOI: 10.5061/dryad.gv395hd/1
title: R code for simulations

description: The R code file is commented and can be used to simulate data, illustrated in figures in the publication: Zajitschek, F. and T. Connallon. Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness. 2018. Evolution.
DOI: 10.5061/dryad.h508g38/1
title: Souissi_Final_working_dataset

description: The  SNP dataset used in all analysis except newhybrids analysis . The VCF file contains 10758  SNPs typed in 161 individuals.Only one single SNP for each pair of RAD loci associated with the same restriction site (i.e. within a distance less than 200 bp) was kept.
DOI: 10.5061/dryad.h508g38/2
title: Souissi_AEG_SEN_JAFS

description: The JAFS dadi input file for Solea senegalensis and Solea aegyptiaca
DOI: 10.5061/dryad.h508g38/3
title: Souissi_DADI_input_to_generate_fs

description: Dataset from Souissi_VCF_dadi_analysis used as input in DADI to generate the FS file
DOI: 10.5061/dryad.h508g38/4
title: Souissi_VCF_DADI_analysis

description: The  SNP dataset used in DADI analysis . The VCF file contains 10758 SNPs typed in 94 individuals.Only one single SNP for each pair of RAD loci associated with the same restriction site (i.e. within a distance less than 200 bp) was kept.
DOI: 10.5061/dryad.hg2g312/1
title: Calf Clinical Data

description: Sheet S1: Fecal oocyst shedding and severity of diarrhea for infected calves, including data on housing system, sample type, and sample time for days 0-10 post-infection. Sheet S2: Clinical outcomes for days 0-10 post-infection. Sheet S3: Calf body weights and calculation of average daily weight gain. Sheet S4: Frequency and type of morbidities and treatments for each calf. Sheet S5: Data Dictionary
DOI: 10.5061/dryad.jv3gm12/1
title: Garces-Restrepo et al 2018. Sloth_Natal_dispersal

description: Resigths data of Sloths in an agroecosystem in Costa Rica, during July 2012 to December 2016.
DOI: 10.5061/dryad.jv3gm12/2
title: survival data juvenile sloths

description: Juvenile sloths survival, Encounter occasions=54, twospecies: bradypus=10, choloepues=01, states: Dependent=m, independent=I, dispersing=D. Each column corresponds to whether the individual was detected in a month, the history of capture began in July 2012 and ended in December 2016. The months of February, March, September and October are considered dry seasons and the rest of the months wet season.
DOI: 10.5061/dryad.qf737c2/1
title: Species occurrence data

description: Occurrence points (geographic coordinates) of termite Constrictotermes cyphergaster and eigth plants (Annona crassiflora, Aspidosperma pyrifolium, Caesalpinia pyramidalis, Caryocar brasiliense, Croton blanchetianus, Plathymenia reticulata, Pilosocereus gounellei, Qualea grandiflora
DOI: 10.5061/dryad.qf737c2/2
title: Principal Coordinates of Neighbour Matrices

description: Suitabilities of the models generated by MaxEnt
DOI: 10.5061/dryad.qf916/1
title: sdRADseq vcf subset

description: This is a vcf file containing the individuals genotyped using sdRADseq, analyzed separately. Only the pruned set of loci used in the analysis are contained in this file.
DOI: 10.5061/dryad.rd736/1
title: Main dataset

description: This dataset contains the true number of birds for each colony, as well as the ground counts, RPA-derived manual counts and RPA-derived semi-automated counts for each colony. This dataset was used for all analyses.
DOI: 10.5061/dryad.rd736/3
title: RPA-derived imagery of bird colonies

description: Compressed folder containing photographs of each colony (n=10) at each sample height (n=4).
DOI: 10.5061/dryad.rd736/4
title: R script for analyses

description: Script used to analyse ground counts, RPA-derived manual counts and RPA-derived semi-automated counts.
DOI: 10.5061/dryad.tq3m0/1
title: Diniz_et_al_2018_Duet_seasonality_Horneros

description: This file includes data about seasonal variation in territorial interactions and in many song traits of individuals and pairs of the Rufous Hornero.
DOI: 10.5061/dryad.v17p8m4/1
title: Tewes_Mueller_Neobiota_rawdata

description: raw data for NeoBiota manuscript by Tewes & Müller
DOI: 10.17632/9f2pjx29cj.1
title: Data for: Systemic administration of scAAV9-IGF1 extends survival in SOD1 G93A ALS mice via inhibiting p38MAPK and JNK-mediated apoptosis pathway

description: These are files from Statistical software
DOI: 10.17632/g3hhczkc44.1
title: Data for: The effects of zinc supplementation on primary human retinal pigment epithelium

description: These table contain the fill proteomics data for the apepr by Po-Jung at al submitted JTEMB.
DOI: 10.5061/dryad.32v7b/1
title: TableS9-InVivoData-2017-12-11

description: Plasma concentration vs. time toxicokinetic data collected for a variety of chemicals in Sprague-Dawley rat.
DOI: 10.5061/dryad.32v7b/2
title: TableS11-TKSummaryStats-2017-12-11

description: Model TK statistics (Cmax, AUC) for in vivo rat studies.
DOI: 10.5061/dryad.32v7b/3
title: TableS10-PropertiesandEstimates-2017-12-11

description: Estimated TK properties (e.g., Volume of Distribution, Fraction bioavailable) for in vivo rat studies.
DOI: 10.5061/dryad.3340hc4/1
title: Rockers et al (2018)

description: Data from 377 caregiver-child pairs collected at baseline (2015) and year two follow-up (2017) of a cluster-randomized controlled trial conducted in Zambia. Includes household demographics, child anthropometry including stunting status, and child development scores using Bayley Scale for Infant and Toddler Development, 3rd Edition (BSID-III).
DOI: 10.5061/dryad.3q67545/1
title: Villar&Naya_DatasetS1

description: Body mass, year of collection and geoprhafic coordinates for 17 rodents speces (taken from Arctos database).
DOI: 10.5061/dryad.43cp320/2
title: Genomic sequence variation in wild social amoebas

description: Archive of the variant call format files used to generate the
population genetic data.
DOI: 10.5061/dryad.752153b/1
title: Radiomics.PET.features

description: PET features used in model development: imaging features computed for tumor (Tumor) and merging structure including involved lymph nodes (Nodes). Survival information (in years) is available for all patients under analysis (status: 1 - deceased, 0 - alive).
DOI: 10.5061/dryad.752153b/2
title: PET.Nodes.Features

description: This file comprises the data used in the sub-analysis as described in the "Supporting Information - Feature Selection" file.
DOI: 10.5061/dryad.873bn/1
title: Fold change calculations for Mouse XL Cytokine Arrays

description: Each tab contains raw densitometry data for Mouse XL Cytokine arrays performed on samples from skin and soft tissue infection, 7 day mesh infection, or 21 day mesh infection. Fold changes for each of three array sets per infection (infected/uninfected) were used to calculate the mean log2 fold change for each cytokine and chemokine(reported in Supplemental Table 2 of paper).
DOI: 10.5061/dryad.873bn/2
title: Sample arrays

description: Representative Mouse XL cytokine arrays for SSTI, Day 7 biofilm, and day 21 biofilm infections.
DOI: 10.5061/dryad.9202s/1
title: Ortholog trees

description: All ortholog trees in newick format (n=1306) used in the current study.
DOI: 10.5061/dryad.9202s/2
title: Ortholog alignments

description: All ortholog alignments in fasta format (n=1306) used in the current study.
DOI: 10.5061/dryad.9202s/3
title: Ortholog bootstrap replicates

description: All ortholog bootstrap replicates in newick format (n=1306) used in the current study.
DOI: 10.5061/dryad.9202s/4
title: Species trees and input files

description: Inferred species trees from RAxML, ASTRAL, and ASTRID. Additional files include the concatenated sequence alignment (in phylip format) used for RAxML analysis and the two files (newick trees and bootstrap replicates) used in ASTRAL and ASTRID analyses.
DOI: 10.5061/dryad.9mc8j51/1
title: consensus_tree

description: Trimmed majority-rule consensus tree that was constructed using the full post-burnin distribution from Cacho et al., 2014 and consensus branch lengths calculated using the least squares method via the ‘consensus.edges’ function in the package “phytools.”
DOI: 10.5061/dryad.9mc8j51/2
title: 1000_trees

description: 1,000 trimmed trees randomly drawn from the posterior distribution of Cacho et al., 2014.
DOI: 10.5061/dryad.9mc8j51/3
title: Data
DOI: 10.5061/dryad.9qh7t9t/1
title: Supporting figures
DOI: 10.5061/dryad.d8sv77t/1
title: Monthly Observations of Disease and Bleaching

description: This spreadsheet tracks individual ramets (numbered 1-10) within several genets (labelled A-Z) of Acropora cervicornis through the 2014 bleaching event and subsequent disease outbreak. From this, ramets are categorized as either bleached, diseased, bleached and diseased, or healthy, per the associated journal article.
DOI: 10.5061/dryad.g38qb00/1
title: All data from Experiment 1 (no hormonal manipulation) and Experiment 2 (mesotocin manipulation)

description: These data come from a prosocial choice task conducted on captive pinyon jays. Experiment 1 measured baseline preferences (i.e. without hormonal manipulation), and Experiment 2 involved administration of a high or low dose of mesotocin (the avian homolog of oxytocin) or a saline control. Description of the relevant columns for "all_data.csv":
A: dataset - either 1 (for Experiment 1, no hormones) or 2 (for Experiment 2, with hormonal manipulation) 
B: donor - a unique numeric identifier for each subject in the study 
C: date - date that session in corresponding row was conducted
D: session - sequential numbering for each subject's session
E: trial - specific trial number within a session
F: partner - location of partner (either N- no partner, L-left sidecage, or R-right sidecage)
G: recipient - if present, a unique numeric identifier for each recipient in the study 
H: payoff_condition - trial type; either Pre-Test (attention trials), Side bias (bias trials), or Prosocial/Altruistic
I: partner_present - either 'Partner absent' or 'Partner present'
J: hormone - hormone condition: NA for Experiment 1; A, B, C, or SAL for Experiment 2 (experimenters were blind to condition)
K: right.left - subject's choice on that trial, either right or left wire
L: response - FOR PRE-TEST (i.e. attention trials): 1 if subject correctly chose side with food, 0 if incorrect
L: response - FOR SIDE BIAS (i.e. bias trials): 1 if subject chose LEFT, 0 if RIGHT
L: response - FOR PROSOCIAL/ALTRUISTIC: IF partner absent, 1 if subject chose LEFT, 0 if RIGHT
L: response - FOR PROSOCIAL/ALTRUISTIC: IF partner present, 1 if subject chose same side as partner, 0 if not.
DOI: 10.5061/dryad.g38qb00/3
title: Supp. Materials for Duque et al 2018 Jay Prosociality

description: This document contains Supplementary Methods (Subject information, detailed procedure for habituation/training and experimental phases, and additional analyses (weighted prosocial/altruistic tendency) and figures.
DOI: 10.5061/dryad.g38qb00/5
title: Duque_et_al_2018_rcode

description: This Rcode is for Duque et al. 2018 Mesotocin influences pinyon jay prosociality. It is annotated for replication of all results, figures, and analyses.  Absolute tendency appears in main text; Weighted tendency in supplementary.
DOI: 10.5061/dryad.g6b2f/1
title: Cascadae_Bd_inhibitory_taxa_Summarized_by_liefestage_Test_significant_OTUs

description: Cascadae_Bd_inhibitory_taxa_Summarized_by_liefestage_significant_OTUs
DOI: 10.5061/dryad.g6b2f/2
title: Cascadae_biom_file_16_18s_fungi_combined
DOI: 10.5061/dryad.g6b2f/3
title: Cascadae_Supplemental_Table_2_Positive_Co_occurance_w_Bd

description: Cascadae_Supplemental_Table_2_Positive_Co_occurance_w_Bd
DOI: 10.5061/dryad.g6b2f/4
title: Cascadae_Supplemental_Table_3_Negitive_Co_occurance_w_Bd

description: Cascadae_Supplemental_Table_3_Negitive_Co_occurance_w_Bd
DOI: 10.5061/dryad.g6b2f/5
title: Cascadae_Supplemental_Table_4_Complete_list_Bd_inhibitory_OTUs_Ids_7459

description: Cascadae_Supplemental_Table_4_Complete_list_Bd_inhibitory_OTUs_Ids_7459
DOI: 10.5061/dryad.g6b2f/6
title: Cascadae_Supplemental_Table_5_Results_of_ANCOM

description: Cascadae_Supplemental_Table_5_Results_of_ANCOM
DOI: 10.5061/dryad.ks622/1
title: 1.donelan&trussell.behavior

description: Data used in analysis of refuge use and to construct Fig. 1.
DOI: 10.5061/dryad.ks622/2
title: 2.donelan&trussell.avgforaging

description: Data used in analysis of foraging activity and to construct Fig. S1 in Electronic Supplementary Material.
DOI: 10.5061/dryad.ks622/3
title: 3.donelan&trussell.growth&GE

description: Data used in analyses of Nucella offspring growth and growth efficiency and to construct Figs. 2 and 3.
DOI: 10.5061/dryad.ks622/4
title: 4.donelan&trussell.mussels

description: Raw data of mussels that were consumed by Nucella offspring during the experiment. Used to calculate total energy consumed by offspring in File 2 and per capita foraging activity and in Fig. S1 in Electronic Supplementary Material.
DOI: 10.5061/dryad.m2763r3/1
title: Experimental Data on Phoradendron californicum infrapopulation experiment

description: All data from the associated manuscript are provided. Natural_infrapopulations sheet provides observational data on infrapopulations assessed in the field. Pollinator_visitation sheet provides data on observation of pollinator visitation to infrapopulations of different characteristics. Pollen_deposition sheet provides data on pollen receipt to flowers of female parasitic plants on control and treated host plants. Fruit_success_removal provides data on fruit set and fruit removal for female parasitic plants on control and treated host plants. Please see the metadata sheet for definitions of all column names provided in the data sheets.
DOI: 10.5061/dryad.mh206/6
title: Sequencing data
DOI: 10.5061/dryad.qf916/2
title: ddRADseq vcf subset

description: A vcf file containing the individuals genotyped using ddRADseq, analyzed separately. This file only contains the pruned subset of loci used in the analyses.
DOI: 10.5061/dryad.qf916/3
title: Both sdRADseq and ddRADseq vcf subset

description: A vcf file containing all individuals, both sdRADseq and ddRADseq, when analyzed together using stacks. This file only contains the pruned subset of loci used in the analysis.
DOI: 10.5061/dryad.qf916/4
title: in silico digest raw data

description: A compressed file containing all of the raw output from the in silico digestions using different sources of error.
DOI: 10.5061/dryad.qf916/5
title: Both sdRADseq and ddRADseq from samtools vcf

description: Variant Call File from the samtools analysis on 60 ddRAD-seq individuals and 60 sdRAD-seq individuals analyzed together.
DOI: 10.5061/dryad.qf916/6
title: ddRADseq from samtools vcf

description: vcf file from the samtools analysis of 60 ddRAD-seq individuals.
DOI: 10.5061/dryad.qf916/7
title: sdRADseq from samtools vcf

description: vcf file from a samtools analysis of the 60 sdRAD-seq individuals.