cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0jm1dt2/5
title: Waraniak_18S_OTUseq_counts

description: Data file with information on the read count for each of the OTUs from the mothur analysis in each of the predator diet samples. Also contains information on the taxonomic group assigned to each OTU based on the NCBI blast protocol outlined in the manuscript.
DOI: 10.5061/dryad.0jm1dt2/6
title: Waraniak_18S_Preyseq_Props

description: Data file that contains the proportions of read counts from the different prey ESUs found in the predator diet samples. Also contains data for the environmental variables associated with each diet sample. Necessary input file for the analyses in the R code.
DOI: 10.5061/dryad.0sn4046.1
title: Data from: The impact of income, land, and wealth inequality on agricultural expansion in Latin America
DOI: 10.5061/dryad.0sn4046.1/1.1
title: PNAS_Data

description: Data for the PNAS publication "The impact of income, land and wealth inequality on agricultural expansion in Latin America" by M.G. Ceddia
DOI: 10.5061/dryad.0sn4046.2
title: Data from: The impact of income, land, and wealth inequality on agricultural expansion in Latin America
DOI: 10.5061/dryad.0sn4046.2/1.2
title: PNAS_Data

description: Data for the PNAS publication "The impact of income, land and wealth inequality on agricultural expansion in Latin America" by M.G. Ceddia
DOI: 10.5061/dryad.15p1k05/1
title: Information on data files used for this publication
DOI: 10.5061/dryad.15p1k05/2
title: ASR_Analyses

description: See Readme file
DOI: 10.5061/dryad.15p1k05/3
title: Brood_Sex_Ratio_Data

description: See Readme file
DOI: 10.5061/dryad.15p1k05/4
title: female_helpers

description: See Readme file
DOI: 10.5061/dryad.15p1k05/5
title: Helper_Present

description: See Readme file
DOI: 10.5061/dryad.15p1k05/6
title: Large_CB_Groups

description: See Readme file
DOI: 10.5061/dryad.15p1k05/7
title: Male_Dispersal

description: See Readme file
DOI: 10.5061/dryad.15p1k05/8
title: SY_Helpers

description: See Readme file
DOI: 10.5061/dryad.2g75hp3.1
title: Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition
DOI: 10.5061/dryad.2g75hp3.1/1.1
title: BioControlDatabase

description: This pest-control database encompasses 132 studies and 6,759 sites worldwide. Data discussed and interpreted in Karp et al. (2018) Crop pests and predators exhibit inconsistent responses to surrounding landscape composition. PNAS.
DOI: 10.5061/dryad.2g75hp3.2
title: Data from: Crop pests and predators exhibit inconsistent responses to surrounding landscape composition
DOI: 10.5061/dryad.2g75hp3.2/1.2
title: BioControlDatabase

description: This pest-control database encompasses 132 studies and 6,759 sites worldwide. Data discussed and interpreted in Karp et al. (2018) Crop pests and predators exhibit inconsistent responses to surrounding landscape composition. PNAS.
DOI: 10.5061/dryad.2h0k50s/10
title: Measurements of Specimens of Limia rivasi
DOI: 10.5061/dryad.2h0k50s/11
title: Measurements of Specimens of Limia sulfurophila
DOI: 10.5061/dryad.2h0k50s/12
title: Measurements of Specimens of Limia tridens
DOI: 10.5061/dryad.2h0k50s/13
title: Measurements of Specimens of Limia versicolor
DOI: 10.5061/dryad.2h0k50s/14
title: Measurements of Specimens of Limia vittata
DOI: 10.5061/dryad.2h0k50s/6
title: Measurements of Specimens of Limia melanonotata
DOI: 10.5061/dryad.2h0k50s/7
title: Measurements of Specimens of Limia nigrofasciata
DOI: 10.5061/dryad.2h0k50s/8
title: Measurements of Specimens of Limia pauciradiata
DOI: 10.5061/dryad.2h0k50s/9
title: Measurements of Specimens of Limia perugiae
DOI: 10.5061/dryad.42g78nj/1
title: Cardinal-McTeague_2018

description: This package includes the LiteBlueDevil v0.3 python script, archived alignment, tree files, and seed dimension dataset, and R script and files needed to reproduce the seed evolution analyses in the following paper: Cardinal-McTeague et al. 2018. Seed size evolution and biogeography of Plukenetia (Euphorbiaceae), a pantropical genus with traditionally cultivated oilseed species. BMC Evolutionary Biology.
DOI: 10.5061/dryad.4521vq2/1
title: Experimental_disturbances_species

description: Vegetation composition data from permanent experimental plots (artificial disturbances and undisturbed controls). Plot size is 0.5 × 0.5 m. Cover of all vascular plants are on percentage scale.
DOI: 10.5061/dryad.4d3f4g3/1
title: EnvironmentalDNA_SubstrateSelection_Albany_GardenIsland_Ersai_Bautino_CaspianSea

description: Fasta files were generated through usearch9.2 from Miseq .fastq reads. Fasta files are labelled by their unique sample name, place sampled and substrate type. All fasta files were filtered following the methods from the paper "Environmental DNA metabarcoding studies are critically affected by substrate selection"
DOI: 10.5061/dryad.50t6sq6/11
title: Red + Purple urchin mortality data for loess analysis

description: Data set to visualize red + purple urchin mortality patterns using LOESS
DOI: 10.5061/dryad.50t6sq6/12
title: Predator aggregation and species richness analyses

description: Script to analyze predator aggregation and species richness datasets from field experiment conducted in Pt Loma and S La Jolla in 2014 and 2017
DOI: 10.5061/dryad.50t6sq6/13
title: Predator video data

description: Data set from video recordings of predators foraging in field experiment conducted in Pt Loma and S La Jolla kelp forests in 2014 and 2017
DOI: 10.5061/dryad.90473mt/1
title: Data used for the analyses; Verheyen and Stoks

description: DTF = Daily Temperature Fluctuation; PO = phenoloxidase; MDA = malondialdehyde; CAT = catalase; ETS = electron transport system; SOD = superoxide dismutase
DOI: 10.5061/dryad.c58539p/1
title: Compressed raw data set

description: The uploaded data file includes the raw data for the figures and tables in our paper.
DOI: 10.5061/dryad.cj05t65/10
title: AFSmicrobiome_SI_otuRDPclassification_phyloseqIn_Rinput_DatasetS8

description: R markdown input file containing the OTU RDP classifications prepared for phyloseq input
DOI: 10.5061/dryad.cj05t65/11
title: AFSmicrobiome_SI_OTUtable_final_trimmed_allSamples_Rinput_DatasetS9

description: R markdown input file containing the trimmed OTU table for all samples
DOI: 10.5061/dryad.cj05t65/2
title: AFSmicrobiome_SI_OTUprocessingPipelineStatistics_DatasetS2

description: Summary statistics for the OTU processing pipeline
DOI: 10.5061/dryad.cj05t65/3
title: AFSmicrobiome_SI_Rmarkdown_DatasetS3_html

description: R Markdown file in .html format containing all the R code used for the analyses of the Antarctic fur seal microbiome
DOI: 10.5061/dryad.cj05t65/4
title: AFSmicrobiome_SI_Rmarkdown_DatasetS3_Rmd

description: R Markdown file in Rmd format containing all the R code used for the analyses of the Antarctic fur seal microbiome
DOI: 10.5061/dryad.cj05t65/5
title: AFSmicrobiome_SI_SequencingStatsFile_Rinput_DatasetS4

description: R markdown input file containing sequencing statistics
DOI: 10.5061/dryad.cj05t65/6
title: AFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5

description: R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Contains table header with loci names.
DOI: 10.5061/dryad.cj05t65/7
title: AFSmicrobiome_SI_MicrosatelliteGenotypes50_P22removed_colnames_Rinput_DatasetS5.1

description: R markdown input file containing genotypes at 50 microsatellite loci for 95 fur seal individuals (pup P22 was removed due to large number of missing genotypes). Header line removed.
DOI: 10.5061/dryad.cj05t65/8
title: AFSmicrobiome_SI_relatednessWang50Msats_Rinput_DatasetS6

description: R markdown input file containing pairwise relatedness estimates
DOI: 10.5061/dryad.cj05t65/9
title: AFSmicrobiome_SI_otuRDPclassification_Rinput_DatasetS7

description: R markdown input file containing the OTU RDP classifications obtained with the USEARCH sintax command
DOI: 10.5061/dryad.d22q6vh/1
title: Combination of NEWS and inflammatory biomarkers datafile

description: This datafile contains parts of the data used for our retrospective analyses.
DOI: 10.5061/dryad.d90bc74/1
title: Data associated to Maxwell et al.
DOI: 10.5061/dryad.hj0005k/2
title: wood_traits_Erythrophleum

description: Tangential vessel diameter, vessel density, vessel grouping index (ratio of total number of vessels to total number of vessel groupings), proportion of vessel lumen, fibre, axial and radial parenchyma measured for the two species, E. ivorense and E. suaveolens, in their natural habitat (branch and stem samples) and in a common garden experiement (only branch samples). On branch sections, these measurements were done on 0.16 mm² quadrats systematically distributed from the pith to the bark (from [0;400] to [2800;3200]), in order to include radial variation in wood traits. For stem sections, measurements were done on two quadrats of 9.40 mm². Intervessel wall thickness and fiber wall thickness (measured as the double wall between two adjacent fibers) were also measured at higher magnification. Conduit wall reinforcement was calculated by determining the wall thickness (t) to conduit wall span (b) ratio . On tangential sections, we measured the horizontal pit membrane diameter at its widest point but only for branch samples from natural habitat.
DOI: 10.5061/dryad.js11601/1
title: README

description: Description of repository contents, organization, and file types.
DOI: 10.5061/dryad.js11601/2
title: Summary Table

description: A summary table for the entire set of simulations
DOI: 10.5061/dryad.js11601/3
title: Syllable Table

description: A table of syllable start and stop times for the stimulus set
DOI: 10.5061/dryad.js11601/4
title: Example Notebook

description: A Jupyter Python notebook that shows how to load the data.
DOI: 10.5061/dryad.js11601/5
title: Receptive Fields

description: A compressed directory of spectrotemporal receptive fields used to simulate the responses.
DOI: 10.5061/dryad.js11601/6
title: Stimuli

description: A compressed directory of stimulus files
DOI: 10.5061/dryad.js7r696/1
title: Cytochrome-b_alignment_Abrothrix_manni

description: DNA sequences of the first 801bp of the gene Cytochrome-b of specimens of Abrothrix manni. This is a non-redundant alignment, i.e., only one sequence representative of each haplotypic class is included. These sequences were also deposited in GenBank. Accession numbers area provided as sequence header in this file.
DOI: 10.5061/dryad.n541d0t/1
title: Cotter01_densities

description: Estimated densities of organisms from the Cotter River. These data have had all taxa common to Cunningham and Cotter or Cunningham only removed.
DOI: 10.5061/dryad.n541d0t/2
title: Environmental data.

description: Corresponding environmental data.
DOI: 10.5061/dryad.q91784t/1
title: Dryad.Chang.Larracuente.Genetics.11.12.2018
DOI: 10.5061/dryad.r4v94tc/2
title: Poa_ITS_OCHLOPOA

description: Alignment file of the ITS sequences (ITS1-5.8S rRNA gene-ITS2 region, nuclear genome)
DOI: 10.5061/dryad.r4v94tc/3
title: Ochlopoa table -ALL SPECIES

description: Sequences used for our analysis with the references to collectors, location and GenBank numbers
DOI: 10.5061/dryad.v2k8nf2/1
title: Qualitative database for focus group discussions

description: This data file includes qualitative data that is based on focus group discussions and the attached file is the axial coding of themes that emerged from these discussions.
DOI: 10.17632/y9k69pvrhp.1
title: Data for: 2-D numerical model for lithospheric temperature distribution at 33°S, central Chile: a thermal properties approach

description: This data is the result of different measurements in the upper crustal units at the 33S latitude in central Chile
DOI: 10.5061/dryad.23j8p68/1
title: Ionosporus rpb2 fasta alignment

description: A FASTA file of 35 exemplars with aligned rpb2 sequences. 7 of those exemplars were newly seqeunced.
DOI: 10.5061/dryad.2ff8mv9/1
title: Levy_Data

description: Contains microsatellite and mitochondrial haplotype data used to estimate genetic diversity and genetic connectivity of three small mammal species (Ningaui timealeyi, Pseudomys chapmani, Pseudomys hermannsburgensis) in the Pilbara bioregion of Western Australia, Australia.
DOI: 10.5061/dryad.2h0k50s/15
title: Measurements of Specimens of Limia zonata
DOI: 10.5061/dryad.2h0k50s/16
title: Measurements of Specimens of Pseudolimia heterandria
DOI: 10.5061/dryad.2h0k50s/17
title: Measurements of Specimens of Allopoecilia caucana
DOI: 10.5061/dryad.2h0k50s/18
title: Measurements of Specimens of Psychropoecilia hispaniolana
DOI: 10.5061/dryad.2h0k50s/19
title: Measurements of Specimens of Pamphorichthys araguaiensis
DOI: 10.5061/dryad.2h0k50s/20
title: Measurements of Specimens of Pamphorichthys hasemani
DOI: 10.5061/dryad.2h0k50s/21
title: Measurements of Specimens of Pamphorichthys hollandi
DOI: 10.5061/dryad.2h0k50s/22
title: Measurements of Specimens of Pamphorichthys minor
DOI: 10.5061/dryad.2h0k50s/23
title: Measurements of Specimens of Pamphorichthys scalpridens
DOI: 10.5061/dryad.32q9q5d/4
title: Appendix e-3 Glossary of Terms
DOI: 10.5061/dryad.32q9q5d/5
title: Appendix e-4 Full ALS Clinical Trial Guidelines
DOI: 10.5061/dryad.32q9q5d/6
title: Appendix e-5 Statistical Considerations
DOI: 10.5061/dryad.3p4s413/1
title: Eye_Growth_Dataset_FuncEcol

description: Data associated with growth analyses
DOI: 10.5061/dryad.3p4s413/2
title: Eye_Survival_Dataset_FuncEcol

description: Data associated with survival analyses
DOI: 10.5061/dryad.3sp331p/1
title: Forest stand structure and biotic community data from Fort Robinson State Park, Nebraska, USA

description: Data includes coarse woody debris percent coverage, tree density, bird community composition, and understory woody plant community composition/cover taken in 2016 at Fort Robinson State Park, Nebraska, USA. Sampling location coordinates (latitude, longitude) are also included. Sampling locations were distributed in a stratified-random design according to burn severity classes from a wildfire that occurred in 1989.
DOI: 10.5061/dryad.4h16331/1
title: video observations

description: raw behavioral data from video-observations of incubating lesser black backed gulls
DOI: 10.5061/dryad.4rf13r8/2
title: Wind profile for West wind

description: Wind profile for West wind
DOI: 10.5061/dryad.4rf13r8/3
title: Wind porfile for West southwest wind

description: Wind porfile for West southwest wind
DOI: 10.5061/dryad.4rf13r8/4
title: Passive tracer concentration

description: Passive tracer concentration
DOI: 10.5061/dryad.5757d42/1
title: Genotypic and phenotypic data

description: This excel file contains phenotypic data (male color) and microsatellite genotypes (two datasets) from guppies located in the Marianne and Paria rivers, Trinidad.
DOI: 10.5061/dryad.5hg71mj/1
title: Complete data set accompanying manuscript

description: Complete data set including cryo-SEM, turbidity, rheology and dynamic light scattering data and scripts in open standard data formats.
DOI: 10.5061/dryad.5hv83rt/1
title: Experiment 1 data

description: Summary file of the results of mating experiment 1. Detailed column header descriptions are given in the README file.
DOI: 10.5061/dryad.5hv83rt/2
title: Mate_choice_Exp2_dryad

description: Summary file of the results of mating experiment 2. Detailed column header descriptions are given in the README file
DOI: 10.5061/dryad.631j930/1
title: Lab Experiment Infection Load Data

description: Data on echinostome infection load in tadpoles in three groups (near surface, near bottom, or free) in laboratory experiment.
DOI: 10.5061/dryad.631j930/2
title: Field Experiment Infection Load and SVL data

description: Final infection load (intrarenal and extrarenal cysts) in tadpoles from near-surface or near-bottom enclosures in a field experiment in a pond in Illinois.
DOI: 10.5061/dryad.631j930/3
title: Field Experiment Survival and Prevalence Data

description: Data for survival of tadpoles and prevalence (proportion of tadpoles infected with intrarenal and extrarenal trematode cysts).
DOI: 10.5061/dryad.64c32m5/1
title: Data_Cuomo_et_al_2018
DOI: 10.5061/dryad.994f813/2
title: RCode for Analyses_R2

description: Condensed version of R code used to implement analyses outlined in the main text.
DOI: 10.5061/dryad.99k4n5s/1
title: Life table Assay

description: This is a life table assay to quantify individual variation in life history traits of Daphnia. Method details are in corresponding mansucript
DOI: 10.5061/dryad.cj05t65/12
title: AFSmicrobiome_SI_OTUtable_final_trimmed_raref10000_Rinput_DatasetS10

description: R markdown input file containing the trimmed and rarefied OTU table for 94 samples
DOI: 10.5061/dryad.cj05t65/13
title: AFSmicrobiome_SI_Metadata_allSamples_Rinput_DatasetS11

description: R markdown input file containing metadata for all samples
DOI: 10.5061/dryad.cj05t65/14
title: AFSmicrobiome_SI_alphaDiversity_Rinput_DatasetS12

description: R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated from the non-normalised and rarefied OTU tables in USEARCH for all sampled individuals
DOI: 10.5061/dryad.cj05t65/15
title: AFSmicrobiome_SI_alphaDiversity_MainPhyla_Rinput_DatasetS13

description: R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for OTUs belonging to the main phyla
DOI: 10.5061/dryad.cj05t65/16
title: AFSmicrobiome_SI_outgroup_pynastAligned_filtered_Rinput_DatasetS14

description: R markdown input file containing a phylogenetic tree needed for UniFrac distance calculations (created with FastTree in QIIME).
DOI: 10.5061/dryad.cj05t65/17
title: AFSmicrobiome_SI_PuppingLocations_Rinput_DatasetS15

description: R markdown input file containing pupping locations at SSB
DOI: 10.5061/dryad.cj05t65/18
title: AFSmicrobiome_SI_alphaDiversityMultiRaref_Rinput_DatasetS16

description: R markdown input file containing alpha diversity estimates (Effective number of species–Jost1) calculated for 100 rarefied OTU tables in USEARCH for all sampled individuals
DOI: 10.5061/dryad.cj05t65/19
title: AFSmicrobiome_SI_NSTIvalues_filteredTrimmed_rarefied_Rinput_DatasetS17

description: R markdown input file containing NSTI values calculated from PICRUSt
DOI: 10.5061/dryad.cj05t65/20
title: AFSmicrobiome_SI_Categorize_by_FunctionL3_FilteredTrimmed_rarefied_Rinput_DatasetS18

description: R markdown input file containing read counts for KEGG functional predictions calculated with PICRUSt
DOI: 10.5061/dryad.cj62621/1
title: Read me (data file explanations)
DOI: 10.5061/dryad.cj62621/2
title: Data file

description: This data file contains data from the kiddivax study at 2009-2010. This is in a wide format that each row is a household.
DOI: 10.5061/dryad.h3j360r/1
title: Nest Exodus Data

description: This data was collected during two experiments that examined the effect of incubation temperature on the nest exodus behavior of wood duck ducklings. Wood duck eggs were collected from nest boxes at the Savannah River Site in South Carolina, USA. Eggs were incubated and experiments were conducted at Virginia Tech. The zip file contains two Excel spreadsheets. One is data from the Individual Experiment, where ducklings were tested on their ability to exit a nest box individually. The other is data from the Pairs Experiment, where ducklings were tested in mixed incubation temperature pairs.
DOI: 10.5061/dryad.hj0005k/3
title: growth_common_garden

description: Growth in diameter in the common garden experiement  for E. ivorense and E. suaveolens.
DOI: 10.5061/dryad.hj0005k/4
title: growth_natural_habitat

description: Growth in diameter and diameter classes for the two species E. suaveolens and E. ivorense in their respective natural habitat.
DOI: 10.5061/dryad.jc5616h/1
title: Bird Movement and EVI Homogeneity Data

description: Data from Tucker et al. Large birds travel farther in homogeneous environments. Data includes species names, median displacement (km), 0.95 quantile displacement (km), body mass (g), mean EVI value and EVI homogeneity values.
DOI: 10.5061/dryad.js11601/7
title: Spike Data

description: A compressed directory of response spike times.
DOI: 10.5061/dryad.js11601/8
title: Raw Simulation Data

description: A compressed directory of raw simulated responses.
DOI: 10.5061/dryad.m0h05rt/1
title: DataS1: Simulated data and custom modelling functions

description: The two files in DataS1 are used within Appendix S2 to create the example in the manuscript. 

1) modelling_functions.R: Custom functions used to estimate edge weights within an intrinsic conditional autoregressive (ICAR) model by incorporating resistance covariates into the off-diagonal elements of the precision matrix. These functions are used with the rwc package for R. 

2) SimData.Rdata: The Rdata file contains three simulated genetic datasets based on resistance matrices generated under isolation by distance (popsIBD), isolation by resistance (popsIBR), and isolation by barrier (popsIBB) hypotheses. The data were simulated using the PopGenReport package. The simulation was based on 20 loci with 20 alleles, a sex ratio of 0.5, migration rate of 0.05, dispersal rate of 0.05, and a mutation rate of 0.001. However, the maximum dispersal distance (i.e., disp.max) varied depending on the simulation. The simulations were run for 400 generations and the carrying capacity for each of the 30 sub-populations was set to 15. The R code used to generate these datasets can be found in Appendix S2.

The R code used to fit the models is provided in Appendix S2.
DOI: 10.5061/dryad.m0h05rt/2
title: dataS2: Fitted models

description: The file in DataS2 is used within Appendix S2 to create the example in the manuscript. 

1.	DataS2.Rdata: This file contains 9 ICAR models fit to simulated genetic distance matrices and resistance matrices using a generalized Wishart distribution. The simulated genetic distance matrices and resistance matrices were based on the isolation by distance (IBD), isolation by resistance (IBR), and isolation by barrier (IBB) hypotheses. There are 9 models in total (3 simulated genetic distances x 3 resistance types = 9 models). The naming convention for the models is: 
•	IBD.IBD = IBD genetic distance matrix and IBD resistance matrix 
•	IBD.IBR = IBD genetic distance matrix and IBR resistance matrix 
•	IBD.IBB = IBD genetic distance matrix and IBB resistance matrix 
•	IBR.IBD = IBR genetic distance matrix and IBD resistance matrix 
•	IBR.IBR = IBR genetic distance matrix and IBR resistance matrix 
•	IBR.IBB = IBR genetic distance matrix and IBB resistance matrix 
•	IBB.IBD = IBB genetic distance matrix and IBD resistance matrix 
•	IBB.IBR = IBB genetic distance matrix and IBR resistance matrix 
•	IBB.IBB = IBB genetic distance matrix and IBB resistance matrix 

The R code used to fit the models is provided in Appendix S2.
DOI: 10.5061/dryad.m0h05rt/3
title: AppendixS2:  Modelling tutorial

description: In this example we demonstrate how edge weights can be estimated within an intrinsic conditional autoregressive (ICAR) model by incorporating resistance covariates into the off-diagonal elements of the precision matrix. The example is based on genetic simulations generated using the PopGenReport package and implemented using R statistical software version 3.4.4. Resistance distances are generated using the gdistance package and the models are fit using the rwc package; all of which are available on the CRAN website (https://cran.r-project.org/). R code has been provided in AppendixS2.pdf and in dataS1.zip so that the methods are more accessible to readers, who can recreate the example provided in the manuscript and apply these methods to their own landscape genetic datasets.
DOI: 10.5061/dryad.m5d8f45/1
title: peromyscus photos

description: Observations of Peromyscus leucopus activity timing from motion-activated cameras. Cameras were deployed for 6 one-week sessions in spring, summer, and fall of 2017, in plots invaded by buckthorn (Rhamnus cathartica) or plots with buckthorn removed.