cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.01n2q/1
title: Pedigree File

description: the pedigree file, refering to the identity of the individual("ID"), its mother ("MotherID") and its father ("FatherID") when it has been assigned
DOI: 10.5061/dryad.01n2q/2
title: Phenotype File

description: the phenotypic file, contained the ID of the offspring in the common garden experiment ("ID"), the ID of its mother ("Mother"), information about the block and observer effects ("Block" and "Mp") and the values of the 12 functional traits described in the manuscript
DOI: 10.5061/dryad.01n2q/3
title: RelationshipIDCommonGarden_Genotype

description: correspondences between the ID of the phenotyped offspring in the common garden ("ID_CG") and their genotyping ID ("ID_Geno")
DOI: 10.5061/dryad.01n2q/4
title: GenotypeAdult_N1

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for all the potentially reproductive adults of plot N1
DOI: 10.5061/dryad.01n2q/5
title: GenotypeAdult_N2

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for all the potentially reproductive adults of plot N2
DOI: 10.5061/dryad.01n2q/6
title: GenotypeAdult_N4

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for all the potentially reproductive adults of plot N4
DOI: 10.5061/dryad.01n2q/7
title: GenotypeOffspring_N1

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for a subset of offspring per family sampled from plot N1
DOI: 10.5061/dryad.01n2q/8
title: GenotypeOffspring_N2

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for a subset of offspring per family sampled from plot N2
DOI: 10.5061/dryad.04tq4/3
title: Banzai parameters

description: Parameters for bioinformatics pipeline used for dataset.
DOI: 10.5061/dryad.04tq4/4
title: Banzai script

description: Analytical script for bioinformatics (Banzai Pipeline, O'Donnell, available at: https://github.com/jimmyodonnell/banzai/) used in publication.
DOI: 10.5061/dryad.0j4m5/18
title: Haplotype counts
DOI: 10.5061/dryad.0j6s6/1
title: Faunal data

description: The presence (1) or absence (0) of the 74 benthic taxa.
DOI: 10.5061/dryad.0j6s6/2
title: Substrate data

description: The category of substrate type; where the ten categories are defined by the presence and percent-cover of sediment and debris.
DOI: 10.5061/dryad.0j6s6/3
title: Environmental data

description: The quantitative value of four seafloor characteristics at the location of the image (i.e., depth, slope, and small- and large-scale rugosity).
DOI: 10.5061/dryad.0j6s6/4
title: Location data

description: The coordinates of each image in UTM (WGS_1984_UTM_zone_9N).
DOI: 10.5061/dryad.1hb1f/1
title: Colonization projects

description: Spreadsheet of project data used for modeling. id - code, ColPro -development and colonization project name,Country -country of project, Colpro2 -another development and colonization project name.
DOI: 10.5061/dryad.1hb1f/2
title: Grid data

description: Spreadsheet of pixel data used for modeling. POINTID -pixel id,GRID_CODE -codr on grid, X_DD -longitude decimal degree, Y_DD -latitude decimal degree, NEAR_FID -id of nearest project, NEAR_DIST -nearest project distance, NEAR_X -nearest horizontal distance,NEAR_Y -nearest vertical distance, coca -absence (0) or presence (1) of coca in 2014, coca1992 -absence (0) or presence (1) of coca in 1990/1992
DOI: 10.5061/dryad.1hb1f/3
title: Zip file of municipalities in shapefile format

description: Shapefile of municipality units used in modeling.
DOI: 10.5061/dryad.1hb1f/4
title: Deforestation rates by study

description: Spreadsheet of deforestation rates caused by coca or other crops. forest - kind of forest, type -old-growth (primary) orsecondary forest, loss - quantity lost during time step, start - starting forest quantity, defrate_old - Puyravaud 2004 deforestation rate, defrate -revised deforestation rate in which positive values represent loss, illicit -rate is from coca (1) or legal use (0), study -source study. Based on: Armenteras, D., Rodriguez, N. & Retana, J. 2013 Landscape dynamics innorthwestern Amazonia: an assessment of pastures, fire and illicit crops as drivers of tropical deforestation. PLoS ONE 8, e54310.Chadid, M., Davalos, L., Molina, J. & Armenteras, D. 2015 A Bayesian Spatial Model Highlights Distinct Dynamics in Deforestation from Coca and Pastures in an Andean Biodiversity Hotspot. Forests 6, 3828.Davalos, L. M., Bejarano, A. C., Hall, M. A., Correa, H. L., Corthals, A. & Espejo, O. J. 2011 Forests and Drugs: Coca-Driven Deforestation in Tropical Biodiversity Hotspots. Environ. Sci. Technol. 45, 1219-1227.(10.1021/es102373d.)UNODC & Peru Ministerio del Medio Ambiente. Analisis economico de las actividades causantes de la deforestacion en Pichis-Palcazu. Lima: UNODC and Ministerio del Medio Ambiente, Peru2011.
DOI: 10.5061/dryad.1hb1f/5
title: R script for INLA modeling

description: Takes in data in cpn.csv, grid.csv, and mpios.shp and produces map.graph for defining neighboring spatial units, runs and prints spatially explicit binomial models of Table 2. Saves results as d_models3.Rdata
DOI: 10.5061/dryad.1hb1f/6
title: R script to make predictions based on INLA modeling

description: Obtains predictions from models of Table 2, runs AUC analyses of pixel predictions, and prints predictions of model without predictor (no influence of distance to projects), model using the nearest project as random effect along with influence of distance to projects (pred2), and the modelusing municipality intercepts as random effects along with with influence of distance to projects (pred6). The latter is the best-fit model. The script also saves the three-model results as GeoTIFF rasters, the best model is listed as best_auc_hr.tif. NOTE: This R script must run after d2pro3_hires.R, or after loading d_models3.Rdata
DOI: 10.5061/dryad.1qh4c/1
title: Figure 2

description: Prism files for Figure 2 - see read me.
DOI: 10.5061/dryad.1qh4c/2
title: Figure S3

description: Prism Files for Fig. S3 - see read me.
DOI: 10.5061/dryad.1qh4c/3
title: Figure S4

description: Prism Files for Figure S4 - see read me
DOI: 10.5061/dryad.25rm2/1
title: Benowitz_etal_JETH_2016_data

description: This data file contains parental care measurements and larval numbers for N. orbicollis and N. vespilloides males and females.
DOI: 10.5061/dryad.27mk2/1
title: Black rail microsatellite genotypes

description: Microsatellite genotypes for California black rails captured in the San Francisco Bay Area (population 1) and Sierra Nevada Foothills (population 2). Data are formatted for Genepop and can be used as an input file for GeneClass2.
DOI: 10.5061/dryad.38nh3/6
title: PLINK ped file for subset of SNPs

description: This file is the map file for the 1753 unlinked SNPs that are in Hardy Weinberg Equilibrium.
DOI: 10.5061/dryad.38nh3/7
title: Sample_information

description: This file contains the information linking the individuals to the raw sequence data. Each individual has a barcode and a plate ID. Barcodes are unique to each plate but repeated between plates. This file also contains the population of origin for each individual and the latitude/longitude for that population. This file contains data for additional populations not used in this study.
DOI: 10.5061/dryad.683n3/1
title: Tick abundance on blue-footed booby broods

description: In February of 2008, we selected 50 focal nests, located in forest, grassland and beach, with 15 day-old (±2 days) first-hatched or singleton chicks. Locations of all nests in the study area were mapped, and local nest density was the number of pairs within 5 m and local breeding synchrony was the standard deviation of their laying dates.When these broods (their first-hatched chicks) were 15, 29 and 43 days old, we estimated tick abundance on all 1-3 broodmates.
DOI: 10.5061/dryad.7g2c9/1
title: Hudson_et_al_Managing_Cryptic_Biodiv_archived_data

description: Raw data: Sampling event, genotypic, phenotypic (gill-raker, age, standard length) data
DOI: 10.5061/dryad.896cs/1
title: Venney_et_al_inbreeding_fastq

description: Fastq files for each tissue in each individual split using mothur. File name includes the population (H=inbred, P=outbred), individual number (fry: P1-10, H1-11, yearling: P11-20, H12-21), and the tissue denoted by the first letter of each word (Fin, Gill, Liver, Spleen).
DOI: 10.5061/dryad.896cs/2
title: Venney_final_pct_meth_data

description: Final percent methylation data after outlier exclusion and quality control.
DOI: 10.5061/dryad.896cs/3
title: Venney_et_al_geneseqs_bwameth

description: Gene sequences used for bwa-meth alignment and methylation analysis.
DOI: 10.5061/dryad.93633/1
title: Data for manuscript MEC-16-0220

description: This file contains two sheets: the first one describes the samples and their locations while the second sheet presents the genotypes at 20 SSR and SSLP loci as they were used for diversity and differentiation analysis in the MEC-16-0220 manuscript.N/A: missing data.
DOI: 10.5061/dryad.b16n8/1
title: FGCS GP Knowledge, experience, management, attitudes Survey Data Tables Dryad.org  221015

description: Cross sectional survey completed by Australian GPs - regarding GP's experience, knowledge, attitudes and management of FGCS requests: responses anonymous.
DOI: 10.5061/dryad.ck0ts/1
title: BTBW_model1_data

description: Data for Model 1: Testing the effects of ecological and social factors on the probability of siring extra-pair young
DOI: 10.5061/dryad.ck0ts/2
title: BTBW_model2_data

description: Data for Model 2: Testing the effect of food availability on breeding distance
DOI: 10.5061/dryad.d468t/10
title: Philotrypesis_cytb

description: Sequence data for cytochrome b for Philotrypesis individuals.
DOI: 10.5061/dryad.d468t/11
title: Philotrypesis_ITS2
DOI: 10.5061/dryad.d468t/2
title: Phib_Morph

description: Morphological measurements of ovipositor and tibia lengths for Philotrypesis ‘black’ wasps. Includes species assignment.
DOI: 10.5061/dryad.d468t/3
title: Phiy_Morph

description: Morphological measurements of ovipositor and tibia lengths for Philotrypesis ‘yellow wasps. Includes species assignment.
DOI: 10.5061/dryad.d468t/4
title: SycLS_Morph

description: Morphological measurements of ovipositor and tibia lengths for Sycoscapter ‘long’ and ‘short’ wasps. Includes assignments to either long or short ovipositor wasp groupings.
DOI: 10.5061/dryad.d468t/5
title: SycSH_Morph

description: Morphological measurements of ovipositor and tibia lengths for Sycoscapter ‘short’ wasps only. Includes species assignment designations.
DOI: 10.5061/dryad.d468t/6
title: Wat_Morph

description: Morphological measurements of ovipositor and tibia lengths for Watshamiella wasps. Includes species assignment designations.
DOI: 10.5061/dryad.d468t/7
title: Table_Locations

description: GPS location data for all non-pollinating fig wasps in study.
DOI: 10.5061/dryad.d468t/8
title: Eukobelea_cytb

description: Sequence data for cytochrome b for Eukobelea individuals.
DOI: 10.5061/dryad.f68th/1
title: Hove et al. Seed Set Data 2008-2010

description: This Excel file contains data on seed set in Clarkia unguiculata and Clarkia xantiana ssp. xantiana from 2008-2010.
DOI: 10.5061/dryad.f68th/2
title: Hove et al. Pollen Deposition Data

description: This Excel file contains data on pollen deposition for the plants used in a floral emasculation study that estimated the relative contribution of outcrossing, geitonogamous selfing, and autogamous selfing to seed set in Clarkia unguiculata and Clarkia xantiana ssp. xantiana.
DOI: 10.5061/dryad.f68th/3
title: Hove et al. Allozyme Data

description: This Excel file contains data reporting the allozyme genotypes used to estimate outcrossing rates in Clarkia unguiculata and Clarkia xantiana ssp. xantiana populations in 2008.
DOI: 10.5061/dryad.j9q7h/1
title: Annex 2 - extracts from coding tree in english

description: Extracts from the coding trees (non-exhaustive) used for qualitative phases (phases 1 and 3), from N-Vivo 11.
DOI: 10.5061/dryad.m2r17/1
title: Algal biomass, bacterial abundance, and bacterial diversity estimates

description: These data include mean chlorophyll a (ug/cm2; header - Chlor) and bacterial cell abundance (cells/cm2; header - Bacteria) within each site (1-3) and each time point. Bacterial 16S rRNA (archaea and chloroplasts were removed) data are also included - goods coverage (header - Goods_coverage), OTU richness (header - Sobs_16S), the complement of Simpsons Diversity (header - Simpsons_Diversity), and Simpsons Evenness (header - Simpsons_Evenness).
DOI: 10.5061/dryad.m2r17/2
title: Bacterial communities

description: The sequence count (mothur-derived) for each OTU within each sample. Sequence counts were averaged for replicates within each site and time point to avoid pseudo replication. Each sample is noted as time point (2, 4, 8, 16, 35, 64 days) and site (S1, S2, S3). For sequences prior to bioinformatic analysis, and after joining reads, see NCBI SRA: SRP077840.
DOI: 10.5061/dryad.m2r17/3
title: 16S OTU taxonomy

description: The mothur-derived 16S OTU taxonomy. Archaea, chloroplast, and unclassified sequences are not included.
DOI: 10.5061/dryad.t2m75/10
title: Dataset_S10

description: Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed  model statistics of models with a cumulative BIC-weight of at least 0.8
DOI: 10.5061/dryad.t2m75/11
title: HBL/Perl/R scripts

description: Example scripts (HyPhy batch language, perl) for analysing evolutionary rates and indels; R scripts for producing heatmaps from relative rate data and reconstructing the indel history over a given phylogeny after indel-coding with SeqState; includes five example data and tree files.
DOI: 10.5061/dryad.t2m75/6
title: Dataset_S6

description: Results of phylogenetic principal component analysis
DOI: 10.5061/dryad.t2m75/7
title: Dataset_S7

description: Phylogenetic principal regression using MCMC-GLMM
DOI: 10.5061/dryad.t2m75/8
title: Dataset_S8

description: Indel frequency as length variation per gene per species relative to the average length of the respective intact gene
DOI: 10.5061/dryad.t2m75/9
title: Dataset_S9

description: Model-ranked results of Monte Carlo Markov chain coupled generalized linear mixed models with cumulative BIC weights
DOI: 10.5061/dryad.tk0b8/10
title: Lateral (right) view of gonopods (leg pairs 9 and 10) of I. tobini n. sp. (Fig. 4C)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/11
title: Ventral view of gonopods of I. tobini n. sp. (centered on right posterior gonopod, leg-pair 10) (Fig. 4E)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/12
title: Lateral (right) view of gonopods of I. tobini n. sp. (centered on right posterior gonopod) (Figs 5A, C; 11C; 19C)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/5
title: Lateral (right) view of antenna of I. tobini n. sp. (Fig. 3A)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/6
title: Ventral view of head and rings 1 – 5 of I. tobini n. sp. (Fig. 3C)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/7
title: Ventral view of head and rings 1 – 3 (leg pairs 2 – 6 broken off at prefemur-femur joint) (Fig. 3D)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/8
title: Ventral view of rings 6 and 7 with sternites, pleurites and leg bases of I. tobini n. sp. (Figs 3E, 17F)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.tk0b8/9
title: Anterior view of ring 6 sterna of I. tobini n. sp. (Figs 4A, 18A)

description: Scanning electron micrograph taken of palladium/platinum coated structures with an FEI Quanta 600 FEG environmental scanning electron microscope.
DOI: 10.5061/dryad.v3s0k/12
title: ModelInitializer

description: Model --&gt; Model Initializer
DOI: 10.5061/dryad.v3s0k/13
title: ModelInitializer

description: Model --&gt; Model Initializer groovy
DOI: 10.5061/dryad.v3s0k/14
title: CobbDouglas

description: Network --&gt; Function --&gt; CobbDouglas
DOI: 10.5061/dryad.v3s0k/15
title: DistanceFunction

description: Network --&gt; Function --&gt; Distance Function
DOI: 10.5061/dryad.v3s0k/16
title: IncrementDistance

description: Network --&gt; Function --&gt; Increment distance
DOI: 10.5061/dryad.v3s0k/17
title: RouletteWheel

description: Network --&gt; Function --&gt; Roulette wheel
DOI: 10.5061/dryad.v3s0k/18
title: SelectionMechanism

description: Network --&gt; Function --&gt; Selection Mechanism
DOI: 10.5061/dryad.v3s0k/19
title: UtilityFunction

description: Network --&gt; Function --&gt; Utility Function
DOI: 10.5061/dryad.v3s0k/20
title: WeightDistance

description: Network --&gt; Function --&gt; Weight Distance
DOI: 10.5061/dryad.01n2q/9
title: GenotypeOffspring_N4

description: genotyping at the 13 microsatellite markers (presented in Gauzere et al. 2013 Molecular Ecology) for a subset of offspring per family sampled from plot N4
DOI: 10.5061/dryad.038q1/1
title: Analytical code

description: R script for the analyses reported in the article.
DOI: 10.5061/dryad.038q1/2
title: Phenotypic measures

description: Phenotypic records for sampled individuals.
DOI: 10.5061/dryad.038q1/3
title: Selection dataset

description: File detailing the annual survival and realised productivity (i.e., number of successfully recruited offspring) for sampled males included in the selection analyses.
DOI: 10.5061/dryad.1hb1f/7
title: R script to plot logistic model

description: Loads the data generated by script d2pro3_hires.R and generates a decay function plot based on the posteriors of the relationship between probability of finding coca by pixel and the log10 distance to the nearest development project. It also plots the observations. NOTE: this script must run after  d2pro3_hires.R, or after loading d_models3.Rdata
DOI: 10.5061/dryad.1hb1f/8
title: R script to plot deforestation rates

description: Takes in data from ic_noic.csv, and makes a bar plot ofdeforestation rates from different studies and locations. NOTE: this R script must run in the same folder as the data ic_noic.csv
DOI: 10.5061/dryad.1qh4c/10
title: Figure 4B
DOI: 10.5061/dryad.1qh4c/11
title: Figure 4D
DOI: 10.5061/dryad.1qh4c/4
title: Figure 3A
DOI: 10.5061/dryad.1qh4c/5
title: Figure 3B
DOI: 10.5061/dryad.1qh4c/6
title: Figure 3C
DOI: 10.5061/dryad.1qh4c/7
title: Figure 3D
DOI: 10.5061/dryad.1qh4c/8
title: Figure 4A
DOI: 10.5061/dryad.1qh4c/9
title: Figure 4C
DOI: 10.5061/dryad.22709/1
title: Snow et al_Wild Pig Invasion_Data

description: Data file by county. Response variables and predictor variables included, by time period (i.e., Expand_1, Expand_2, etc.)
DOI: 10.5061/dryad.27mk2/2
title: Stable isotopes for black rails

description: Stable C, N, and S values measured from feathers of California black rails captured in the San Francisco Bay Area and Sierra Nevada Foothills.
DOI: 10.5061/dryad.27mk2/3
title: Stable isotopes for wetland soils

description: Stable C, N, and S values measured from wetland soils collected in the home ranges of rails in the Sierra Nevada Foothills.
DOI: 10.5061/dryad.2n22h/1
title: Villafranca et al consent form template data Dryad

description: Raw data file with outputs from Coh-metrix and subsequent conversions of linguistic variables to grade levels. Conversion was done using the formulas described in the manuscript.
DOI: 10.5061/dryad.35b38/1
title: Cyrtandra_dentata_matrices_2010_2014

description: This file contains mean transition matrices from 2010–2011, 2011–2012, 2012–2013, and 2013–2014 from a geographically isolated population of a long lived shrub, Cyrtandra dentata, from the Kahanahāiki Management Unit (36 ha), located in the northern Wai‘anae Mountain Range, on the island of O‘ahu (21° 32’ N, -158°12’ W)
DOI: 10.5061/dryad.37b53/1
title: Raw Short Reads of Insects in Yinggeling National Nature Reserve

description: The data is for insect samples from Malaise traps in Yinggeling National Nature Reserve, Hainan Province, China. Samples were prepared by using one leg from all specimens equal to or larger than a large fly (~5 mm length) and whole bodies of everything smaller. Following the protocol of Ji et al. (2013), samples were homogenized, and DNA was extracted, quality-checked, PCR-amplified with indexed, degenerate primers for the standard mtCOI barcode region, and gel-purified. The PCR products were A-amplicon-sequenced on a Roche GS FLX at the Kunming Institute of Zoology. The 21 Yinggeling samples were sequenced on two 1/8 regions (one 1/8 region shared with other samples), producing 40 261 raw reads.
DOI: 10.5061/dryad.37b53/2
title: Environmental variables in Mengsong

description: The data includes environmental variables in Mengsong. The row names are IDs of survey plots (i.e. 7, which corresponds to PLOT007 in the data of raw short reads). Abbreviations for column names are: HAB = habitat types (RF: regenerating forest, OL: open lands, MF: mature forest), UTM_E and UTM_N = geographic coordinates of each survey plot, F_NR = the survey plots inside the forests of Bulong Nature Reserve? (TRUE: yes, FALSE: no)
DOI: 10.5061/dryad.37b53/4
title: The Operational Taxonomic Unit (OTU) representative sequences in Yinggeling

description: After denoising and deconvoluting, we clustered the reads into 97%-similarity Operational Taxonomic Units (OTUs), which should approximate or somewhat underestimate biological species. We further assigned taxonomic information to the OTUs. The data here shows the OTU representative sequences in Yinggeling.
DOI: 10.5061/dryad.37b53/5
title: The Operational Taxonomic Unit (OTU) representative sequences in Mengsong

description: After denoising and deconvoluting, we clustered the reads into 97%-similarity Operational Taxonomic Units (OTUs), which should approximate or somewhat underestimate biological species. We further assigned taxonomic information to the OTUs. The data here shows the OTU representative sequences in Mengsong.
DOI: 10.5061/dryad.37b53/6
title: The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Mengsong

description: Arthropod community composition of each survey plot in both seasons of Mengsong.MS1 = November-December 2010 (the end of wet season),MS2 = May-June 2011 (the end of dry season).The rows are OTUs, and columns are survey plots together with taxonomies of each OTU. The formats of the dataset are slightly modified for input to R.
DOI: 10.5061/dryad.37b53/7
title: The Operational Taxonomic Unit (OTU) table with assigned taxonomies in Yinggeling

description: Arthropod community composition of each survey plot in Yinggeling.The rows are OTUs, and columns are survey plots together with taxonomies of each OTU. The formats of the dataset are slightly modified for input to R.
DOI: 10.5061/dryad.37b53/8
title: Plant community composition in Mengsong

description: Plant community composition of each survey plot in Mengsong.The rows are survey plots and columns are plant species. This is an input file for R.