cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qb79/4
title: Meyer Science 2016 Fig 3

description: Data collected for results shown in figure 3, see notes within the file and the manuscript for further guidance.
DOI: 10.5061/dryad.51ft1/2
title: Data for the two main analyses

description: The first sheet has data for focal trees followed by data for comparison trees; the second sheet has data for growth and reproduction standardized (from 0 to 1), as described in the text. Fields are described in the README.xls file.
DOI: 10.5061/dryad.5k5k0/1
title: beta defensin BKA tree swallows

description: Data collected in the field from tree swallows individuals in southern Quebec during the reproductive season 2013 and 2014. Contains alleles of beta-defensin, innate immune function BKA. Consult the ReadMe file for more info.
DOI: 10.5061/dryad.5q783/1
title: EcoEvoParasite_rawData_Dryad

description: physiological measurements and gene expression data from all fish in the experiment plus ecosystem data
DOI: 10.5061/dryad.5vr09/1
title: Avian Community Composition of primary and logged forest, Sabah Borneo - PDF

description: Data originally collected in the field (see Edwards et al. 2013; doi: 10.1111/cobi.12059) and published previously in Edwards et al. (2013) supplementary information. Data represent species identity and abundance for all bird species originally recorded in Edwards et al. (2013). (PDF format)
DOI: 10.5061/dryad.7s212/1
title: Data_Mueller_etal2017_EcolAppl
DOI: 10.5061/dryad.804j3/11
title: Timeseries of joints positions of participants

description: Tracked positions of 25 skeletal joints of 12 dyads (24 participants) who were recorded during scientific conversations. All participants had at least three consecutive rounds of conversation on their primary session. Five dyads participated in an additional round conducted six months after the primary session. Rounds ranged up to 15min each. Data in each file corresponds to a specific dyad, round, and participant. The data is synchronized both in time and space. Namely, data points of a specific dyad are synchronized in their timestamps (between participants, but also across rounds 1-3) and share a global spatial coordinate system.
DOI: 10.5061/dryad.8mv03/1
title: Data_for_heritability_exp

description: Main data set to estimate the heritability of nu
DOI: 10.5061/dryad.8mv03/2
title: Main data to estimate fecundity costs of nu
DOI: 10.5061/dryad.8mv03/3
title: Pupal_weight_field_data

description: Pupal weights to calculate costs of nu
DOI: 10.5061/dryad.8mv03/4
title: Pupal_weight_lab_data

description: Pupal weights measured in the lab to estimate costs of low nu
DOI: 10.5061/dryad.9km73/1
title: Proteomic data in long format

description: Protein abundances used for all analyses.
DOI: 10.5061/dryad.9vr0c/1
title: Dewlap size data

description: Data on residual dewlap area of Anolis species from a log-log phylogenetic regression on head length (cm) as a measure of body size. Standard deviations and standard errors are calculated for species with multiple individuals; otherwise the mean intraspecific standard deviation is used. Absolute log dewlap area (cm^2) is also provided. Sample sizes are provided, as well as a column for the number of individuals measured from field guides for each species.
DOI: 10.5061/dryad.9vr0c/2
title: Speciational analysis script

description: Script for running the "multi-psi" analysis presented in the manuscript. Functions and code are annotated to indicate the steps in a basic analysis.
DOI: 10.5061/dryad.9vr0c/3
title: Gamble et al MCC phylogeny of Anolis

description: Phylogenetic tree used in the analyses. The tree is from Gamble et al. (2013) and is available elsewhere on Dryad (doi:10.5061/dryad.dp848.2), but this lightly processed version is provided for ease of running analyses while ensuring taxa names match the data set.
DOI: 10.5061/dryad.b031n/1
title: Distance data of medium and large-sized vertebrates in French Guiana

description: This .csv file contains all data to repeat the distance sampling study on animal detection presented in the associated paper. Perpendicular distance data were not truncated at 50 m.
DOI: 10.5061/dryad.b1410/1
title: Experimental evolution under divergent larval diets in medfly_datasheet

description: Data file containing raw data for all figures in the paper.
DOI: 10.5061/dryad.b327c/5
title: Sap Flow Data for SERC

description: This file contains sap flux density measured at SERC by 30 Granier-style probes on 30 tree stems (see list of trees equipped with sap flow probes).
DOI: 10.5061/dryad.b327c/6
title: List of trees equipped with sap flow probes

description: This is the list of trees that were equipped with Granier-style probes to measure sap flux density.
DOI: 10.5061/dryad.b327c/8
title: List of trees equipped with automated dendrometer bands

description: This is the list of 121 trees that were equipped with automated dendrometer bands in 4 different sites.
DOI: 10.5061/dryad.bn3kd/1
title: Demographic data of two palm species of the Amazon

description: The sheet datep contains data of Euterpe precatoria, the sheet datmf contains data of Mauritia flexuosa. Both sheets have data of: plot, individuals, size category, survival, stem appearance, height and height increase, number of leaves produced, number of pinnae in time t, number of pinnae in time t+1, fertility and number of racemes produced.    The sheet sedep contains data of Euterpe precatoria germinated seedlings in the last census and so does the sheet seedmf, but for Mauritia flexuosa. The two sheets contain information of plot, survival, number of leaves produced, number of pinnae in time t and number of pinnae in time t+1
DOI: 10.5061/dryad.c494p/11
title: Fig. S11 - Serpentes HiSSE states

description: Figure S11. Ancestral state reconstruction of viviparity for Serpentes from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/13
title: Fig. S13 - Anguimorpha HiSSE states

description: Figure S13. Ancestral state reconstruction of viviparity for Anguimorpha from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/14
title: Fig. S14 - Phrynosomatidae HiSSE states

description: Figure S14. Ancestral state reconstruction of viviparity for Phrynosomatidae from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/15
title: Fig. S15 - Liolaemidae HiSSE states with corrected sampling fraction

description: Figure S15. Ancestral state reconstruction of viviparity for Liolaemidae using the corrected sampling fraction from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/16
title: Table S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fraction

description: Table S1. HiSSE model fits for Liolaemidae using the ucorrected sampling fraction
DOI: 10.5061/dryad.c494p/17
title: Table S2. Diversitree and BiSSE-like HiSSE Gekkota parameter estimates

description: Table S2. Parameters estimated using the BiSSE model in Diversitree and the BiSSE-like model in the HiSSE package for Gamble et al. dataset.
DOI: 10.5061/dryad.c494p/18
title: R code, tree, and data for Gekkota HiSSE analyses

description: This zip file contains the tree, trait data, and commented R script to run HiSSE analyses. The null-four nine-rate model requires the separately uploaded file containing the modified null-four function.
DOI: 10.5061/dryad.c494p/19
title: HiSSE.null4.9rate.R

description: Null-four function modified to allow nine transition rates among hidden states. To run this with 9 transition rates, set trans.type = "All.no.dual", all other arguments are identical to the hisse.null4 in the HiSSE package.
DOI: 10.5061/dryad.f4s16/1
title: Zak_Lipo_tag_recapture

description: Tag-recapture data for the marble trout populations of Zakojska and Lipovscek (two .csv files). Mark = fish ID; Year = year of sampling; Month = month of sampling;	Run = first pass (1) or second pass (2); Sector = stream section in which the fish was sampled; Length = total length of fish (mm); Weight = weight of the fish (g); Age = age of fish - fish emerge in May/June, they are 0+ up to first winter, then 1+ and so on; Cohort: year of birth (format Cyy); Adc: 1 if adipose fin was cut - only for fish with no tag when sampled; Adip = additional tag associated with a piece of the adipose cut.
DOI: 10.5061/dryad.f4s16/2
title: Zak_Lipo_SNP_genotype

description: Genotype data for the marble trout populations of Zakojska and Lipovscek. LOCATION = name of the stream/population; 	SAMPLE_ID  fish ID, corresponds to Mark in the tag-recapture dataset; SEX = sex of fish - ? and NA mean not available/uncertain;	YOB = year of birth of fish. Additional columns are the bi-allelic SNPs (0 means not genotyped).
DOI: 10.5061/dryad.fn368/1
title: Lemmens et al., Functional Ecology

description: This isotopic data of food web components  and fish community data of Lake Abaya and Lake Chamo
DOI: 10.5061/dryad.j2130/1
title: Bladderwort-bluegill exp't data

description: Growth and survival data for Bluegill along with zooplankton counts by treatment
DOI: 10.5061/dryad.kj666/4
title: SGA output for analysis sets 21-30.

description: Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 21-30.
DOI: 10.5061/dryad.kj666/5
title: SGA output for analysis sets 31-37.

description: Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 31-37.
DOI: 10.5061/dryad.m17c8/2
title: Data file 4

description: Supplementary figures
DOI: 10.5061/dryad.n0g90/1
title: Data of samplings

description: Data of samplings to evaluate the effect of wind in number of active workers and loaded and unloaded ants speed, and to measure load area carried by workers in natural conditions.
DOI: 10.5061/dryad.r2445/1
title: Arthropod survey data

description: A species matrix of arthropods observed on focal plants.
DOI: 10.5061/dryad.rv08j/3
title: Fasta file of the 2010 orthologs for each of the three species

description: Ortholog identification and alignment are described in the paper.  Briefly, clusters of orthologous genes (with a single member from each species) were identified using blast and mcl clustering.  Alignments were made using MUSCLE.
DOI: 10.5061/dryad.116q7/1
title: Genotypes8loci213samplingunits

description: Microsatellite dataset formatted for GenClone program, with the first column indicating the identifier of sampling units (a concatenation of the location of sampling andunique number), two columns indicating 999 as no sampling coordinates were available, and the remaining 8 columns containing the diploid genotypes at the 8 mirosatelites used, with 3 digits per allele corresponding to the size of the amplified fragment (primers included). The first lines summarize as for GenClone infile the number of sampling units, the maximum coordinates (here missing data), the number of loci, the 2 for diploid dataset and the name of the eight microsatellite loci .
DOI: 10.5061/dryad.116q7/2
title: Experiment: ERX267379

description: Bacterial community dataset: 454 GSLX Data related to the Sample SAMEA1976875 and  ERS251417
DOI: 10.5061/dryad.1414v/1
title: SupplementaryMaterials_PHRAPL_tutorial

description: A detailed tutorial for using PHRAPL
DOI: 10.5061/dryad.1414v/2
title: SupplementaryMaterials_Figures

description: Supplemental figures
DOI: 10.5061/dryad.1414v/3
title: SupplementaryMaterials_Methods

description: Supplemental methods
DOI: 10.5061/dryad.1414v/4
title: SupplementalMaterials_Data&Scripts

description: Datasets simulated and scripts used for this paper
DOI: 10.5061/dryad.19gp1/1
title: Mitochondrial DNA alignment

description: Mitochondrial DNA alignment (ND1 gene) in phylip format.
DOI: 10.5061/dryad.19gp1/2
title: Unlinked SNP, phylip

description: Unlinked SNPs in phylip format.
DOI: 10.5061/dryad.1h2ft/1
title: Parker_data

description: Data used to create manuscript figures, including: egg size (diameter), total lipid content of eggs, shell length of larvae (day 15), standard metabolic rate of larvae (day 15), percentage of umbonate larvae (day 9), percentage survival of larvae (day 15).
DOI: 10.5061/dryad.25nj1/1
title: dataset_AP

description: The file includes raw data of binocular rivalry tracking results in .mat format for each participant. Eye tracking data (.asc) per trial for each participant are also included.
DOI: 10.5061/dryad.31br0/1
title: Female Weights

description: Contains the weight data of the females in the study population.
DOI: 10.5061/dryad.31br0/2
title: Male Weights

description: Contains the weights of the males in the study population.
DOI: 10.5061/dryad.31br0/3
title: Growth Parameters

description: Growth parameters as described in the paper. Tab delimited.
DOI: 10.5061/dryad.3264f/2
title: Mound coordinates - termite model
DOI: 10.5061/dryad.3264f/3
title: Mound coordinates - field data
DOI: 10.5061/dryad.3264f/4
title: Matrix vegetation - FT analysis (model and data)
DOI: 10.5061/dryad.3264f/5
title: Voronoi analysis of mounds
DOI: 10.5061/dryad.344qn/1
title: GrowthDataSEH

description: Growth rates, cells size and chlorophyll measurements for O. tauri under different environments
DOI: 10.5061/dryad.344qn/2
title: VirusInoculation

description: Cell counts for O. tauri populations after virus inoculation in different environments
DOI: 10.5061/dryad.344qn/3
title: CodeFiguresSEH

description: R code for all figures presented in the manuscript
DOI: 10.5061/dryad.344qn/4
title: CodeModelsSEH

description: R code for all mixed effects models presented in the manuscript
DOI: 10.5061/dryad.344qn/5
title: Growthranked

description: Mean O. tauri growth rates ranked in order from fastest to slowest growing for each environment
DOI: 10.5061/dryad.34k42/4
title: 4.Total_Number_of_Affiliative_and_Agonistic_Submissive_interactions_in_dog_packs

description: This file contains ten tables. Each table is a squared matrix reporting the total number of affiliative or agonistic submissive gestures exchanged among dogs belonging to the same pack (see Bonanni et al. 2017, Behav Ecol, for a definition of both types of submission). So, there are two tables for each dog pack, one reporting the outcomes of affiliative submissive gestures and the other one reporting the outcomes of agonistic submissive gestures. Performers of affiliative/agonistic submissive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of affiliative/agonistic submissive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the directional consistency of affiliative and agonistic submissive gestures separately, and mostly to calculate the correlation between matrices of affiliative submissions and those of agonistic submissions for each pack separately.
DOI: 10.5061/dryad.34k42/5
title: 5.Measures_of_social_tolerance_in_dog_packs

description: This file contains a table reporting several measures of social tolerance (and other related variables) in domestic dog packs, comprising both the packs presented in the paper by Bonanni et al. (2017), and others for which data were published in other papers (data source is also reported). Measures of social tolerance comprised: directional consistency index of total submissive behaviour, hierarchy steepness (calculated from matrices reporting total submissive behavior, and based on Dij, i.e. dyadic dominance indexes corrected by chance), and proportion of bites in relation to the total number of agonistic interactions (obtained by summing up aggressive and dominance interactions). Related variables comprised: percentage of dyadic unknown relationships in matrices reporting total submissive behaviour, number of pack members, and proportion of pack members who were either spayed or castrated. In the original paper, these data were used to assess Spearman correlation between measures of social tolerance and related variables.
DOI: 10.5061/dryad.34k42/6
title: 6.Measures_of_social_tolerance_in_free-ranging_dogs_and_wolves

description: This file contains a table reporting measures of social tolerance (and some related variables) in packs of free-ranging dogs and wolves. The latter comprises both packs presented in the paper by Bonanni et al. 2017, as well as packs studied in other papers (data source is also reported in the table). Measures of social tolerance comprised 1) directional consistency indexes of total submissive behaviour and 2) hierarchy steepness (calculated from matrices reporting total submissive behavior, and based on Dij, i.e. dyadic dominance indexes corrected by chance). The table also reports the number of pack members, and the percentage of unknown dyadic relationships in matrices reporting total submissive behaviour, i.e. the same matrices used to calculate measures of social tolerance. In the original paper, these data were used to compare the degree of social tolerance displayed by dogs with that displayed by wolves.
DOI: 10.5061/dryad.34k42/7
title: 7.Total_Number_of_Aggressive_interactions_in_dog_packs

description: This file contains six tables. Each table is a squared matrix reporting the total number of aggressive gestures exchanged among dogs belonging to the same pack. So, each table corresponds to a different dog pack. Performers of aggressive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of aggressive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the statistical parameters reported in Table S6, i.e. hierarchy linearity, directional consistency of aggressive behaviour, hierarchy steepness, as well as percentage of unknown, 1-way, 2-ways, and tied dyadic relationships.
DOI: 10.5061/dryad.34k42/8
title: 8.Total_Number_of_Dominance_interactions_in_dog_packs

description: This file contains six tables. Each table is a squared matrix reporting the total number of dominance displays exchanged among dogs belonging to the same pack. So, each table corresponds to a different dog pack. Performers of dominance displays are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of dominance displays are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). Also, note that the data concerning the Caraffa pack are missing because they were lost. In the original paper, the data reported in these tables were used to calculate the statistical parameters reported in Table S6, i.e. hierarchy linearity, directional consistency of dominance behaviour, hierarchy steepness, as well as percentage of unknown, 1-way, 2-ways, and tied dyadic relationships.
DOI: 10.5061/dryad.3bc74/1
title: Data_for_Dryad_Rusch

description: Excel
DOI: 10.5061/dryad.3mn1t/1
title: Species list and protection attributes

description: The Excel table lists all species included in the analyses, their IUCN Red List status at the time of the analyses, the amount of their range overlapping with various IUCN categories of protected areas (category 7 indicates no IUCN category assigned), and the value of the priority index for the species.  PA overlap area is in meters square.
DOI: 10.5061/dryad.3mn1t/2
title: GeoTIFF rasters of results in figures

description: Raster files are in TIFF format, LZW compressed, and georeferenced (datum WGS84). Rasters of biodiversity and priorities are in the World Eckert IV projection, which is equal area. Files should be compatible with any standard GIS software.
DOI: 10.5061/dryad.41f8t/1
title: Fine scale modelling dataset

description: Variable collected in the investigated caves. A description of each variable is found in the read me file
DOI: 10.5061/dryad.42m1p/1
title: Anopheles moucheti_part2

description: Fastq files for Anopheles moucheti individuals from Cameroon - part 2
DOI: 10.5061/dryad.42m1p/2
title: Anopheles moucheti_part1

description: Fastq files for Anopheles moucheti individuals from Cameroon - part 1
DOI: 10.5061/dryad.43bv0/1
title: Climate Similarity Support Scripts

description: This compressed file contains scripts and supporting data necessary to reproduce the analyses and products associated with Doherty et al. (2017), “Matching seed to site by climate similarity: Techniques to prioritize plant materials development and use in restoration.”
DOI: 10.5061/dryad.4qb79/5
title: Meyer Science 2016 Fig 4C

description: Data collected for results shown in figure 4c, see notes within the file and the manuscript for further guidance.