cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tr360/1
title: Body temperature of Aardvarks in the Kalahari and meteorological data

description: This file provides the body temperature of four aardvarks (Orycteropus afer) recorded in 2012-2013 in the South African Kalahari (Tswalu Game Reserve) and black globe temperature measured on site. Data were recorded at a 30 min interval. Body temperature was recorded using miniaturized data logger implanted surgically. Three of the aardvarks died during the course of the study, one did survive the planned year.
DOI: 10.5061/dryad.v861k/1
title: Microsat25_2991Plectropomus

description: 25 microsatellite loci for 2991 Plectropomus app collected from the southern Great Barrier Reef, Australia
DOI: 10.5061/dryad.0008d/6
title: Fig 7. IHC analyses of Abeta deposits in TG mice 9 months post-irradiation

description: Immunohistochemical analyses of Abeta deposition analyses of Aβ deposits in TG APP/PS1 mice 9 months post-irradiation.
DOI: 10.5061/dryad.0008d/7
title: Fig 8. WB analyses of synaptophysin in the cortex of TG and WT mice at 9 months

description: Western Blot analyses of synaptophysin in the cortex of TG and WT mice 9 months post-irradiation.
DOI: 10.5061/dryad.0008d/8
title: Fig 9. Cytokine levels in the cortex of TG and WT mice 9 months post-irradiation.

description: Luminex analyses of cytokine levels in the cortex of TG and WT mice 9 months post-irradiation.
DOI: 10.5061/dryad.24tm0/1
title: Comments to data sets

description: Background information to the data sets
DOI: 10.5061/dryad.24tm0/2
title: FemaleFledge_Dryad_Tot

description: Females Fledged
DOI: 10.5061/dryad.2v0hj/1
title: Hormones, ovaries and CHCs

description: Self explanatory data for hormone titers in hemolymph (radioimmunoassay for juvenile hormone and ecdysteroids), measurements of oocyte area  for all females (using ImageJ) and the cuticular hydrocarbon proportions for all individuals in study. The latter data was log transformed for analyses in paper (see methods).
DOI: 10.5061/dryad.3324n/1
title: RAW DATA_Pointing Gesture Experiment-Free-ranging dogs

description: All data decoded from the videos used for the pointing gesture experiment.
DOI: 10.5061/dryad.38jp6/2
title: HD_SNP

description: map file of the high density SNP data ped file
DOI: 10.5061/dryad.3jg7h/1
title: Alignment from Heinicke et al.

description: Concatenated alignment of 389 loci for 35 species of frog. File is in phylip format. Gene boundaries are identified in associated partition file
DOI: 10.5061/dryad.4mt00/1
title: Fisher Detections

description: The binary detection history of fisher via camera at non-invasive detection stations.  Fisher detections were used as a covariate for the probability of falsely detecting American marten; the dimensions of the file represent the number of detection stations (238 rows) and the maximum number of sampling occasions (9 columns) for any given station; 0 indicates no fisher detection, 1 indicates fisher detection, and NA indicates the station was not active for a particular check.
DOI: 10.5061/dryad.4mt00/2
title: MartenOccupancyEncounters

description: Encounter history for American martens at 238 detection stations in Maine, used to model marten occurrence. Rows represent unique stations (238), columns represent sampling occasions (maximum of 9). Cell values correspond to detection outcomes: 1 indicates a marten was detected by a camera only, 2 indicates a marten was detected via snow-tracking, 3 indicates that both a camera image and marten snow tracks were observed, and 4 indicates no marten detection.
DOI: 10.5061/dryad.4mt00/3
title: Detection Station Locations

description: This file provides the x and y coordinates of 238 detection stations used to survey American marten in Maine, USA. Units are UTM/1000 (thus, km units); original projection of the data was UTM Zone 19N.
DOI: 10.5061/dryad.4mt00/4
title: Detection Station Activity History

description: The detection station activity history used for Spatial Capture-Recapture modeling of American marten density. 238 rows correspond to distinct station, with 22 total checks corresponding to columns. Cell values of 1 indicate that a detection station was active during a specific check period, and cell values of 0 indicate it was not active.
DOI: 10.5061/dryad.4mt00/5
title: Marten site covariates, occupancy models

description: Two site covariates used for occupancy modeling. each row corresponds to 1 of 238 detection stations: "Early" is a binary variable indicating whether a station was active during early winter (Jan. & Feb.), "MNEVC" corresponds to the z-standardized proportion of existing Tree vegetation cover within a 1km buffer surrounding the detection station location.
DOI: 10.5061/dryad.4mt00/6
title: Individual Marten Captures

description: Individual marten encounter history used for Spatial Capture-recapture modeling of marten density in 'flat format': data must be coerced to a 3-dimensional array for model fitting using the BUGS language. Individual represents the identity of the marten encountered, trap represents the trap number at which the individual was encountered, check corresponds to the check # during which the individual marten was detected at the specific detection station, and detection type corresponds to the type of detection: 2 represents detection by camera only, 3 represents detection by non-invasive genetic sampling only, and 4 represents detection by both camera and non-invasive genetic sampling.
DOI: 10.5061/dryad.54tv7/1
title: Single tabulated data set

description: Contains all data used in the analyses published in the paper.
DOI: 10.5061/dryad.5fr18/1
title: Houle et al. Nature.

description: Data used in Houle et al. Nature "Mutation predicts 40 million years of fly wing evolution"
DOI: 10.5061/dryad.6n1q4/1
title: Anti-feedant assay data
DOI: 10.5061/dryad.6n1q4/2
title: Behavioural experiments data
DOI: 10.5061/dryad.6n1q4/3
title: Colour contrast data
DOI: 10.5061/dryad.6n1q4/4
title: Pattern fraction of transitions data
DOI: 10.5061/dryad.6n1q4/5
title: Sequence data
DOI: 10.5061/dryad.771p1/1
title: Dunlin (Calidris alpina) counts

description: Total number of dunlins (Calidris alpina) counted in high-tide roost regular counts at the Tagus estuary (Portugal) during spring migration.
DOI: 10.5061/dryad.771p1/2
title: Carbon and nitrogen stable isotopic ratios of Dunlin (Calidris alpina)

description: Carbon and nitrogen stable isotopic signatures of dunlin (Calidris alpina) toenails, red blood cells (RBC) and plasma collected at the Tagus estuary (Portugal) and Banc d'Arguin (Mauritania) during the winters of 2012-2013 and 2013-2014, and at the Tagus estuary (Portugal) during spring migration of 2013 and 2014. Wintering origins of dunlins sampled during spring migration at the Tagus estuary, as determined by a discriminant analysis based on isotopic signatures of toenails (see Catry et al. 2016, 10.1016/j.baae.2015.10.005), are also included. Birds identified as originating from wintering areas outside Mauritania and Portugal (e.g. Morocco) are included in the dataset but were excluded from further analyses, as well as two birds with low classification scores.
DOI: 10.5061/dryad.79822/1
title: Data, analysis scripts, and results

description: This is the main working directory for the project and it contains clean data, all scripts needed to reproduce the analysis, results, figures, notes from the development process, and assorted ancillary files. These files are also available on GitHub (https://github.com/infotroph/efrhizo); this zip file is a snapshot of that repository at revision 8783e81.
DOI: 10.5061/dryad.79822/2
title: Full Stan output

description: Full output (~900 MB) from the Stan models, including saved HMC chains and a lot of diagnostic plots.
DOI: 10.5061/dryad.79822/3
title: Image tracing data

description: Full outputs from the manual image-tracing stage of the analysis. Includes the same data and log files included in the working directory's `rawdata/` folder, plus `.pat` files containing pixel-by-pixel coordinates of every root in each image traced in the experiment... but in an undocumented format :(
DOI: 10.5061/dryad.7hn1j/1
title: Combined alignment: benA caM RPB2

description: Combined dataset of BenA, CaM and RPB2 sequences for 164 taxa belonging to section Aspergillus (formerly Eurotium). Hamigera avellanea NRRL 1938T represents an outgroup. BenA: positions 1-408; CaM: positions 409-1124; RPB2: positions 1125-2093
DOI: 10.5061/dryad.7hn1j/10
title: Aspergillus sect. Aspergillus: Tree based on ITS rDNA

description: A 50% majority rule Maximum likelihood consensus tree based on ITS rDNA sequences. Maximum likelihood bootstrap proportion (bs) and Bayesian posterior probability (pp) are appended to nodes; only bs ≥ 70 % and pp ≥ 95% are shown, lower supports are indicated with a hyphen, whereas asterisks indicate full support (100% bs or 1.00 pp); ex-type strains are designated by a superscript T. The tree is rooted with Hamigera avellanea NRRL 1938T.
DOI: 10.5061/dryad.7hn1j/2
title: Phylogeny of sect. Aspergillus inferred from combined data: BenA, CaM, RPB2

description: A 50% majority rule Maximum likelihood consensus tree based on combined dataset of BenA, CaM and RPB2 sequences showing the relationship of species within Aspergillus sect. Aspergillus. Dataset contained 164 taxa. Maximum likelihood bootstrap proportion (bs) and Bayesian posterior probability (pp) are appended to nodes; only bs ≥ 70 % and pp ≥ 95% are shown, lower supports are indicated with a hyphen, whereas asterisks indicate full support (100% bs or 1.00 pp); ex-type strains are designated by a superscript T. The tree is rooted with Hamigera avellanea NRRL 1938T.
DOI: 10.5061/dryad.7hn1j/3
title: β-tubulin (BenA) alignment

description: Alignment: β-tubulin (BenA) sequences for 164 taxa belonging to section Aspergillus (formerly Eurotium). Hamigera avellanea NRRL 1938T represents an outgroup.
DOI: 10.5061/dryad.7hn1j/4
title: Aspergillus sect. Aspergillus: Tree based on benA

description: A 50% majority rule Maximum likelihood consensus tree based on partial β-tubulin (BenA) sequences showing the relationship of species within Aspergillus sect. Aspergillus. Maximum likelihood bootstrap proportion (bs) and Bayesian posterior probability (pp) are appended to nodes; only bs ≥ 70 % and pp ≥ 95% are shown, lower supports are indicated with a hyphen, whereas asterisks indicate full support (100% bs or 1.00 pp); ex-type strains are designated by a superscript T. The tree is rooted with Hamigera avellanea NRRL 1938T.
DOI: 10.5061/dryad.7hn1j/5
title: Calmodulin (caM) alignment

description: Alignment: calmodulin (caM)  sequences for 164 taxa belonging to section Aspergillus (formerly Eurotium). Hamigera avellanea NRRL 1938T represents an outgroup.
DOI: 10.5061/dryad.7hn1j/6
title: Aspergillus sect. Aspergillus: Tree based on CaM

description: A 50% majority rule Maximum likelihood consensus tree based on partial calmodulin (CaM) sequences showing the relationship of species within Aspergillus sect. Aspergillus. Maximum likelihood bootstrap proportion (bs) and Bayesian posterior probability (pp) are appended to nodes; only bs ≥ 70 % and pp ≥ 95% are shown, lower supports are indicated with a hyphen, whereas asterisks indicate full support (100% bs or 1.00 pp); ex-type strains are designated by a superscript T. The tree is rooted with Hamigera avellanea NRRL 1938T.
DOI: 10.5061/dryad.7hn1j/7
title: RPB2 alignment

description: Alignment: RNA polymerase II second largest subunit (RPB2) sequences for 164 taxa belonging to section Aspergillus (formerly Eurotium). Hamigera avellanea NRRL 1938T represents an outgroup.
DOI: 10.5061/dryad.7hn1j/8
title: Aspergillus sect. Aspergillus: Tree based on RPB2

description: A 50% majority rule Maximum likelihood consensus tree based on partial RNA polymerase II second largest subunit (RPB2) sequences showing the relationship of species within Aspergillus sect. Aspergillus. Maximum likelihood bootstrap proportion (bs) and Bayesian posterior probability (pp) are appended to nodes; only bs ≥ 70 % and pp ≥ 95% are shown, lower supports are indicated with a hyphen, whereas asterisks indicate full support (100% bs or 1.00 pp); ex-type strains are designated by a superscript T. The tree is rooted with Hamigera avellanea NRRL 1938T.
DOI: 10.5061/dryad.7hn1j/9
title: ITS rDNA alignmet

description: Alignment: RNA polymerase II second largest subunit (RPB2) sequences for 164 taxa belonging to section Aspergillus (formerly Eurotium). Hamigera avellanea NRRL 1938T represents an outgroup.
DOI: 10.5061/dryad.7p2cv/3
title: collembola.csv

description: Categorical observations of Collembola abundance before each harvest (0 = no individual in the microcosm; 1 = 1-10 individuals; 2 = 10-100 individuals; and 3 = more than 100 individuals).
DOI: 10.5061/dryad.8n4f6/1
title: Salas-Morales et al DataBase

description: The data contained in this data base are from 15 localities in Coastal Oaxaca, Mexico. The format is an Excel Book. Page 'Location' includes names and geographical coordinates of the localities. Page 'Height' contains the heights in m for all trees recorded in 10 2 x 50-m transects at each locality; next to the height of each individual the growth form of the plant is provided; the number of individuals varies between localities. The third page ('Environment') includes results of soil analyses for soil samples from each location; these analyses may come from the upper or the lower soil horizon; additionally, climatic data for each location are included, which were obtained through linear interpolation of data recorded at meteorological stations in the region with long climatic records.
DOI: 10.5061/dryad.8sm32/1
title: Raeymaekers et al-NatCommun-2017

description: Morphological, spatial and environmental data of populations of the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) from eight sites in the Belgian-Dutch lowlands.
DOI: 10.5061/dryad.8sm32/2
title: Raeymaekers et al-NatCommun-2017_three_spined_reference_based_genotypes

description: Reference-based SNP genotypes of the three-spined stickleback (VCF file). Individuals are labelled as Population_ID.
DOI: 10.5061/dryad.9c5s0/1
title: Seasonal_genetic_structure_Pygospio_elegans

description: The file 'Seasonal_genetic_structure_Pygospio_elegans.xlsx' contains information about samples used in this study including:
SampleID	
Sampling.Data (population codes include location name and a 2 digit code for the sampling month)
Phenotypic.Data	(Length is measured in mm; cohort refers to cohort assignments described in Thonig et al. 2016 Invertebrate Biology 135(4): 370–384) 
Microsatellite.Data	(11 microsatellite loci, 2 columns for each) 
Structure: Cluster Membership Coefficients	(results of the structure analysis presented in the paper: membership coefficients and final cluster assignment for each individual)
DOI: 10.5061/dryad.b1m2s/1
title: origin sequence data

description: origin sequence data
DOI: 10.5061/dryad.bh7mc/1
title: PhysconiaLabrataAlignmentForDryad

description: Alignment trimmed to nearly equal length sequences, including all of ITS1 and 2.
DOI: 10.5061/dryad.bp096/3
title: Sites
DOI: 10.5061/dryad.bp096/4
title: Readme
DOI: 10.5061/dryad.dc92c/1
title: Lamb et al Necturus microsatellites

description: Microsatellite data (GenePop format from GenAlEx)
DOI: 10.5061/dryad.f8j0n/1
title: pre_post_cop_code.tar

description: This compressed directory contains the 45 files needed to compile the code underlying the paper and run all simulations. Parameter values for simulations are set in the PolyIn.c file, which outputs results in three separate TXT files. The output TXT files can be used in the analysis.R file to recreate all analyses and figures from the paper. This code is also publicly available, with additional documentation, on Brad Duthie's GitHub repository: https://github.com/bradduthie/pre_post_cop
DOI: 10.5061/dryad.g582t/1
title: Data File 1 Symbiodinium LSU rDNA

description: Data File 1. Nexus file of aligned sequences of the partial LSU rDNA from various described species of Symbiodinium including new species under formal description in Clade G.  This was used to generate the phylogeny presented in Figure 1 (Ramsby et al. 2017 J. of Phycology).
DOI: 10.5061/dryad.hq08g/1
title: Data for non-invasive brain stimulation in stroke and healthy controls meta analysis

description: We provide data on non-invasive brain stimulation for fine motor recovery after stroke and for healthy controls. The data consists mainly of pre- and post- means, standard deviations and the sample size of the populations studied.
DOI: 10.5061/dryad.jk183/1
title: cytb (80 sequence) (2)
DOI: 10.5061/dryad.jk183/2
title: KIF24withOG
DOI: 10.5061/dryad.jk183/3
title: LDB5BwithOG
DOI: 10.5061/dryad.jk183/4
title: Microsatellite
DOI: 10.5061/dryad.jk183/5
title: Haplotype List
DOI: 10.5061/dryad.m0q5s/1
title: M_australiense-ForwardReads
DOI: 10.5061/dryad.m0q5s/2
title: M_australiense-ReverseReads
DOI: 10.5061/dryad.qn119/1
title: Predictor variables for model averaging procedure

description: Litter mass, plant species richness, soil pH and litter carbon to element ratios for N, P, K, Ca, Mg, Na, and S measured on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-land use system-replicate (two landscapes: Bukit Duabelas (B) and Harapan (H); four land-use systems: Forest (F), Jungle rubber (J), Rubber (R), Oil palm (O); four replicates). Litter_mass gives the dry litter mass per ground area in g cm-2 (Krashevska et al., Biol. Fertil. Soils, 2015). Plant_rich gives the species richness of all trees with a diameter equal to or larger than 10 cm at breast height as well as all vascular plants per site. Soil pH, analysed in a 1:4 soil-to-water ratio, was taken from Allen et al. (PLoS ONE, 2015). Elemental ratios (CX) were calculated based on mg per g dry weight of the analysed leaf litter material. To obtain these site-averaged ratios, ratios of single leaf samples were weighted according to their relative importance in local leaf litter at each site (Jochum et al., The American Naturalist, 2017). Note that prior to analyses, predictor variables were transformed and standardized (see main article).
DOI: 10.5061/dryad.qn119/2
title: Observed litter macro-invertebrate species richness per consumer group and site

description: Litter macro-invertebrate species richness of 14 consumer groups observed on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-land use system-replicate (two landscapes: Bukit Duabelas (B) and Harapan (H); four land-use systems: Forest (F), Jungle rubber (J), Rubber (R), Oil palm (O); four replicates). Values represent species richness observed on 3 square metres per site for ten selected taxonomic groups (ants, blattodea, chilopoda, coleoptera, diplopoda, isopoda, isoptera, opiliones, orthoptera, spiders), three functional feeding guilds (detritivores, predators, omnivores) and the complete consumer community (all). It should be noted that the values for the selected taxonomic consumer groups do not necessarily add up to the values of the functional feeding guilds or the complete community as these aggregated groups contained more individuals than just the selected groups. These values are given as reference points for the extrapolated consumer species richness values actually used in the model averaging procedure.
DOI: 10.5061/dryad.qn119/3
title: Extrapolated litter macro-invertebrate species richness per consumer group and site

description: Extrapolated litter macro-invertebrate species richness of 14 consumer groups for the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-land use system-replicate (two landscapes: Bukit Duabelas (B) and Harapan (H); four land-use systems: Forest (F), Jungle rubber (J), Rubber (R), Oil palm (O); four replicates). Values represent extrapolated species richness per site for ten selected taxonomic groups (ants, blattodea, chilopoda, coleoptera, diplopoda, isopoda, isoptera, opiliones, orthoptera, spiders), three functional feeding guilds (detritivores, predators, omnivores) and the complete consumer community (all). For each consumer group, extrapolated species richness was calculated based on the three subplot samples, using the nonparametric “jacknife 2” estimator (Brose et al., Ecology, 2003).
DOI: 10.5061/dryad.qn119/4
title: Litter macro-invertebrate biomass per consumer group and site

description: Fresh biomass of 14 litter macro-invertebrate groups from the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-land use system-replicate (two landscapes: Bukit Duabelas (B) and Harapan (H); four land-use systems: Forest (F), Jungle rubber (J), Rubber (R), Oil palm (O); four replicates). Values represent fresh biomass per site for ten selected taxonomic groups (ants, blattodea, chilopoda, coleoptera, diplopoda, isopoda, isoptera, opiliones, orthoptera, spiders), three functional feeding guilds (detritivores, predators, omnivores) and the complete consumer community (all). Fresh biomass in mg m-2 was calculated as the sum of individual body masses of all sampled individuals that were, in turn, calculated using length-mass regressions from the literature (Barnes et al., Nat. Commun., 2014). It should be noted that the values for the selected taxonomic consumer groups do not necessarily add up to the values of the functional feeding guilds or the complete community as these aggregated groups contained more individuals than just the selected groups.
DOI: 10.5061/dryad.qn119/5
title: Coefficients and 95% confidence intervals for averaged consumer species richness models (Fig1)

description: Standardized coefficients and 95% confidence intervals for each of the ten predictors from each of 14 averaged consumer species richness models presented in Figure 1. Consumer groups are the ten selected taxonomic groups (ants, blattodea, chilopoda, coleoptera, diplopoda, isopoda, isoptera, opiliones, orthoptera, spiders), three functional feeding guilds (detritivores, predators, omnivores) and the complete consumer community (all). Predictor variables are litter mass (LM), plant species richness (prich), soil pH (pH), and litter carbon to element ratios for N, P, K, Ca, Mg, Na, and S. Coef gives the standardized coefficient of each predictor for each averaged model. Confint_lower_boundary and confint_upper_boundary give the 95% confidence interval for the coefficients. It should be noted that for all stoichiometric parameters, negative coefficients indicate a positive effect of the respective elemental availability as the models were run on C:element ratios. As such, a positive effect of e.g. C:N corresponds to a negative effect of N in main text Fig. 1.
DOI: 10.5061/dryad.qn186/1
title: Britton et al. Functional Ecology

description: Data for experiment of Britton et al. 2017, 'Trophic consequences of introduced species: comparative impacts of increased inter-specific versus intra-specific competitive interactions'
DOI: 10.5061/dryad.rv77v/2
title: Midwest Leptinotarsa decemlineata SNP genotype matrix

description: Curated SNP x individual genotype matrix for 24 Lepinotarsa decemlineata populations in the Midwest, USA. Genotypes are encoded in a {0,1,2} format. Contains genotypes for 188 individuals at 34,186 SNPs.
DOI: 10.5061/dryad.rv77v/3
title: Environmental variables

description: Values of potato intensification and percent non-forest habitat associated with 16 Leptinotarsa decemlineata populations in Wisconsin, USA.
DOI: 10.5061/dryad.rv77v/4
title: Imidacloprid LC50 data

description: Coordinates and imidacloprid LC50 estimates for 47 Leptinotarsa decemlineata populations in Wisconsin, USA