cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r1d8q/13
title: BEAST A. kanna lineage BSP analysis input file

description: Input data file in XML format used in Bayesian skyline plot (BSP) historical demographical analysis of the cytb dataset corresponding to the A. kanna lineage (supported by BFD species delimitation analyses; see Results) in BEAST v1.8.3. Results from one run of this datafile, as summarized in Tracer, are presented in Fig. 4B.
DOI: 10.5061/dryad.r1d8q/14
title: full-cytb GARLI ML tree

description: Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the full-cytb dataset in GARLI v2.0.
DOI: 10.5061/dryad.r1d8q/15
title: cytb haplotype GARLI ML tree

description: Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the cytb haplotype dataset in GARLI v2.0. A portion of this tree is shown in Fig. 2.
DOI: 10.5061/dryad.r1d8q/16
title: reduced-cytb *BEAST species tree

description: NEXUS format tree file containing the species tree inferred in the best-supported species delimitation model identified during Bayes factor delimitation, the 'two-species allopatric' model. This file is readable in FigTree v1.4.0, and the species tree within it is shown in Fig. S4.
DOI: 10.5061/dryad.r1d8q/17
title: full-cytb BEAST time tree

description: Newick format tree file containing the relaxed-clock time tree (gene tree) inferred in the BEAST analysis of the full-cytb dataset. This tree is shown in Fig. S2.
DOI: 10.5061/dryad.r1d8q/18
title: cytb haplotype BEAST time tree

description: Newick format tree file containing the relaxed-clock time tree (gene tree) inferred in the BEAST analysis of the cytb haplotype dataset. This tree is shown in Fig. S3.
DOI: 10.5061/dryad.r1d8q/19
title: nuclear RPS7 intron 1 dataset

description: NEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 1 dataset alignment, which includes 24 sequences.
DOI: 10.5061/dryad.r1d8q/20
title: nuclear RPS7 intron 2 dataset

description: NEXUS file containing the nuclear ribosomal protein S7 (RPS7) intron 2 dataset alignment, which includes 53 sequences of Amatitlania samples.
DOI: 10.5061/dryad.s089p/1
title: New Zealand sea lion microsatellite dataset

description: 1205 NZSL individuals at 17 microsatellite loci.
DOI: 10.5061/dryad.10877.2
title: Data from: Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants
DOI: 10.5061/dryad.10877.2/1.2
title: Supplemental Dataset 1

description: Module figures for all modules learned from the residuals dataset.
DOI: 10.5061/dryad.10877.2/3.2
title: Supplemental Dataset 2

description: Excel file containing predicted GO annotations for all modules in Supplemental Data Set 1.
DOI: 10.5061/dryad.337dr/1
title: Data Package

description: This is the data package to accompany Senior et al. 2016: Meta-analysis of variance: an illustration comparing the effects of two dietary interventions on variability in weight. The zip file contains three R files. 1) "Analysis.R" is the script to perform the analysis and is heavily commented. 2) "Data.Objects.Rdata" is a R datafile containing all of the necessary to replicate the analysis (see comments in "Analysis.R"). 3) "EffectSizeFunctions.R" contains various functions to calculate effect sizes, and is called in "Analysis.R".
DOI: 10.5061/dryad.4ht86/1
title: Data spreadsheet for Carbon and nitrogen

description: Data spreadsheet for Carbon and nitrogen ANOVA analyses and Fig. 2. Habitat 1 = shallow mud, 2 = muddy sand, 3 = detrital mud, 4 = deep mud
DOI: 10.5061/dryad.4ht86/2
title: CHNData2 - Statistics for Carbon and Nitrogen

description: Statistics for Carbon and Nitrogen ANOVA analyses and Fig. 2.Habitat 1 = shallow mud, 2 = muddy sand, 3 = detrital mud, 4 = deep mud
DOI: 10.5061/dryad.4ht86/3
title: AbunVsCHN2 -data spreadsheet for regression equation

description: Data spreadsheet for regression equation of CHN vs M. balthica density
DOI: 10.5061/dryad.4ht86/4
title: AbunVsCHN2 -statistics from Minitab CHN vs M. balthica density

description: Statistics from Minitab for regression equation of CHN vs M. balthica density
DOI: 10.5061/dryad.4ht86/5
title: Abund&SizeSmLg_05-31-16 -Data spreadsheet Ambient clam density

description: Ambient M. balthica density and size Small (juvenile) and Large (Adult) and Fig. 3
DOI: 10.5061/dryad.5h50p/1
title: Lanes et al 2016 Macaw palm genetic data

description: Excel file containing microsatellite genotypes of A. aculeata adult plants and their offspring, collected from the southeastern region of Brazil.Genetic data of nine microsatellite for  27 mother trees (adult plants) and 157 offspring (juvenile plants). The locus names are listed in the first line. The offspring are identified by alphanumeric code  of genebank listed in the first column of the sheet.The genotypes of each accession are from columns 3 to 20. The allelic description of each offspring was determined by informative numerical codes. Missing genetic data are coded as "0".
DOI: 10.5061/dryad.5kb61/1
title: biomass data

description: These are observations on biomass, which form the core of the study. See Supplemental Figure S1 for a graphical representation. COLUMN HEADINGS: 'spcode' the number of the species (names available in 'species data' file). 'house': Which shadehouse did the seedling grow in? 'indiv' Which individual was the observation made on?, 'light' the light (in %) in the shadehouse. 'day' how many days since the start of the study did the observation occur? 'biomass': the estimated biomass on this day in grams (see Methods for details on how biomass was estimated).
DOI: 10.5061/dryad.5kb61/2
title: Species descriptions

description: THis is basically Table 1. It summarises chaarcteristics of each species used in the study, linking the species codes (spcode) to the famil, genus and species of each taxon. column 'deciduous' indicates whether the species is deciduous or evergreen. Max height is in meters. Successional stage gives the rough shade tolerance of the taxon.
DOI: 10.5061/dryad.5kb61/3
title: harvest data

description: This file contains data from the two destructive harvests. The first six columns are just like in the biomass data file. 'Harvest' indicates which of the two harvests the observation was made. 'date' gives the number of days since the start of the study of the harvest. 'height' is the height of teh measured individual. girth_1 and girth_2 are two perpendicular basal diameters of the stem. BiomassR, BiomassS, BiomassL, and BiomassA give, respectively, the individual's biomass of roots, stem, leaves and all (the sum of the three prior). THickness gives leaf thickness in micrometers (measured only at harvest 3). Leaf area is leaf area of the individual, in cm^2.
DOI: 10.5061/dryad.5kb61/4
title: gas exchange data

description: This file provides details on rates of gas exchange made at the time of the second harvest. The first six columns are just as in the biomass data file. 'Area' represents the leaf area measured for photosynthetic rate in the cuvette, in cm^2. 'N' leaf nitrogen  concetration, on a mass basis, in percent. 'thickness': leaf blade thickness, in micrometers. 'LMR' leaf mass ratio. 'Lcp' Light compensation point - the amount of light (in µmol m-2·s-1) at which photosynthesis is zero. 'Amax': the predicted maximal rate of photosynthesis per unit area in CO2·m-2·s-1. SLA_photo: specific leaf area, 'Amass': predicted maximal photosynthetic rate per unit leaf biomass in nmol CO2·g-1·s-1.
DOI: 10.5061/dryad.648jt/1
title: Bat community data for 15 landscapes in southeastern Brazil

description: All information on bats was collected in the field by Renata  Muylaert. Metadata is described on file.
DOI: 10.5061/dryad.709d4/1
title: Genotype data of 16 UTR-derived SSRs

description: Genotype data for 16 UTR-derived SSRs
DOI: 10.5061/dryad.7cf5j/1
title: Supporting Data

description: Raw data used to generate figures
DOI: 10.5061/dryad.8kd35/1
title: Laser ablation–inductively coupled plasma mass spectrometry raw data for Amazonian fishes

description: Laser ablation–inductively coupled plasma mass spectrometry raw data (background- and drift-corrected) for Brachyplatystoma rousseauxii (Ecuador and Colombia), Brachyplatystoma filamentosum (Colombia), and six Prochilodus nigricans.  Data include Ca, Sr, and Ba for both Brachyplatystoma species and localities, and Ca, Ba, and Mn for all six P. nigricans.
DOI: 10.5061/dryad.8kd35/2
title: Scanning x-ray fluorescence microscopy raw data for Brachyplatystoma rousseauxii

description: Scanning x-ray fluorescence microscopy raw data (drift-corrected) for Brachyplatystoma rousseauxii (Colombia), including Ca, Se, and Sr.  Calculations of Se:Ca × 1000 and Sr:Ca × 1000 are also included.
DOI: 10.5061/dryad.8kd35/3
title: Scanning x-ray fluorescence microscopy data for Arapaima sp.

description: Scanning x-ray fluorescence microscopy raw data (drift-corrected) for Arapaima sp., including Ca, Zn, and Sr.  Calculations of Zn:Ca × 1000 and Sr:Ca × 1000 are also included.
DOI: 10.5061/dryad.8kd35/4
title: Scanning x-ray fluorescence microscopy data for Brachyplatystoma filamentosum (Colombia)

description: Scanning x-ray fluorescence microscopy raw data (drift-corrected) for Brachyplatystoma filamentosum (Colombia), including Ca, Se, and Sr.  Calculations of Se:Ca × 1000 and Sr:Ca × 1000 are also included.
DOI: 10.5061/dryad.8kd35/5
title: Scanning x-ray fluorescence microscopy data for Plagioscion squamosissimus

description: Scanning x-ray fluorescence microscopy raw data (drift-corrected) for Plagioscion squamosissimus, including Ca, Mn, and Sr.  Calculations of Mn:Ca × 1000 and Sr:Ca × 1000 are also included.
DOI: 10.5061/dryad.98q2r/1
title: individual dip sampling data for mosquito larvae in Ethiopia

description: Site: sites visited labelled from A-Z (with 2 meaning second visit). Sample: count of individual samples taken at each site. Depth: depth in cm at the point of each individual dip sample. Area: area of the water body being sampled. Mean_depth: mean of depth measures from site. ph: ph at each site. Tall_rip: percentage estimate of tall (&gt;20cm) riparian vegetation around the water body. Temp: temperature in degrees celsius at the sampling point. Anoph10: yes/no variable for whether Anopheles larvae were found in an individual dip sample. Algae: whether algae were visibly present in the water body. Sunny: if it was sunny on the surface of the water body at the time of collection.
DOI: 10.5061/dryad.bc80r/2
title: Chanderbali et al_Gamma_Data
DOI: 10.5061/dryad.cc5v0/1
title: Euphorbia rosescens demography dataset

description: Dataset includes vital rates (survival, # stems, reproductive stage, flowering sex, stem length and # cyathia) collected for a demographic study of Euphorbia rosescens from 2004-2012. Data were collected on 1567 individuals among 13 subpopulations that encompassed a variety of habitats and fire histories.
DOI: 10.5061/dryad.cc5v0/2
title: Euphorbia rosescens excavation

description: Dataset includes stem length of above- and belowground plant material collected in a single excavation of 68 Euphorbia rosescens individuals. Above- and belowground root weights were used to calculate below- to aboveground ratios.
DOI: 10.5061/dryad.cj421/1
title: README
DOI: 10.5061/dryad.cj421/2
title: Yangetal_beheco_2016_owsurvival_B
DOI: 10.5061/dryad.cj421/3
title: Yangetal_beheco_2016_glmm
DOI: 10.5061/dryad.fj4f2/1
title: Long-term impacts of variable retention harvesting on ground-layer plant communities in Pinus resinosa forests. Roberts, D'Amato, Kern, Palik.
DOI: 10.5061/dryad.gf036/1
title: Data of nutrient budget section

description: Data used in Figs 2-4 in the nutrient budget section of the paper. See notes in data file for variable description.
DOI: 10.5061/dryad.gf036/2
title: Data of consumer-driven nutrient recycling section

description: Data used in Figs 5-8 in the consumer-driven nutrient recycling section of the paper. See notes in data file for variable description.
DOI: 10.5061/dryad.h7vb0/4
title: LeMoan_4_pops_all_samples_anchovy_working_dataset_MAC2_1SNPperRAD

description: The global SNP dataset used in NewHybrids analysis and in the PCA analysis containing hybrids (Figure 1A). The VCF file contains 5638 SNPs typed in 128 individuals. The minor allele count (MAC) threshold is 2 and only one SNP per RAD was kept.
DOI: 10.5061/dryad.h7vb0/5
title: LeMoan_Atlantic_anchovy_JAFS

description: The JAFS dadi input file for the Atlantic ecotype pair.
DOI: 10.5061/dryad.h7vb0/6
title: LeMoan_Mediterranean_anchovy_JAFS

description: The JAFS dadi input file for the Mediterranean ecotype pair.
DOI: 10.5061/dryad.jd150/1
title: Simulated phylogenies and lineage through time plot Yguel et al 2016 AmNat

description: The Rdata files are simulated phylogenies and lineage through time plot of these simulated phylogenies, used in Yguel et al. 2016 AmNat. The code to extract the LTT plot from the phylogenies is given in the Appendices of the article as well as the method used to make these simulations.The name of the Rdata file indicates which simulation the file is refering to. The Excel files contain measures of phylogenetic structure of these simulated phylogenies (Measure phylogenetic structure parameters on simulated phylogenies.xlsx) and phylogenies of the experimental communities used in the article (Measure phylogenetic structure parameters on Cadotte Zanne phylog.xlsx). The code to calculate a1, a2, a3, and to measure S1 and S2 are given in the method of the article. In all excel files, a1 a2 a3 are the polynomial parameters fitted on the LTT plots. S1 and S2 are respectively ES1 and ES2, the "elderness surface" presented in the article. MPD, MNTD, gamma, and Colless are the common phylogenetic structure measurement (see also method), and invNRI and invNTI the standardized version of MPD and MNTD. RichSpe or Sps correspond to the species richness. PlotID corresponds to the identification of the plot. Mean19962007 corresponds to the mean productivity from 1996 to 2007.
DOI: 10.5061/dryad.m550m/1
title: XML files. Datasets for swine influenza phylogenetic analysis

description: Datasets containing sets of sequences used for the phylogenetic analysis of the different genomic segments of swine influenza
DOI: 10.5061/dryad.m550m/2
title: Supplementary Data file 1

description: acknowledgement of the authors and research laboratories that contributed sequence data
DOI: 10.5061/dryad.m550m/3
title: Supplementary Data file 2

description: acknowledgement of the authors and research laboratories that contributed sequence data
DOI: 10.5061/dryad.m550m/4
title: Supplementary data file 3

description: 2009 pandemic H1N1 genome sequences used in the analysis
DOI: 10.5061/dryad.m550m/5
title: genebank acc numbers

description: accession numbers of the 58 new genomes of swine influenza from Mexico analyzed in this study
DOI: 10.5061/dryad.m550m/6
title: Figure 1 - source data 1

description: source data used in figure 1 of the manuscript
DOI: 10.5061/dryad.mp089/1
title: Experiment_1

description: Redirection Experiment: Experiment 1
DOI: 10.5061/dryad.mp089/2
title: Experiment_2

description: Redirection Experiment : Experiment 2
DOI: 10.5061/dryad.mp089/3
title: Experiment_3

description: Redirection Experiment: Experiment 3
DOI: 10.5061/dryad.mp089/4
title: Experiment_4

description: Speed match experiment : Experiment 4
DOI: 10.5061/dryad.pc307/2
title: Transect Descriptions

description: Notes on locating garlic mustard transects along North Lake Road.
DOI: 10.5061/dryad.pr2v3/1
title: Radman et al. data
DOI: 10.5061/dryad.r0160/1
title: Study 1 Data

description: Primate species represented in Study 1, including the following data per sex for each: number of individuals and recordings, vocal fundamental frequency, body mass, habitat, and mating system, as well as sexual dimorphism (male/female) in vocal fundamental frequency
DOI: 10.5061/dryad.r0160/2
title: Study 2 Data

description: Participants represented in Study 2, including the following data for each: age, sex, ethnicity, ratings of attractiveness and dominance from voice recordings, duration of recordings, and acoustic parameters
DOI: 10.5061/dryad.r1d8q/21
title: RPS7 intron 1 GARLI ML tree

description: Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the ribosomal protein S7 (RPS7) intron 1 dataset in GARLI v2.0. This tree is shown at the top of Fig. S1.
DOI: 10.5061/dryad.r1d8q/22
title: RPS7 intron 2 GARLI ML tree

description: Newick format tree file containing the single 'best' maximum-likelihood tree resulting from analysis of the ribosomal protein S7 (RPS7) intron 2 dataset in GARLI v2.0. This tree is shown at the bottom of Fig. S1.
DOI: 10.5061/dryad.r1d8q/23
title: *BEAST 'four-species' model input file

description: Input data file in XML format used in *BEAST (multispecies coalescent) species tree analysis of the reduced-cytb dataset in BEAST v1.8.3 under a 'four-species' model grouping sequences into the corresponding three currently recognized species of Amatitlania, as well as A. nigrofasciata samples from Lago Coatepeque formerly known as 'A. coatepeque'. The final section of this file calls a post-run analysis estimating the log-marginal likelihood of the model using path sampling (PS) and stepping-stone (SS) sampling approaches.
DOI: 10.5061/dryad.s41s2/1
title: Trocha_Data_FE2015-00294

description: The file contains data on respiration (RS) (nmol O2 g-1 s-1) and nitrogen concentration (%N) of 93 species of fungal sporocarps of different fungal guilds (ECM-ectomycorrhizal, SAP-saprotrophic, and PAR-parasitic); the file contains also information on RS and %N in fungal "tissues" (cap, stipe, and as 'sporocarp' for those species do not form cap-and-stipe fruiting bodies); the number of each RS and %N measurement and sporocarp repeat is also included;
DOI: 10.5061/dryad.vm32c/1
title: Laying date data
DOI: 10.5061/dryad.vm32c/2
title: Nestling mass
DOI: 10.5061/dryad.0kn60/1
title: Pope NEJM 2009

description: air quality, longevity and demographic variables for 211 US cities
DOI: 10.5061/dryad.10877.1
title: Data from: Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants
DOI: 10.5061/dryad.10877.2/2.2
title: Supplemental Dataset 3

description: Module figures for all modules learned from the original dataset, without removing lab and accession effects.
DOI: 10.5061/dryad.10877.2/4.2
title: Supplemental Dataset 4

description: Excel file containing predicted GO annotations for all modules in Supplemental Data Set 3.
DOI: 10.5061/dryad.10877.2/5.2
title: Supplemental Dataset 5

description: Excel file with gene counts in the residuals and sample networks for all GO processes with at least 10 nodes in the residuals network.
DOI: 10.5061/dryad.10877.2/6.2
title: Supplemental Dataset 6

description: Category-specific function prediction performance figures for all GO categories scored in Supplemental Figure 5.
DOI: 10.5061/dryad.20627/10
title: Environment Dataset

description: Environmental variables including mean monthly rainfall, dry season length, original forest cover, and surface water cover, aggregated by municipality in the Brazilian Amazon.
DOI: 10.5061/dryad.20627/8
title: Hydrology Datasets

description: Point data on river water level, river discharge/flow, and daily precipitation for the Amazon, Tocantins/Araguaia, Paraná, and Atlantic watersheds contained within the Brazilian Amazon.
DOI: 10.5061/dryad.20627/9
title: Health Datasets

description: Disease incidence data by municipality of residence, including malaria, dengue fever, cutaneous leishmaniasis, and HIV/AIDS, for the Amazon region of Brazil.
DOI: 10.5061/dryad.2r025/1
title: LeGouez_PlosOne2016

description: Neonatal data from a cohort of children with esophageal atresia and their parents' psychological responses (PPQ and STAI questionnaires).
DOI: 10.5061/dryad.2v77j/1
title: Vijay_et_al_2016_oilpalm

description: Contains shapefile and georeferenced TIFFs from the paper.
DOI: 10.5061/dryad.38537/1
title: Ichthyolith Counts for DSDP Site 596 and ODP Site 886

description: IODP Sample identifiers, downcore depth, age, ichthyolith counts and ichthyolith accumulation rates for DSDP Site 596 and ODP Site 886.
DOI: 10.5061/dryad.40c7c/1
title: ALL-samples-Q30-snps-recal-beagle-polymorphic.vcf

description: Variant call format (VCF) file for 16 Gopherus polyphemus samples for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2016) Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Molecular Ecology Resources. For detailed steps on how this file was created see: https://github.com/jelber2/immunome_2014/blob/master/README.md
DOI: 10.5061/dryad.40c7c/2
title: ALL-samples-recal03.bam

description: Binary alignment map (BAM) file for 16 Gopherus polyphemus samples for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2016) Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Molecular Ecology Resources. For detailed steps on how this file was created see: https://github.com/jelber2/immunome_2014/blob/master/README.md
DOI: 10.5061/dryad.4ht86/10
title: ForagEff - Statistics in Minitab of foraging efficiency of crabs on clams

description: Statistics in Minitab of foraging efficiency of crabs on clams, and foraging efficiency ANOVAs (log-transformed data)
DOI: 10.5061/dryad.4ht86/11
title: GrowSplitPlot - Data spreadsheet for clam growth using split plot design

description: Data spreadsheet for clam growth in caging experiment using split plot design
DOI: 10.5061/dryad.4ht86/12
title: GrowSplitPlot -Statistics from Minitab for clam growth from caging experiments

description: Statistics from Minitab for clam growth from caging experiments; stats for Table 2, growth from split plot analysis
DOI: 10.5061/dryad.4ht86/13
title: OpAmbient2 - Data spreadsheet ambient clams from experimental plots

description: Data spreadsheet ambient clams from experimental plots; mean ambient abundance in experimental plots for Fig. 5
DOI: 10.5061/dryad.4ht86/14
title: OpAmbient2 - Statistics from Minitab mean ambient clam abundance

description: Statistics from Minitab; mean ambient clam abundance in experimental plots for Fig. 5
DOI: 10.5061/dryad.4ht86/6
title: Abund&SizeSmLg_05-31-16 - Statistics for ambient clam density

description: ANOVAs for M. balthica density and size Small (juvenile) and Large (Adult) and Fig. 3
DOI: 10.5061/dryad.4ht86/7
title: Preds2_05-31-16 - Data spreadsheet predator abundance

description: Data for predator abundance ANOVAs, and number of clams per crab ANOVAs and means
DOI: 10.5061/dryad.4ht86/8
title: Preds2_05-31-16 - Statistics from Minitab for predator abundance

description: Statistics from Minitab for predator abundance ANOVAs, and number of clams per crab ANOVAs and means
DOI: 10.5061/dryad.4ht86/9
title: ForagEff -Data spreadsheet Foraging efficiency of crabs on clams

description: Data spreadsheet of foraging efficiency of crabs and clams
DOI: 10.5061/dryad.4nj8n/1
title: Data_041916

description: S. purpuratus asymmetry data (including all feeding data)
DOI: 10.5061/dryad.4nj8n/2
title: Dendraster_Data042816

description: Dendraster asymmetry data
DOI: 10.5061/dryad.4nj8n/3
title: DoubleRudiment_Data_Final

description: S. purpuratus double rudiment data
DOI: 10.5061/dryad.67g5d/1
title: upload for Dryad

description: The zip files contains a WORD file that explains all contents of the uploaded data. There are two sub-directories ('analysis' and 'recorded files'), which contain the originally recorded files and the files created during analysis, respectively. All details about these files are provided within the WORD file ('Files uploaded to Dryad').