cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p5hd0/1
title: Bootstrap31

description: Example of Bootstrap Iteration for 3 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 3 m segment, ntc = proportion of non-treed corridors in 3 m segment, road = proportion of roads in 3 m segment, grass = proportion of grassland in 3 m segment, shrub = proportion of shrubland in 3 m segment, treedcorr = proportion of treed corridors in 3 m segment, urban = proportion of urban land in 3 m segment, water = proportion of water/wetland in 3 m segment
DOI: 10.5061/dryad.p5hd0/2
title: Bootstrap101

description: Example of Bootstrap Iteration for 10 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 10 m segment, ntc = proportion of non-treed corridors in 10 m segment, road = proportion of roads in 10 m segment, grass = proportion of grassland in 10 m segment, shrub = proportion of shrubland in 10 m segment, treedcorr = proportion of treed corridors in 10 m segment, urban = proportion of urban land in 10 m segment, water = proportion of water/wetland in 10 m segment
DOI: 10.5061/dryad.s2h01/1
title: DATA Dryad Venail et al. Functional Ecology
DOI: 10.5061/dryad.t6859/3
title: program covariates

description: The file ‘program covariates.csv’ includes the percentage of nine habitat types (water, development, barren, forest, grassland, pasture, crop, woodywetland, emergentwetland; see Appendix S4 for details) within a buffer (of radius 500 m, 1,000 m, 2,500 m, 5,000 m, and 10,000 m) from the 2006 National Land Cover Database at 99,997 locations (equally spaced) in the Platte River Recovery Implementation Program associated habitat area. For example, the column ‘water.500’ is the percentage of water within a 500 m radius buffer. The columns ‘lat’ and ‘long’ indicate the latitude and longitude of the location where the predictor was calculated.
DOI: 10.5061/dryad.t6859/4
title: state covariates

description: The file ‘state covariates.csv’ includes the percentage of nine habitat types (water, development, barren, forest, grassland, pasture, crop, woodywetland, emergentwetland;see Appendix S4 for details) within a buffer (of radius 500 m, 1,000 m, 2,500 m, 5,000 m, and 10,000 m) from the 2006 National Land Cover Database at 100,044 locations (equally spaced) in Nebraska, USA. For example, the column ‘water.500’ is the percentage of water within a 500 m radius buffer. The columns ‘lat’ and ‘long’ indicate the latitude and longitude of the location where the predictor was calculated.
DOI: 10.5061/dryad.t6859/5
title: whooping crane data with all covariates

description: The file ‘whooping crane data with all covariates.csv’ includes information and predictors for 407 whooping crane group locations in Nebraska from 1988‒2012. The file also contains 10,000 Monte Carlo integration points with predictors calculated from the 1992, 2001, and 2006 National Land Cover Database (NLCD) for a total of 30,000 points. The column ‘ID’ is the United States Fish and Wildlife Service unique identifier for the whooping crane group. The column ‘y’ indicates if the row is a record of a whooping crane group (y = 1) or a Monte Carlo integration point (y = 0). The column ‘group.size’ is the number of whooping cranes in each group. The column ‘sample’ indicates if the whooping crane group location was used in the training (75%) or test (25%) partition of the data. The column ‘water.500’ is the percentage of water within a 500 m radius buffer around whooping crane group locations and Monte Carlo integration points. Names for other covariates of similar form to ‘water.500’ indicate the type of habitat and the buffer size (water, development, barren, forest, grassland, pasture, crop, woodywetland, and emergentwetland (see Appendix S4 for details); 500 m, 1,000 m, 2,500 m, 5,000 m, and 10,000 m). The columns ‘day’, ‘month’ and ‘year’ identify the date the group was first observed on or a date associated with the Monte Carlo integration point. The column ‘population’ is the estimated number of whooping cranes in the Aransas-Wood Buffalo population. The columns ‘lat’ and ‘long’ refer to the latitude and longitude of where the whooping crane group or Monte Carlo integration point was located. The column ‘accuracy’ is the accuracy of the whooping crane group location (2 = ‘1/2-Section’, 3  = ‘1/4-Section’, 5 = ‘section’, 7 = ‘GPS’, and 10 = ‘Landmark’; see Appendix S1 of manuscript for more information and Hefley et al. (2014) citation in manuscript). The column ‘NLCDclass’ refers to the NLCD that was used to calculate the predictors (e.g., 1992).  Note that Monte Carlo integration points (y=0) will have NA recorded in the columns ‘ID’, ‘group.size’, ‘sample’, and ‘accuracy’.

To obtain the original whooping crane group location records and associated information for Nebraska please contact the author (Trevor Hefley) or the Nebraska Field Office of the United States Fish and Wildlife Service (http://www.fws.gov/nebraskaes/).
DOI: 10.5061/dryad.t6859/6
title: Niobrara shapefiles

description: A shapefile of a portion of the Niobrara National Scenic River, Nebraska.
DOI: 10.5061/dryad.t6859/7
title: associated habitat area shapefile

description: A shapefile of the Platte River Recovery Implementation Program associated habitat area along the central Platte River, Nebraska.
DOI: 10.5061/dryad.t6859/8
title: Nebraska

description: A shapefile of Nebraska, USA.
DOI: 10.5061/dryad.v150f/1
title: Susi_etal_2015_AmNat

description: The data contains results of a common garden experiment on Plantago lanceolata and Podosphaera plantaginis.
DOI: 10.5061/dryad.18ng6/4
title: MI_harvest_COMBINED

description: Michigan Harvest Files
DOI: 10.5061/dryad.18ng6/5
title: MN_DYNAMIC_INPUTS_COMBINED_CLIMATES

description: Minnesota Dynamic Input Files (All three climate scenarios)
DOI: 10.5061/dryad.18ng6/6
title: MI_DYNAMIC_INPUTS_COMBINED_CLIMATES

description: Michigan Dynamic Input Files (All three climate scenarios)
DOI: 10.5061/dryad.18ng6/7
title: ReadMe

description: ReadMe file is a general metadata file for all the data associated with the article.
DOI: 10.5061/dryad.1n14c.2/10.2
title: tfile

description: posterior distribution of time calibrated mammaliaforme trees from MrBayes analysis
DOI: 10.5061/dryad.1n14c.2/2.2
title: MCCT

description: Maximum clade credibility tree from simultaneous phylogenetic and dating analysis of living and fossil mammals. extant clade names reflect those in Meredith et al.
DOI: 10.5061/dryad.1n14c.2/3.2
title: body_mass

description: a csv file containing mean and standard errors for ln body mass in living and fossil mammals and mammaliaformes
DOI: 10.5061/dryad.1n14c.2/4.2
title: fitContinuous_paleoModels

description: A corrected version of the functions used in Slater (2013) to fit mode shift models to phylogenetic data. This version uses direct conversion of the variance covariance matrix to fit OU models to non-ultrametric data.
DOI: 10.5061/dryad.1n14c.2/5.2
title: mammaliaformes tree

description: The pruned, renamed tree used in model fitting
DOI: 10.5061/dryad.1n14c.2/6.2
title: fit_mammal_models

description: An R script that allows the user to repeat model fitting analyses performed in the manuscript using the pruned and renamed mammal tree.
DOI: 10.5061/dryad.1n14c.2/7.2
title: fit_models_posterior

description: R script to fit macroevolutionary models to trees from MrBayes Posterior distribution
DOI: 10.5061/dryad.1n14c.2/8.2
title: mammal_mass_posterior

description: mammaliaforme body mass data with row names corresponding to those in the posterior distribution of trees. Used when fitting models to posterior distribution.
DOI: 10.5061/dryad.1n14c.2/9.2
title: pfile

description: parameter (.p) file from dating analysis of living and fossil mammals conducted in MrBayes. This file is required to rescale branch lengths in the posterior distribution of trees
DOI: 10.5061/dryad.4b565/1
title: GLMM and GLM models

description: Includes raw MLPA data files, R scripts and output
DOI: 10.5061/dryad.4b565/2
title: Misc statistics

description: R code script and data for true prevalence estimates, tests of proportions and kolmogorov-smirnov tests
DOI: 10.5061/dryad.4b565/3
title: qPCR

description: Ct values for qPCR data
DOI: 10.5061/dryad.4b565/4
title: Sequences and trees

description: Tree files in newick format for BQCV and SBPV; raw cloned sequences in fasta format for BQCV, SBPV and ABPV
DOI: 10.5061/dryad.92961/1
title: D concolor broad scale surveys

description: Latitude and longitude of survey locations of the pollinators of Drakaea concolor. Includes the number of wasps detected in surveys
DOI: 10.5061/dryad.92961/2
title: D concolor microsat scores

description: Microsatellite scores for a population genetic study of Drakaea concolor
DOI: 10.5061/dryad.92961/3
title: D concolor pollinator choice trials

description: Choice trials with the wasp Pogonothynnus sp., responding to different populations of the orchid Drakaea concolor
DOI: 10.5061/dryad.p5hd0/10
title: Chip_MultipleRegressionResults

description: Results of multiple regression models across 1000 bootstrap iterations. This file includes estimates, t values and p-values for parameter estimates and full models.
DOI: 10.5061/dryad.p5hd0/11
title: ChipmunkFull3

description: Full dataset for 3 m segment. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 3 m segment, ntc = proportion of non-treed corridors in 3 m segment, road = proportion of roads in 3 m segment, grass = proportion of grassland in 3 m segment, shrub = proportion of shrubland in 3 m segment, treedcorr = proportion of treed corridors in 3 m segment, urban = proportion of urban land in 3 m segment, water = proportion of water/wetland in 3 m segment
DOI: 10.5061/dryad.p5hd0/12
title: ChipmunkFull10

description: Full dataset for 10 m segment. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 10 m segment, ntc = proportion of non-treed corridors in 10 m segment, road = proportion of roads in 10 m segment, grass = proportion of grassland in 10 m segment, shrub = proportion of shrubland in 10 m segment, treedcorr = proportion of treed corridors in 10 m segment, urban = proportion of urban land in 10 m segment, water = proportion of water/wetland in 10 m segment
DOI: 10.5061/dryad.p5hd0/3
title: Bootstrap251

description: Example of Bootstrap Iteration for 25 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 25 m segment, ntc = proportion of non-treed corridors in 25 m segment, road = proportion of roads in 25 m segment, grass = proportion of grassland in 25 m segment, shrub = proportion of shrubland in 25 m segment, treedcorr = proportion of treed corridors in 25 m segment, urban = proportion of urban land in 25 m segment, water = proportion of water/wetland in 25 m segment
DOI: 10.5061/dryad.p5hd0/4
title: Bootstrap501

description: Example of Bootstrap Iteration for 50 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 50 m segment, ntc = proportion of non-treed corridors in 50 m segment, road = proportion of roads in 50 m segment, grass = proportion of grassland in 50 m segment, shrub = proportion of shrubland in 50 m segment, treedcorr = proportion of treed corridors in 50 m segment, urban = proportion of urban land in 50 m segment, water = proportion of water/wetland in 50 m segment
DOI: 10.5061/dryad.p5hd0/5
title: Bootstrap1001

description: Example of Bootstrap Iteration for 100 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 100 m segment, ntc = proportion of non-treed corridors in 100 m segment, road = proportion of roads in 100 m segment, grass = proportion of grassland in 100 m segment, shrub = proportion of shrubland in 100 m segment, treedcorr = proportion of treed corridors in 100 m segment, urban = proportion of urban land in 100 m segment, water = proportion of water/wetland in 100 m segment
DOI: 10.5061/dryad.p5hd0/6
title: Bootstrap2001

description: Example of Bootstrap Iteration for 200 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 200 m segment, ntc = proportion of non-treed corridors in 200 m segment, road = proportion of roads in 200 m segment, grass = proportion of grassland in 200 m segment, shrub = proportion of shrubland in 200 m segment, treedcorr = proportion of treed corridors in 200 m segment, urban = proportion of urban land in 200 m segment, water = proportion of water/wetland in 200 m segment
DOI: 10.5061/dryad.p5hd0/7
title: Bootstrap4001

description: Example of Bootstrap Iteration for 400 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 400 m segment, ntc = proportion of non-treed corridors in 400 m segment, road = proportion of roads in 400 m segment, grass = proportion of grassland in 400 m segment, shrub = proportion of shrubland in 400 m segment, treedcorr = proportion of treed corridors in 400 m segment, urban = proportion of urban land in 400 m segment, water = proportion of water/wetland in 400 m segment
DOI: 10.5061/dryad.p5hd0/8
title: Bootstrap10001

description: Example of Bootstrap Iteration for 1000 m segment width. ID = pair-wise comparison, cat = dependent variable for logistic regression, pmem = dependent variable for multiple regression, forest = proportion of forest in 1000 m segment, ntc = proportion of non-treed corridors in 1000 m segment, road = proportion of roads in 1000 m segment, grass = proportion of grassland in 1000 m segment, shrub = proportion of shrubland in 1000 m segment, treedcorr = proportion of treed corridors in 1000 m segment, urban = proportion of urban land in 1000 m segment, water = proportion of water/wetland in 1000 m segment
DOI: 10.5061/dryad.p5hd0/9
title: Chip_LogisticRegressionResults

description: Results of logistic regression models across 1000 bootstrap iterations. This file includes estimates, z values and p-values for parameter estimates and full models.
DOI: 10.5061/dryad.vm752/1
title: nuoM competition data

description: Colony count data from 6-day competitions between admixtures of nuoM+ and nuoM- clones.
DOI: 10.5061/dryad.vm752/2
title: S and L competition data

description: Colony count data from 6-day and 12-day competitions between S and L clones.
DOI: 10.5061/dryad.vm752/3
title: Fit competition data to linear frequency dependence

description: Mathematica notebook that fits competition data to a linear paramaterization of frequency-dependent fitness.
DOI: 10.5061/dryad.vm752/4
title: Fit competition data to quadratic frequency dependence

description: Mathematica notebook that fits competition data to a quadratic paramaterization of frequency-dependent fitness.
DOI: 10.5061/dryad.vm752/5
title: Cross-feeding Monod model and fit to linear frequency dependence

description: Monod model of a cross-feeding interaction, including dynamics of daily resource use and growth. Fits post-growth cycle relative frequencies to a linear parameterization of frequency dependent fitness.
DOI: 10.5061/dryad.033ds/1
title: Neottia_18S+ITS+trnL(UAA)intron_alignment

description: Combined alignment of 18S, ITS, and trnL(UAA) intron of five Neottia species used for infering phylogeny under a partitioned model. This file is in nexus format and contains sequence alignment and MrBayes input data.
DOI: 10.5061/dryad.033ds/2
title: Neottia_18S+ITS+trnL(UAA)intron_tree

description: Bayesian phylogenetic tree of the Neottia genus based on a concatenation of ITS, 18S, and trnL(UAA) intron, with photosynthetic N. ovata, N. cordata, and N. smallii, putatively photosynthetic and likely partially mycoheterotrophic N. camtschatea, and non-photosynthetic mycoheterotrophic N. nidus-avis in adulthood. The tree is in the newick format.
DOI: 10.5061/dryad.033ds/3
title: Neottia_18S_alignment

description: Alignment of 18S of Neottia species produced by MAFFT and used for infering phylogeny. This file is in nexus format and contains sequence alignment and MrBayes input data.
DOI: 10.5061/dryad.0g2f5/1
title: DNA sequence alignments

description: DNA sequence alignments for haplotype as well as individual sequences (two alignments per gene: with one sequence per haplotype and with one sequence per individual).
DOI: 10.5061/dryad.0g2f5/2
title: Occurence data for ENM

description: Occurence data used for ENM (ecological niche modelling).
DOI: 10.5061/dryad.0g2f5/3
title: GenBank accession numbers

description: Text file with GenBank accession number of each haplotype sequence.
DOI: 10.5061/dryad.0g2f5/4
title: Population IDs & coordinates

description: Excel file with population ID, coordinates and location of each sampled population.
DOI: 10.5061/dryad.11h73/1
title: Predator-prey survival data for native and non-native aquatic plants

description: Prey survival data was collected in a series of three aquarium experiments. The file is split into two tabs: realplant-survival used for Figure 1 and artificialplant-survival used for Figure 2. The first tab contains data about prey survival under mirror carp or dragonfly larvae predation in monocultures of real aquatic plants, at low and high stem density. The column headings in the first tab are: totalID (distinct ID per record), testSpecies (gives scientific name of plant species tested), preySurvival (%-prey survival), stemDensity (plant stem density), plantOrigin (plant native status in Northwestern Europe), dayExperiment (day that data record was collected in predator-prey trial), periodDay (time of the day that data record was collected in predator-prey trial), preySpecies (type of prey for data record), predatorSpecies (type of predator for data record), predatorIndividual (unique ID for dragonfly individual or unique ID for fish pairs). The second tab contains data about prey survival under mirror carp predation, in monocultures of artificial plant analogues resembling aquatic plants, at low and high stem density. For information on column headings in the second tab, see descriptions given for headings in the first tab. Information on the number of prey at t0, the duration of predation trials, plant density and other ifnormation is provided in the corresponding publication.
DOI: 10.5061/dryad.1n14c.1
title: Data from: Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Paleogene boundary
DOI: 10.5061/dryad.54bm8/1
title: Map File

description: See ReadMe file
DOI: 10.5061/dryad.54bm8/2
title: Microsatellite genotypes

description: Microsatellite genotypes for all samples (focal and reference) across 21 loci. Each individual is represented by a single row. Unknown alleles are denoted by zero (0). Genotype calls generated and confirmed using GeneMarker (SoftGenetics).
DOI: 10.5061/dryad.54bm8/3
title: Sample UTM coordinates

description: GPS coordinates are provided in the Universal Transverse Mercator (UTM) coordinate system for UTM zone 17N.
DOI: 10.5061/dryad.54bm8/4
title: Gutmicrobiomes_16SV4

description: Raw sequence and barcode files from MiSeq.
DOI: 10.5061/dryad.54bm8/5
title: OTU Tables

description: QIIME generated OTU tables (.biom format) used in this study. See ReadMe file for further information.
DOI: 10.5061/dryad.92961/4
title: D concolor pollinator size

description: Comparison of the sizes of the two pollinators of Drakaea concolor, Pogonothynnus sp. and Zaspilothynnus gilesi
DOI: 10.5061/dryad.b999q/1
title: genotypes and mean x, y coordinates for adult kangaroos by sex each year

description: Genotypes were assessed in GeneMapper 4.1.  Each line represents an individual.  Sex 1 = male, Sex 2 = female.  Year 1 = 2010-2011, Year 2 = 2011-2012, Both Years = 2010-2012.
DOI: 10.5061/dryad.b999q/2
title: distances between mothers and young of different ages and sexes

description: Each line represents a mother-young pair for a certain age period.  Period 1 = 10-13 months, Period 2 = 14-17 months, Period 3 = 18-21 months, Period 4 = 22-25 months, Period 5 = 26-29 months, Period 6 = 30-33 months, Period 7 = 34-37 months, Period 8 = 38-41 months.  Young and Mother refer to individuals but are not the tag numbers.  Sex 1 = male, Sex 2 = female.  Year 1 = 2010-2011, Year 2 = 2011-2012.  Distance Mother Moved is from the previous age period.
DOI: 10.5061/dryad.b999q/3
title: range sizes of 95% and 50% kernels for different sex-age classes

description: Sizes of kernels were calculated in Ranges8 v. 2.5.  Each line represents an individual.  Width refers to the distance between the two outermost points of kernels.
DOI: 10.5061/dryad.b999q/4
title: known dispersers with sex, age and distance moved

description: Each line represents an individual.  Sex 1 = male, Sex 2 = female.  Cohort 2007 = born 2006/2007, Cohort 2008 = born 2007/2008, Cohort 2009 = born 2008/2009.  Age last seen = age when last seen on study area.
DOI: 10.5061/dryad.gf6tq/1
title: year-conecondition-key

description: To connect phenotypic data to cone conditions for a specific year.
DOI: 10.5061/dryad.kv3q7/1
title: Compilation of publication data

description: This Excel file contains all tables and the appendix present in the manuscript. There is no other data available.
DOI: 10.15156/bio/sh2696107.08fu
title: SH2696107.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh2696108.08fu
title: SH2696108.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.