cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.23qp6/2
title: Cougar Survival Data

description: Survival data for cougars monitored the Colorado Front Range from 2007-2013. Data is in CSV format, and is intended for Kaplan-Meier survival analysis. Entry and exit dates are given in months and describe either the date the cougar was first captured, or the date an individual reached adulthood (24 months).  "TotalMonths" is the amount of time each cougar was monitored. "Event" describes whether monitoring ended due to censorship (0) or death (1). Censorship included lost communication with GPS collar or cessation of the study. We include covariates that may be linked to survival, including sex, isotopic signature (in delta-13C or delta15N), housing density (see manuscript for details), and percent of diet from native herbivores. We also include mortality cause where available (see manuscript for category descriptions). Complete data was not available for all cougars in the study.
DOI: 10.5061/dryad.23qp6/3
title: Cougar prey isotopic signatures

description: Isotopic signatures of potential prey species of cougars in the Colorado Front Range, in CSV format. Prey hair were collected between 2007 and 2013 throughout the study area, and analyzed for isotopic signature, in delta-13C and delta-15N (see manuscript for details).
DOI: 10.5061/dryad.2d1d7/1
title: bat_data_covariates

description: This dataset contains acoustic data from multiple bat species and various environmental covariates collected around detector sites. Full details are provided in Caryl F.M., Lumsden L., van der Ree R., Wintle B. 2015 Functional responses of insectivorous bats to increasing housing density support 'land-sparing' rather than ‘land-sharing’ urban growth strategies. Journal of Applied Ecology. Insectivorous bats were surveyed with acoustic detectors at 176 sites separated by &gt;250 m grouped into clusters of four within 9 km2 landscapes in February to April 2010. Four detectors suffered mechanical failure and data from the successful 172 detectors are published here. Landscape-context and site-specific environmental covariates were generated for each site (see metadata tab for details) and used to examine drivers of bat species distributions in urban landscape and identify critical environmental thresholds.
DOI: 10.5061/dryad.2ds6h/3
title: Habitat, nest counts and sampling effort

description: Habitat variables as described in the manuscript. Electrofishing effort (effort) is reported in seconds. The variables "agri.rank" and "wsa.rank" represent ranked values of each raw measurement of %agriculture and watershed area (km2), respectively. These two variables were added to calculate the variable "stress.bin", which served as the independent variable in regressions testing predictions of the stress-gradient hypothesis.
DOI: 10.5061/dryad.2ds6h/4
title: Nest web observations

description: Cyprinid nesting observations, including which species constructed the nest and which species used those nests for reproduction. These data were used for generating the nest webs.
DOI: 10.5061/dryad.3b37k/1
title: Supporting Information
DOI: 10.5061/dryad.605j6/1
title: Data for repository_final

description: The Excelfile provided comprises two data sheets. On the first sheet the calibration data for measurement 2-4 for the 60 sensors are given. On the second sheet, the minimum conductivity value measured in the field without any water present is given. The values are already temperature-corrected.
DOI: 10.5061/dryad.62247/10
title: SupplTable1

description: Supplementary Table 1
DOI: 10.5061/dryad.62247/7
title: SupplFig4

description: Supplementary Figure 4
DOI: 10.5061/dryad.62247/8
title: SupplFig5

description: Supplementary Figure 5
DOI: 10.5061/dryad.62247/9
title: SupplFig6

description: Supplementary Figure 6
DOI: 10.5061/dryad.63f26/1
title: mismatch-uv.r

description: R-functions for simulating the process, solving for the joint evolutionary outcome and for generating the different plots in the paper.
DOI: 10.5061/dryad.63f26/2
title: dryad-examples

description: Example R-code generating Figs. 1, 2 and 3 in the paper, a contourplot of the joint evolutionary outcome, as well as code solving for the joint evolutionary outcome and simulating the process.  Calls the functions in mismatch-uv.r which needs to be in the working directory.
DOI: 10.5061/dryad.66f8c/2
title: Simulated.dataS2

description: Simulated species 2 file to input into R Simulation file
DOI: 10.5061/dryad.66f8c/3
title: Simulating data

description: R script for processing the pure simulated genotypes into mixed sexual and clonal samples as would be sampled naturally
DOI: 10.5061/dryad.66f8c/4
title: fdata

description: raw unprocessed output of Simulated data processing script with mixed MLGs
DOI: 10.5061/dryad.66f8c/5
title: Simulated data

description: Data processing of simulated data
DOI: 10.5061/dryad.66f8c/6
title: C1and3

description: Processed Symbiodinium C1 and C1 data
DOI: 10.5061/dryad.66f8c/7
title: Howellsetal2013

description: Presence/absence file from Howells et al. 2013 processed into a list of alleles observed in each sample used to create Figure 4
DOI: 10.5061/dryad.66f8c/8
title: Wirshingetal 2013 Partitioned

description: Data from Wirshing et al. 2013 after partitioning into the two species ( Figure 5c)
DOI: 10.5061/dryad.74cj2/1
title: Fuiman and Perez PRSB data

description: Data file includes results from experiments 1, 2, and 3 plus complete fatty acid profiles for all samples of eggs, larval diets, and larvae. File contains notes to explain variables.
DOI: 10.5061/dryad.76qd7/1
title: EEG-fMRI Data part 1

description: Rat 1 - Rat 4
DOI: 10.5061/dryad.76qd7/2
title: EEG-fMRI study part 2

description: Rat 5 - Rat 6
DOI: 10.5061/dryad.78h38.1
title: Data from: Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics
DOI: 10.5061/dryad.78h38.2
title: Data from: Adaptive radiation driven by the interplay of eco-evolutionary and landscape dynamics
DOI: 10.5061/dryad.78h38.2/1.2
title: revised_simul_DL

description: Code for simulation and diversity estimation. NOTE: Please use revised_simul_DL.zip and not simul_DL.zip. Version 1 was uploaded by mistake, and this is not the simulation code corresponding to the published paper. Version 2 is the correct simulation code.
DOI: 10.5061/dryad.7gr50/1
title: Abundance and Biomass of trophic guilds
DOI: 10.5061/dryad.8n2d5/1
title: Sphagnum_Metacommunity_otu_table

description: The complete OTU-table of the partial 16S rRNA genes of the microbiome associated with the vegetation in two Alpine bogs in Austria.
DOI: 10.5061/dryad.c27k5/1
title: raw data of the study-Retrospective Study using Magnetic Resonance Imaging (MRI) to Measure Depths of Acupuncture Points in Neck and Shoulder Region

description: This document contains the raw data of 394 subjects including sex,BMI and measured depth of each point in the study: Retrospective Study using Magnetic Resonance Imaging (MRI) to Measure Depths of Acupuncture Points in Neck and Shoulder Region.
DOI: 10.5061/dryad.c2ss6/1
title: BBS_Routes_Housing_and_Bird_Guild_Abundance_Richness_inside_outside_USA_Protected_Areas

description: This file contains Data on 45 USA Breeding Bird Survey Routes, their associated Bird Conservation Region, housing density summarized within 400 m of BBS routes, and bird guilds, as described in our paper. Further, we provide summarized (proportion of 400 m buffers of BBS routes) National Land Cover Database layers. Additionally, this file contains housing density for paired BBS routes (routes located outside Protected Areas). The outside protected area housing density was summarized within 400 m of BBS Routes.
DOI: 10.5061/dryad.c2v35/1
title: Morphological data - species averages

description: Morphological data: body depth, body width, standard length, dorsal fin spine length, anal fin spine length and pectoral fin spine lengths. Measured on a single exemplar species for 347 teleost fish families at the California Academy of Sciences
DOI: 10.5061/dryad.g28c8/3
title: Diaspidid_phylogeny

description: Phylogenetic tree of armored scale insects used in the paper.
DOI: 10.5061/dryad.g28c8/4
title: Analysis_R_scripts

description: R scripts for running the analyses from this paper.
DOI: 10.5061/dryad.g94676pg.1
title: Data from: Islands and streams: clusters and gene flow in wild barley populations from the Levant
DOI: 10.5061/dryad.g94676pg.2
title: Data from: Islands and streams: clusters and gene flow in wild barley populations from the Levant
DOI: 10.5061/dryad.g94676pg.2/1.2
title: Barley1K_microsatellites
DOI: 10.5061/dryad.g94676pg.2/2.2
title: B1K illumina
DOI: 10.5061/dryad.g94676pg.2/3.2
title: Barley1k location

description: MS Excel spreadsheet showing Barley1k locations.
DOI: 10.5061/dryad.mk966/1
title: Lehndal and Agren PLOS ONE
DOI: 10.5061/dryad.pd7r6/5
title: Barcode_and_type

description: tab separated table of location and relative type percentage with barcodes.
DOI: 10.5061/dryad.pd7r6/6
title: CYTB_sequences_used_to_identify_groups

description: CYTB_sequences_used_to_identify_groups
DOI: 10.5061/dryad.qm30m/1
title: Unigene
DOI: 10.5061/dryad.qm30m/2
title: single_copy
DOI: 10.5061/dryad.qt3c9/1
title: Marxan Files

description: Input files used in the Marxan software to derive optimized monitoring networks for the four stratification methods - No stratification (NS), Protection stratification (PA), Environmental Stratification (ENV), and Environmental and Protection stratification (ENVPA); and the three target scenarios: T10, T30 and T50
DOI: 10.5061/dryad.qt3c9/2
title: Carvalho_S_et_al_2015-JAE_DATA_&_RCODE

description: Input files and r scripts used to derive non-optimized monitoring schemes for the four stratification strategies (No stratification (NS), Protection stratification (PA), Environmental Stratification (ENV), and Environmental and Protection stratification (ENVPA)) and the three target scenarios (T10, T30 and T50);  and to evaluate the performance of both optimized and non-optimized networks using the different indicators.
DOI: 10.5061/dryad.rg7s7/1
title: Field data used to parameterise the mesquite population model

description: An overview of what field data was used to estimate each parameter is provided in the first tab. Subsequent tabs contain the raw field data that was collected, including a text box providing a brief description of the data source. Notes on column headings provide information on data fields where it is not self-explanatory.
DOI: 10.5061/dryad.rr611/1
title: Genotype and spatial data for Udzungwa red colobus monkeys

description: The data set includes the genotypes and spatial data for the samples used in the study: "A novel landscape genetics approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum)". The data set includes: i) the genotypes for all the unique individuals identified; ii) the subset of genotypes for the individuals that were not related in first degree and were used for the landscape analyses; iii) the pairwise Rousset matrix for the individuals that were not related in first degree and were included in the landscape analyses and iv) the spatial coordinates for the individuals that were not related in first degree and were included in the landscape analyses.
DOI: 10.5061/dryad.rs7b0.1
title: Data from: Novel forests maintain ecosystem processes after the decline of native tree species
DOI: 10.5061/dryad.s06br/1
title: Biometric data for centrodorsals of Glenotremites paradoxus from Turonian samples

description: Biometric data for centrodorsals of Glenotremites paradoxus from five Turonian samples
DOI: 10.5061/dryad.t5c10/1
title: Salin et al 2015 Biol let - SMR and ROS in vivo
DOI: 10.5061/dryad.t741c/1
title: Processed_inspection_data

description: Data table with meta data for all the trials and inspection variables.
DOI: 10.5061/dryad.t741c/2
title: Raw_inspection_data

description: Raw JWatcher files for the inspection data.
DOI: 10.5061/dryad.t741c/3
title: Raw_tracks_control_trials

description: Raw ctrax output (after manual correction) for novel object control trials.
DOI: 10.5061/dryad.vp18t/1
title: Breeding Pair Estimator Spreadsheet

description: This is a user-friendly spreadsheet that allows users the ability to obtain estimates of avian breeding pairs using the Breeding Pair Estimator (BPE). The associated 'ReadMe' file is a tutorial with instructions for how to input data successfully into the BPE spreadsheet.
DOI: 10.5061/dryad.0vf86nb1.1
title: Data from: How depressed? Estimates of inbreeding effects during seed development depend on reproductive conditions
DOI: 10.5061/dryad.0vf86nb1.2
title: Data from: How depressed? Estimates of inbreeding effects during seed development depend on reproductive conditions
DOI: 10.5061/dryad.0vf86nb1.2/1.2
title: Harder etal data

description: The file contains two worksheets with data for Disa ferruginea and D. ophrydea concerning the proportion of outcross pollen applied to stigmas (pcmass), the number of ovules counted (ovule cnt), and the numbers of those ovules that were fertilized (fertilized) and developed into seeds (seeds). Each row represents the results from a single flower, with multiple flowers per plant. These data were used to estimate the relative success of self- and cross-pollen in fertilizing ovules, the relative survival of self- and cross-zygotes and inbreeding depression.
DOI: 10.5061/dryad.0vf86nb1.2/2.2
title: Simulation model

description: This spreadsheet implements simulations of seed production under specific conditions (including pollen, ovule or resource limitation) and was used to produce the results presented in Fig. 3e. Instructions are presented on the spreadsheet.
DOI: 10.5061/dryad.10278/10
title: Bumble bee visits - Front Range

description: This is the number of individuals of each bumble bee species visiting each plant species as collected by Macior (1974) and Miller-Struttmann in the past (1966-1969) and present (2012-2014). Visitation data from Mt. Evans Wilderness Area and Niwot Ridge Long Term Ecological Research combined as in Macior 1974. Used in “Tube depth density function parameter estimation.r”
DOI: 10.5061/dryad.10278/11
title: Flower tube depth mean and standard deviation

description: Mean and standard deviation of flower tube depth for plant species visited by resident alpine bumble bees (Bombus balteatus and B. sylvicola). Plant species determined according to Webber and Wittmann 2012. Used in “Tube depth density function parameter estimation.r”COLUMN DETAILS:PLANT.SPECIES - plant species name MEAN - mean flower tube depth (mm)STANDARD.DEVIATION - standard deviation of flower tube depth (mm).
DOI: 10.5061/dryad.10278/12
title: Data from 'Tube depth density function parameter estimation'

description: Sample output (used in the above manuscript) from the R script “Tube depth density function parameter estimation.r”. Provides the mean and standard deviation of flowers visited by bumble bees in the past (1966-1969) and present (2012-2014) in the Front Range (visitation data from Mt. Evans Wilderness Area and Niwot Ridge Long Term Ecological Research site combined as in Macior 1974).COLUMN DETAILS:REPLICATE - iteration from the resampling code (ranges from 1-1000)mean - mean tube depth (mm) of flowers visited by resident alpine bumble bees during each of 1000 resampled visitation iterationsst.dev - standard deviation in tube depth (mm) of flowers visited by resident alpine bumble bees during each of 1000 resampled visitation iterationsvariance - variance in tube depth (mm) of flowers visited by resident alpine bumble bees during each of 1000 resampled visitation iterationsTIME – the timeframe of the original visitation data used to simulate the tube depth density function
DOI: 10.5061/dryad.10278/13
title: Bumble bee foraging data - Lubinski

description: Foraging behavior of bumble bees (B. balteatus) followed while foraging in the field on Pennsylvania Mountain, CO. COLUMN DETAILS:SEQUENCE - the order in which a given flower was visited by a beeSPECIES FROM - the plant from which a bee departsSPECIES TO -  the plant which the bee visits nextSWITCH - describes whether a bee chose to switch to a different plant species (1) or remained consistent (0) between SPECIES FROM and SPECIES TO visitsFLOWER DENSITY - density of flowers (flowers per m2) in the original foraging patchFLIGHT DISTANCE - distance flown between SPECIES FROM and SPECIES TO (m)FROM TUBE - tube depth (mm) of species the bee departs TO TUBE - tube depth (mm) of plant species the individual bee visits next
DOI: 10.5061/dryad.10278/14
title: Bumble bee morphology data

description: Morphological measurements of bumble bee specimens collected by various individuals at Mt. Evans Wilderness Area, Niwot Ridge Long Term Ecological Research site, and Pennsylvania Mountain.COLUMN DETAILS:GLOSSA LENGTH ANALYSIS - a bivariate operator indicating if a specimen was (1) or was not (0) used in the analyses of tongue length presenting in the above articleINTERTEGULAR SPACE ANALYSIS - a bivariate operator indicating if a specimen was (1) or was not (0) used in the analyses of intertegular space presenting in the above articlePLANT.SPECIES - the plant species on which the bee was visiting when collected
DOI: 10.5061/dryad.10278/15
title: Niwot change in vegetative cover

description: Proportional change in vegetative cover and flower depth for eleven historic bumble bee host plant species as measured on Niwot Ridge Long Term Ecological Research site (Johnson et al. 2011). Vegetative cover in each year (1971 and 2011) was summed across all plots, and proportional change in vegetative cover for each species was calculated as the difference between vegetative cover in 2011 and 1971 weighted by cover in 1971.
DOI: 10.5061/dryad.10278/16
title: Penn flower density

description: Peak flower density (flowers per meter squared) for six plant species surveyed across five habitats [krummholz (KRUM); south and south-east facing slopes (SLOPE); wet tundra (SWALE), false summit (FSUMMIT); and true summit (SUMMIT)] on Pennsylvania Mountain in the past (1977-1980) and present (2012-2014).
DOI: 10.5061/dryad.10278/17
title: Plant specimens with flower measurements

description: Flower tube depth measurements of plant specimens collected by various individuals collected at or with 15km of at Mt. Evans Wilderness Area, Niwot Ridge Long Term Ecological Research site.
DOI: 10.5061/dryad.10278/8
title: Data from 'Tongue length density function parameters estimation' - Pennsylvania Mountain

description: Sample output (used in the associated manuscript) from the R script “Tongue length density function parameter estimation.r”. Provides the proportion of individual bumble bees in each subpopulation (short and long-tongued) and mean and standard deviation of tongue length in each subpopulation of bumble bees at Pennsylvania Mountain Wilderness Area in the past and present.COLUMN DETAILS:REPLICATE - iteration from the resampling code (ranges from 1-1000)lambda1 - proportion of individuals in the short-tongued subpopulation of bumble bees mu1 - mean tongue length of the individuals in the short-tongued subpopulation of bumble bees sigma1 - standard deviation of tongue length for individuals in the short-tongued subpopulation of bumble beeslambda2 - proportion of individuals in the long-tongued subpopulation of bumble bees mu2 - mean tongue length of the individuals in the long-tongued subpopulation of bumble bees sigma2 - standard deviation of tongue length for individuals in the long-tongued subpopulation of bumble beesTIME – the timeframe during which the bees were originally collected in the Front Range (Mt. Evans and Niwot Ridge combined) and Pennsylvania Mountain (1966-1969 and 1977-1980, respectively)
DOI: 10.5061/dryad.10278/9
title: Tube depth density function parameter estimation

description: This is R script when run with the following two files [“Bumble bee visits - Front Range.csv”, ”Flower tube depth mean and standard deviation.csv”] will produce the parameter estimates for the uni-modal tongue length density function of 1000 simulated bumble bee visitation bouts. One example output from this R script (which was analyzed statistically for the above manuscript) is included in this set of datafiles [i.e., “Data from 'Tube depth density function parameter estimation'.csv”]
DOI: 10.5061/dryad.128p6/1
title: Appendix S1. Localities of Kaninospirifer, Fasciculatia, Imperiospira, and Quadrospira with their current- and palaeo-coordinates
DOI: 10.5061/dryad.239sm/1
title: Semantic Similarity Results
DOI: 10.5061/dryad.239sm/2
title: Ontology
DOI: 10.5061/dryad.239sm/3
title: Phenotype profiles
DOI: 10.5061/dryad.2d53k/1
title: Per-individual microsatellite and MC1R genotypes, coloration, and sex data

description: Columns contain the following data: Individual ID, Population, Sex, Brown chroma (coloration), MC1R genotype at amino acid position 126 (Ile126Val polymorphism), Microsatellite genotypes (the two alleles of each locus are given in two subsequent rows)
DOI: 10.5061/dryad.2d53k/2
title: MC1R sequences

description: Columns contain the following data: Individual ID, Population, MC1R sequence (unphased, heterozygous positions are provided in IUPAC degenerate code)
DOI: 10.5061/dryad.2d53k/3
title: ND6 haplotypes

description: Columns contain the following data: Individual ID, Population, ND6 haplotype
DOI: 10.5061/dryad.2qg54/1
title: Df and Dxy values for 10kb blocks from Victoria pair
DOI: 10.5061/dryad.2qg54/2
title: Df and Dxy values for 10kb blocks from Kivu pair
DOI: 10.5061/dryad.2qg54/3
title: Df and Dxy values for 10kb blocks from Mweru pair
DOI: 10.5061/dryad.44372/1
title: Align_12S_62samples_substitution.rate.estimation

description: This file contains aligned sequences used to estimate a 12S substitution rate for Teiidae.
DOI: 10.5061/dryad.44372/2
title: Align_12S_137samples.outgroup_gblock

description: This file contains aligned sequences used to estimate 12S gene tree.
DOI: 10.5061/dryad.44372/3
title: Align_ATPSB_126samples.outgroup_gblock

description: This file contains aligned sequences used to estimate ATPSB gene tree.
DOI: 10.5061/dryad.44372/4
title: Align_NKTR_115samples.outgroup

description: This file contains aligned sequences used to estimate NKTR gene tree.
DOI: 10.5061/dryad.44372/5
title: Align_R35_134samples.outgroup

description: This file contains aligned sequences used to estimate R35 gene tree.
DOI: 10.5061/dryad.44372/6
title: Align_RP40_132samples.outgroup

description: This file contains aligned sequences used to estimate RP40 gene tree.
DOI: 10.5061/dryad.44372/7
title: Align_NE.SW_12S_398samples_gblock

description: This file contains 12S aligned sequences used to calculate the number of polymorphic sites (S), haplotype number (h), haplotype diversity (Hd), nucleotide diversity (π), and Tajima’s D for Northeast (NE) and Southwest (SW) lineages.  This file was also used to to estimate uncorrected pairwise genetic distances between and within lineages and to investigate genetic structure with analyses of molecular variance (AMOVA).
DOI: 10.5061/dryad.44372/8
title: Align_NE.SW_12S_137samples_gblock

description: This file contains 12S aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) and Southwest (SW) sequence clusters were used separately in historical demography analyses and phylogeographic reconstruction.
DOI: 10.5061/dryad.4h40n/1
title: Terrestrial arthropods of Steel Creek - Coleoptera

description: The beetles included within this data set were collected at Steel Creek, Buffalo National River, Newton County, Arkansas between April and December 2013 using a variety of collecting techniques.  The spreadsheet uses Darwin Core headings, which are defined in the ReadMe file.
DOI: 10.5061/dryad.60hh0/2
title: Gene copy numbers of Rickettsia felis 17-kDa in individual flea lysates

description: Raw data for gene copy numbers of Rickettsia felis 17-kDa in individual flea lysates from rickettsial horizontal transmission bioassays.