cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r14bv/1
title: Voltammetric recordings of behaving monkeys

description: Each folder contain data files of one experimental day.Original COLOR.txt files.Each FSCV recording consists of 500 voltage points for 10ms (50kHz sampling).Recording was repeated at 10Hz, every 0.1s. In MFB stimulation, each trial was made for 20s (200 time points) and the electrical stimulation was delivered from 5s (from recording 50).Original COLOR data of MFB stimulation is a table of 200 x 500.In behavioral analysis, each recoring was made for 300s block (3000 time points), simultaneously for 4 channels. In most cases, Ch0:ventral striatum (acc, Cd), Ch1:putamen, Ch3:CS signal and Ch4:IR sensor monitoring the facial movement.To export full waveform data of multi-channel recording on TH-1, backgound subtraction was turned off. The original data, recorded as nA value, was exported as COLOR.txt files. Original COLOR data of behavioral task is a table of 3000 x 500.CS signal was simultaneously recorded on Ch2, and the CS timing during 300s block was exported as IT.txt files. The hight of CS signal indicate the type of trials, and the offset of CS is the timing of juice delivery. For free trials, similar timing signal is recorded and the juice was delivered at the offset of the signal, but no visual stimuli appeared on the screen.Original ITCS data of CS is a table of 3000 x 1.For food trials, the pulses in ITCS data indicate the timing of reaching of the food to the mouth.These data were loaded on MATLAB, background subtracted for each trials, and PCR was performed using princomp function. Templates for Principle Component Regression (PCR) analysis.Voltage-current curves (500 points) at the peak MFB responses were collected as in-vivo dopamine template.Also, presumably pH curves were collected 10-15s after the stimulation. PCR resultsResult of PCR: 1zz, 2zz and 3zz files, each columns indicate one trial for 8s (80 points). Each column started with the Block number, timing point of CS onset in the block and hight of CS signal.The trials judged as "extreme" have more than 1000 value of CS signal.1zz is the dopamine-like component and 2zz is the pH-like component. 3zz is the current at the peak of dopamine oxidation potential (120/500 points)Point 40 is the CS onset. Timing cue was shown from point 30, and the onset of juice delivery was point 55. One behavioral session consists of multiple 5-min blocks.Review on EXEL show the average of each trial type within the session.  In original analysis to calculate PCR result of 1zz, timing of the trials were aligned by CS onset, so time 0 is the time just before the CS onset. For final graph presentation of the results, the timing of juice delivery/CS offset is shown as time 0. In some review tables of EXEL, you need to find which timing determination is applied.
DOI: 10.5061/dryad.r22h4/122
title: MRI_subject_9
DOI: 10.5061/dryad.r22h4/123
title: MRI_subject_8
DOI: 10.5061/dryad.rq8n5/1
title: pin points reading along elevation gradients in wetlands

description: This data corresponds to the reading of plant vegetation surveys conducted on plots 25x25 cm large, with 18 readings (R1 to R18) on each plot. Each count is the number of hits per species. They were recorded on  70 plots, 25 x 25cm large, placed every 20 cm along two elevation transects used as replicates (35 plots per sequence). Plots were proteted from grazing by cattle and horses. On each plot, vegetation relevés were performed along both diagonals using the pinpoint method, with a record every 4 cm. Three readings were made: on the 23-29 October, 2008 (Year 1, period 2), on the 3-12 June, 2009 (Year 2, period 1) and on the 19-20 October, 2009 (Year 2, period 2). Aeration Sum Exceedance values were measured based on water table field monitoring, and foflowing Gowing et al. 1998. Predicting the effect of change in water regime on plant communities. In: Wheater H, Kirby C, editors. Hydrology in a Changing Environment vol. I.  John Wiley, Chichester: pp. 473–483
DOI: 10.5061/dryad.ss2g7/2
title: Foot Area data file

description: CSV file containing measures of foot area for all specimens used in the study
DOI: 10.5061/dryad.tf704/1
title: Haplotypes for all loci and individuals

description: Output of the final step of the pyRAD software pipeline (Eaton and Ree, 2013). File contains both haplotypes for 125 individuals at 144,699 loci. This is the "raw" data set subjected to additional filtering (see scripts) before phylogenetic analysis.
DOI: 10.5061/dryad.tf704/2
title: Partitioning Scripts

description: This folder contains a short pipeline (3 Python scripts) for partitioning loci haplotype data by the number of individuals without data. A README file explains how to use the scripts.
DOI: 10.5061/dryad.tf704/3
title: Phylogenetic Trees

description: Readable trees (.tre) corresponding to paper figures as follows: RAxML_concat--Figure 2; BEAST--Figure 3; RAxML_presabs, RAxML_SNP, and NJst--Figure S3; RAxML_PartitionX--Figure S4.
DOI: 10.5061/dryad.tf704/4
title: Raw_Reads_AGTCAG

description: Raw reads with index AGTCAG.
DOI: 10.5061/dryad.tf704/5
title: Raw_Reads_CTGAGA

description: Raw reads with index CTGAGA.
DOI: 10.5061/dryad.tf704/6
title: Raw_Reads_GACTTC

description: Raw reads with index GACTTC.
DOI: 10.5061/dryad.vb53h/2
title: long-term zebrafish study

description: These data provide the information on tankno, generation, numred, numwt, pctredmorph, and simulationredpct. Tankno provides information on each of the 18 tanks; generation for each of the 18 tanks varies from 1 to a maximum of 15; how the generations were collected is explained in the paper as no overlapping generations were permitted, numred is the number of red adults counted at the end of each generation; numwt is the number of wild-type adults counted at the end of each generation; pctredmorph is calculated as: (numred/ numred + numwt) * 100; simulationredpct is the predicted percent red individuals by the demographic model described in the paper.
DOI: 10.5061/dryad.vb53h/3
title: malemale chases for sas

description: These data provide the information on the number of male directed chases toward another male and indicate if the male chasing was red or wild type, and if the male being chased was red or wild type.  Data are given for group, %red male category, number of chases, collection, type of chase, and chases per male. Group is referred to as aquarium in the paper; pctred is the %red male category of which there are five types (25%, 33$, 50%, 66%, and 75%; number of chases observed is how many chases were observed during the 10 min observation period each day; collection refers to the number of days that data were collected for each group; Chasetype: 1 = wild-type male chasing a red male, 2 = a red male chasing a wild-type male; chasepermale divides the numbchases by how many males of each type were in the aquarium to allow for comparison of different %red male categories.
DOI: 10.5061/dryad.vb53h/4
title: malefemale chases for sas

description: Data file: Malefemale chases:
These data provide the information on the number of male directed chases toward females and indicate if the male chasing was red or wild type.  Data are given for collection, type of chase, number of chases, group, %red male category, chases per male, and chase type. Collection refers to the number of days that data were collected for each group, type of chase: either red male or wild-type male chasing a female, number of chases observed is how many chases were observed during the 10 min observation period each day; group is referred to as aquarium in the paper; pctred is the %red male category of which there are five types (25%, 33$, 50%, 66%, and 75%. Chasespermale divides the numbchases by how many males were in the aquarium to allow for comparison of different %red male categories. Chasetype codes typechase numerically (1 = wild-type male chasing female; 2 = red male chasing female).
DOI: 10.5061/dryad.24061/2
title: Raw Throat Relfectance Measures

description: Raw values of throat reflectance measures of all fish used.  Data are separated into 2010 and 2011 year categories, for both male and female fish.  Male ID (numbers) correspond to that year's trials, and not to male ID in the combined data set.  For the combined data set, males are numbered 1-63, starting with the first male in 2010 and continuing sequentially through the end of the 2011 year. Con-specific or intruder males used in the con-specific male sequential choice trials are indicated with an 'I' (for example M7-I is the con-specific male presented to subject male 7)
DOI: 10.5061/dryad.3ss6p/1
title: AdditionalFile1_Alignment_NexusFormat

description: Nexus formatted alignment of all protein sequences used for POR phylogeny inference.
DOI: 10.5061/dryad.4h462/2
title: Simulated Data

description: Simulated site pattern data files from ms used for DFOIL analysis
DOI: 10.5061/dryad.4kh20/1
title: Brazilian_efficiency

description: This file offers the data behind Fig. 3A of Lähteenmäki et al., estimating the efficiency of the Brazilian MESOCLOSURES in preventing the inflow of beetles as a function of MESOCLOSURE size. Included are counts of beetles caught by identical traps in two settings: traps within the MESOCLOSURES and traps outside the MESOCLOSURES. The specific columns are the following: Time: day of experiment (with individual trapping periods extending over 24 hours)Size: the dimension of the MESOCLOSURE (given as the length of MESOCLOSURE side, in metres)Replicate: the identity of the replicate cageTotal: the summed number of beetles caught inside and outside of the MESOCLOSUREInside: the number of beetles caught inside of the MESOCLOSURE
DOI: 10.5061/dryad.4kh20/2
title: Dungweight

description: This file offers the data behind Fig. 4A-C of Lähteenmäki et al., estimating the effects of time, grazing regime (i.e. of grass length) and beetle taxa present on dung pat weight in the temperate experiment (for an in-depth description, see Appendix 1, section Experimental design, Finland). The specific columns are the following:BlockID: block identityCageID: cage identityPat: dung pat replicateGrass height: simulated grazing regime, with L identifying long grass and S identifying short grassGeotrupes presence: design variable indicating whether Geotrupes was present or not Aphodius presence: design variable whether Aphodius was present or not Measurement: measurement day (treated as a categorical variable)Weight: dung weight, in grams
DOI: 10.5061/dryad.4kh20/3
title: Finnish_efficiency

description: This file offers the data behind Fig. 3B of Lähteenmäki et al., estimating the efficiency of the Finnish MESOCLOSURES in preventing the inflow of beetles as a function of species identity. Included are counts of beetles caught by bait pats in two settings: baits within the MESOCLOSURES, and baits outside the MESOCLOSURES. The specific columns are the following: Replicate: the identity of the replicate MESOCLOSURESpecies: the identity of the speciesTotal: the summed number of beetles caught inside and outside of the MESOCLOSURESInside: the number of beetles caught inside of the MESOCLOSURE
DOI: 10.5061/dryad.4kh20/4
title: Soil temperatures

description: This file offers data on soil temperature, as recorded in each of four subplots on 27th July and reported verbally in the Results. The specific columns are the following:Replicate: the identity of the replicate MESOCLOSUREEnclosure type: treatment applied at the MESOCLOSURE level (for an in-depth description of treatment types, see main paper)Grass height: simulated grazing regime, with L identifying long grass and S identifying short grassTemperature: temperature recorded, in °C, with missing data indicated by an empty cell
DOI: 10.5061/dryad.71gt8/1
title: VCF Files of 7 Datasets used for Analysis

description: VCF files for all 7 datasets used for analysis, along with a csv file of individual ID #s and a csv file with a description of each dataset (see Table 1 in publication for more information).
DOI: 10.5061/dryad.77220/1
title: Kyogoku&Sota(2015)JEB

description: The data was produced by the laboratory experiment, in which C. chinensis males with various genital morphology interfered with the reproduction of C. maculatus females through interspecific copulation, which does not result in hybridization. The table includes the strain of the C. chinensis males, C. maculatus female fecundity and elytral length, the occurrence of externally identifiable genital injury in C. maculatus females, and morphological dimensions of the genitalia of C. chinensis males.
DOI: 10.5061/dryad.8sb8v/6
title: vanProosdij_etal_2015_Ecography_A9_Plotting_script

description: This R script is used to plot the results. It is a general plotting function that is applicable to any taxonomi clade or group, study area or climate chance scenario.
DOI: 10.5061/dryad.8sb8v/7
title: vanProosdij_et_al_2015_Ecography_A3_ReadMe

description: This manual provides a brief explanation of the Appendices A4-A9. It describes the input, output and data fromat requirements of each R script in the Appendices.
DOI: 10.5061/dryad.91d70/3
title: Fueling Data

description: This file contains data pertaining to the foraging rates of female Black-tailed Godwits in our study area in Friesland, The Netherlands during the spring of 2013. Data are grouped by individual by day and averaged across all of the three-minute periods for which that individual was observed on that day. Successes refers to the number of prey items consumed by an individual during a three minute period.
DOI: 10.5061/dryad.91d70/4
title: Response Data

description: This file contains data pertaining to the behavioral response of all individual Black-tailed Godwits that were seen in our study in Friesland during the spring of 2013. It includes their reproductive parameters in both 2013 and 2014, as well as their individual arrival date history. Response type is coded as: 1 (stayed), 2 (reverse migrated), 3 (delayed arrival), and 4 (normally late arriving). For all other categories, 0 denotes a negative result (e.g., nest failed), while 1 denotes a positive result (e.g., fledged successfully).
DOI: 10.5061/dryad.91d70/5
title: All nests 2005-2014

description: This file contains data on nests found in our study area in Friesland between 2005-2014. It includes their hatching success, fledging success, clutch size, average egg volume, and initiation date, as well as the colour code of the corresponding adults. In all cases, 0 denotes a negative result (i.e., nest failed to hatch), and 1 a positive result (i.e., nest hatched).
DOI: 10.5061/dryad.91d70/6
title: Breeding Propensity

description: This files contains data on the breeding propensity of Black-tailed Godwits seen in our study area prior to the initiation of the first nest from 2005-2014. A 0 denotes that an individual was not found nesting, a 1 that it was found nesting, and a blank that it was not seen in that year.
DOI: 10.5061/dryad.91d70/7
title: Polder Counts

description: This file contains data on the number of territorial Black-tailed Godwits seen during our weekly survey of every parcel of every polder in our study area in Friesland during the pre-breeding period. In this file, NA = 0 territorial godwits during a survey period.
DOI: 10.5061/dryad.9mb00/1
title: Plant diversity & abundance, Aspen stand characteristics

description: This data was collected in the field during the summer of 2007. The excel file contains all data used in our analyses. Data is separated into different sheets. We sampled the grassland matrix and aspen stands using Modified-Whittaker plots (Stohlgren et al. 1995 Vegetatio).  We identified all species at the level of microplot (mp - 10 per plot), subplot (sp - 2 per plot), midplot (mi - 1 per plot) and wholeplot (wp - i.e., the entire plot). Within each microplot we measured the percent cover of herbaceous plants using Daubenmire cover classes (Daubenmire 1959 Northwest Science). Aspen stands that were not sampled, but were included to calculate stand connectivity, are coded in the distance matrix with letters (i.e., a,b,c etc.), while stands that were sampled are coded numerically.
DOI: 10.5061/dryad.b7156/10
title: 1112 Empirical UCE Nexus Files

description: All 1,112 UCE nexus alignments.
DOI: 10.5061/dryad.b7156/2
title: Online Appendix 2 - Locus Info

description: Excel file containing information on each UCE locus used in this study. This information includes: locus length, number of informative sites, number of SNPs, and best fitting model. There are two sheets: one listing all of the loci included in our final dataset (1,112 loci) and another listing only the loci that had phylogenetically informative sites (919 loci).
DOI: 10.5061/dryad.b7156/3
title: Online Appendix 3 - BPP Results

description: Theta and tau estimates, and corresponding ESS values, from eight BP&P runs corresponding to eight subsets of the 919-locus dataset. These values were used to construct a species tree that was used as the "true" tree from which we simulated character data.
DOI: 10.5061/dryad.b7156/4
title: Figure S1 Smilogram

description: Figure S1. Scatter plot of the frequency of variant bases relative to the position of those sites in their alignments
DOI: 10.5061/dryad.b7156/5
title: Figure S2 Concatenated Full MrBayes

description: Figure S2. Non-condensed trees from concatenated analyses. Condensed trees are shown in Fig. 3 in the main text. Numbers at nodes indicate Bayesian posterior probabilities.
DOI: 10.5061/dryad.b7156/6
title: Figure S3 Empirical StarBEAST

description: Figure S3. All 19 empirical *BEAST subsets. Subsets 1–18 are based on random subsets of 50 loci each; subset 19 includes the remaining 19 loci not included in the othersubsets. Numbers at nodes denote Bayesian PPs. Black circles at nodes indicate PPs ≥ 0.95.
DOI: 10.5061/dryad.b7156/7
title: Figure S4 Sim-Matching StarBEAST

description: Figure S4. All 10 Sim-Matching *BEAST subsets.Each species tree is based on analysis of a differentsubset of 50 simulated loci. Numbers at nodesdenote Bayesian PPs.
DOI: 10.5061/dryad.b7156/8
title: Figure S5 Sim-Multi-Individual StarBEAST

description: Figure S5. All 10 Sim-Multi-Individual *BEASTsubsets. Each species tree is based on analysis of adifferent subset of 50 simulated loci. Numbers atnodes denote Bayesian PPs.
DOI: 10.5061/dryad.cs5b4/1
title: Dataset_ExtinctionDebt_Gonzalez-Varo_et_al_JAPPLECOL

description: Please see the README file
DOI: 10.5061/dryad.jr81f/1
title: Sphagnum height and biomass increment in undrained, drained and rewetted boreal spruce swamp forests

description: Measured using grow-through mesh nets located in nine undrained, nine drained and 18 rewetted sites in 2011-2012.
DOI: 10.5061/dryad.jr81f/2
title: Sphagnum cover in undrained, drained and rewetted boreal spruce swamp forests

description: Sphagnum cover results from a vegetation survey conducted in 2009 (sphagcover_veg). Estimated Sphagnum cover of the growth measurement patches in 2011-2012 (sphagcover_patch). Vegetation survey results first published in: Maanavilja, L., Aapala, K., Haapalehto, T., Kotiaho, J.S. & Tuittila, E. (2014) Impact of drainage and hydrological restoration on vegetation structure in boreal spruce swamp forests. Forest Ecology and Management, 330, 115-125.
DOI: 10.5061/dryad.nt18c/1
title: LDBS1_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on July 26th, 2011.
DOI: 10.5061/dryad.nt18c/2
title: LDBS2_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 2nd, 2011
DOI: 10.5061/dryad.nt18c/3
title: LDBS3_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 3rd, 2011
DOI: 10.5061/dryad.nt18c/4
title: LDBS4_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 15th, 2011
DOI: 10.5061/dryad.q018v/1
title: README

description: Summary of all files in this Dryad package
DOI: 10.5061/dryad.q018v/2
title: FileS4 NewScaffoldOrder.csv

description: Revised scaffold order for each chromosome (consensus of FTC and BEPA). Revised coordinates (based on this study) and original assembly coordinates are presented. Orientations are defined relative to original genome assembly. The orientation of some scaffolds was not detected in this study. These scaffolds are labeled as having 'unknown' orientation; their orientation was not altered relative to their orientation in the original genome assembly. Chromosome 'M' is the mitochondrial genome sequence, which was not analyzed in this study but is replicated in the revised genome assembly.
DOI: 10.5061/dryad.q5270/1
title: Ectoparasites and fitness

description: Excel spreadsheets of data on 1) ectoparasite manipulation on female fitness and 2) treatment vs female parasite loads. The data were collected under natural conditions in the field.
DOI: 10.5061/dryad.r22h4/1
title: LTAS data
DOI: 10.5061/dryad.r22h4/124
title: MRI_subject_7
DOI: 10.5061/dryad.r22h4/125
title: MRI_subject_6
DOI: 10.5061/dryad.r22h4/126
title: MRI_subject_5
DOI: 10.5061/dryad.r22h4/127
title: MRI_subject_4
DOI: 10.5061/dryad.r22h4/128
title: MRI_subject_3
DOI: 10.5061/dryad.r22h4/129
title: MRI_subject_2
DOI: 10.5061/dryad.r22h4/130
title: MRI_subject_1
DOI: 10.5061/dryad.r7122/1
title: Mitogenome assemblies

description: File 'UKbees_mitogenomes_of_48_species_20150529.gb' (GenBank format) contains the mitochondrial assemblies of the 48 bee species.
DOI: 10.5061/dryad.r7122/2
title: Metabarcoding data

description: This dataset includes the post-denoising (BLUE) and post-merging (FLASH) sequence data, the map files for library splitting, the merged *.fna file for all sequences from all samples, the representative sequence of each OTU, and the command files.
DOI: 10.5061/dryad.rb3jp/1
title: AllYears_4000mBuffer

description: Coordinates of the centroids of every horse movement-based (4000m radius) buffer and counts of individuals and bands inside those buffers for each year (2008-2013).
DOI: 10.5061/dryad.rb3jp/2
title: distancewater_density

description: For each random location calculated for the RSF analysis: distance to water, number of horses centroids in a 4000m buffer (centered on the random location) during the year associated with the random location.
DOI: 10.5061/dryad.rb3jp/3
title: RSFdata

description: Real and random locations used for the RSF analysis with zone, distance to water, and habitat type.
DOI: 10.5061/dryad.rb3jp/4
title: Time_at_water

description: Drinking time table describing for each horse studied the time spent drinking, the number of horses present, and the type of water source.
DOI: 10.5061/dryad.sp20s/1
title: Supplementary Data File - spider & nectar

description: Data from 'Rapid nectar-meal effects on a predator’s capacity to kill mosquitoes'
DOI: 10.5061/dryad.tf704/7
title: Raw_Reads_TCAGCT

description: Raw reads with index TCAGCT.
DOI: 10.5061/dryad.vq080/1
title: Singh et al data

description: Contains data from four experiments reported in the paper.
DOI: 10.5061/dryad.34t55/1
title: Challands2015Analysis1

description: Challands 2015 matrix - Friedman 2007 Dipnoan matrix ammended for Dipterus valenciennesi without Rhinodipterus kimberleyensis.
DOI: 10.5061/dryad.3ss6p/2
title: AdditionalFile2_BayesianTree_NexusFormat4FigTree

description: Bayesian POR phylogeny in Nexus format, readable in the program FigTree.
DOI: 10.5061/dryad.3ss6p/3
title: AdditionalFile3_MaximumLikelihoodTree_NewickFormat

description: Maximum-likelihood POR phylogeny in Newick format.
DOI: 10.5061/dryad.3ss6p/4
title: AdditionalFile4_PorSpeciesTable

description: Excel spreadsheet of identifying information (e.g., accessions) for all sequences used in the POR phylogeny.
DOI: 10.5061/dryad.3ss6p/5
title: AdditionalFile5_PrimerTable

description: Table of degenerate and species-specific primers used to amplify por gene sequences from stramenopile algae.
DOI: 10.5061/dryad.4h462/5
title: dfoil analysis script

description: main analysis script, use --help for full options