cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dg0747n/1
title: Dry matter partitioning coefficient,water budget and evapotranspiration data observed in drip irrigated rice cultivation

description: Dry matter partitioning coefficient (PC) of aerobic rice (Conventional) compared to drip irrigation with aerobic rice treatments. Crop evapotranspiration calculated for the cropping period. Total Water Applied (TWA: mm), Irrigated Water (IW: mm) and Effective Rainfall (ER: mm) of aerobic rice cultivated under drip and conventional practice.
DOI: 10.5061/dryad.j91d66c/3
title: Rabbit multi-state, dead recovery models

description: Multi-state, dead-recovery models for 18 years of data from Turretfield rabbit population, South Australia. 

Code by Louise K. Barnett, November 2017

Before running the script you will need to install program MARK from http://www.phidot.org/software/mark/downloads/

Mac and Linux users might find this post helpful: http://www.phidot.org/forum/viewtopic.php?f=21&t=3233&p=10967&hilit=install+RMark#p10967
DOI: 10.5061/dryad.j91d66c/4
title: Plotting output of multi-state, dead-recovery model

description: This script is for plotting the output from the multi-state model script. Run the models and save the output first.

Notes-

Immunity state / previous exposure categories: N - Immunity to neither virus M - Immunity to myxoma virus only R - Immunity to rabbit haemorrhagic disease virus (RHDV) only B - Immunity to both viruses

Age groups: Kittens ≤ 600 g (may have residual maternal immunity to RHD) Adults &gt; 600 g (unlikely to have residual maternal immunity)
DOI: 10.5061/dryad.mb756c7/3
title: Jacobsen_wood2018_pool_A_S1_L001_R1_001.fastq

description: Raw sequence data (gzipped fastq-file) from high-throughput sequencing of wood samples. Pool A, forward reads.
DOI: 10.5061/dryad.mb756c7/4
title: Jacobsen_wood2018_pool_A_S1_L001_R2_001.fastq

description: Raw sequence data (gzipped fastq-file) from high-throughput sequencing of wood samples. Pool A, reverse reads.
DOI: 10.5061/dryad.mb756c7/5
title: Jacobsen_wood2018_pool_B_S1_L001_R1_001.fastq

description: Raw sequence data (gzipped fastq-file) from high-throughput sequencing of wood samples. Pool B, forward reads.
DOI: 10.5061/dryad.mb756c7/6
title: Jacobsen_wood2018_pool_B_S1_L001_R2_001.fastq

description: Raw sequence data (gzipped fastq-file) from high-throughput sequencing of wood samples. Pool B, reverse reads.
DOI: 10.5061/dryad.p1j7n43/59
title: WangEtAl2017_fam1_m_Mb.cM.line
DOI: 10.5061/dryad.p1j7n43/60
title: WangEtAl2017_fam2_f_Mb.cM.line
DOI: 10.5061/dryad.p1j7n43/61
title: WangEtAl2017_fam2_m_Mb.cM.line
DOI: 10.5061/dryad.p1j7n43/62
title: WangEtAl2017_fam3_f_Mb.cM.line
DOI: 10.5061/dryad.p1j7n43/63
title: WangEtAl2017_fam3_m_Mb.cM.line
DOI: 10.5061/dryad.p1j7n43/64
title: WongEtAl2010_Mb.RR.line
DOI: 10.5061/dryad.p1j7n43/65
title: WuEtAl2014_Mb.cM.dot
DOI: 10.5061/dryad.p1j7n43/66
title: XuEtAl2014_Mb.cM.dot
DOI: 10.5061/dryad.p1j7n43/67
title: ZhangEtAl2012_Mb.cM.dot
DOI: 10.5061/dryad.rc78g29/1
title: Ho_and_Agrawal_2018_SimulationData

description: File contains data from the simulations.
DOI: 10.5061/dryad.rg098gq/1
title: Venom HPLC Peak Areas

description: The percent area of each of 34 high pressure liquid chromatography (HPLC) peaks for each snake used in the study. Peaks locations are identified in figure 1 of the associated manuscript.
DOI: 10.5061/dryad.rg098gq/2
title: Mammals_Presence_Absence_Matrix

description: Presences (1) and absences (0) for each study locality, as determined by range map overlap for California small mammal species available as prey to Crotalus oreganus.
DOI: 10.5061/dryad.0t67n/4
title: Supporting Material
DOI: 10.5061/dryad.1h48b38/17
title: Genotypes for CR genes in Lissotriton kosswigi

description: Genotypes for CR genes called with GATK in Lissotriton kosswigi
DOI: 10.5061/dryad.1h48b38/18
title: Genotypes for CR genes in Lissotriton montandoni

description: Genotypes for CR genes called with GATK in Lissotriton montandoni
DOI: 10.5061/dryad.1h48b38/19
title: Genotypes for CR genes in Lissotriton schmidtleri

description: Genotypes for CR genes called with GATK in Lissotriton schmidtleri
DOI: 10.5061/dryad.1h48b38/20
title: Genotypes for CR genes in Lissotriton vulgaris vulgaris

description: Genotypes for CR genes called with GATK in Lissotriton vulgaris vulgaris
DOI: 10.5061/dryad.1h48b38/21
title: Genotypes for TAP1 gene in Lissotriton

description: Fasta sequences containing concatenated exon sequences of TAP1 gene genotyped in six Lissotriton lineages and an outgroup
DOI: 10.5061/dryad.1h48b38/22
title: MHCI alleles

description: MHC class I gene alleles in Lissotriton lineages
DOI: 10.5061/dryad.1h48b38/23
title: MHC class I gene genotypes in Lissotriton

description: MHC class I gene genotypes in Lissotriton lineages
DOI: 10.5061/dryad.1h48b38/24
title: Forward simulation script NEUTRALITY M0

description: Forward simulation script for the scenario: Neutrality, migration = 0. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.
DOI: 10.5061/dryad.1h48b38/25
title: SLiM simulation script NEUTRALITY M1

description: Forward simulation script for the scenario: Neutrality, migration M1 = 5.0E-07. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.
DOI: 10.5061/dryad.45b5g/1
title: Scaling of fish length
DOI: 10.5061/dryad.45b5g/2
title: Scaling of grain size
DOI: 10.5061/dryad.50554tg.1/1.1
title: Fasta file - with sequences

description: This Fasta file contains all unique sequences accompanied by a unique identification number from 1 to 9193, which corresponds to a number in the file ’Frequency table.xls’
DOI: 10.5061/dryad.50554tg.1/2.1
title: Frequency table

description: This file tabulates sequences for all spider individuals. Each row in this file represents a unique sequence with the identification number (in column 1) corresponding to the sequence number in the file ’Fasta file – with sequences.txt’. The following columns have the following descriptions:

Sequence count = the total number of sequence across all spider individuals
Order = Arthropod order corresponding to the sequence
Sequence identity = The identity based on best match in Barcode of Life Data bas
Match = best match where 1.00 corresponds to perfect match (100%)
Spindel_1 .. Spindel_504 = unique identity for each spider individual, which corresponds to a number in the file ’GutTesta.txt’. The numbers in this column indicates the number of sequences for each unique sequence and spider individual
DOI: 10.5061/dryad.50554tg.1/3.1
title: Tabulated gut contents

description: This file summarises presence-absences for a given prey group in the gut of a spider individual. The columns have the following descriptions:

Spider no = unique identity for each spider individual, with a number corresponding to columns in the file ’Frequency table.xls’
Site = Collection site, see Figure 1 in the paper
Date = Collection date
Month = Collection month
Identity = Identification of spider individual: ’Pardosa prativaga’, ’Pardosa agricola’, ’Pardosa sp’
Sex, f = female, m = male, x = unidentified
Age, ad = adult, subad = subadult, juv = spiderling
Predation events = total number of predation events
Pepred = Predation events – occurrence of predator in gut
Weight = Weight in mg
Two group columns, Aqua = Aquatic larvae, Terr = Terrestrial larvae
Nine group columns, Chir = Chironomids, Aqu = other aquatic diptera, Det = detritivores, Pred = predators, Herb = herbivores, Leps = Lepidoptera, Cole = Coleoptera, Hete = Heteroptera, Coll = Collembola
22 columns for taxonomic categories.
DOI: 10.5061/dryad.50554tg.1/4.1
title: Network data

description: This ’consumer’ file was used for the null model analysis in econullnetr, and is based on occurrence in spider gut contents. The columns have the following descriptions:

Period, 1 = May-July, 2 = August-October
Sample, Site_Period
Identity = Identification of spider individual: ’Pardosa prativaga’, ’Pardosa agricola’, ’Pardosa sp’
Group
15 columns for taxonomic categories
DOI: 10.5061/dryad.50554tg.1/5.1
title: Prey abundances

description: This ’resource’ file was used for the null model analysis in econullnetr, and is based on the data from malaise traps. The columns have the following descriptions:

Period, 1 = May-July, 2 = August-October
Sample, Site_Period
15 columns for taxonomic categories
DOI: 10.5061/dryad.5cn37rr/3
title: invade-exp-data-output-taxa-table-biomass

description: Taxa description table
DOI: 10.5061/dryad.5fj6t/10
title: Cdil3
DOI: 10.5061/dryad.5fj6t/11
title: Cdil2
DOI: 10.5061/dryad.5fj6t/4
title: Cp4
DOI: 10.5061/dryad.5fj6t/5
title: Cp3
DOI: 10.5061/dryad.5fj6t/6
title: Cp5
DOI: 10.5061/dryad.5fj6t/7
title: Cdor_egg
DOI: 10.5061/dryad.5fj6t/8
title: Cdor3
DOI: 10.5061/dryad.5fj6t/9
title: Cdor2
DOI: 10.5061/dryad.640v21f/1
title: Standardized data used in structural equation models

description: The standardized (Z-scores) values for all variables used in a structural equation model for testing the relative importance of pollination and conventional agricultural management on crop yield. For the methods of collection and pre-calculation, see original manuscript.
DOI: 10.5061/dryad.7mf14t0/1
title: Raw Data for Social Cognition Playback

description: This file contains the values of all response variables measured as part of a playback experiment to test whether acorn woodpeckers can recognize the associations between members of other social groups. The file also contains the identifying information for each subject and the specific stimuli to which she was exposed, the date and time of each playback trial, and a number of factors and covariates
DOI: 10.5061/dryad.9bn4443/1
title: Repository data Madden et al

description: Data for The quick are the dead: Pheasants that are slow to reverse a learned association survive for longer in the wild
DOI: 10.5061/dryad.9ff3r4v/1
title: Columella tiers

description: Counts of columella tiers on mutant and rescued lines
DOI: 10.5061/dryad.9ff3r4v/2
title: HYD1sense3 Fig. 3A,B

description: Root growth data, Fig. 3A,B
DOI: 10.5061/dryad.9ff3r4v/3
title: HYD1sense auxin genes Fig 4

description: Gene expression data Fig. 4G
DOI: 10.5061/dryad.9s03863/1
title: Oxpecker Data

description: Each row represents a five minute observation of  an individual mammal and associated number of red-billed (RBO) and yellow-billed oxpeckers (YBO). For each individual, general data (date, time, location) as well as specific data (group size, wound presence, demographics) are provided.
DOI: 10.5061/dryad.b06f3s2/1
title: Code for the figures

description: The zip file contains seven folders containing the MATLAB code needed to reproduce the two figures and five supplementary figures presented in the paper. The code for each figure is contained within a separate and appropriately numbered folder, with the letter S denoting supplementary figures. Each code folder contains a main file named either plot X or Figure X which can be run to reproduce the figures with the help of auxiliary functions. The code files contain added comments and documentation to explain their organization further.
DOI: 10.5061/dryad.dh7cd36/1
title: Trap Deployment File (TDF)

description: Site location data
DOI: 10.5061/dryad.dh7cd36/2
title: Encounter Data File (EDF)

description: Individual encounter histories for SCR models.
DOI: 10.5061/dryad.dh7cd36/3
title: Fisher Camera Detections

description: Unmarked fisher camera detection data
DOI: 10.5061/dryad.f8j00mn/1
title: input file 1 for ABGD, pairwise TrN-corrected COI distances

description: Matrix of pairwise TrN-corrected COI distances for all Placida and nominal Stiliger haplotypes, used as input for ABGD analysis.
DOI: 10.5061/dryad.f8j00mn/2
title: input file 2 for RaxML, mtDNA haplotypes

description: RaxML input (nexus file type) of concatenated mtDNA (COI + 16S) haplotypes representing Sacoproteus gen. nov. (11 unique haplotypes representing 5 supported taxa) and Placida/Stiliger s.s. species (49 unique haplotypes representing 14 candidate taxa).
DOI: 10.5061/dryad.g7v1b.3
title: Data from: A framework for resolving cryptic species: a case study from the lizards of the Australian Wet Tropics
DOI: 10.5061/dryad.g7v1b.3/2.3
title: Supplementary Information
DOI: 10.5061/dryad.g7v1b.3/3.3
title: Appendix 1: Taxonomic revisions of the species groups
DOI: 10.5061/dryad.g7v1b/3
title: Appendix 1: Taxonomic revisions of the species groups
DOI: 10.5061/dryad.gp350rt/1
title: dryad id accessions

description: The submitted table includes the accessions' names of the species Pennisetum glaucum L.  collected from coastal North Africa along with their origin, their respective conservation sites, the characteristics of the prospecting sites and the microsatellite fingerprint data.
DOI: 10.5061/dryad.gq6326t/1
title: Experiment 1 Data (9 crickets per 6 minute trial)
DOI: 10.5061/dryad.gq6326t/2
title: Experiment 2 Data (1 cricket per 10 minute trial)
DOI: 10.5061/dryad.hc54664/1
title: alignments and partition schemes

description: The alignments and their partitions/models used in this study. For content of each alignment, please check the details in the original publication.
DOI: 10.5061/dryad.j0r8127/1
title: Supplementary_Data

description: Counts of sites by county for Cenozoic fossil marine invertebrates used to create Figure 1, specifically the number of sites (collections) from the Paleobiology Database download, and the number of sites (localities) digitally mobilized from nine institutions of the EPICC  TCN.  The Paleobiology Database download was performed on November 10 2017 using the following query: 
http://paleobiodb.org/data1.2/colls/list.csv?datainfo&rowcount&interval=Cenozoic,Cenozoic&cc=US&envtype=marine&show=loc,paleoloc,strat,stratext,lith,geo,methods,resgroup,refattr,secref,ent,entname.  The nine institutions are:  Burke Museum of Natural History and Culture, University of Washington, Seattle, WA; California Academy of Sciences, San Francisco, CA; Natural History Museum of Los Angeles County, Los Angeles, CA; National Museum of Natural History, Smithsonian Institution, Washington, DC; Orange County Paleontological Collection, Fullerton, CA; Paleontological Research Institution, Ithaca, NY; University of Alaska Museum, University of Alaska, Anchorage, AK; University of California Museum of Paleontology, Berkeley, CA; University of Oregon Museum of Natural History, Eugene, OR.  Data from both Paleobiology Database collections and museum collections were cleaned to remove terrestrial strata erroneously categorized as marine.
DOI: 10.5061/dryad.jf75dq3/1
title: Data for A domesticus social density and sex ratio

description: This data file has two pages--a metadata page explaining the meaning of each column label, and a datasheet containing 27 columns and 100 rows of data.
DOI: 10.5061/dryad.k082rv8/1
title: Graph Drawing Program Using Search Based Techniques

description: This package contains the source code of a Java program which includes the algorithms of 4 search based techniques (hill climbing, simulated annealing, tabu search, and path relinking) used to draw general graph layouts with undirected straight edges. The program includes a GUI which allows the user to adjust the parameters for each method according to user's preferences.
DOI: 10.5061/dryad.kg3d57r/1
title: Environmental variables used to generate the ENMs

description: Environmental variables used to generate the ENMs, including the raw layers and the PCA layers calculated from the raw datasets.
DOI: 10.5061/dryad.kg3d57r/2
title: Virtual species

description: Nine virtual species generated via NicheA (http://nichea.sourceforge.net/).
DOI: 10.5061/dryad.kg3d57r/3
title: Seperated virtual species

description: 6 regions for each virtual species, which were separated based on the areas of the potential distribution of each species.
DOI: 10.5061/dryad.kg3d57r/4
title: README
DOI: 10.5061/dryad.n73v54m/1
title: Maize plant population and row spacing data

description: To collate peer-reviewed articles, a literature search was conducted using the Institute for Scientific Information Web of Science Database (http://apps.webofknowledge.com). The “Web of Science Core Collection” option was used. No timeframe limitation was set and the last online search was conducted on 5 September 2017. The keywords used included combinations of “corn yield”, “maize yield”, “plant population”, “planting density”, “sowing rate”, “planting rate”, “corn population”, and “maize population”. When articles were unavailable online or from local libraries, a request was made directly to author(s) of the particular article to provide a reprint. Articles were read in full text and examined on the basis of the following eligibility criteria: (i) plant population was evaluated as a treatment to investigate the effects thereof on maize grain yield, (ii) data reported were generated by field experiments with sound statistical designs, and (iii) field trials received no irrigation prior to planting or during the growing season. Any article that was not in English or did not meet the abovementioned eligibility criteria was excluded. Field trial data generated for modelling purposes were included. To overcome publication bias challenges, studies selected for analysis were not geographically limited. This ensured the inclusion of field trial data from various climatic conditions, combined with different agronomic management systems.
DOI: 10.5061/dryad.q8kb971/1
title: Riesch et al 2018 Data

description: The first data sheet provides the environmental data we measured at each site (conductivity and chlorophyll a) as well as the climate data we downloaded from the WorldClim database (Hijmans et al. 2005 International Journal of Climatology 25:1965–1978); the second data sheet provides all the male life history data; the third data sheet provides all the female life history data; the fourth data sheet provides all the microsatellite fragment lengths we used for the population genetic analyses presented in the online supplement of our publication.
DOI: 10.5061/dryad.rg098gq/3
title: Bioclim-Variables_by-Site

description: 19 WorldClim BioClim variables and elevation of each rattlesnake population locality.
DOI: 10.5061/dryad.rg098gq/4
title: SnakeData

description: Size, sex, identification number, and clade/population membership of the rattlesnakes used in the study.
DOI: 10.5061/dryad.rg098gq/5
title: StructureInput_popflag

description: STRUCTURE input file created from loci obtained from Crotalus oreganus used in this study. Loci were obtained using double-digest restriction-site-associated DNA sequencing (RAD-seq). This file was used to run the Bayesian clustering approach of STRUCTURE and for calculation of pairwise population F-statistics.
DOI: 10.5061/dryad.s4n5t51/1
title: plastid genome sequeces

description: Complete plastid genome sequeces of Quercus acutissima and Quercus chenii, the format are .fasta and .geneious.
DOI: 10.5061/dryad.ss0k19q/1
title: Seersholm2018_NZ_BBM

description: Obitools style filtered OTUs, assigned to the lowest possible taxonomic node based Blast hits. Reads with a best hit below 95% similarity to the database have not been assigned to a node (taxon_name=NA).
DOI: 10.17632/78t2yz2xrf.1
title: Data for: Pollen records of the Little Ice Age humidity flip in the middle Yangtze River catchment

description: Grain size was determined using a Malvern Mastersizer 2000 type particle size analyzer, guided by Lu and An (1998). The grain-size distribution was then transformed into different end-members for better characterization of the depositional environments (Weltje and Prins, 2003).Assessment of the detrital grain-size distributions yielded an optimal model with four end-members (EMs) explaining 99.8% of the original data variance. The mean total R2 between the original and modeled data is generally &gt;0.9. EM1 and EM2 explain 58.3% and 27.1% of data variance, respectively. The grain-size distribution reveals diverse kurtosis, which can reflect different soil conservation and vegetation conditions when there is no flowing water. EM1 has a narrow range from 10µm to 100µm with a peak at ~18µm; EM2 has a broad range from 10µm to 1000µm with a peak at ~129µm; EM3 has a range greater than 100µm with a peak at almost 1000µm, and EM4 has a complex kurtosis (Fig. 3A). The results of the grain-size temporal distribution suggest that EM1 and EM2 are the main components and together account for almost 90% of the total, while EM3 and EM4 are persistently low. The median grain size shows high fluctuations and varies from 0 to 150μm.
DOI: 10.17632/78t2yz2xrf.2
title: Data for: Pollen records of the Little Ice Age humidity flip in the middle Yangtze River catchment

description: Grain size was determined using a Malvern Mastersizer 2000 type particle size analyzer, guided by Lu and An (1998). The grain-size distribution was then transformed into different end-members for better characterization of the depositional environments (Weltje and Prins, 2003).Assessment of the detrital grain-size distributions yielded an optimal model with four end-members (EMs) explaining 99.8% of the original data variance. The mean total R2 between the original and modeled data is generally &gt;0.9. EM1 and EM2 explain 58.3% and 27.1% of data variance, respectively. The grain-size distribution reveals diverse kurtosis, which can reflect different soil conservation and vegetation conditions when there is no flowing water. EM1 has a narrow range from 10µm to 100µm with a peak at ~18µm; EM2 has a broad range from 10µm to 1000µm with a peak at ~129µm; EM3 has a range greater than 100µm with a peak at almost 1000µm, and EM4 has a complex kurtosis (Fig. 3A). The results of the grain-size temporal distribution suggest that EM1 and EM2 are the main components and together account for almost 90% of the total, while EM3 and EM4 are persistently low. The median grain size shows high fluctuations and varies from 0 to 150μm.