cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j2906/1
title: Great Lakes piping plover population data

description: Great Lakes piping plover population data from 1993 - 2016 used to build a coupled integrated population model-Bayesian population viability analysis (IPM-BPVA). The first tab includes capture-mark-resight (CMR) data for hatch-year and after hatch-year birds. Note that the CMR data included here represent a partial list (proprietary records omitted) because of the endangered status of Great Lakes piping plovers, but are sufficient for conducting the IPM-BPVA analysis. The second tab includes census data (number of breeding pairs annually). The third tab includes 2 columns on productivity: FLEDGE is the number of fledglings observed annually and SURV_BROOD is the number of surveyed broods annually. The last tab includes merlin census data collected at 2 observatories annually: Hawk Mountain (HM) and Whitefish Point (WP).
DOI: 10.5061/dryad.kg262/1
title: FE_Data
DOI: 10.5061/dryad.kg5s5/4
title: accessory_binary_genes

description: The binary representation of accessory genes present (A) or absent (C) from the 20 P. freudenreichii genomes as determined by Roary analysis.
DOI: 10.5061/dryad.kt741/1
title: Hermoso et al

description: Distribution of key species in Natura 2000, used in this study
DOI: 10.5061/dryad.n5d23/1
title: Data Table 1. Main biologic characteristics of the randomly selected 24 patients suffering from chronic (over 6-Months) tempormandibular joint disorders (TMD) with substantial selfreported unilateral pain

description: Biological characteristics of patients
DOI: 10.5061/dryad.n5d23/2
title: Data Table 2. Condylar Path

description: Table 2 shows mean (from 2 independent assessor’s measurements) values of Condylar Path angles on each side of patients. Measurement units: degrees.
DOI: 10.5061/dryad.n5d23/3
title: Data Table 3. Lateral Guidance

description: Lateral anterior guidance (LG) angles of patients suffering from susbstantial chronic unilateral TMD pain.
DOI: 10.5061/dryad.n5d23/5
title: Data Table 5. CP and LG outcomes reliability

description: Raw measurements of condylar path (CP), and lateral anterior guidances (LG) from two independent assessors
DOI: 10.5061/dryad.n5d23/7
title: Data Table 4. Asymmetry and Equation indexes of condylar path and lateral guidance angles

description: Asymmetry indexes (quotient between differences and sums of a particular outcome) of condylar path (CP) and lateral guidance (LG) angles. The algorithm “Equation” correlates both CP and LG outcomes: (Right CP × left LG) / (left CP × right LG)
DOI: 10.5061/dryad.p58c0/1
title: SI Figures S1-S17

description: All 17 SI figures with captions.
DOI: 10.5061/dryad.p58c0/2
title: SI tables S1-S7

description: All 7 SI tables with captions.
DOI: 10.5061/dryad.p58c0/3
title: Analysis.files

description: Input and output files for analyses with R code.
DOI: 10.5061/dryad.pj475/2
title: Results presented in figure 8 (a) and (b).

description: (a) The sensor response to different nitrite concentrations in the sample, (b) nitrite concentration calibration curve (Line fitted to the experimental S values obtained for different nitrite concentrations using Griess reagents).
DOI: 10.5061/dryad.pj475/3
title: Results presented in figure 9.

description: A Linear relationship between the pH values obtained using the pH meter and those obtained using the portable device.
DOI: 10.5061/dryad.pj475/4
title: Results presented in figure 10.

description: A Linear relationship between the concentrations of the prepared nitrite solutions and those obtained using the portable device.
DOI: 10.5061/dryad.pj475/5
title: Results presented in figure .11 (Top) and (Botoom)

description: UV-vis measurements for nitrite concentrations (top) UV-vis spectrum for the determination of different nitrite concentration, (bottom) nitrite concentration calibration curve (Line fitted to the experimental absorbance values at 540 nm obtained for different nitrite concentrations using Griess reagents)
DOI: 10.5061/dryad.pj475/6
title: Photocolorimeter algorithm
DOI: 10.5061/dryad.pp06m3k/1
title: Kostermanetal_Data_EcoApps
DOI: 10.5061/dryad.qf731/24
title: sifaka_trimmed_phyloseq_markedonly_normalized_openref

description: Phyloseq object containing normalized OTU counts for sifaka of known identity only. Place in "data" folder before running analyses.
DOI: 10.5061/dryad.qf731/25
title: mantel_tests_social_distance_vs_microbiome

description: R script that tests for correlations between social distance and microbiome dissimilarity.
DOI: 10.5061/dryad.qf731/27
title: samseq_differential_abundance_across_groups

description: R script that tests for differential abundance of bacterial phyla, families, and genera among sifaka social groups.
DOI: 10.5061/dryad.qf731/28
title: alpha_diversity

description: R script that rarefies the raw OTU table 100 times to calculate  microbiome diversity for individual samples.
DOI: 10.5061/dryad.qf731/29
title: social_data

description: R script that loads in census, focal, and scan data.
DOI: 10.5061/dryad.qf731/30
title: diet_analyses

description: R script that tests between-group and between-individual differences in diet.
DOI: 10.5061/dryad.qf731/31
title: beta_div_glmms

description: R script that uses generalized linear mixed models (GLMMs) to estimate the effects of pairwise predictors (social distance, relatedness, group membership) on microbiome dissimilarity.
DOI: 10.5061/dryad.qf731/32
title: mantel_tests_relatedness_vs_microbiome

description: R script that tests for correlations between genetic relatedness and microbiome dissimilarity.
DOI: 10.5061/dryad.qf731/33
title: pairwise_dissimilarity_predictors

description: R script testing the effects of habitat overlap, dispersal history, and vertical inheritance on microbiome dissimilarity among samples.
DOI: 10.5061/dryad.rv6b7/1
title: Contrast sensitivity across the menstrual cycle

description: contrast sensitivity from a control sample of male participants, and across the menstrual cycles of naturally cycling women and users of combined oral contraception.
DOI: 10.5061/dryad.st621/1
title: Fig2C_Blot3

description: Original blot used to quantify Fig2C
DOI: 10.5061/dryad.st621/2
title: Fig2C Blot2

description: Original blot to quantify Fig2C
DOI: 10.5061/dryad.st621/3
title: Fig2C_Blot1

description: Original blot to quantify Fig2C
DOI: 10.17632/dcgzyyxfdh.1
title: Data for: Long-term effects of zero tillage and grazing on soil quality and land productivity in a semiarid environment

description: supplementary information
DOI: 10.17632/dcgzyyxfdh.2
title: Data for: Long-term effects of zero tillage and grazing on soil quality and land productivity in a semiarid environment

description: supplementary information
DOI: 10.17632/fdgp5gh3j9.1
title: Data for: Conservation professionals agree on challenges to coexisting with large carnivores but not on solutions

description: Although many studies explore characteristics of stakeholders or publics “for” or “against” carnivores, disagreements among conservation professionals advocating different conservation strategies also occur and are not well recognized. Differing viewpoints on whether and how humans can share landscapes with large carnivores can influence conservation actions. To characterize current viewpoints about terrestrial carnivore conservation, we conducted an online survey assessing a wide range of viewpoints about large carnivore conservation among international professionals (n=505). We explored how variation in viewpoints was related to expertise, background, and broader institutional contexts in which one lives and works. The majority of participants agreed people and large carnivores can share the same landscapes (86%). Human adaptation to carnivores (95% agreement) and acceptance of some conflict (93%) were the highest ranked requirements for human-carnivore coexistence. We found broad consensus regarding intrinsic value of carnivores, reasons carnivores are imperilled, conflict drivers, and importance of proactive solutions, such as adopting preventative livestock husbandry methods or avoiding situations that put people at risk. The greatest polarization was observed in issues related to lethal control, where we only found broad consensus for killing carnivores in situations where humans are in immediate risk. Participants did not support killing large carnivores for purposes of decreasing population sizes or increasing human tolerance, profits, livelihoods, or fear of humans. Results point to considerable diversity, perhaps driven by local context, concerning how to proceed with large carnivore conservation in increasingly human-influenced landscapes of the Anthropocene. The different observed viewpoints represent both different strategies about how to best conserve, but also different moral platforms about what, how, where, and for whom conservation should occur. Our study underlines that challenges to adopting and implementing long-lasting carnivore conservation strategies may well occur as much within the conservation community as outside it.
DOI: 10.17632/rf3zh2x4xc.1
title: Data for: Molecular systematics and phylogenetics of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae)

description: Bait-120-60-R4-both4434.fas, sequences of all 120 bp baits Goby4434.fas, sequences of the markers that were used for baits design OdontobutidsSequences.txt, the sequence alignments in nexus format for all loci PartitionFinderScheme.txt, the best partitioning scheme for the 4,397 loci suggested by PartitionFinder.
DOI: 10.5061/dryad.15qf2/2
title: STRUCTURE individual output file

description: STRUCTURE output file with inferred population assignment probabilities for individual samples (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.
DOI: 10.5061/dryad.15qf2/3
title: STRUCTURE population output file

description: STRUCTURE output file with mean assignment probabilities for each of ten populations, pre-defined by sampling location (K=5). Burn-in period of 300,000 followed by 1,000,000 MCMC repetitions.
DOI: 10.5061/dryad.22tq8/2
title: Data for spatial analysis

description: Contains geographic coordinates, year, and plot code for each tree, as well as a status code and whether the tree is dead or alive.
DOI: 10.5061/dryad.2n0v8/1
title: FDS4d

description: This is the code, which we used  to generate the blue points in Fig. 5
DOI: 10.5061/dryad.2n0v8/2
title: INSTRUCTIONS  --  Program FDS4d.m
DOI: 10.5061/dryad.4k03n/1
title: Leaf trait and light measurements Jena Experiment 2011

description: The data folder comprises three csv-files with plant trait and light measurements conducted within the Jena Experiment in 2011. Information of each column is given in the header of each file.
DOI: 10.5061/dryad.74gd7/1
title: Supplementary Structure input file

description: Genotype calls for all sampled individuals. SNP numpers in columns and individuals in rows. Genotype calls (1-4) corresponds to bases A, T, C, and G respectively. The file works as an input file in Structure
DOI: 10.5061/dryad.871c7/10
title: North_high_vs_mid

description: DESeq2 differential gene expression results for the north 60psu vs north 35psu exposure
DOI: 10.5061/dryad.871c7/11
title: North_low_vs_mid

description: DESeq2 differential gene expression results for the north 15psu vs north 35psu exposure
DOI: 10.5061/dryad.871c7/12
title: Orthogroups_All

description: All the orthogroups inferred for the northern and southern copepod populations. Includes orthogroups that were present only in the north or only in the south population.
DOI: 10.5061/dryad.871c7/13
title: Orthogroups_in_both_pops

description: Orthogroups that were present in both the northern and southern populations
DOI: 10.5061/dryad.871c7/14
title: SA_transcriptome

description: The transcriptome from the Salt Point (northern) copepod population originally published in Kelly et al. 2017 DOI: 10.1111/1365-2435.12725
DOI: 10.5061/dryad.871c7/6
title: count_matrix_BR_genes

description: The count matrix at the gene level for the Bodega Reserve population
DOI: 10.5061/dryad.871c7/7
title: count_matrix_SD_genes

description: The count matrix at the gene level for the San Diego population
DOI: 10.5061/dryad.871c7/8
title: Count_orthos

description: Script that sums the counts of reads mapped to all genes within an orthogroup
DOI: 10.5061/dryad.871c7/9
title: full_count_matrix_orthogroups

description: The count matrix at the orthogroup level for orthogroups present in both populations
DOI: 10.5061/dryad.8g1bb/1
title: Dryad1_PCRandSeqconditions

description: PCR and sequencing conditions for song sparrow MHC class IIß
DOI: 10.5061/dryad.8g1bb/2
title: Dryad2_FigS1_MHCalleletree

description: Figure S1. Phylogeny of MHC class IIß amino acid alleles amplified from 32 male song sparrows. Evolutionary history was inferred using the maximum likelihood method based on the WAG amino acid substitution model. The tree with the highest likelihood is shown. The percentage of replicate trees in which the associated alleles cluster together in the bootstrap test (500 replicates) is shown at each node. The tree is drawn to scale, with branch lengths corresponding to number of substitutions per site. The analysis involved 186 amino acid sequences (SOSP-DAB*#). Each vertical red line indicates a superallele (SA) composed of multiple similar sequences, and each black arrow indicates a single sequence that belonged to its own SA.
DOI: 10.5061/dryad.8g1bb/3
title: Dryad3_Rcode

description: Annotated R code used in data analysis.
DOI: 10.5061/dryad.8g1bb/4
title: Dryad4_MHC_composition_table

description: MHC composition table for 32 male song sparrows. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (allele). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.
DOI: 10.5061/dryad.8g1bb/5
title: Dryad5_MHC_composition_table_with_IDs

description: MHC composition table for 32 male song sparrows, including individual identifiers. Each row corresponds to an individual bird, and each column corresponds to a unique amino acid sequence at MHC IIß (“allele”). Presence or absence of each allele in each individual’s genotype is denoted by 1 or 0, respectively. Alleles are listed here as X1, X2, … and correspond to sequences SOSP-DAB*1, SOSP-DAB*2, … on Figure S1 and on GenBank.
DOI: 10.5061/dryad.8g1bb/6
title: Dryad6_MHC_AA_sequences

description: Amino acid sequences for 32 male song sparrows genotyped at MHC IIß (FASTA format).
DOI: 10.5061/dryad.8g1bb/7
title: Dryad7_MHC_AA_tree

description: Newick tree topography for amino acid alleles characterized at MHC IIß. Evolutionary history was inferred as described in Figure S1 (file Dryad2).
DOI: 10.5061/dryad.9b9c1/1
title: Combined matrix of Spiranthinae and outgroups (matK-trnK, trnL-F and nrITS)

description: Interleaved matrix in NEXUS format including nucleotide sequences of matK-trnK (2169 characters), trnL-F (2002 characters) and nrITS (760 characters) regions.
DOI: 10.5061/dryad.gc46s/1
title: DelayInEmergenceEABFitness_DataAnalyses

description: Data and R code to reproduce analyses and figures. R code is given in .Rmd & R files. The .Rmd files are best viewed in RStudio, but can be opened in any text editor. All code is commented.
DOI: 10.5061/dryad.hf124/1
title: Camuropiscis_Suborbital_SAMP53772
DOI: 10.5061/dryad.hf124/2
title: Eastmanosteus_postsuborbital_MVP231104
DOI: 10.5061/dryad.hf124/3
title: Eastmanosteus_Postsuborbital_subsection_MVP231104
DOI: 10.5061/dryad.hf124/4
title: Kimberleyichthys_Postsuborbital_ANUV1037
DOI: 10.5061/dryad.hf124/5
title: Ligulalepis_ANUV3628_sensory pits
DOI: 10.5061/dryad.hf124/6
title: Parabuchanosteus_Suborbital_ANUV1686
DOI: 10.5061/dryad.md268/1
title: GPS data for all of the terminal attack trajectories of peregrine falcons (Falco peregrinus) that were analysed in the paper.

description: The raw GPS data relating to our publication are stored in the MAT-file Brighton2017.mat, readable in MATLAB Version 8 (The MathWorks, Inc.) or later. This MAT-file holds a single structure array, terminalTrajectories, containing the GPS data for all of the terminal attack trajectories of peregrine falcons (Falco peregrinus) that were analysed in the paper. A detailed description of the fields of this structure array can be found in the accompanying README file.
DOI: 10.5061/dryad.qf731/1
title: diet_diversity_table_for_poisson_glmm

description: Place in "data" folder before running analyses. For use in poisson_glmms.R script.
DOI: 10.5061/dryad.qf731/11
title: sifaka_allotus_phyloseq_openref

description: Phyloseq object containing raw OTU counts (but singletons are removed). Place in "data" folder before running analyses.
DOI: 10.5061/dryad.qf731/12
title: diet_diversity_df

description: Table of individual dietary richness values. Place in "data" folder before running analyses. For use in diet_analyses.R script.
DOI: 10.5061/dryad.qf731/36
title: network_duration_function_dyad

description: R script that creates a social network using census, focal, and scan data.
DOI: 10.5061/dryad.qf731/37
title: poisson_glmms

description: R script that uses generalized linear mixed models (GLMMs) to estimate the effects of age, network centrality, diet, and scent-marking rate on within-host microbiome richness.
DOI: 10.5061/dryad.qf731/38
title: beta_diversity_adonis

description: R script for PERMANOVA analyses.
DOI: 10.5061/dryad.qf731/39
title: sifaka_trimmed_phyloseq_normalized_openref

description: Phyloseq object containing normalized OTU counts for all individuals. Place in "data" folder before running analyses.
DOI: 10.5061/dryad.qf731/9
title: sifaka_braycurtis_marked_openref

description: Matrix of Bray Curtis dissimilarities among microbiome samples. Place in "data" folder before running analyses.
DOI: 10.5061/dryad.qq11c/1
title: 18S V1-V3
DOI: 10.5061/dryad.qq11c/2
title: 18S V4
DOI: 10.5061/dryad.qq11c/3
title: COI
DOI: 10.5061/dryad.qq11c/4
title: Fish 16S
DOI: 10.5061/dryad.qq11c/6
title: Ceph 16S
DOI: 10.5061/dryad.sq4f7/1
title: ShigellaDataFor2016Paper_labelled_dryad
DOI: 10.5061/dryad.st621/4
title: Fig2B_Blot2

description: Original blot to quantify Fig2B
DOI: 10.5061/dryad.st621/5
title: Fig2B_Blot1

description: Original blot to quantify Fig2B
DOI: 10.5061/dryad.v2q3v/1
title: Data from Experiment 1 of Wale et al. 2017, PNAS.

description: Excel file containing (sheet 1) raw data from Experiment 1 & (sheet 2) information describing the contents.
DOI: 10.5061/dryad.v2q3v/2
title: Data from Experiment 2 of Wale et al. 2017, PNAS.

description: Excel file containing (sheet 1) raw data from Experiment 2 & (sheet 2) information describing the contents.
DOI: 10.5061/dryad.v2q3v/3
title: Data from Experiment 3 of Wale et al. 2017, PNAS.

description: Excel file containing (sheet 1) raw data from Experiment 3 & (sheet 2) information describing the contents.
DOI: 10.5061/dryad.v2q3v/4
title: Data from Experiment 4 of Wale et al. 2017, PNAS.

description: Excel file containing (sheet 1) raw data from Experiment 4 & (sheet 2) information describing the contents.
DOI: 10.5061/dryad.v6q0p/1
title: Assembly of Buddleja globosa genome

description: Assembly of Buddleja globosa genome (voucher: R.G. Olmstead 2010-46 [WTU]) from whole-genome shotgun Illumina sequencing. De novo assembly performed with CLC Genomics Server 5.0.2.
DOI: 10.5061/dryad.v6q0p/2
title: Target locus sequences for probe design

description: Set of sequences from Buddleja globosa of putative single-copy nuclear loci used for probe design. Includes taxon-specific loci (sequence name beginning with GRFT or XRLM) and COSII, APVO SSC, and PPR loci.
DOI: 10.5061/dryad.v6q0p/3
title: Buddleja APVO SSC loci concatenated alignment
DOI: 10.5061/dryad.16r1r/1
title: raw data

description: raw data, Couple Functionality Assessment Tool (CFAT) Malawi validation study
DOI: 10.5061/dryad.16r1r/2
title: women's questionnaire

description: Couple Functionality Assessment Tool (CFAT) Malawi validation questionnaire, women's version, Q1-Q141. This tool is copyrighted by Catholic Relief Services (CRS). CRS has granted permission to place the tool in open access with no restrictions on usage and requests that CRS is credited for any usage of the tool.
DOI: 10.5061/dryad.16r1r/3
title: men's questionnaire

description: Couple Functionality Assessment Tool (CFAT) Malawi validation questionnaire, men's version, Q1-Q141, This tool is copyrighted by Catholic Relief Services (CRS). CRS has granted permission to place the tool in open access with no restrictions on usage and requests that CRS is credited for any usage of the tool.
DOI: 10.5061/dryad.1j05f/1
title: Lammers et al MINEX Acoustic Monitoring data

description: Spreadsheet containing the data used for statistical calculations
DOI: 10.5061/dryad.1j05f/2
title: MINEX GAM Output

description: Explanation of generalized additive model
DOI: 10.5061/dryad.1j05f/3
title: MINEX_linear_array_dep_01-14_raw
DOI: 10.5061/dryad.1j05f/4
title: Explosions detected to date_EJZ

description: Data file used for creating GAM
DOI: 10.5061/dryad.22tq8/3
title: Data for mortality model

description: Contains data for each individual tree used for mortality modeling: whether the tree is dead/alive, its DBH, the temperature and precipitation in the preceding wet and dry seasons, and the Competition Index using radii of 5 and 10 meters.
DOI: 10.5061/dryad.25m10/1
title: Supplemental Figure 2 from Chapter 5

description: Hierarchal tree of overrepresented GO terms within the set of
downregulated genes in ΔrpnR. Boxes highlighted in green represent GO terms that are
overrepresented, a black edge between two nodes means “regulates”, a blue edge “is a”,
and a light blue edge “is part of”.
DOI: 10.5061/dryad.678rp/1
title: Figure_S1_RADseq_SVDquartets_trees_high_res

description: High resolution version of Figure S1 depicting the Crenicichla phylogeny across different matrix sizes and data
DOI: 10.5061/dryad.678rp/2
title: Burress_et_al_Supporting_Information

description: This file contains the supplemental tables and figures referenced in the main text as well as Methods and Results associated with the SVDquartets trees. A high resolution version of figure S1 is provided separately.
DOI: 10.5061/dryad.678rp/3
title: Crenicichla_dated_ML_tree

description: The unpruned time-calibrated maximum likelihood tree used for phylogenetic comparative analyses in the paper. File is in tree format.
DOI: 10.5061/dryad.6g8n1/1
title: DeBoeck et al. meta-analysis

description: Data used in the meta-analysis
DOI: 10.5061/dryad.6h68k/1
title: Trevathan-Tackett_etal_JAE_rawdata

description: All data is included in one file and includes, sampling descriptions, GPS points, organic matter data, elemental and isotope data, thermogravimetric analysis data, and age-dating data.
DOI: 10.5061/dryad.7d8k0/1
title: data
DOI: 10.5061/dryad.871c7/15
title: SA_transcriptome.pep

description: The translated Salt Point transcriptome
DOI: 10.5061/dryad.871c7/16
title: sal_high_vs_mid

description: The log p-value for orthogroups differentially expressed under high salinity stress. This file is used in the functional enrichment analysis
DOI: 10.5061/dryad.871c7/17
title: sal_low_vs_mid

description: The log p-value for orthogroups differentially expressed under low salinity stress. This file is used in the functional enrichment analysis
DOI: 10.5061/dryad.871c7/18
title: South_high_vs_mid

description: DESeq2 differential gene expression results for the south 60psu vs north 35psu exposure
DOI: 10.5061/dryad.871c7/19
title: South_low_vs_mid

description: DESeq2 differential gene expression results for the south 15psu vs north 35psu exposure
DOI: 10.5061/dryad.871c7/20
title: tig_ogs_with_goterms

description: List of gene ontology terms associated with the orthogroups that were present in both the northern and southern population