cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr00820/3
title: Coyote Pup Hormones_pt.1

description: This datafile contains information for both pup cortisol and testosterone, to perform univariate animal models used to measure repeatability and partition components of variance in each hormone. This file was also used for univariate model selection analyses, which are detailed in the Supporting Information Table S3.  This file, however, was not used for multivariate analyses to determine correlation estimates among traits; that file is designated "Coyote Pup Hormones_pt.2".  In this file, all of the identical columns from the "Coyote Risk-taking Assays.csv" file are include, sans the columns that pertain to coyote risk-taking. The values for the "Cortisol" and "Testo" columns are in units "ng/g", and pertain specifically to the values from the hair sample collected at the particular developmental time (i.e. AGE=WK5, WK10, and WK15).
DOI: 10.5061/dryad.pr00820/4
title: Coyote Pup Hormones_pt.2

description: This aggregated file contains information on pup cortisol, testosterone, and risk-taking behavior to perform the multivariate analyses used to determine correlation estimates among traits (risk-taking with cortisol; cortisol with testosterone; and risk-taking with testosterone). Data for each individual were binned according to the period of hair sample collection. Hence, hair collected at 10 weeks of age were paired with the aggregate number of foraging "successes" (i.e. "1") over the 5-10 week developmental period. To use a "multinomial2" distribution, the column "FR.total" was included with "FR.success", which creates a proportional matrix of how often the individual ate in front of an observer.  All other columns are identical to the files "Coyote Pup Hormones_pt.2" and "Coyote Risk-taking Assays"
DOI: 10.5061/dryad.pr00820/5
title: R Code_Coyote Parental Fear

description: Complete and annotated R script used for all analyses. The data files denoted in this Dryad repository are named and linked to all of the code in this file. Thus, Bayesian animal models performed, model selection analyses, correlation estimates, highest posterior density intervals (HPDI), and model assessment lines of code are all contained in this file.
DOI: 10.5061/dryad.pv814j1/26
title: Specimen 10_1cut
DOI: 10.5061/dryad.pv814j1/27
title: Specimen 11 Control
DOI: 10.5061/dryad.pv814j1/28
title: Specimen 11_1cut
DOI: 10.5061/dryad.pv814j1/29
title: Specimen 12 Control
DOI: 10.5061/dryad.pv814j1/30
title: Specimen 12_1cut
DOI: 10.5061/dryad.pv814j1/31
title: Specimen 13 Control
DOI: 10.5061/dryad.pv814j1/32
title: Specimen 13_5cut
DOI: 10.5061/dryad.pv814j1/33
title: Specimen 14 Control
DOI: 10.5061/dryad.pv814j1/34
title: Specimen 14_2cut
DOI: 10.5061/dryad.pv814j1/35
title: Specimen 15 Control
DOI: 10.5061/dryad.q0b78b5/1
title: Garrick_etal_2018b_Simulated_Data.zip

description: Simulated DNA sequence haplotype data sets associated with Garrick et al. Extending phylogeography to account for lineage fusion. J. Biogeography.
DOI: 10.5061/dryad.v273bt1/1
title: Data on for an experimental selection experiment selecting for or against host manipulation

description: The data file consists of three spreadsheets. Spreadsheet 1 (copepod data) contains data on each copepod (Macrocyclops albidus) used in the study, spreadsheet 2 (fish data) contains data on each fish (three-spined stickleback, Gasterosteus aculeatus) used to allow the parasites to mature and spreadsheet 3 contains data on each parasite (Schistocephalus solidus) family used in this experiment. Descriptions of variable names for all three spreadsheets are provided in the readme file.
DOI: 10.5061/dryad.3ds11g5/2
title: Cover types and heights of cover types

description: Cover types and heights of all cover types measured at random sites
DOI: 10.5061/dryad.4769955/2
title: Haverkamp et al_Flight height

description: Flight height approach from Manduca sexta in wind tunnel
DOI: 10.5061/dryad.4769955/3
title: Haverkamp et al_Flight responce_Nectar_Pollen

description: Manduca response in wind tunnel to flowers
DOI: 10.5061/dryad.4769955/4
title: Haverkamp et al_Flower energy calculation

description: Physical flower energy estimation of movement
DOI: 10.5061/dryad.4769955/5
title: Haverkamp et al_Flower temperature

description: Flower temperature at corolla when directly exposed to high energy lamps to mimic light in natural habitat
DOI: 10.5061/dryad.4769955/6
title: Haverkamp et al_Relative germination rate

description: Pollen germination rate after light exposure
DOI: 10.5061/dryad.76j14s5/10
title: Maximum likelihood tree nAChR gene family

description: The phylogenetic maximum likelihood tree of the nAChR genes in nexus format. The tree topology is supported by a non-parametric Ultra-Fast Bootstrap (UFBoot) and approximate Likelihood-Ratio Test (aLRT) with 1000 replicates. For simplicity only UFBoot values are shown. The taxa ID contains the species, the localization of the gene (chromosome/scaffold/contig number) and a number indicating the order on the chromosome/scaffold/contig if several genes are located on the same one. The taxa ID of human and zebrafish genes with annotated HGNC or ZFIN names, respectively, also contain these names. The assigned taxa ID and sequence information details are provided in Additional file 4.
DOI: 10.5061/dryad.76j14s5/4
title: Table paralogon 3

description: Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 3. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
DOI: 10.5061/dryad.76j14s5/5
title: aLRT SH-like trees paralogon 5

description: Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 5. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
DOI: 10.5061/dryad.76j14s5/6
title: Table paralogon 5

description: Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 5. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
DOI: 10.5061/dryad.76j14s5/7
title: aLRT SH-like trees paralogon 1 in teleosts

description: Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 1 in relation to 3R in teleosts. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
DOI: 10.5061/dryad.76j14s5/8
title: Table paralogon 1 in teleosts

description: Table containing information about the nAChR neighboring gene families included in the analysis of nAChR paralogon 1 in relation to 3R event in teleosts. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
DOI: 10.5061/dryad.80c1rq2/1
title: Roth2019-MEE-IncubationChambers-Data
DOI: 10.5061/dryad.82j677c/4
title: Emergence in Nature

description: Adult B. treatae caught in traps used to estimate emergence phenology in nature
DOI: 10.5061/dryad.82j677c/5
title: Emergence in Laboratory

description: Adult B. treatae emerged from root galls in the laboratory used to estimate emergence phenology
DOI: 10.5061/dryad.82j677c/6
title: Adult Longevity

description: Measurements of adult B. treatae longevity
DOI: 10.5061/dryad.83765sm/1
title: Genotypes and biological data

description: Genotypes and biological data. Genotypes are coded with three digit alleles.
DOI: 10.5061/dryad.83m50j8/1
title: Wildlife responses to UAS approaches

description: Responses by seven species of African herbivore to vertical and horizontal approaches by UAS. Various co-variates are included
DOI: 10.5061/dryad.83pm53m/1
title: Data and R scripts water level body size

description: The data sheets of the male signaling experiment, female phonotaxis experiment and male field playback experiment, including metadata on the columns. Followed by R scripts that show our analyses.
DOI: 10.5061/dryad.b433hv8/1
title: Data for E&E
DOI: 10.5061/dryad.fk01r01/4
title: performance_fmri

description: The file "performance_fmri.xlsx" contains the behavioral data under fMRI scanning for each subject (Dataset 1-fMRI).
DOI: 10.5061/dryad.ft4sn88/16
title: Dryad Supplementary File 16. Constrained ML phylogeny of vascular plants after genera in file genera removed.

description: Dryad Supplementary File 16. Constrained ML phylogeny of vascular plants after genera in file genera removed.
DOI: 10.5061/dryad.ft4sn88/17
title: Dryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magallón et al. (2013).

description: Dryad Supplementary File 17. Time-scaled phylogeny of plant genera based on age estimates in Magallón et al. (2013).
DOI: 10.5061/dryad.ft4sn88/18
title: Dryad Supplementary File 18. treePL file used to time-scale vascular plant phylogeny.

description: Dryad Supplementary File 18. treePL file used to time-scale vascular plant phylogeny.
DOI: 10.5061/dryad.ft4sn88/19
title: Dryad Supplementary File 19. Time-calibrated maximum-likelihood phylogeny of 10785 vascular plant genera.

description: Dryad Supplementary File 19. Time-calibrated maximum-likelihood phylogeny of 10785 vascular plant genera.
DOI: 10.5061/dryad.ft4sn88/20
title: Dryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderized

description: Dryad Supplementary File 20. Time-calibrated maximum-likelihood phylogeny of 1731 ant species. Outgroup taxa removed and tree ladderized
DOI: 10.5061/dryad.ft4sn88/21
title: Dryad_Supplementary_File_21_BAMM_controlfile

description: Dryad_Supplementary_File_21_bamm_controlfile
DOI: 10.5061/dryad.ft4sn88/22
title: Dryad_Supplementary_File_22_BAMM_chain_swap_info

description: Dryad_Supplementary_File_22_BAMM_chain_swap_info
DOI: 10.5061/dryad.ft4sn88/23
title: Dryad_Supplementary_File_23_BAMM_event_data

description: Dryad_Supplementary_File_23_BAMM_event_data
DOI: 10.5061/dryad.g07kg88/1
title: Data for antibiotic coinfection experiment

description: virulence experiment data
DOI: 10.5061/dryad.kd1qt0p.1/1.1
title: Figure 2 - Source Data 1

description: This zip archive contains the original z-stack used for Figure 2, panels A-C. It is provided as a TIF file, which is readable by FIJI. All imaging parameters are included in the image metadata.
DOI: 10.5061/dryad.kd1qt0p.1/13.1
title: Figure 5 - source data 2

description: This zip archive contains the original z-stacks used for Figure 5, panels B and D. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS303_s9_t1 = WT LSI, Dilution factor = 1
A7PS303_s10_t1 = WT LSI, Dilution factor = 1/2
A7PS303_s11_t1 = WT LSI, Dilution factor = 1/4
A7PS303_s12_t1 = WT LSI, Dilution factor = 1/8
A7PS303_s25_t1 = MUC2KO LSI, Dilution factor = 1
A7PS303_s26_t1 = MUC2KO LSI, Dilution factor = 1/2
A7PS303_s27_t1 = MUC2KO LSI, Dilution factor = 1/4
A7PS303_s28_t1 = MUC2KO LSI, Dilution factor = 1/8
A7PS284_s13_t1 = HBSS

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure 5, panels B and D.
DOI: 10.5061/dryad.kd1qt0p.1/16.1
title: Figure 7 - source data 1

description: This zip archive contains the original z-stacks used for Figure 7, panel A. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS320_s1_t1 = 6.66 mg/mL Pectin
A7PS320_s2_t1 = 3.33 mg/mL Pectin
A7PS320_s3_t1 = 1.67 mg/mL Pectin
A7PS320_s4_t1 = 0.835 mg/mL Pectin
A7PS320_s5_t1 = 0.417 mg/mL Pectin
A7PS320_s6_t1 = 0.209 mg/mL Pectin
A7PS320_s7_t1 = 0.105 mg/mL Pectin
A7PS320_s8_t1 = 0.053 mg/mL Pectin
A7PS320_s11_t1 = 236 mg/mL Fibersol-2
A7PS320_s12_t1 = 118 mg/mL Fibersol-2
A7PS320_s13_t1 = 59.0 mg/mL Fibersol-2
A7PS320_s14_t1 = 29.5 mg/mL Fibersol-2
A7PS320_s15_t1 = 14.8 mg/mL Fibersol-2
A7PS322_s1_t1 =  6.66 mg/mL Fibersol-2
A7PS322_s2_t1 =  3.33 mg/mL Fibersol-2
A7PS322_s3_t1 =  1.67 mg/mL Fibersol-2
A7PS322_s4_t1 =  0.835 mg/mL Fibersol-2
A7PS322_s5_t1 =  0.417 mg/mL Fibersol-2
A7PS322_s6_t1 =  0.209 mg/mL Fibersol-2
A7PS322_s7_t1 =  0.105 mg/mL Fibersol-2
A7PS322_s8_t1 =  0.053 mg/mL Fibersol-2


Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to this paper to generate Figure 7, panel A.
DOI: 10.5061/dryad.kd1qt0p.1/2.1
title: Figure 2 - Source Data 2

description: This zip archive contains the original z-stack used for Figure 2, panel D. It is provided as a TIF file, which is readable by FIJI. All imaging parameters are included in the image metadata.
DOI: 10.5061/dryad.kd1qt0p.1/23.1
title: Figure S5 - source data 1

description: This zip archive contains the original z-stacks used for Figure S5, panels A and C. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS308_s1_t1 = WT USI, Dilution factor = 1
A7PS308_s2_t1 = WT USI, Dilution factor = 1/2
A7PS308_s3_t1 = WT USI, Dilution factor = 1/4
A7PS308_s4_t1 = WT USI, Dilution factor = 1/8
A7PS308_s17_t1 = Rag1KO USI, Dilution factor = 1
A7PS308_s18_t1 = Rag1KO USI, Dilution factor = 1/2
A7PS308_s19_t1 = Rag1KO USI, Dilution factor = 1/4
A7PS308_s20_t1 = Rag1KO USI, Dilution factor = 1/8
A7PS284_s13_t1 = HBSS

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure S5, panels A and C.
DOI: 10.5061/dryad.kd1qt0p.1/26.1
title: Table S2 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S2. “WT_LSI_raw_data.xlsx” contains the data for the wild-type lower small intestine, “KO_LSI_raw_data.xlsx” contains the data for the MUC2 knockout lower small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S2 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table.
DOI: 10.5061/dryad.kd1qt0p.1/3.1
title: Figure 2 - Source Data 3

description: This zip archive contains the original z-stack used for Figure 2, panel E. It is provided as a TIF file, which is readable by FIJI. All imaging parameters are included in the image metadata.
DOI: 10.5061/dryad.kd1qt0p.1/35.1
title: Depletion Calculations Code

description: This zip folder contains the source code to generate the plots of the interparticle potential minima displayed in Figure 4H. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p.1/36.1
title: Diffusion coefficients Code

description: This zip folder contains the source code to generate the plots of the diffusion coefficients displayed in Figure 4I. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p.1/5.1
title: Figure 2 - Source Data 5

description: This zip archive contains the original z-stacks used for Figure 2, panels H-I. These are provided as TIF files, which are readable by FIJI. All imaging parameters are included in the image metadata. They are labeled by “Group#” (indicating which CDF they below to in the figure) and “Trial#” if multiple technical replicates were done for a given sample from a Group. The control done in Hanks’ Balanced Salt Solution (HBSS) is labeled as “HBSS”. 

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “Group#_trial#_automated_counting_statistics”. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “Group#_trial#_singlet_IDs”. These .csv files were used in combination with the jupyter notebooks provided (also provided in this submission) to generate Figure 2, panels H-I. If multiple technical replicates were performed on a sample, the resulting ECDFs were combined to create one master ECDF for that sample.
DOI: 10.5061/dryad.m8v146p/1
title: PONE-D-18-26939R2 final dataset

description: Data concerning morphine administration and plasma concentrations f morphine and metabolites in neonates during and after therapeutic hypothermia
DOI: 10.5061/dryad.mj2j4v2/4
title: Online Appendix 4_Specimen_List_&_Observations

description: Online Appendix 4 - List of specimens and observations of cingulum distribution, Excel file
DOI: 10.5061/dryad.mj2j4v2/5
title: Online Appendix 5_Tree_nodes_numbered

description: Online Appendix 5 - Dated tree with node/taxa numbers, PDF file
DOI: 10.5061/dryad.mj2j4v2/6
title: Online Appendix 1_Cingulum_Observation_&_Tree_Construction

description: Online Appendix 1 - Details on cingulum observation and tree construction, Word document
DOI: 10.5061/dryad.mj2j4v2/7
title: Online Appendix 2_Ages_Divergences_Used_Tree

description: Online Appendix 2 - Details on Ages used for divergences, Excel file.
DOI: 10.5061/dryad.n66q0nv/2
title: Studies omitted from review

description: This table provides a list of studies that did not meet the criteria for review.
DOI: 10.5061/dryad.pm4n81q/1
title: Turnover_dendritic_network_(20170320)

description: Data in text format to reproduce experimental results from the article. Please note that the associated R code is available at: https://github.com/harveye/Turnover_dendritic_network
DOI: 10.5061/dryad.pv814j1/36
title: Specimen 15_1cut
DOI: 10.5061/dryad.pv814j1/37
title: Specimen 16 Control
DOI: 10.5061/dryad.pv814j1/38
title: Specimen 16_1cut
DOI: 10.5061/dryad.pv814j1/39
title: Specimen 17 Control
DOI: 10.5061/dryad.pv814j1/40
title: Specimen 17_2cut
DOI: 10.5061/dryad.pv814j1/41
title: Specimen 18 Control
DOI: 10.5061/dryad.pv814j1/42
title: Specimen 18_2cut
DOI: 10.5061/dryad.pv814j1/43
title: Specimen 19 Control
DOI: 10.5061/dryad.pv814j1/44
title: Specimen 19_2cut
DOI: 10.5061/dryad.q5n39p4/1
title: R PerSIMPER function

description: Based on a presence/absence matrix, this function allows the identification of the first-order process of assembly underlying a set of taxonomic assemblages. Its use should therefore be limited to the comparison of significantly distinct taxonomic sets. But at the same time connected enough to allow the potential dispersal of species between these different sets. The PER-SIMPER method distinguishes the main ecological assembly process (between species dispersal capacity and niche richness) at the origin of the observed taxonomic differences between two (or more) compared sets of assemblages. The PER-SIMPER method is associated with the calculation of the E index (the logarithm of the sum of squared deviations between empirical and simulated SIMPER profiles) to assist in distinguishing the result of PER-SIMPER analyses.
DOI: 10.5061/dryad.q5n39p4/2
title: Help notes PER-SIMPER

description: Help notes of the PER-SIMPER R function. R function included too.
DOI: 10.5061/dryad.qb701kq/1
title: Micorsatellites data in genepop format

description: Micorsatellites data in genepop format for 10 populations of Tetranychus uticae
DOI: 10.5061/dryad.qb701kq/2
title: The cytb gene sequences for all individuals of Tetranychus uticae

description: The cytb gene sequences for all individuals of Tetranychus uticae from 10 populations
DOI: 10.5061/dryad.qb701kq/3
title: Thirteen haplotypes of cytb gene for Tetranychus uticae

description: Thirteen haplotypes of cytb gene for Tetranychus uticae
DOI: 10.5061/dryad.r2d5451/1
title: Data files

description: Data and output files produced by pyrad.
DOI: 10.5061/dryad.r2d5451/2
title: AMOVA and Fst analyses

description: Data and script for AMOVA and Fst analyses.
DOI: 10.5061/dryad.r2d5451/3
title: SNAPP analyses

description: Data and script for converting snp files into snapp input files.
DOI: 10.5061/dryad.r2d5451/4
title: Population genetic summary statistics

description: Script for calculating population genetic summary statistics.
DOI: 10.5061/dryad.r2d5451/5
title: Phylogeographic concordance factor analysis

description: Data and scripts for running Phylogeographic Concordance Factors (PCFs) and testing for significance with the analysis.
DOI: 10.5061/dryad.vb76b45/1
title: Database S1

description: GGI genes trees and species trees analyses using ASTRAL-2
DOI: 10.5061/dryad.vb76b45/2
title: Database S4

description: Subsets of exon capture