cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd1qt0p.1/9.1
title: Figure 4 - source data 2

description: This zip archive contains the original z-stacks used for the PEG 1 MDa data in Figure 4, panel D. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS290_s1_t1 = 6.52 mg/mL PEG 1 MDa
A7PS290_s2_t1 = 3.26 mg/mL PEG 1 MDa 
A7PS290_s3_t1 = 1.63 mg/mL PEG 1 MDa
A7PS290_s4_t1 = 0.815 mg/mL PEG 1 MDa
A7PS290_s5_t1 = 0.407 mg/mL PEG 1 MDa
A7PS290_s6_t1 = 0.204 mg/mL PEG 1 MDa
A7PS290_s7_t1 = 0.102 mg/mL PEG 1 MDa
A7PS290_s8_t1 = 0.0509 mg/mL PEG 1 MDa

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 as additional files to this paper to generate Figure 4, panel D.
DOI: 10.5061/dryad.kd1r166/3
title: Claytonia_SeedSet
DOI: 10.5061/dryad.kd1r166/4
title: Delphinium_SeedSet
DOI: 10.5061/dryad.kt24554/1
title: Alignments used for comparative genomics

description: Multiple species alignment for each HOG. NCBI gene IDs for HOGs can be found in R_data_and_scripts/02_output_annotated_data/raw_results_sptrees_all_annotations.csv from zipped R_data_and_scripts file.
DOI: 10.5061/dryad.kt24554/3
title: R Scripts and Data Files

description: All selection scan and differential expression results (PAML results, HyPhy results, Sleuth results), and all scripts for subsequent analyses. There are seven modules that include and R script, directory with any necessary input data, and directory with any output files. The scripts do the following: 1. process all PAML and HyPhy output into analysis-ready formats. 2. Annotate all HOGs with NCBI and Ensembl gene IDs. 3. General dataset statistic calculations 4. Bird KEGG pathway enrichment analyses. 5. Comparisons of bird and mammal selection scan results 6. Clustering and analysis of bird aBS-REL results. 7. Transcriptome analyses for both birds and mammals.
DOI: 10.5061/dryad.mj2j4v2/10
title: Online_Appendix_7_Matrices_Q

description: Online Appendix 7 - Illustration of matrices used for likelihood tests of character models, PDF file.
DOI: 10.5061/dryad.mj2j4v2/11
title: Online_Appendix_8_Results_Rates_models_EntireSample

description: Online Appendix 8 - Excel sheets with the estimated transition rates for all models for the anterior and posterior cingula in the entire sample (Placentalia)
DOI: 10.5061/dryad.mj2j4v2/8
title: Online Appendix 3_Results-Likelihood_Models

description: Online Appendix 3 - ML results, Excel file.
DOI: 10.5061/dryad.mj2j4v2/9
title: Online Appendix 6_Details_Node_Positioning

description: Online Appendix 6 - Illustration of methodology for node positioning on the analyzed tree, PDF file.
DOI: 10.5061/dryad.pv814j1/45
title: Specimen 20 Control
DOI: 10.5061/dryad.pv814j1/46
title: Specimen 20_1cut
DOI: 10.5061/dryad.pv814j1/47
title: Specimen 21 Control
DOI: 10.5061/dryad.pv814j1/48
title: Specimen 21_1cut
DOI: 10.5061/dryad.pv814j1/49
title: Specimen 22 Control
DOI: 10.5061/dryad.pv814j1/50
title: Specimen 22_1cut
DOI: 10.5061/dryad.pv814j1/51
title: Specimen 23 Control
DOI: 10.5061/dryad.pv814j1/52
title: Specimen 23_1cut
DOI: 10.5061/dryad.rf79641/1
title: Variant file in VCF format

description: 23,667 SNPs genotyped in 91 individuals aligned to Trinidadian guppy genome assembly used for population genomic characterization. Individual IDs correspond to population codes in Table 1.
DOI: 10.5061/dryad.v309h90/1
title: Data_phen_conn_dryad

description: Phenotypic information and mean connectome feature data for Bernhardt et al. (2019) Temporal lobe epilepsy: hippocampal pathology modulates white matter connectome topology and controllability. Neurology
DOI: 10.5061/dryad.15d8dq8/3
title: uSNPs input file for STRUCTURE

description: uSNPs input file for STRUCTURE
DOI: 10.5061/dryad.3hp84t0/1
title: Naylor Davidson Manusript Dryad spreadsheet

description: This data file includes empirical scoring data for the manuscript submitted for full review to the eLife journal. Each spreadsheet contains the scoring data for individual experiments and are so titled in terms that refer to the Figure in question.
DOI: 10.5061/dryad.3hp84t0/2
title: Naylor Davidson Manuscript Dryad spreadsheet

description: Contains empirical data for the resubmitted version of the paper entitled "A novel mechanism of gland formation in zebrafish involving transdifferentiation of kidney cells and live cell extrusion". Each spreadsheet contains data for the individual figures where quantitation was performed.
DOI: 10.5061/dryad.485b1c3/1
title: Transition Probabilities

description: Transition probabilities used to conduct a baseline analysis as well as cohort-level Markov simulations.
DOI: 10.5061/dryad.485b1c3/2
title: Tibial Neurolysis Markov Model (discounted)

description: TreeAge decision tree used for a cost-effectiveness analysis and cohort-level Markov simulations.
DOI: 10.5061/dryad.4f1n785/1
title: OTUS

description: Otus as fasta format file. See Otutable.xls to link sample names to data.
DOI: 10.5061/dryad.4f1n785/2
title: OTU table

description: Reads assigned for each OTU in each sample. Contains the metadata information of the samples.
DOI: 10.5061/dryad.4r34459/1
title: T2 curve of coal samples

description: The data is the original data of the test process, which can be opened by Excel software.
DOI: 10.5061/dryad.4t46jj6/1
title: site data

description: Sites are defined as a single slope within an abandoned field or pasture. Information on land-use history and time since abandonment was obtained from interviews with former landowners and local residents. All study sites were former pastures, although small areas within pastures may have been used temporarily for crop cultivation. No records exist of within-site land-use dynamics but extensive discussions with former land owners and neighbors indicate that such areas were generally small and cultivated for one to two years before being converted back to pasture. In each site, two 20×50 m plots were established, one on the upper portion of the slope and another on the lower portion of the slope. In each plot, all stems of trees, shrubs, and palms with a diameter ≥ 5 cm and all stems of woody climbing plants with a diameter of ≥ 1 cm were tagged, identified and measured. In one-half of each plot, stems with 1 ≤ DBH &lt; 5 cm of woody, non-climbing plants were treated similarly. This data file contains site-level data: "site+ = site id; "age" = forest age since abandonment, in years; "BA" = average of the basal areas of the two plots, in m2/ha; "dist" = distance between the two plots, in meters; "nutr" = dissimilarity in soil nutrients between the upper and lower plots, calculated using Al, P, Ca, Mg, and Cu, and Euclidean distances; "abdis" = species dissimilarity, calculated using the abundance-weighted Jaccard index.
DOI: 10.5061/dryad.4t46jj6/3
title: plot_data

description: This data file contains plot-level data: "site" = site id; "transect" = plot id; "TP" = topographic position, either upper slope (UP) or lower slope (LS); "BA" = basal areas of the plot, in m2/ha; “P” = P concentration, in ppm; “Mg” = Mg concentration, in ppm; “Ca” = Ca concentration, in ppm; “Cu” = Cu concentration, in ppm; “Al” = Al concentration, in ppm.

Soils were sampled at the end of the wet season (late November–early December) at nine points along the mid line of each plot at 5 m intervals. Soil cores were taken from the upper 15 cm of the mineral soil, bulked, thoroughly mixed, and then sub-sampled for nutrient analysis. Concentrations of base cations and plant available phosphorus were extracted using the Mehlich III method.
DOI: 10.5061/dryad.4t46jj6/4
title: Species abundances per plot

description: Species abundances per plot. Sampling was nested, with plants with 1-5 cm dbh sampled in 500 m2 per plot, and plants with dbh &gt; 5 cm sampled in 1000 m2 per plot. To account for difference in sample effort, we counted each plant with a diameter less than 5 cm double in the calculation of abundance. "transect" = plot number; "specid" = species identification codes used by the Center for Tropical Forest Studies; "nr" = estimated number of plants per species.
DOI: 10.5061/dryad.5bg107j/1
title: Wood frog mating trials and offspring summary data

description: This file contains data from wood frog mating trials (males divided into two treatments, to mate with preferred or non-preferred females) and includes summary data for the resulting offspring.
DOI: 10.5061/dryad.5bg107j/2
title: Laboratory-reared offspring

description: This file contains body size, date of metamorphosis, and parent morphology of all wood frog larvae that were reared in the laboratory.
DOI: 10.5061/dryad.5bg107j/3
title: Field-reared offspring

description: This file contains the Gosner stages, sizes, and parent sizes of the wood frog larvae that were reared in field enclosures.
DOI: 10.5061/dryad.5s12fr6/1
title: Wilde et al., 2019FE_data

description: Data from ME and RM low sites, Spring Gulch (SG) and Big Elk (BE) respectively. 
Data is organized by site, individual mouse ID (format: site_season_number), and descending year (2018, 2017, 2016). 
Associated demographic characters Sex and Age are in binary, with 1 representing Male and Adult, and 0 representing Female and Juvenile. 
RMR and SMR are uncorrected flow rate’s (ml O2 min-1) from respirometry trials, done only in 2016 and 2017.
Infection is organized with 0 ‘no infection’, 1 ‘recovering’, and 2 ‘active infection’. 
See methods of Wilde et al., 2019 for further details.
DOI: 10.5061/dryad.61r43kd/1
title: Supplementary_Metadata

description: Metadata describing information regarding each sample included in the study. The metadata includes sequence ID, DNA yield following DNA extraction and library generation, storage conditions, DNA quality and donor.
DOI: 10.5061/dryad.64s8h65/6
title: Waraniak_Rana_pipiens_population_sturcture_analyses

description: R code detailing the analyses of population structure and landscape genetics as described in Waraniak et al.
DOI: 10.5061/dryad.64s8h65/7
title: R._pipiens_records-2965a1e1a3034dcca2186fd124c90386

description: Records of northern leopard frogs taken from the VertNet database.
DOI: 10.5061/dryad.64s8h65/8
title: Waraniak_Rana_pipiens_species_distribution_model

description: R code detailing how the species distribution model presented in Waraniak et al. was built and how results were mapped onto climate scenarios.
DOI: 10.5061/dryad.6n5g482/1
title: Yu et al JOE-data
DOI: 10.5061/dryad.73rj625/1
title: Vocalizations

description: Data from the vocalization analyses of Ramphotrigon megacephalum and Pipraeidea melanonota.
DOI: 10.5061/dryad.73rj625/2
title: Coloration

description: Reflectance spectrum measurements and spectral variables values from the coloration analyses of Pipraeidea melanonota.
DOI: 10.5061/dryad.73rj625/3
title: Traditional mitochondrial and nuclear markers

description: This file contains the FASTA alignments for the Sanger loci (traditional mitochondrial and nuclear markers) for Ramphotrigon megacephalum and Pipraeidea melanonota.
Files have been organized in two folders, one for each species. Inside these folders you will find several fasta files, one for each marker.
DOI: 10.5061/dryad.73rj625/4
title: Restriction Site Associated DNA data (ddRAD) - GPHOCS

description: GPhoCS input file and control files for the 2 and 3 population models.
DOI: 10.5061/dryad.73rj625/5
title: Restriction Site Associated DNA data (ddRAD) - STRUCTURE

description: Structure input file
DOI: 10.5061/dryad.92dj50c/1
title: Preisler et al. 2019_ Climatic panel_Figure 1

description: Climatic data and evapotranspiration recorded measured by the Yatir forest Eddy covariance flux tower
DOI: 10.5061/dryad.92dj50c/2
title: Preisler et al. 2019_ WP_figure 2

description: Pre-dawn water potential measurements data from 5 seasons that were held at the trees in different stress stages. rainfall amount of the corresponding period is also noted
DOI: 10.5061/dryad.92dj50c/3
title: Preisler et al. 2019_ BAI-tree rings_Figure 3

description: Tree ring data recorded from all tree in the study period for the period of 1972 to 2012. Annual rainfall for the same period is also noted
DOI: 10.5061/dryad.92dj50c/4
title: Preisler et al. 2019_ Stoniness and root density_Figure 4

description: Root density and stoniness % measurements as obtained from the soil trenches in the Live and dead plots
DOI: 10.5061/dryad.96bk480/1
title: cs_initiation_date

description: This file contains data used to estimate the effects of clutch and brood size manipulations on clutch size and initiation date of female black brant in year t+1.  Variable descriptions are as follows: "METAL" is the unique number on a female's steel leg band; "CSM1" is the laid clutch size of a female in year t -1; "CS" is the laid clutch size of a female in year t. "IDM1" is the initiation date, in Julian days, of the female's nest in year t - 1; "ID" is the initiation date, in Julian days, of a female's nest in year t; "MCSM1" is the manipulated clutch size of a female in year t - 1, this variable was z-standardized with mean = 0 and sd =1 to enable replacement of missing values with 0; "GLNM1" is the manipulated initial brood size of the female in year t - 1; "YEAR" represents breeding season t; "RELID" is the relative initiation date (Julian initiation date - median initiation date) of a female's nest in year t; "RELIDM1" is the relative initiation date of a female's nest in year t - 1.
DOI: 10.5061/dryad.96bk480/2
title: mass_nthprim

description: This file contains the data for the analyses of nesting mass, change in mass between nesting and banding, and ninth primary length.  Note the some nesting mass (nmass) data is blank when the change in mass variable (chng_mass) is not, this is because in this case the female did not undergo a clutch manipulation and therefore was not used in the nest mass analysis.  The variables are as follows: "METAL" is the unique code on the female's steel band, "emcs" is the final manipulated clutch size a female incubated,"gln" is the initial brood size of the female, "nmass" is the mass (g) of the female if she was captured within 24 hrs of hatch and underwent a clutch manipulation, "YEAR" references breeding season t, "NINTHPRIM" is the length of a female's ninth primary feather on the day she was captured during brood rearing,"DSH" is the days between when a female's nest hatched and she was captured during brood rearing,"chng_mass" is the change in the mass of a female between hatch and when she was captured during brood rearing.
DOI: 10.5061/dryad.96bk480/3
title: return_rate_data

description: This file contains the reencounter data used in the return rate (logistic regression) analysis.  The variables in the file are as follows: "return" indicates if a female was seen nesting and/or captured at banding with a brood patch (return = 1) or not (return = 0); "gln" is the initial manipulated brood size of a female in year t -1.
DOI: 10.5061/dryad.96bk480/4
title: cmr_file

description: This file contains the capture-mark-recapture data used to estimate the effects of clutch and brood size on adult female breeding probability and survival.  Variables are as follows: "ch" is the capture histories, which are in an LDLD format with two secondary occasions (nesting and banding) each represented by "L", followed by non-breeding season (represented by second "D") reencounter data (0=not encountered, 1=encountered dead, 2=re-sighted alive), primary occasions are 2008-2015.  Note that the first "D" in the capture history for each primary occasion is essentially a dummy variable, which are all "0".  "mbha 2008:2012" indicates if a female's reproductive output was manipulated and she was captured and marked at the nest during that year; "age 2008:2015" is the z-standardized age (mean = 8.64, sd = 5.59) of a female in year t, "ageq 2008:2015" is the squared z-standardized age value for use in models with a quadratic effect of age; "emcs 2008:2015" is the z-standardized (mean = 4.22, sd = 1.87) final manipulated clutch size value in year t; "emcsq" is the squared z-standardized emcs value for use in models with a quadratic effect of emcs; "gln" is the z-standardized (mean = 3.49, sd = 1.73) initial brood size value for the female in year t; "glnq" is the squared z-standardized gln value for use in models with a quadratic effect of brood size; and "grp" is a grouping variable that indicates that all females were manipulated during our study.  Note that for variables "emcs" and "gln" the years 2013-2015 have values that are all 0 but are needed because program Mark requires time varying covariates for each primary occasion.  Zeros for other variables mean the female had not yet been captured and released or was not manipulated that year.
DOI: 10.5061/dryad.980538t/7
title: battles

description: Contains pairwise bryozoan colony battle outcomes, assessments of whether one or the other combatant was larger and difference in relative commonness. A few other trait differences are also given, but these are recalculated in the production line, which also adds other traits and trait-trait interaction terms.
DOI: 10.5061/dryad.980538t/8
title: species_traits

description: Contains trait values for each species found in the battle outcome file.
DOI: 10.5061/dryad.b698s18/1
title: Behavioural observations of mating strategy and mate choice preferences of male eastern mosquitofish reported in Fox et al.

description: Behavioural observations of mating strategy and mate choice preferences of male eastern mosquitofish maintained on either 'high" or "low" quality diets. Datafile contains raw data used in the analyses reported in Fox et al "Variation in the condition-dependence of individual sexual traits in male eastern mosquitofish, Gambusia holbrooki"
DOI: 10.5061/dryad.fq3d127/5
title: Time spent at sea total

description: Minutes and days spent at sea per fish, also divided by season. Also contains length, weight, gender and status. Status is awarded to the fish as described in the paper.
DOI: 10.5061/dryad.fq3d127/6
title: Time spent at sea per excursion

description: Time spent at sea per excursion.
DOI: 10.5061/dryad.fq3d127/7
title: Time spent in river total

description: Time spent in the river per fish, also related to season.
DOI: 10.5061/dryad.fq3d127/8
title: Time spent in river per excursion

description: Time in river per excursion.
DOI: 10.5061/dryad.hb0338g/3
title: Supplemental

description: Supplemental methods, data and result
DOI: 10.5061/dryad.kd1qt0p.1/19.1
title: Figure 7 - source data 4

description: This zip archive contains the original z-stacks used for Figure 7, panel G. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS318_s1_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/4
A7PS318_s2_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/8
A7PS318_s3_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/16
A7PS318_s4_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/32
A7PS318_s5_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/64
A7PS318_s6_t1 = 30-µm-filtered Pectin LSI, Dilution factor = 1/128
A7PS314_s25_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1
A7PS314_s26_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/2
A7PS314_s27_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/4
A7PS314_s28_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/8
A7PS314_s29_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/16
A7PS314_s30_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/32
A7PS314_s31_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/64
A7PS314_s32_t1 = 30-µm-filtered Fibersol-2 LSI, Dilution factor = 1/128
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 7, panel G.
DOI: 10.5061/dryad.kd1qt0p.1/20.1
title: Figure 7 - source data 5

description: This zip archive contains the original z-stacks used for Figure 7, panel H. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS313_s9_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1
A7PS313_s10_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/2
A7PS313_s11_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/4
A7PS313_s12_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/8
A7PS313_s13_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/16
A7PS313_s14_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/32
A7PS313_s15_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/64
A7PS313_s16_t1 = 0.45-µm-filtered Pectin LSI, Dilution factor = 1/128
A7PS314_s9_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1
A7PS314_s10_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/2
A7PS314_s11_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/4
A7PS314_s12_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/8
A7PS314_s13_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/16
A7PS314_s14_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/32
A7PS314_s15_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/64
A7PS314_s16_t1 = 0.45-µm-filtered Fibersol-2 LSI, Dilution factor = 1/128
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 7, panel H.