cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qb6b5/2
title: ABC estimator - non equilibrium population

description: R script for running the ABC estimator assuming a non-equilibrium population
DOI: 10.5061/dryad.qb6b5/3
title: equilibrium_mouse_sims

description: Text file containing 500,000 simulations for the mouse data assuming an equilibrium population
DOI: 10.5061/dryad.qb6b5/4
title: plssummary_mice_eqm

description: Text file containing the required information for calculating PLS components for the mouse data assuming an equilibrium population
DOI: 10.5061/dryad.qb6b5/5
title: non_equilibrium_mouse_sims

description: Text file containing 500,000 simulations for the mouse data assuming a non-equilibrium population
DOI: 10.5061/dryad.qb6b5/6
title: plssummary_mice_non_eqm

description: Text file containing the required information for calculating PLS components for the mouse data assuming a non-equilibrium population
DOI: 10.5061/dryad.s0054/2
title: Proportional Opsin Expression Data

description: Opsin expression data for each individual.
DOI: 10.5061/dryad.s0054/3
title: Relative to housekeeping measure of opsin expression

description: Opsin expression for each individual.
DOI: 10.5061/dryad.s0054/4
title: LWS-1 genotypes

description: Alleles of the LWS-1 for each individual.
DOI: 10.5061/dryad.v8m1p/1
title: Gruntman et al., Data
DOI: 10.5061/dryad.02tf9/4
title: Supplementary Data Files

description: Species tree, gene tree and BEAST 2 XML files used for simulation studies
DOI: 10.5061/dryad.02tf9/5
title: New Supplementary Information

description: Supplementary tables, figures and descriptions of experiments.
DOI: 10.5061/dryad.0817m/1
title: Original SNP data ch6 12 15_replace

description: SNPs in three chromosomes (6, 12, 15) for 50 reference individuals (25 pure Populus balsamifera and 25 pure P. trichocarpa) and 68 admixed individuals
DOI: 10.5061/dryad.0817m/2
title: alpha estimates in introgressed regions

description: Data from Table 2. Alpha estimate for three introgressed P. balsamifera regions in P. trichocarpa, one in chromosome (Chr) 06 (region A) and two in chromosome 15 (B and C).
DOI: 10.5061/dryad.0c116/1
title: HP1beta paper raw/original microscopy images

description: All raw images used in this study at 60X oil NA1.4 lens, were taken using a spinning disk confocal microscope (CSUX, Yokogawa, Japan) equipped with an iXon+ DU-897-BV monochrome EMCCD camera (Andor, UK) mounted on an Olympus IX81 fully automated microscope, or with an Olympus IX71 epifluorescent microscope equipped with a Dp71 camera (Olympus).
DOI: 10.5061/dryad.0g6hq/1
title: Allele Frequencies

description: Allele Frequencies - The frequency of the major allele (P) is indicated for each of 19,703 SNP loci for each population (indicated by abbreviation as described in Table 1), including the global average MAF, and the global average genotype success rate (GSR).
DOI: 10.5061/dryad.0g6hq/2
title: Genotypes

description: Genotypes: Individual genotypes for each sample at each of the 19,703 loci.  Sample ID is population abbreviation (see Table 1) followed by "xXXX", where XXX is a three digit numerical identifier.
DOI: 10.5061/dryad.11bn8/1
title: Anchor damage data

description: Data collected in the field in Crab Cove, British Virgin Islands.
DOI: 10.5061/dryad.31430/1
title: Colony Keystone Removal_NOA_1_17_2015 (1)

description: Boldness measures and colony-level foraging aggressiveness in colonies that contained keystone individuals for variable amounts of time
DOI: 10.5061/dryad.353gc/1
title: Supplementary Table S1 (a) and (b)

description: Supplementary table S1 (a) and (b) detailing the reference Internally transcribed spacer region (ITS) and beta-tubulin (BTUB) sequences of the five populations used in the study
DOI: 10.5061/dryad.3n2j5/10
title: 4 years data for reproductive success analysis (poisson fledged response)
DOI: 10.5061/dryad.3n2j5/4
title: 4 years data for PCA on survival
DOI: 10.5061/dryad.3n2j5/5
title: 2 years data for survival analysis
DOI: 10.5061/dryad.3n2j5/6
title: 4 years data for survival analysis
DOI: 10.5061/dryad.3n2j5/7
title: 2 years data for reproductive success analysis (binomial fledged response)
DOI: 10.5061/dryad.3n2j5/8
title: 4 years data for reproductive success analysis (binomial fledged response)
DOI: 10.5061/dryad.3n2j5/9
title: 2 years data for reproductive success analysis (poisson fledged response)
DOI: 10.5061/dryad.4622g/1
title: DYNAMICS

description: Dynamics of populations through time.  Every 4 transfers populations were measured for bacterial and phage density, colony morphology and plasmid prevalence. Treatments comprise plasmid and phage free (F), phage free, plasmid containing (P), plasmid free and phage containing (FP),  plasmid and phage containing (P).
DOI: 10.5061/dryad.4622g/2
title: RBG

description: Infection/resistance estimates as 'Reduction in Bacterial Growth' (RBG) for 20 clones isolated from each of the phage containing populations at transfer 20.  Each clone was estimated against each of the 12 phage populations. The morphology and plasmid status (0, plasmid free or 1, plasmid containing) of each clone is also included. Treatments are identified as plasmid free (FP) and plasmid containing (PP).
DOI: 10.5061/dryad.4622g/3
title: GROWTH RATES

description: Growth rates of the ancestral starting strain with and without the plasmid in the presence and absence of mercury (hg).
DOI: 10.5061/dryad.4622g/4
title: RESISTANCE MUTS

description: Fitness of resistance mutants relative to a marked reference strain in 0 and 8 µM of HgCl2 with and without the plasmid.  Mutants A1-4 were derived from challenge with the ancestral phage while mutants E1-5 were challenged with evolved phages. WT denotes the wild type, susceptible strain.
DOI: 10.5061/dryad.469vn/2
title: call data

description: Raw data for jeet call analysis
DOI: 10.5061/dryad.4m6s6/1
title: Alignments
DOI: 10.5061/dryad.4m6s6/2
title: ML_analysis
DOI: 10.5061/dryad.4m6s6/3
title: Bayesian_analysis
DOI: 10.5061/dryad.74ms0/13
title: mussel750_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/14
title: mussel1000_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/15
title: mussel1000_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/16
title: mussel1000_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/17
title: mussel1000_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/18
title: mussel750+2_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/19
title: mussel750+2_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/20
title: mussel750+2_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/21
title: mussel750+2_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.855m4/4
title: 97-04 yuhina ms_7loci_171birds_for_dryad_051815

description: 10 microsatellite genetic markers data from 171 Taiwan yuhina (Yuhina brunneiceps).
DOI: 10.5061/dryad.8rv01/1
title: O'Meara & Asher Supplementary Material

description: O'Meara and Asher Supplementary Material. Summary statistics for all species, complete results from main analysis and all additional discriminant function analyses, and life history data and sources. Additional analyses include those assessing the position of marsupials, those in which species with small sample size are removed, and those assessing the effects of body size and life history.
DOI: 10.5061/dryad.bd4gs/1
title: AAA_maindata

description: Behavioural and SCR data from 4 experiments combined. Experiment scripts and a script for collection of individual data files into the repository are contained in AAA_metadata.zip
DOI: 10.5061/dryad.c1sd4/8
title: Sample Locality Data

description: A table that includes sample locality for all specimens in the study.
DOI: 10.5061/dryad.c4k68/1
title: Hippolais genotypes

description: This file holds the genotypes and spatial locations of both Hippolais warblers in a format to read in by the converter program Transformer 4 http://www.demiurge-project.org/transformer4
DOI: 10.5061/dryad.d331n/1
title: Lord1: Supplementary Data

description: Raw data used to draw conclusions in paper and figures. Concat Lord[1-5].bin together into Lord.zip
DOI: 10.5061/dryad.d331n/2
title: Lord2: Supplementary Data

description: Concat Lord[1-5].bin together into Lord.zip
DOI: 10.5061/dryad.d331n/3
title: Lord3: Supplementary Data

description: Concat Lord[1-5].bin together into Lord.zip
DOI: 10.5061/dryad.d331n/4
title: Lord4: Supplementary Data

description: Concat Lord[1-5].bin together into Lord.zip
DOI: 10.5061/dryad.d331n/5
title: Lord5: Supplementary Data

description: Concat Lord[1-5].bin together into Lord.zip
DOI: 10.5061/dryad.fs950/1
title: Simulation Code

description: Mathematica code for stochastic simulations
DOI: 10.5061/dryad.h8p4n/1
title: Seed arrival, recruitment and presence in vegetation along riparian gradients

description: 11 worksheets with data on seed arrival, experimentally studied recruitment processes (germination, seedling survival and seedling growth), and natural developing vegetation (worksheets 3-7), model predictions of seed arrival and recruitment processes (worksheets 8-11), abiotic variables (worksheet 2) and description of column headers (worksheet 1).
DOI: 10.5061/dryad.j5r51/14
title: LIF network output variables for input 1.0 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 1.0 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/15
title: LIF network output variables for input 2.0 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 2.0 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/16
title: LIF network output variables for input 2.5 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 2.5 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/17
title: LIF network output variables for input 3.0 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 3.0 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/18
title: LIF network output variables for input 6.0 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 6.0 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/19
title: Simulated laminar recordings 125 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 125 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms
DOI: 10.5061/dryad.j5r51/20
title: Simulated laminar recordings 250 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 250 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/21
title: Simulated laminar recordings 375 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 375 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/22
title: Simulated laminar recordings 500 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 500 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.n63j0/1
title: Data Influenza Burden

description: Complete data used for the article
DOI: 10.5061/dryad.pj69f/1
title: MartinetalSupp data

description: Tables 1 and 2, Figures 1 and 2
DOI: 10.5061/dryad.pm5rt/1
title: Collins et al SOM - isotopes

description: Isotope data from crassatellid bivalves, associated with analyses of heterochrony
DOI: 10.5061/dryad.q6ds5/3
title: Statistical details

description: This file includes all of the statistical details, as well as R code and output for the analyses presented in the main text of this paper, as well as some ancillary supporting analyses not reported in the paper.
DOI: 10.5061/dryad.qb6b5/7
title: mousedata80kb

description: Text file containing SNP information for the mouse data in msms format (80kb)
DOI: 10.5061/dryad.qb6b5/8
title: pythonscript1

description: First python script required for running the ABC estimator in non-equilibrium populations
DOI: 10.5061/dryad.qb6b5/9
title: pythonscript2

description: Second python script required for running the ABC estimator in non-equilibrium populations
DOI: 10.5061/dryad.rr7q5/1
title: Supplemental Data

description: Supplemental data includes a table summarizing number of Paleobiology Database collection entries and fossil individuals used in the analysis per time bin, collection references, and localities.
DOI: 10.5061/dryad.sk800/1
title: emesis dataset 14NOV2015
DOI: 10.5061/dryad.t9q11/1
title: Appendix S1

description: Micro-CT sections through the three specimens (left) with black line indicating position on corresponding 3D surfaces (right). A, Transverse section through the left first intercoronoid fossa of MHMN 06-538. B, Transverse section through the right precoronoid fossa of UMZC GN.792. C, Transverse section through the anterior lower jaw of UMZC GN.1147.
DOI: 10.5061/dryad.t9q11/2
title: Appendix S2

description: Transformation matrices for three-dimensional surface models of individual bones of the lower jaw of Eusthenopteron foordi.
DOI: 10.5061/dryad.vq4j4/1
title: Dryad-MS-HDY-15-OR0093RR-Coordinates/Genotypes

description: Coordinates of sample locations and plastid and nuclear genetic data
DOI: 10.5061/dryad.0817m/3
title: Tajima and Nucleotide Diversity estimates

description: Data for Figure 2, Figure 4 Supporting Information (Tajimas' D) and Figure 7 Supporting Information (Nucleotide diversity).
DOI: 10.5061/dryad.0817m/4
title: RASPberry

description: Data for Figure 1, Figure 2 supportive information and Figure 3 supportive information.
DOI: 10.5061/dryad.0817m/5
title: LD_Haploview

description: Data for Figure 3 and Figure 6 supportive information.
DOI: 10.5061/dryad.0817m/6
title: NJ analysis

description: Data from Figure 1 Supporting information and Figure 5 Supporting information
DOI: 10.5061/dryad.0817m/7
title: Gene_sequences

description: Data for Figure 4, Figure 8 supportive information and Figure 9 supportive information.
DOI: 10.5061/dryad.0817m/8
title: 971Kb_filtered_dataset

description: This dataset was filtered based on minimum allele frequency (MAF &gt;0.1) and missing data (GR 0.95), for 25 reference P. trichocarpa, 25 reference P. balsamifera and 68 admixed accessions. The initial dataset consisted of 971K SNPs from 3691 genes in all 19 chromosomes.
DOI: 10.5061/dryad.0g6hq/10
title: RDA_BIOCLIMDATA

description: Input file of environmental factors included for RDA
DOI: 10.5061/dryad.0g6hq/11
title: RDA_AlleleFreq

description: Input file of allele frequencies for 19,703 SNPs for RDA