cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5jg20/4
title: GEV_Fig3

description: R script for figure 3.
DOI: 10.5061/dryad.5jg20/5
title: GEV_Fig5

description: R script for figure 5.
DOI: 10.5061/dryad.5vb8v.2
title: Data from: Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus)
DOI: 10.5061/dryad.5vb8v.2/1.2
title: 13688snps-562individus.recode

description: The file contains 13,688 SNPs and 562 individuals.
DOI: 10.5061/dryad.5vb8v.2/2.2
title: RDA-selection

description: The script used for performing RDA on the putatively under selection SNPs.
DOI: 10.5061/dryad.5vb8v.2/3.2
title: RDA-neutral

description: The script used for performing RDA on the putatively neutral SNPs.
DOI: 10.5061/dryad.5vb8v.2/4.2
title: 9770snps-neutral.frq

description: The file containing all the allele frequencies for the putatively neutral SNPs.
DOI: 10.5061/dryad.6h5b7/1
title: data.zip

description: Compressed file containing point cloud data and orthomosaic images of habitat used by baboons at Mpala Research Centre, Kenya. For associated baboon movement data, see: Crofoot MC, Kays RW, Wikelski M (2015) Data from: Shared decision-making drives collective movement in wild baboons. Movebank Data Repository. doi:10.5441/001/1.kn0816jn
DOI: 10.5061/dryad.6q5t4.2
title: Data from: Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators
DOI: 10.5061/dryad.6q5t4.2/1.2
title: Pimiento&Balk.Dataset

description: Carcharocles megalodon tooth measurements and body size estimations from different geologic formations around the world.
DOI: 10.5061/dryad.731fm/1
title: data

description: all.csv contains the results of cross-inoculation experiments; each line is a specific parasite * host combination. The column "Virulence" is infectivity (0 or 1)Variables_dynamique.xlsx contains host and parasite population sizespopulation_sizes_dynamics contains R code to analyse the dynamics of host and parasite populationscorrelations_and_nestedness contains R code to analyse the infectivity matrices (analyses ii to iv in the paper)temporal_trends_infectivity contains R code to analyse temporal trends in infectivity (analysis v in the paper)
DOI: 10.5061/dryad.86h2k/1
title: Lichen abundance data

description: Lichen abundance data obtained using the US Forest service and EU (total and macrolichens only) lichen diversity standard sampling methodologies. Data corresponds to 28 sites sampled across climate and pollution gradients in northwestern USA.
DOI: 10.5061/dryad.8gg68/1
title: Total Model Data

description: This csv file contains all of the data needed to run scripts provided with this manuscript.  Contains plot, environmental, and vegetation data.
DOI: 10.5061/dryad.8gg68/2
title: Mitchell_EcolApp_Script_160923

description: Scripts for running all analyses in manuscript using Total Model Data file.
DOI: 10.5061/dryad.bm2cg/1
title: Data used in all figures and Tables.
DOI: 10.5061/dryad.c3n62/1
title: Tara V9 ciliate data

description: This file contains ciliate sequences (V9 SSU rDNA) from ocean surface waters (SRF) and the deep chlorophyll maximum (DCM) of 47 sampling stations in the world's oceans. The data has been collected during the Tara Oceans expedition (2009 - 2012). For details on sampling procedure and sequence handling please refer to 'De Vargas et al. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science, 348:1261605'.The complete Tara Oceans sequence data is available at the European Nucleotide Archive under project PRJEB6610.
DOI: 10.5061/dryad.d1m02/1
title: Data_Impact of Forest Degradation and Invasive species on Mimusops andongensis in Lama Forest Reserve in Benin

description: Data on trees occurrence, dbh and height, data on regeneration occurence, diameter and height, and data on Chromolaena odorata cover
DOI: 10.5061/dryad.d5842/1
title: Microsatellite genotypes

description: Microsatellite genotypes for all sampled populations and individuals
DOI: 10.5061/dryad.fj0f8/1
title: Human cardiac miRNA sequencing of paired frozen and FFPE samples

description: MicroRNA deep sequencing of human cardiac tissues. 3 pairs of fresh and formalin-fixed paraffin-embedded (FFPE) samples are analyzed by Ion PGM system.
DOI: 10.5061/dryad.j626h/1
title: Supplementary Table 1 - Surface Size Data

description: Long axis measurements of vertebrate bioclasts from six vertebrate microfossils bonebeds in the Judith River Formation, Montana
DOI: 10.5061/dryad.j626h/2
title: Supplementary Table 2 - Sieve Size Data

description: Long axis measurements of vertebrate bioclasts from six vertebrate microfossils bonebeds in the Judith River Formation, Montana
DOI: 10.5061/dryad.k83h6/1
title: Teegalapalli & Datta FE&M

description: Vegetation data (trees and regeneration) was collected from different-aged successional sites formed following shifting cultivation and uncut forest sites. Data was collected from two replicate sites each from 2 year, 12 year, 25 year and 50 year old successional sites and two uncut forest sites. Trees (diameter at breast height, dbh&gt;=3 cm) were inventoried and identified to species or genus level in twelve 7 m radius plots located 25 m from each other on alternating sides of a 250-m transect. We enumerated the regeneration comprising of seedlings (height&lt;=25 cm) and saplings (height&gt;25 cm & &lt;=100 cm) of tree species in each of the four successional stages and the uncut forest sites in 1-m and 3-m radius nested within the 7-m radius plots, respectively. Detailed methods are provided in the methods section of the main article.
DOI: 10.5061/dryad.kv898/2
title: Pseudamara Miquihuana untrimmed DNA sequence matrix

description: This file contains all of the untrimmed DNA sequence data gathered for the paper. It is formatted as a NEXUS file, and is compatible with Mesquite version 3.10
DOI: 10.5061/dryad.kv898/3
title: Miquihuana rhadiniformis kww999 CLC de novo assembly

description: This assembly was built using CLC Genomics Workbench v. 8.5.1 and the default de novo assembly options after using CLC's default trimming of the input reads. The input data consisted of 100-base paired-end Illumina HiSeq 2000 reads and were imported into CLC as paired-end reads. The raw reads are accessible through the NCBI Sequence Read Archive with the accession number SRP073745.
DOI: 10.5061/dryad.kv898/4
title: Pseudamara arenaria kww998 CLC de novo assembly

description: This assembly was built using CLC Genomics Workbench v. 8.5.1 and the default de novo assembly options after using CLC's default trimming of the input reads. The input data consisted of 150-base paired-end Illumina HiSeq 3000 reads and were imported into CLC as paired-end reads. The raw reads are accessible through the NCBI Sequence Read Archive with the accession number SRP073745.
DOI: 10.5061/dryad.mg363/1
title: Pyrenoid_S.glynnii_example1

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/2
title: Pyrenoid_S.glynnii_example2

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mg363/3
title: Pyrenoid_S.glynnii_example3

description: 3-D movie reconstruction of pyrenoid ultrastructure showing connections (stalks) to the cell cytoplasm and chloroplast lobes. Data were obtained from serial block face scanning electron microscopy on preserved cells of Symbiodinium glynnii sp. nov. Detailed protocol concerning the chemical fixation and preparation of specimens for serial block face scanning electron microscopy available at Deerinck TJ, Bushong EA, Thor A, and Ellisman EH (2010). NCMIR Methods for 3D EM: A New Protocol for Preparation of Biological Specimens for Serial Blockface Scanning Electron Microscopy. SBEM Protocol version 7_01_10. Center for Research in Biological Systems and the National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA. https://ncmir.ucsd.edu/sbem-protocol
DOI: 10.5061/dryad.mq3mq/1
title: Forest Vital Rates

description: Vital rate means and variances from Forest site - needed to run Population Projection R script
DOI: 10.5061/dryad.mq3mq/2
title: Germination Seed Grid

description: Germination data from seed grid experiment - used to calculate g11
DOI: 10.5061/dryad.mq3mq/3
title: Lupinus constancei Monitoring Data

description: Monitoring data from Lassics lupine (Lupinus constancei) - used to calculate vital rate means and variances
DOI: 10.5061/dryad.mq3mq/4
title: Seed Production Data

description: Seed production data from 2010/2011 - needed to run Seed Production Analysis R script
DOI: 10.5061/dryad.nb1hc/1
title: Almawi PLoS One data

description: VEGF SNP analysis in 382 women with PCOS and 393 control women. Genotyping was done by real-time PCR (ABI StepOne Plus).
DOI: 10.5061/dryad.nn8kv/1
title: Full analysis and data repository for Putnam et al Evolutionary Applications 2016

description: All Analysis Script, Data, and Output files to reproduce results and figures for Putnam et al Evolutionary Applications 2016
DOI: 10.5061/dryad.pf550.1
title: Data from: Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)
DOI: 10.5061/dryad.pf550.2/18.2
title: YST_EUR_1069loc_BayeScan

description: SNP data file for BayeScan analysis of data set for DIYABC analysis of YST in Eurasia
DOI: 10.5061/dryad.pf550.2/19.2
title: MEC_15-1264_Sample_Data

description: List of samples and sequencing run information
DOI: 10.5061/dryad.qv000/10
title: Hackett tree

description: Phylogeny of the species present in the included studies, following the 'Hackett tree' (see Jetz et al. 2012; birdtree.org)
DOI: 10.5061/dryad.qv000/9
title: Ericson tree

description: Phylogeny of the species present in the included studies, following the 'Ericsson tree' (see Jetz et al. 2012; birdtree.org)
DOI: 10.5061/dryad.rf551/1
title: Biomass of species in mixed-forest simulations

description: This file contains the biomass (t.ha-1.yr-1) of each species (in mixed-forest) after 2000 years of forest dynamic simulation with ForClim. Species biomass are given for each site of the study (column "Site") and for each mixed-forest simulation (column "Simulation number").
DOI: 10.5061/dryad.rf551/2
title: Biomass of species in monocultures

description: This file contains the biomass (t.ha-1.yr-1) of each species (in monoculture) after 2000 years of forest dynamic simulation with ForClim. Species biomass are given for each site of the study (column "Site") and for each monoculture simulation (column "Simulation number").
DOI: 10.5061/dryad.rf551/3
title: Trait matrix

description: This file contains parameters (considered as traits in our study) of species modelled in ForClim. We used these parameters to explore community assembly processes.
DOI: 10.5061/dryad.t6md2/1
title: Mapped canopy boundaries of single species plots

description: In December 2013 and July 2014, we mapped the canopy boundaries of 87 single species plots, using a handheld GPS unit (Bad Elf GPS Pro, manufactured by Bad Elf, LLC; http://bad-elf.com) and tablet displaying the aerial image. The attached kml file includes the boundaries of those plots, named according to the plot number of the PRORENA field planting trial plots. This plot number can be used to merge the tree growth data and this spatial data on plot boundaries.
DOI: 10.5061/dryad.t6md2/2
title: Tree growth data for PRORENA plots 2008-2010

description: This file presents the growth data from the PRORENA field planting trials for the 87 plots used in the growth study. The field codes are as follows: SPEC_ID (the species code), TREE_ID (unique tree identification number), DIAM_2008 (Diameter in mm measured at 1.3 m high for all trees in 2008. For trees with multiple stems, the value represents the square root of the sum of all squared trunk stem diameters). DIAM_2010 (same as DIAM_2008, but for 2010), BLOCK (the treatment groups of plots), PLOT (a numeric identifier for each plot. Note that this is the same PLOT value in the spatial data of mapped canopy boundaries), ABSOLUTE GROWTH (the difference between diameter in mm between 2000 and 2010), STD.GROWTH (growth rate standardized within species by centering around the mean absolute growth rate for that species and dividing by two standard deviations of the absolute growth rate for that species), Species (the scientific name for each species).
DOI: 10.5061/dryad.vj32s/20
title: Reduced_Sequence_Files

description: -contains .phy files for subset of 354 loci and 60 taxa
DOI: 10.5061/dryad.vj32s/21
title: Tree_Files

description: -Astral_Bootstrap.trenewick formatted 100 bootstrap replicates from the COMPLETE ASTRAL-II species analysis-Gene_Trees_Full.tre newick formatted 498 "best" gene trees from RAxML (in ascending order)-Gene_Trees_Reduced.tre newick formatted reduced 354 "best" gene trees form RAxML (in ascending order)-Individual_Trees.trenewick formatted trees based on 326 sequences to check for monophyly-RAxML_Bootstrap.tre-neewick formatted bootstrap replicates from the RAxML species analysis-Species_Trees_Complete.trenewick formatted species trees (ASTRAL-II and SVDquartets) with support values for all 65 taxa, 498 loci (COMPLETE dataset)-Species_Trees_Consensus.trenewick formatted species trees generated using the CONSENSUS dataset-Species_Trees_OnePer.trenewick formatted species trees generated using the ONEPER dataset-Species_Trees_Reduced.trenewick formatted species trees with support values for REDUCED set of 60 taxa, 354 loci-Species_Trees_Schnitzler.trenewick formatted species trees with species and data from Schnitzler et al. included (AUGMENTED dataset)-SVD_bootstrap.trenewick formatted 100 bootstrap replicates from the SVDquartets species analysis
DOI: 10.5061/dryad.vj32s/22
title: Distances

description: contains pairwise distances among gene trees, among species trees, and between gene trees (observed, randomly generated, and simulated using COAL)
DOI: 10.5061/dryad.vj32s/23
title: Internode_Certainty

description: for all four species trees, contains internode certainty and internode certainty all values from RAxML, along with branch lengths
DOI: 10.5061/dryad.vj32s/24
title: Locus_Info

description: matches Table 2 in manuscript, contains information on all loci, including length, parsimony informative sites, and distance to species trees.
DOI: 10.5061/dryad.vq6m6.2
title: Data from: Tropical Drosophila pandora carry Wolbachia infections causing cytoplasmic incompatibility or male killing
DOI: 10.5061/dryad.vq6m6.2/1.2
title: CI strain_Cytoplasmic Incompatibility

description: Lab collected crossing data for CI strain of Drosophila pandora, used to evaluate Cytoplasmic Incompatibility. Data from two experiments (Jan 2014 and April 2014), showing the number of hatched/unhatched eggs collected and scored, and the number of male and female progeny collected and scored. Crosses where no mating occurred excluded for analysis but identified here for completeness.
DOI: 10.5061/dryad.vq6m6.2/2.2
title: MK strain_Crosses

description: Lab collected crossing data for MK strain of Drosophila pandora, used to evaluate Cytoplasmic Incompatibility where CI68+ is the MK strain. Data showing the number of hatched/unhatched eggs collected and scored, and the number of male and female progeny collected and scored. Crosses where no mating occurred excluded for analysis but identified here for completeness.
DOI: 10.5061/dryad.vq6m6.2/3.2
title: MK strain_28 Degree Age

description: Lab collected data evaluating female age and progeny sex ratio for MK strain of Drosophila pandora (strain C168+). Data shows the number of male and female progeny collected and scored when females at 28 degrees.
DOI: 10.5061/dryad.vq6m6.2/4.2
title: MK strain_28 Degree Male Crosses

description: Lab collected data for crosses between the CI and MK strains of Drosophila pandora, using males reared at 28 degrees (and including rare males from the MK line). Data shows the number of hatched/unhatched eggs collected and scored, and the number of male and female progeny collected and scored. Crosses where no mating occurred excluded for analysis but identified here for completeness.
DOI: 10.5061/dryad.08803/11
title: Video 1. Macrophage and neutrophil behavior at the lag phase of Mm infection.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm (red) were imaged alive every ~60 sec from 1 hpi to 12 hpi by CLSM (Nikon A1). In the top panel the dynamics of GFP-positive (green) macrophages and DsRed-positive (blue) neutrophils are shown, whereas in the bottom panels the trajectories for macrophages (left) and neutrophils (right) are indicated. The magenta and red lines represent infected macrophages and neutrophils, whereas the yellow and blue lines represent uninfected leukocytes. The infected cells remain in the tail fin, except for one of the neutrophils (red line), which undergoes reverse migration along the caudal vein. The uninfected macrophages show short trajectories in the tail fin and the neutrophils show longer tracks, of which one neutrophil (blue line) seems to be scanning a large area of the tail fin. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 100 µm.
DOI: 10.5061/dryad.08803/12
title: Video 2. Cell death Mm infected neutrophils showing fragmentation and roundup morphologies followed by efferocytosis.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm (red) were imaged alive every ~60 sec using CLSM (Nikon A1). In the top panel the dynamics of DsRed-positive (blue) neutrophils are visualized separately, whereas in the bottom panels GFP-positive (green) macrophages and Mm (red) are also included. The white arrow in top panel indicates an infected neutrophil that undergoes cell death showing clear fragmentation morphology after ~1,5 hours. Subsequently, the bacteria and probably remains of this neutrophil is taken up by a second neutrophil within an hour. This second neutrophil (also indicated by an white arrow in right bottom panel) is taken up by a macrophage at 4 hours. The yellow arrow in the top panel indicates an infected neutrophil that undergoes cell death showing a round up morphology. The fluorescent signal of the neutrophil associated with Mm gradually decreases in several hours. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 20 µm.
DOI: 10.5061/dryad.08803/13
title: Video 3. Cell death of Mm infected macrophages showing fragmentation morphology.

description: Double transgenic Tg(mpeg1:EGFP) and Tg(lyz:DsRed2) larvae infected with Mm (red) were imaged alive every ~60 sec using CLSM (Nikon A1). The GFP-positive (green) macrophage infected with Mm (red) indicated by white arrow undergoes cell death showing clear fragmentation at 57 minutes. The maximum intensity projection from 11 CLSM images (step size in z-direction, 5.56 µm) is shown at 10 frames per second. Scale bar: 20 µm.
DOI: 10.5061/dryad.13074/1
title: Phenotypic data

description: phenotypic data (Lsmeans used for association analysis)
DOI: 10.5061/dryad.13074/2
title: Genotypic data

description: 50 KSNP data used for association genetics, see Ganal et al. 2011 PLos One for method description
DOI: 10.5061/dryad.15981/1
title: Yang&Chiao-Data-2016

description: All data in Figures 2, 3, 4, 5, 6, S1, and S2.
DOI: 10.5061/dryad.1h12r/1
title: Lutheretal2015 playback response data

description: Playback response data used for analysis.
DOI: 10.5061/dryad.28b06.1
title: Data from: High evolutionary constraints limited adaptive responses to past climate changes in toad skulls
DOI: 10.5061/dryad.28b06.2
title: Data from: High evolutionary constraints limited adaptive responses to past climate changes in toad skulls
DOI: 10.5061/dryad.28b06.2/1.2
title: Species means and residual P-matrices

description: The data are species climatic means (bio1 through bio19 extracted fromWorldClim database for all localities the species are reported to occur.For variable definitions see: http://www.worldclim.org/bioclim. Furtherinformation in Hijmans et al. (2005) Int. J. Climatol. 25, 1965–1978.http://dx.doi.org/10.1002/joc.1276. Note bio3 and bio7 were excluded from analysis) and morphological means (21 linear skull distances: definitions of abbreviations are in the ReadMe file). Next are species residual phenotypic variance covariance matrices for which the effects of sex and locality were removed (see table S1 of article). The last data is a data frame that was used as entry on the function oubm.fit of the slouch R package.
DOI: 10.5061/dryad.28b06.2/2.2
title: Table 1. Vector correlations between evolutionary response (Δz), selection (β) and PC1.

description: This is the correct version of Table 1, in which column headings are in the correct positions. Please see the associated README "read_me_table1.txt" for a description of the symbols. Please also see: Correction to ‘High evolutionary constraints limited adaptive responses to past climate changes in toad skulls’ in Proceedings of the Royal Society B at http://dx.doi.org/10.1098/rspb.2016.2354
DOI: 10.5061/dryad.2m19h/10
title: Plantation habitat measurements

description: Data from the five environmental characteristics measured in plantation habitats in order to assess the similarity of sample sites. See ReadMe file for description of column headings.
DOI: 10.5061/dryad.2m19h/6
title: GLMM input variables

description: Input variables used in Generalized Linear Mixed Models (GLMMs) that examine whether the proportion of individuals per species crossing the habitat boundary was influenced by species' traits, abundance and habitat of first capture. See ReadMe file for description of column headings.
DOI: 10.5061/dryad.2m19h/7
title: GLMM input variables with site identity

description: Input variables used in Generalized Linear Mixed Models (GLMMs) that examine whether the proportion of individuals per species crossing the habitat boundary was influenced by species' traits, abundance and habitat of first capture. Site identity was included as a random effect in this analysis. See ReadMe file for description of column headings.