cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t80r9c1/2
title: Per-genotype abundance data

description: Per-genotype abundances from plots in the main experiment in year 1 (ABUND_13) and year 3 (ABUND_15) post-introduction. Abundance in genotypic mixture plots were estimated based on observed plot-level abundances and per-genotype relative abundance (based on a subset of samples that were genotyped for a set of accession-specific SNPs).
DOI: 10.5061/dryad.t80r9c1/3
title: KPC_AT 2015 analysis_EcolMono
DOI: 10.5061/dryad.v5sh63t/16
title: dph09_adult_PC-1086

description: TIFF sequence of interaction PC-1086 (9 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/17
title: dph09_latecopepodite_LC-422

description: TIFF sequence of interaction LC-422 (9 days post-hatch fish targeting a late copepodite).
DOI: 10.5061/dryad.v5sh63t/18
title: dph09_latecopepodite_LE-1147

description: TIFF sequence of interaction LE-1147 (9 days post-hatch fish targeting a late copepodite).
DOI: 10.5061/dryad.v5sh63t/19
title: dph09_latecopepodite_LE-1917

description: TIFF sequence of interaction LE-1917 (9 days post-hatch fish targeting a late copepodite).
DOI: 10.5061/dryad.v5sh63t/20
title: dph11_earlycopepodite_TA-975

description: TIFF sequence of interaction TA-975 (11 days post-hatch fish targeting an early copepodite).
DOI: 10.5061/dryad.v5sh63t/21
title: dph11_earlycopepodite_TE-747

description: TIFF sequence of interaction TE-747 (11 days post-hatch fish targeting an early copepodite).
DOI: 10.5061/dryad.v5sh63t/22
title: dph12_adult_VD-684

description: TIFF sequence of interaction VD-684 (12 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/23
title: dph12_adult_VG-764

description: TIFF sequence of interaction VG-764 (12 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/24
title: dph12_adult_VG-1150

description: TIFF sequence of interaction VG-1150 (12 days post-hatch fish targeting an adult copepod).
DOI: 10.15159/phytop.11
title: Lake Peipsi 2004 (Phytoplankton samples)

description: Method: Phytoplankton samples were preserved in Lugol’s (acidified iodine) solution and counted under an inverted microscope (Utermöhl, 1958). 3 ml of preserved sample was settled overnight and counted in random fields or transects. Biovolumes of algal cells, colonies and/or filaments were calculated using assigned geometric shapes dimensions, and converted to biomass assuming the specific density of 1 g cm-3 in accordance with Edler (1979). Approved by CEN on 14 July 2006 “Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique)” (CEN 15204, 2006) European Standard EN 15204:2006 Utermöhl, H., 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitteilungen der Internationale Vereinigung für Theoretische und Angewandte Limnologie 9, 1- 38. Edler, L. (ed.), 1979. Recommendations on methods for marine biological studies in the Baltic Sea. Phytoplankton and chlorophyll. Baltic Marine Biologists WG 9.
DOI: 10.15159/phytop.12
title: Lake Peipsi 2005 (Phytoplankton samples)

description: Method: Phytoplankton samples were preserved in Lugol’s (acidified iodine) solution and counted under an inverted microscope (Utermöhl, 1958). 3 ml of preserved sample was settled overnight and counted in random fields or transects. Biovolumes of algal cells, colonies and/or filaments were calculated using assigned geometric shapes dimensions, and converted to biomass assuming the specific density of 1 g cm-3 in accordance with Edler (1979). Approved by CEN on 14 July 2006 “Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique)” (CEN 15204, 2006) European Standard EN 15204:2006 Utermöhl, H., 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitteilungen der Internationale Vereinigung für Theoretische und Angewandte Limnologie 9, 1- 38. Edler, L. (ed.), 1979. Recommendations on methods for marine biological studies in the Baltic Sea. Phytoplankton and chlorophyll. Baltic Marine Biologists WG 9.
DOI: 10.15159/phytop.13
title: Lake Peipsi 2006 (Phytoplankton samples)

description: Method: Phytoplankton samples were preserved in Lugol’s (acidified iodine) solution and counted under an inverted microscope (Utermöhl, 1958). 3 ml of preserved sample was settled overnight and counted in random fields or transects. Biovolumes of algal cells, colonies and/or filaments were calculated using assigned geometric shapes dimensions, and converted to biomass assuming the specific density of 1 g cm-3 in accordance with Edler (1979). Approved by CEN on 14 July 2006 “Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique)” (CEN 15204, 2006) European Standard EN 15204:2006 Utermöhl, H., 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitteilungen der Internationale Vereinigung für Theoretische und Angewandte Limnologie 9, 1- 38. Edler, L. (ed.), 1979. Recommendations on methods for marine biological studies in the Baltic Sea. Phytoplankton and chlorophyll. Baltic Marine Biologists WG 9.
DOI: 10.17632/3j84yp5ymb.1
title: Data for: Activation of FLiBe Coolant in the Molten Salt Reactor
DOI: 10.17632/nr5yhdk79j.1
title: The MS data and its structure of peak1-50; TIC of all samples

description: The MS and MSMS data was obtained by UHPLC-QTOF-MS and its structure was identified by molecular ions and fragment ions. The TIC of all samples was obtained by UHPLC-QTOF-MS.
DOI: 10.17632/pb27mw2drp.1
title: Data for: Pb isotope compositions of galena in hydrothermal deposits obtained by drillings from active hydrothermal fields in the middle Okinawa Trough determined by LA-MC-ICP-MS

description: Table 1 Drilled hole location and depth Table 2 Laser and mass spectrometer setup parameters for the femtosecond LA and MC-ICP-MS Table 3 List of samples analyzed for Pb isotope compositions Table 4 List of sulfide ore and chimney samples from the Original site in the Iheya North field and the Jade and Hakurei sites in the Izena field Table 5 Chemical compositions of sphalerite determined by EPMA Table 6 Mean values of Pb isotope compositions of galena determined by LA-MC-ICP-MS and TIMS Table S1 Pb isotope compositions of galena determined by LA-MC-ICP-MS Table S2 Pb isotope compositions of bulk sample determined by P-TIMS
DOI: 10.5061/dryad.11t5s30/10
title: Cross fertility

description: Seed set after pollination within the campions Silene dioica (L.) Clairv. and S. latifolia Poiret, as well as between these species (data from: Rahmé et al., 2009, Journal of Evolutionary Biology 22, 1637-1943 ). Column names: female, female individual; mother.species, species [Dioica: S. dioica, Latifolia: S. latifolia]; treatment, pollination treatment [D.pollen: S. dioica pollen, L.pollen: S. latifolia pollen, M.pollen: 1:1 mixed pollination (not considered)]; normal, number of normal seeds; deformed, number of deformed seeds; aborted, number of aborted seeds; weight, seed weight of normal seed in mg; mean.weight, mean weight per seed in mg, Seed.set, normal seeds divided by total seeds (normal+deformed+aborted), date, pollination date.
DOI: 10.5061/dryad.11t5s30/11
title: R script: Swiss SDM and PCA

description: Species distribution modeling (SDM) with 10-fold cross validation and principal components analysis (PCA) for records of Silene dioica and S. latifolia within Switzerland, where dispersal between habitats scan be expected.
DOI: 10.5061/dryad.11t5s30/12
title: R script: Germination responses

description: Analysis of a seed germination experiment using interval in freshly harvested seeds of Silene dioica, S. latifolia and of different hybrid classes between these species under three conditions, a dormancy breaking treatment and conditions simulating diurnal temperature profiles during the seeding time of S. dioica or S. latifolia. Analyses of seed weight and climate condition during seed fall as well as of reproductive isolation indices with bootstrap confidence intervals are also included.
DOI: 10.5061/dryad.11t5s30/5
title: Germination responses

description: Data from a germination experiment with freshly harvested seeds of crosses within Silene dioica (L.) Clairv., S. latifolia Poiret and of different hybrid classes between these species under three conditions, a dormancy breaking treatment (OPT), and conditions simulating diurnal temperature profiles during the seeding time of S. dioica (SD) or S. latifolia (SL, see methods). Column names: name, unique name of each seed lot, collected on the same day; ct4, cross type (SL: Silene latifolia, SD: Silene dioica, F1: first-generation hybrid, F2: second-generation hybrid, F3: third-generation hybrid, BC-SD: backcross toward SD, BC-SL: backcross toward SL [see also Table S2, Figure S1]); No, cross identity (see Table S2); Date: seed collection date as days from the start of the experiment; OPT, SD, SL, percentage of seeds germinating under OPT, SD, and SL conditions; weight, weight per seed in g (measured for entire seed lot before splitting), no.OPT, no.SD, no.SL, number of hard (likely viable) seeds which had not germinated; dead.OPT, dead.SD, dead.SL, number of dead (soft) seeds under  OPT, SD, and SL conditions; TOTAL.sum, total number of seeds per seed lot (OPT + SD + SL); TOTAL.min, minimum number of seeds per trial (petri dish); comment, information on data pooling where seed number per trial was &lt; 15 (see methods).
DOI: 10.5061/dryad.11t5s30/6
title: Climate data June-August

description: Average temperatures (minimum, mean, maxiumu) during the seed fall period of Silene dioica (L.) Clairv. and S. latifolia Poiret (June – August) for 20 populations of S. dioica and 19 populations of S. latifolia (Table S1). Data are calculated from long-term monthly averages (1960-1990) obtained from WorldClim – Global Climate Data (http://www.worldclim.org/, Hijmans et al., 2005, Int. J. Climatol. 25:1965-1978). Colum names: pop, population name; Sp, species [SD: S. dioica, SL, S. latifolia]; Max, maximum temperature June-August; Mean, mean temperature June-August; Min, minimum temperature June-August.
DOI: 10.5061/dryad.11t5s30/7
title: Transplant experiment

description: Cumulative fitness (times flowered + 1 if the plant survived to the end of the experiment) in crosses within the campions Silene dioica (L.) Clairv. and S. latifolia Poiret, as well as their first- and second-generation hybrids, in a four-year transplant experiment at three sites of each species (data from Favre et al., 2017, New Phytologist 213, 1487-1499). Individuals that died soon after transplantation (transplant shock) or due to mole disturbance or could not be sexed were excluded from the dataset here (see Favre et al. 2017). Column names: Site.ID, identification of individuals across sites; site, transplant site; ID, identification number of individuals within sites; cross, cross type [SD: within S. dioica, SL: within S. latifolia, HD: SD female x SL male, HL: SL female x SD male, F2: second-generation hybrids (pooled)]; habitat, SD: transplanted within SD population, SL: transplanted within SL population; dblock, block within site; family, full-sib family; sex, plant sex; fitness.rev, cumulative fitness (times flowered + 1 if the plant survived to the end of the experiment).
DOI: 10.5061/dryad.11t5s30/8
title: Pollen competition

description: Percent hybrid offspring after mixed pollination with 1:1 mixed pollen loads in the campions Silene dioica (L.) Clairv. and S. latifolia Poiret (data from: Rahmé et al., 2009, Journal of Evolutionary Biology 22, 1637-1943). Column names: mother, individual; mother.sp, species [SD: S. dioica, SL: S. latifolia]; conspecific, number of offspring with con-specific father; heterospecific, number of offspring with hetero-specific father (hybrids); Unknown, number of offspring with unknown father (not considered); date.poll, pollination date(s); prop.consp, proportion of offspring with con-specific father, prop.heterosp, proportion of offspring with hetero-specific father (hybrids).
DOI: 10.5061/dryad.11t5s30/9
title: R script: Range wide SDM and PCA

description: Species distribution modeling (SDM) with 10-fold cross validation and principal components analysis (PCA) for range-wide records of Silene dioica (L.) Clairv. and S. latifolia Poiret as well as principal components analysis of climatic variables.
DOI: 10.5061/dryad.2h9d7sh/1
title: Supplementary Figures_Endocrinology

description: Supplementary Figures 1-7
DOI: 10.5061/dryad.2h9d7sh/2
title: Supplementary Figure Legends_Endocrinology

description: Supplementary Figure Legends 1-7
DOI: 10.5061/dryad.2vd01gr/10
title: Diversification analysis files

description: Files used in diversification analyses in Revbayes and BAMM, including Revbayes and R scripts and summary of parameter estimates in Revbayes
DOI: 10.5061/dryad.2vd01gr/11
title: Unaligned UCE contigs

description: Unaligned UCE contigs grouped by taxon in fasta format
DOI: 10.5061/dryad.2vd01gr/12
title: Passerines per locus alignments gbtrimmed 80%

description: Per locus alignments of UCE sequences aligned with MAFFT and trimmed with Gblocks, each locus containing sequences for at least 80% of 221 taxa.
DOI: 10.5061/dryad.2vd01gr/13
title: Passerines per locus alignments untrimmed and unfiltered

description: Per locus alignments of UCE sequences, no Gblocks trimming, no minimum number of taxa per locus
DOI: 10.5061/dryad.2vd01gr/4
title: Concatenated alignment

description: Concatenated alignment of 4,060 UCE loci for 221 individuals in nexus format.  Charset definition of each UCE locus included. Each UCE locus aligned with MAFFT, trimmed with Gblocks and contains sequence data for at least 80% of individuals.
DOI: 10.5061/dryad.2vd01gr/5
title: Figure 1 tree file

description: Figure 1 annotated tree file
DOI: 10.5061/dryad.2vd01gr/6
title: RAxML gene trees

description: Newick file of gene trees estimated using RAxML
DOI: 10.5061/dryad.2vd01gr/7
title: Files for dating analyses in BEAST, MCMCTree

description: Files for dating analyses in BEAST (BEAUTI files and nucleotide data sets) and MCMCTree (control files and calibrated tree file)
DOI: 10.5061/dryad.2vd01gr/8
title: BioGeoBEARS files

description: Input and output files for BioGeoBEARS analyses, including input tree files, geographic area files, dispersal multiplier files, Rdata output files, and output pdf files. BioGeoBEARS scripts are available on Github (https://github.com/carloliveros/passerines); these scripts cannot be hosted on Dryad because of copyright issues.
DOI: 10.5061/dryad.2vd01gr/9
title: Data assembly notes

description: Notes on data assembly with PHYLUCE
DOI: 10.5061/dryad.325pp2h/1
title: PONE-D-18-04427R1
DOI: 10.5061/dryad.5gk37t8/1
title: Input files for PCA, ADMIXTURE, fineRADstructure, BayeScan, TreeMix, as well as individual & concatenated FASTA files

description: (1) Run-ready input files for (a) ADMIXTURE (i.e, ped/map input files), (b) BAYESCAN, (c) fineRADstructure, (d) PCA, (e) TreeMix for 3,017 Autosomal and 177 Z linked markers identified using ddRAD-seq protocols for 176 Mallards, American black ducks, Mexican ducks, West-gulf Coast Mottled ducks, and Florida Mottled ducks. (2) Individual and concatenated fasta files for 3,017 Autosomal and 177 Z linked markers identified using ddRAD-seq protocols for 176 Mallards, American black ducks, Mexican ducks, West-gulf Coast Mottled ducks, and Florida Mottled ducks.
DOI: 10.5061/dryad.6mn67g0/10
title: Overstory-tree-dbh

description: Overstory tree species diameter at breast height (dbh) for each tree in the sample. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/11
title: Sapling-species-composition-structure

description: Sapling species composition and structure across the study site. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/12
title: Seedling-species-composition-structure

description: Seedling species composition and structure across the study site. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/4
title: Delta-backwater-Missouri-River-species-presence-comparison

description: Woody species presence on the White River delta-backwater and the Garrison and Gavins Point remnant reaches of the Missouri River. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/5
title: GIS-woodland-age-area-distribution-by-year

description: Riparian woodland age-area distribution by year on the White River delta-backwater, based on GIS analysis of historic aerial photos. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/6
title: Lake-Francis-Case-Water-Surface-Elevation-1989-2013

description: Water Surface Elevations of Lake Francis Case, 1989-2013. Data were derived from the US Geological Survey Gage 06442996 at Chamberlain, South Dakota. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/7
title: Liana-presence-absence

description: Liana (woody vine) species presence/absence in sampled stands. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/8
title: List-of-woody-plant-species-sampled

description: A complete list of the woody species sampled. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6mn67g0/9
title: Overstory-species-composition-structure

description: Overstory tree species composition and structure across the study site. A README file is provided on the first worksheet.
DOI: 10.5061/dryad.6n0b28n/2
title: Zonation performance curves

description: Zonation performance curve data resulted from spatial prioritisation analyses based on taxonomic, phylogenetic and functional-trait scenario.
DOI: 10.5061/dryad.6n0b28n/3
title: Maps of conservation priority ranks

description: This zip file contains three maps (in .TIF) of conservation priority ranks based on taxonomic, phylogenetic and functional-trait scenarios.
DOI: 10.5061/dryad.6ph57.1/4.1
title: TESS input file for spatial-genetic analysis of modern samples
DOI: 10.5061/dryad.6ph57.1/5.1
title: GENEPOP input file with populations defined as historical and modern clusters inferred by GENELAND
DOI: 10.5061/dryad.b28t0q7/1
title: radar-observation_strong-migration-nights_2010-2011

description: The data includes radar observations and wind simulations of Australian Plague locust strong migrations on 45 nights in 2010-2011.
DOI: 10.5061/dryad.d0779mb/3
title: Alonso_and_Marder_visualization_code_and_numerical_data

description: There are 4 folders in the zip file. Each folder has an independent set of scripts that are useful to (a) reproduce the exact figures in the manuscript (b) wrap in other projects. See README file for specifics.
DOI: 10.5061/dryad.fp26p04/1
title: Velthuis et al., 2018, GCB

description: Data and R-scripts belonging to the published manuscript. For more detailed information see the README file.
DOI: 10.5061/dryad.gg3g3s5/1
title: AlbaladejoRG_Pistacia

description: Zip file contains each of the datasets that accompany: Albaladejo et al. 2019 (https://doi.org/10.1007/s11295-019-1325-x) Linking DNA methylation with performance in a woody plant species. See README for variable definitions.
DOI: 10.5061/dryad.k57430s.1
title: Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting
DOI: 10.5061/dryad.k57430s.1/1.1
title: Online Appendix 1

description: Extended Methods section including: DNA Extraction and Library Preparation, and Target Enrichment and Sequencing of UCEs.
DOI: 10.5061/dryad.k57430s.1/2.1
title: Online Appendix 2

description: Extended Methods section including: Assembly and Alignment of Sequence Capture Data.
DOI: 10.5061/dryad.k57430s.2/10.2
title: Aldaetal_SystBio_SupplMat

description: Supplementary Tables S1-S4, and Supplementary Figures S1-S16.
DOI: 10.5061/dryad.k57430s.2/11.2
title: pruned_gene_trees

description: All gene trees (best and bootstrapped) inferred in RAxML for
all the filtered datasets.  Contents in README.
DOI: 10.5061/dryad.k57430s.2/3.2
title: all_gene_trees

description: All gene trees (best and bootstrapped) inferred in RAxML for
each individual UCE locus for the full and reduced taxon sets.  Contents in
README.
DOI: 10.5061/dryad.k57430s.2/6.2
title: gymno_reduced_dataset_100_complete

description: Individual UCE loci alignments that are common to 100% of taxa in the reduced dataset of Gymnotiformes (368 loci, 11 taxa). Codes for individual names in README.
DOI: 10.5061/dryad.k57430s.2/7.2
title: gymno_full_dataset_min75_concatenated.nex

description: Concatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes full dataset. Code names in README.txt.
DOI: 10.5061/dryad.k57430s.2/8.2
title: gymno_reduced_dataset_min75_concatenated

description: Concatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.
DOI: 10.5061/dryad.k57430s.2/9.2
title: gymno_reduced_dataset_100_concatenated

description: Concatenated matrix of UCE loci in common to at least 100% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.
DOI: 10.5061/dryad.m29k410/1
title: E&E_CMR_Code_Cleaned

description: CMR code
DOI: 10.5061/dryad.m799h3r/1
title: R_scripts

description: This file contains R scripts for analysis of data in this publication.
DOI: 10.5061/dryad.m799h3r/2
title: Phylogenetic trees based on maximum likelihood analysis of concatenated amino acid sequences of orthologues among fully sequenced invertebrate genomes

description: A phylogenetic tree of 44 invertebrate species drawn using concatenated 35 orthologous sequences.
DOI: 10.5061/dryad.m799h3r/3
title: Phylogenetic trees based on maximum likelihood analysis of concatenated amino acid sequences of orthologues among non-parasites with fully sequenced genomes

description: A phylogenetic tree of 34 non-parasites drawn using concatenated 106 orthologous sequences.
DOI: 10.5061/dryad.q80p8j4/1
title: Table 1. Matrix

description: Matrix of 28 morphological characters recognized in 22 species of the Family Nisusiidae and two species of Kutorginidae listed in the text.
DOI: 10.5061/dryad.q80p8j4/3
title: Table 3. List of the characters and character sets used in the phylogenetic analysis:

description: List of the characters and character sets used in the phylogenetic analysis.
DOI: 10.5061/dryad.v5sh63t/25
title: dph13_adult_VF-711

description: TIFF sequence of interaction VF-711 (13 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/26
title: dph14_adult_BB-1161

description: TIFF sequence of interaction BB-1161 (14 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/27
title: dph14_adult_BE-356

description: TIFF sequence of interaction BE-356 (14 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/28
title: dph14_adult_ZB-2633

description: TIFF sequence of interaction ZB-2633 (14 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/29
title: dph14_adult_ZC-686

description: TIFF sequence of interaction ZC-686 (14 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/30
title: dph14_adult_ZC-1114

description: TIFF sequence of interaction ZC-1114 (14 days post-hatch fish targeting an adult copepod).
DOI: 10.5061/dryad.v5sh63t/31
title: READ ME

description: Provides a description of how data files are organized.
DOI: 10.5061/dryad.v5sh63t/32
title: Tuttle et al 2019 JRSI S1 Data
DOI: 10.5061/dryad.v5sh63t/33
title: Tuttle et al 2019 JRSI S2 Code compute flow
DOI: 10.5061/dryad.v5sh63t/34
title: Tuttle et al 2019 JRSI S3 Code interpolate
DOI: 10.17632/46ynjsp243.1
title: Data for: Accuracy and Confidence in Perceptions of Targets’ Attachment to Former Partners: Do Judges Vary as a Function of Individual Differences in Attachment Style?

description: Sample 2, Aims 2-4