cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.478t9/7
title: fish_ADR1_PHYLIP_MIX_gte5_output

description: the raw maximum parsimony tree set output of GESTALT barcodes collected from adult zebrafish ADR1.  The file contains the all of the raw PHYLIP Mix software package output trees
DOI: 10.5061/dryad.478t9/8
title: cell_culture_gte2_MIX_output

description: the raw maximum parsimony tree set output of GESTALT barcodes collected from a cell culture lineage simulation.  The file contains the all of the raw PHYLIP Mix software package output trees
DOI: 10.5061/dryad.478t9/9
title: all_stats_files.tar

description: contains all the UMI and read alignments used to produce the associated trees
DOI: 10.5061/dryad.4966m/1
title: Isotopic niche indices for estuarine fish

description: Isotopic niche indices for the fish and source assemblages of 9 Australian estuaries. Indices were calculated using bayesian methods of Jackson et al. (2011). Predictor variables are also included.
DOI: 10.5061/dryad.5b8t8/1
title: Data from SABAP1

description: Data from SABAP1
DOI: 10.5061/dryad.5b8t8/2
title: Data from SABAP2

description: Data from SABAP2
DOI: 10.5061/dryad.77kj5/2
title: Maximum Fruit Set and Female to Flower cost Ratio

description: In each of 130 oak trees (Q. petraea) surveyed in 2013 and from various locations in metropolitan France, (1) the fruit set is computed as the proportion of female flowers that successfully develop into mature fruits and (2) the Fruiting-to-Flowering Resource demand ratio (FFR) is computed as the ratio of the resource required to produce one mature fruit to that required for one sexually operational female flower. FFR is computed based on either (i) dry weight, (ii) carbon or (iii) nitrogen content of flowers and mature acorns.
DOI: 10.5061/dryad.83g9k/1
title: Functional trait data for 27 temperate grassland species

description: Traits were measured on plants grown in a common garden in Tartu, Estonia (58°22´N, 26°41´E) using seeds collected from seven grasslands that differed in species richness and composition, soil fertility, pH, and management history (seed origin coordinates supplied). Individual plants of each focal species were subjected to treatments that manipulated a) neighbour identity (surrounded by either conspecifics or heterospecifics), and b) neighbour density (0, 1, 2, 3, 4, 6 or 8 neighbours). Each neighbour identity by density combination was replicated twice. In the heterospecific treatment, each focal species was grown together with a species that it frequently encountered in the field as its nearest neighbour. Five aboveground traits and total aboveground dry mass of focal and neighbour plants were recorded. The maximum vegetative height of the focal plants was measured as the highest point reached by stem leaves (or rosette leaves in the absence of a leafed stem). Leaf water content was calculated by dividing the difference between fresh and dry mass by the fresh mass of two newly produced but fully expanded leaf blades (four leaves for Carex ornithopoda, Juncus gerardii, Veronica chamaedrys; five leaves for Antennaria dioica; ten leaves for Lotus corniculatus; 25 leaves for Galium verum).  Specific leaf area (SLA), was calculated as the ratio of leaf area and leaf dry mass of leaves used for water content measurements. The dry mass of the supportive structures was found by summing the dry mass of stems (including stolons), leaf petioles and leaf sheaths (in the case of graminoids). All above-ground parts of each focal plant and its neighbours were oven-dried at 70C for 48 h and weighed separately as necessary for calculations.
DOI: 10.5061/dryad.8nj00/1
title: Plukenetieae combined partitioned dataset

description: 154 terminal, 2381 character, combined psbA-trnH, psbA-trnH indels, and ITS dataset of tribe Plukenetieae and outgroups (Euphorbiaceae). This nexus file includes the full alignment, exclusion sets, and partitions.
DOI: 10.5061/dryad.9pg8d/1
title: SRA-files.xlsx

description: Accession numbers for raw-reads in NCBI SRA.
DOI: 10.5061/dryad.9pg8d/2
title: trinity-assemblies-for-dryad.tar.gz

description: De novo Trinity (trinityrnaseq_r2013-02-25) assemblies of raw-reads for all individuals included in study.
DOI: 10.5061/dryad.9pg8d/3
title: outgroup-data.tar.gz

description: Outgroup data included in analysis from genome-enabled cichlids.
DOI: 10.5061/dryad.9pg8d/4
title: 11-20-2014-malfaro-cichlids-taxa.conf

description: Configuration file used with PHYLUCE for taxon-set extraction.
DOI: 10.5061/dryad.9pg8d/5
title: skull-mobility-contig-and-alignment-data.tar.gz

description: UCE contigs, alignments, trimmed alignments, coverage information, and configuration and log files used in all phylogenetic analyses.
DOI: 10.5061/dryad.9pg8d/6
title: mafft-gblocks-clean-95p-complete-raxml.tar.gz

description: Partition-finder and RAxML input/output files for ML analysis of the 95 % complete data set.
DOI: 10.5061/dryad.f1d5h/1
title: Supplementary Table S1_S8 and Figure S1_S3.160216

description: Table S1. Samples information of fig and fig wasp for Microsatellite or COI sequences.Table S2. Microsatellite primers of Ficus plants used in this paper.Table S3. Fig volatile samples of receptive phase in Menglun site.Table S4. Genetic distance matrix (Mean± SE) for pollinator clades.Table S5. Frequency of associations between sympatric Ficus species and Ceratosolen species basing on 87 de novo sequenced Ceratosolen wasps.Table S6. Posterior probabilities of assignment of 13 individuals identiﬁed as putative hybrids from Bayesian clustering analysis (K = 5) using a priori species identity information with migration rate priors of 0.10, 0.05, 0.01 are shown.Table S7. Pairwise migration rates (MR) for five sympatric morphological figs estimated in BayesAss.Table S8. Tentatative results of occurrences (Occ) and relative abundances (Mean, SD) of the compounds found in fig volatiles at receptive phase of five morphological fig species.Figure S1. Bayesian tree of all Ceratosolen fig wasps with COI gene recored in GenBank.Figure S2 Bayesian tree of Ficus from Subgenus Sycomorus based on the ITS-G3pdh combined dataset.Figure S3. Bayesian tree of 87 Ceratosolen fig wasps de novo sequenced in this study based on the COI gene.
DOI: 10.5061/dryad.f1d5h/2
title: Appendix S1. Byesian tree of all Ceratosolen species with COI gene recored in GenBank

description: Appendix S1. Byesian tree of all Ceratosolen species with COI gene recored in GenBank.nexus
DOI: 10.5061/dryad.f1d5h/3
title: Appendix S2. Bayesian tree of sympatric figs species from Subgenus Sycomorus.nexus

description: Appendix S2. Bayesian tree of sympatric figs species from Subgenus Sycomorus.nexus
DOI: 10.5061/dryad.f1d5h/4
title: Appendix S3. Byesian tree of 87 de nove sequenced Ceratosolen fig wasps

description: Appendix S3. Byesian tree of 87 de nove sequenced Ceratosolen fig wasps.nexus
DOI: 10.5061/dryad.f1d5h/5
title: Appendix S4. Ficus SSR data 11loci_278ind

description: Appendix S4. Ficus SSR data 11loci_278ind.txt
DOI: 10.5061/dryad.f1d5h/6
title: Appendix S5. List of fig wasp and fig samples used in phylogeny establishment

description: Appendix S5. List of fig wasp and fig samples used in phylogeny establishment.xlsx
DOI: 10.5061/dryad.g0874/26
title: Genotypes Intergenic Part 2 of 3

description: Genotype calls for all individuals at intergenic sites. Part 2 of 3.
DOI: 10.5061/dryad.g0874/27
title: Genotypes Intergenic Part 3 of 3

description: Genotype calls for all individuals at intergenic sites. Part 3 of 3.
DOI: 10.5061/dryad.g0874/28
title: asymptotic_alpha

description: [5 files] Four files give site frequency spectra for each gene separately, sampling down to 16 individuals from the Western population. The four files correspond to i) Autosomal genes, synonymous SNPs, ii) Autosomal genes, non-synonymous SNPs, iii) Z chromosome genes, synonymous SNPs, iv) Z chromosome genes, non-synonymous SNPs. The R script was used to calulcate aplpha and produce the plot in Fig. 4. See the text for further details.
DOI: 10.5061/dryad.g0874/29
title: sfs_v2

description: [18 files] Site frequency spectra for autosomal scaffolds considering different site classes: 4D sites, introns and intergenic sites. Each site was downsampled to 5 individuals per site, either considering all samples, or only those from a similar locality ('close'). Spectra for the Western and Eastern populations down sampling to 20 individuals per site are also given. See the text for further details.
DOI: 10.5061/dryad.g0874/30
title: multiple_regression_v2

description: [14 files] Data and R code used for multiple regression analysis of neutral diversity. The raw unprocessed data are given in the files "set80.Zupdated.realign80.GQ30.4D.lowCUB.autoScafs.PiDxyGC.w100m150s100.csv" (pi, dxy and gc content for 100 kb windows); "set80.Zupdated.realign80.GQ30.4D.autoScafs.PiDxyGC.w100m250s100.csv" (the same but only for low-CUB genes); "mel1_hec1_wal1_hecu1_era1.realign80.GQ30.ALLSITES.cons.codeml_nW.w100m500.csv" (Paml analysis results, where branch 8..1 refers to the branch leading to H. melpomene); and "MK_gene_a.csv" (gene by gene a estimates). The "model data" files give the processed data that is imported by the R scripts to run the model, as described in the text.
DOI: 10.5061/dryad.g0874/31
title: diversity_around_substitutions.tar

description: [5 files]. Nucleotide diversity (pi) and divergece (dx) for each 4D site. The "distToNearest" files give, for each 4D site, the distance to the nearest substitution, either synonymous or nonsynonymous. For synonymous substitutions, the there are 100 bootstrapped distances, obtained by subsampling sysnonymous substitutions. There are distance files for two groups of substitutions, identified using different outgroups, as described in the text.
DOI: 10.5061/dryad.g0874/32
title: simulated_error_rates

description: [20 files] Counts of paires of actual and inferred genotype patterns for simulated data at different percentage divergences and sequence coverage depths. Foer example "counts_01_00" refers to the number of sites at which the actual genotype was 0/1 and the inferred genotype was 0/0.
DOI: 10.5061/dryad.g0874/33
title: Nucleotide diversity for 100 kb windows V2

description: [17 files] Nucleotide diversity for each population calculated in 100kb windows. Seven different types of sites were considered: all sites, intergenic, intron, codon positions 1, 2 and 3, and four-fold degenerate (4D) sites. Dxy values between populations are also given, but these are based on just a single pair of samples and may be less accurate than those given in the dxy data. There are 8 files giving nucleotide diversity statistics considering only samples with at least 25x coverage - which should be more reliable. These correspond to the same seven site types listed above, plus one file for 4D sites only in genes showing minimal codon usage bias (CUB). There are also two files giving nucleotide diversity at intergenic sites and 3rd codon positions that were used to test whether the proportion of missing data in H. melpomene samples was correlated with nucleotide diversity.
DOI: 10.5061/dryad.jr5fd/1
title: Time series of clonal composition and diversity

description: Time series of Daphnia pulex clone frequencies, abundances, log (abundance), log growth rates, and diversity
DOI: 10.5061/dryad.jr5fd/2
title: Daphnia pulex and chlorophyll a time series

description: Time series of Daphnia pulex population density, log D. pulex density, chlorophyll-a concentration and log chlorophyll-a concentration
DOI: 10.5061/dryad.jr5fd/3
title: Temporal variability and synchrony measures

description: Coefficient of variation of Daphnia pulex density and chlorophyll-a concentration over time; synchrony of D. pulex clonal abundances over time
DOI: 10.5061/dryad.n7b7d/1
title: Rosten et al dataset
DOI: 10.5061/dryad.p380b/1
title: addax_Stacks_files

description: Stacks 1.01 catalog output files with summary statistics. This file must be unzipped.
DOI: 10.5061/dryad.p380b/2
title: Allele_Sharing_Results

description: Average pair-wise allele sharing estimates in csv format. The zipped file includes allele sharing estimates and the variance using 500 subsampled loci for both ddRAD and SNP chip approaches. One thousand bootstrap replicates with replacement were performed. Results with minor allele filtering (snpCHIP2 and ddRAD2) and without minor allele filtering (snpCHIPall and ddRADall) are included.
DOI: 10.5061/dryad.ps1h0/1
title: SupplementaryTables:  Data on trophic levels and body lengths of trophic species in 9 pelagic and 9 terrestrial food webs

description: Adult body lengths of all trophic species in these 18 webs were taken from reported values in the literature and on the Internet. The trophic level of each trophic species was determined from food web graphs, designating primary producers as trophic level 1, herbivores as trophic level 2, and so on. Six of 9 pelagic and 2 of 9 terrestrial webs explicitly indicated principal energy flow pathways in the food web graphs. Where food web diagrams indicated the relative strength of multiple trophic pathways (such as a predator consuming a range of prey species from various trophic levels, e.g. by the width of arrows), the strongest pathways were used to determine food chain length and trophic levels. Otherwise, directed trophic links were used as given. The 18 webs are selected from the 113 food webs analyzed by Briand and Cohen (1987, Science 238:956-960). These data were used to estimate geometric mean body length by trophic level for animals in pelagic and terrestrial food webs. Table S1 gives summary information and a description for all 18 webs. Table S2 gives the lengths and trophic levels for all trophic species in the 9 pelagic webs. Table S3 gives the lengths and trophic levels for all trophic species in the 9 terrestrial webs. The 9 pelagic webs chosen were the 9 of 113 Briand and Cohen webs with longest maximum food chain length that also had only one-celled primary producers. The 9 terrestrial webs were individually chosen as those having similar numbers of trophic species as the 9 pelagic webs (to minimize differences between pelagic and terrestrial food webs arising from more detail having been included in the published food web graphs).
DOI: 10.5061/dryad.q9m45/1
title: Data for Figure 1A-D

description: This dataset contains the cell values (for NPP, species richness, sister coexistence and sister age) used in Figure 1A-D.
DOI: 10.5061/dryad.149m8/1
title: Parameters and HMM files

description: Parameter values and HMM model files for all subsets of all humans in the Adaptive and Vollmers data sets.
DOI: 10.5061/dryad.149m8/2
title: Full set of plots

description: Plots of all alleles for all humans in the Adaptive and Vollmers data sets.
DOI: 10.5061/dryad.15rg7/1
title: Data_Kingma_etal_ProspectingCosts

description: Body condition data of resident and prospecting individuals. All additional data used in the analyses are included.
DOI: 10.5061/dryad.1j6sk/1
title: Nest_Temperature_2013_2014_PSWMA_

description: Black bulb temperatures recorded at bobwhite nest sites, and 2m paired sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.27m7h/2
title: GPA Bats & Carnivorans

description: Average coordinates and centroid sizes from Generalized Procrustes Analysis of bats and carnivorans in each of the skull views (cranium ventral, cranium lateral, and mandible lateral). Values were averaged across individuals for each species.
DOI: 10.5061/dryad.35ck3/1
title: proximate dispersal cues in a social spider

description: We manipulated foraging opportunities in field colonies of the social spider Stegodyphus dumicola, and tested how it affects individual reproduction dispersal. We followed colonies cleared of nests around them to count the number of dispersal nests from each colony, their distance, reproductive state, and survival. We used JMP for the statistical analysis.
DOI: 10.5061/dryad.478t9/11
title: fish_ADR2_PHYLIP_MIX_gte5_input data matrix

description: the data matrix for adult fish ADR2, used as input to PHYLIP Mix
DOI: 10.5061/dryad.478t9/12
title: fish_ADR1_PHYLIP_MIX_gte5_input

description: the data matrix for adult fish ADR1, used as input to PHYLIP Mix
DOI: 10.5061/dryad.478t9/13
title: cell_culture_gte2_input_MIX

description: the data matrix for the cell culture experiment, used as input to PHYLIP Mix
DOI: 10.5061/dryad.47dq3/1
title: Phased DNA sequences and aminoacids

description: This file contains all the phased sequences used in the study, with heterozygous gaps resolved. Fasta containing aminoacids translations are also provided for markers used in MK tests.
DOI: 10.5061/dryad.47dq3/2
title: Informations about individuals

description: This file contains for each individual included in the study its identifier, its color form/morph, the locality where it was sampled and its sex.
DOI: 10.5061/dryad.49f83/1
title: data_packet

description: This is a datapacket that contains the input files for all analyses performed in this study as described in the publication. This includes input files for maximum parsimony, maximum likelihood and Bayesian inference analyses of mtSSU; maximum liklihood and Bayesian inference input files for a partitioned ITS dataset; and the distance table of computed ITS Jukes Cantor sequences distances calculated in PAUP.
DOI: 10.5061/dryad.5d4fh/1
title: Data file Stockley&Hobson

description: Excel file containing comparative data on male care and life history traits of mammals
DOI: 10.5061/dryad.5k0g4.1
title: Data from: Coastal landforms and accumulation of mangrove peat increase carbon sequestration and storage
DOI: 10.5061/dryad.5k0g4.2
title: Data from: Coastal landforms and accumulation of mangrove peat increase carbon sequestration and storage
DOI: 10.5061/dryad.5k0g4.2/1.2
title: Carbon content in mangrove sediments in four coastal lagoons of the Mexican Pacific

description: This database contains the carbon contents found in sediments below mangrove forests in four coastal lagoons of the Mexican Pacific coast: (1) Bahía Magdalena, Pacific coast of Baja California Sur, (2) Balandra, Gulf of California coast of Baja California Sur, (3) Marismas Nacionales, State of Nayarit, and (4) La Encrucijada, State of Chiapas. Samples were collected by Paula Ezcurra, Exequiel Ezcurra, and Pedro P. Garcillán. Samples and data form part of Paula Ezcurra's Honors Program project at the University of California Santa Barbara. The datafile in other formats (csv, pdf) can be downloaded from the following URL: http://ezcurralab.ucr.edu/c-sequestration/mangroves.html
DOI: 10.5061/dryad.5k0g4.2/2.2
title: Radiocarbon age of peat in mangrove sediments from the Mexican Pacific

description: This database contains the carbon contents found in sediments below mangrove forests in four coastal lagoons of the Mexican Pacific coast: (1) Bahía Magdalena, Pacific coast of Baja California Sur, (2) Balandra, Gulf of California coast of Baja California Sur, (3) Marismas Nacionales, State of Nayarit, and (4) La Encrucijada, State of Chiapas. Samples were collected by Paula Ezcurra, Exequiel Ezcurra, and Pedro P. Garcillán. Samples and data form part of Paula Ezcurra's Honors Program project at the University of California Santa Barbara. The datafile in other formats (csv, pdf) can be downloaded from the following URL: http://ezcurralab.ucr.edu/c-sequestration/mangroves.html
DOI: 10.5061/dryad.5k0g4.2/3.2
title: Carbon content in mangrove sediments in five Gulf of California sites

description: This database contains the carbon contents found in sediments below mangrove forests in five coastal coastal sites of the Gulf of California, around the Bay of La Paz and neighboring islands. Samples were collected by Matt Costa with field assistance of Paula Ezcurra. Both samples and data form part of Matt Costa's PhD project at Scripps Institution of Oceanography, University of California San Diego. The datafile in other formats (csv, pdf) can be downloaded from the following URL: http://ezcurralab.ucr.edu/c-sequestration/mangroves.html.
DOI: 10.5061/dryad.635ds/1
title: Supplemental File 2

description: Fasta file for Safflower draft genome
DOI: 10.5061/dryad.635ds/2
title: Supplemental File 4

description: Genetic Map File of Recombination Bins
DOI: 10.5061/dryad.762b8/1
title: SM_CN_OK

description: Carbon and Nitrogen data from Swarth Moor (cores SM1-3)
DOI: 10.5061/dryad.762b8/2
title: SM_SCPshortcores_OK

description: Spheroidal carbonaceous particle data from short cores from Swarth Moor
DOI: 10.5061/dryad.8t3v5/1
title: Fig 1 egg-hatching dates experiment 2007

description: Data used in Figure 1
DOI: 10.5061/dryad.9n237/1
title: Anterior supragnathal of an Early Devonian arthrodire (ANU V244)

description: PLY file of the anterior supragnathal (ASG) of an Early Devonian arthrodire (ANU V244).
DOI: 10.5061/dryad.9pg8d/10
title: phylogenetic-analysis-steps.txt

description: Steps used during the phylogenetic analysis.  All used the PHYLUCE software package (available from: https://github.com/faircloth-lab/phyluce).
DOI: 10.5061/dryad.9pg8d/11
title: fish-uce-1k-probes.fasta.gz

description: Fasta file detailing probes targeting UCEs in Acanthomorphs.
DOI: 10.5061/dryad.9pg8d/12
title: all-tre-files.tar.gz

description: An archive of all trees generated for the manuscript text in Newick format.
DOI: 10.5061/dryad.9pg8d/7
title: mafft-gblocks-clean-95p-complete-EXABAYES.tar.gz

description: ExaBayes output files for Bayesian analysis of the 95 % complete data set.
DOI: 10.5061/dryad.9pg8d/8
title: mafft-gblocks-clean-75p-complete-raxml.tar.gz

description: Partition-finder and RAxML input/output files for ML analysis of the 75 % complete data set.
DOI: 10.5061/dryad.9pg8d/9
title: mafft-gblocks-clean-75p-complete-EXABAYES.tar.gz

description: ExaBayes output files for Bayesian analysis of the 75 % complete data set.
DOI: 10.5061/dryad.b1m1h/1
title: Soil biotic and abiotic data

description: SIR, microbial biomass C, N, TOC,TON, pH, VWC.
DOI: 10.5061/dryad.b1m1h/2
title: mycorrhizaeData_dryad

description: AMF colonization (%)
DOI: 10.5061/dryad.b1m1h/3
title: baseline C-N_dryad

description: total (bulk) soil C, N
DOI: 10.5061/dryad.fg7jv/1
title: Pre- and postcopulatory trait measures

description: Sheet 1: Data. Sheet 2: Variable descriptions
DOI: 10.5061/dryad.gr060/1
title: Comparative study
DOI: 10.5061/dryad.k3479/1
title: Crouzeilles_et_al_R code for Meta-Analyses
DOI: 10.5061/dryad.k3479/2
title: Crouzeilles_et_al_R code for Model Selection Analyses
DOI: 10.5061/dryad.k3479/3
title: Meta_analysis
DOI: 10.5061/dryad.k3479/4
title: Model_Selection_Landscape_5kmradius
DOI: 10.5061/dryad.k67j5/1
title: Survival and traits according to the different species and treatments

description: Excel sheet composed of 5 tables. Table 1: descriptors used. Table 2: Survival data. Table 3: Growth data. Table 4. Phenological data. Table 5. Leaf traits data
DOI: 10.5061/dryad.k8h4t/1
title: Cassowary sightings and mortality data

description: The number of sightings and wildlife traffic strikes occurring within georeferenced 1 km grid cells. Also included are the R scripts used to run the CARP models
DOI: 10.5061/dryad.nk3qt/1
title: Debecker et al 2016 JAE repository data

description: Life-history and behavioural data from larvae of four Ischnura species reared under common garden conditions in the laboratory from the egg stage. During the final instar, larvae got an 8-day pesticide treatment (2 µg/l chlorpyrifos present/absent). Behavioural data (feeding activity(=projections) and latency time after a simulated predator attack) were collected just before the start en after the end of the pesticide treatment. See manuscript and Supporting Information on the publisher's website for more guidance.
DOI: 10.5061/dryad.q9m45/2
title: Data for Figure 2A-B

description: This file contains two datasheets. The first sheet provides the underlying sister species, and their values of coexistence and NPP from a single exemplar tree used to plot Figure 2A. The second sheet provides the numerical values plotted in Figure 2B.
DOI: 10.5061/dryad.q9m45/3
title: Data for Figure 3

description: This file contains the individual numeric values plotted in Figure 3.