cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bg4t9/1
title: Raw data for morphological indexs of QWE and  QWLs (Figure 1)

description: This is the raw data of mean (+SE) weight of new born queens and 3-day-old queen larvae, thorax width and length of new born queens, from QWE and QWLs. Data supports the Fig. 1 in paper titlied "Making a queen: an epigenetic analysis of the robustness of the honey bee (Apis mellifera) queen developmental pathway". Data was measured by using an analytical balance (FA3204B, Shanghai Precision Scientific Instrument Co., Ltd.).
DOI: 10.5061/dryad.f6154/1
title: pyRAD parameters file

description: This is the parameter file containing all parameters used for de novo SNP calling using the pyRAD pipeline. Running pyRAD using these parameters on the deposited raw data (accessible in GenBank BioProject PRJNA382467) will produce the "FL-RAD-SphI-ALL.vcf" and "FL-RAD-SphI-ALL.loci" files deposited in this repositiory.
DOI: 10.5061/dryad.f6154/2
title: Unfiltered Called SNPs (VCF format)

description: This file is the output of the pyRAD pipeline (VCF format) ran on the raw sequence reads (accessible via GenBank, BioProject PRJNA382467) using the parameters which are given in the the pyRAD parameter file despoted in this repository ("pyRAD_parameters_file.txt"). It contains several technical replicates (which are denoted by the suffix "_R"), which are used in the study to determine the consistency of SNP calls.
DOI: 10.5061/dryad.f6154/3
title: Unfiltered Called SNPs (".loci" format)

description: This file is the output of the pyRAD pipeline (pyRAD ".loci" format) ran on the raw sequence reads (accessible via GenBank, BioProject PRJNA382467) using the parameters which are given in the the pyRAD parameter file despoted in this repository ("pyRAD_parameters_file.txt"). It contains several technical replicates (which are denoted by the suffix "_R"), which are used in the study to determine the consistency of SNP calls.
DOI: 10.5061/dryad.f6154/4
title: Filtered SNPs

description: SNP genotypes for each individual, filtered according to the parameters explained in the manuscripts (and in the comments to the file). This is the main data-set used for population genetic analyses.
DOI: 10.5061/dryad.f6154/5
title: Alignment for phylogeny

description: This is a multiple sequence alignment file (in PHYLIP format) obtained by concatenating the sequences of the 2051 loci for a subset of 57 individuals. This file is the input file used for phylogenetic analyses.
DOI: 10.5061/dryad.f6154/6
title: Samples and populations list

description: Text file with sampling location information for each individual.
DOI: 10.5061/dryad.f6154/7
title: DIY-ABC Input file

description: This is the input data for all ABC analyses. It includes genotypes of individuals from the North Sea (coded as NS), The Baltic Pelagic (PEL) and the Baltic demersal (DEM) lineages. Outlier loci and individuals from the transition zone were removed from this dataset.
DOI: 10.5061/dryad.hg600/9
title: Estimates of the G x G indirect genetics effects

description: Estimates of the 417 GxG indirect genetic effects in the best model for dataset3 analyses (used for Fig. S6)
DOI: 10.5061/dryad.k505s/1
title: Viburnum phylogeny

description: 120-taxon phylogeny, pruned from Spriggs et al. 2015, used for Viburnum-wide habit/habitat analyses
DOI: 10.5061/dryad.k505s/2
title: Viburnum-wide character data

description: habitat and character codings, and bioclim variables, for Viburnum-wide phylogenetic analyses
DOI: 10.5061/dryad.k505s/3
title: phenology transect data

description: dates of leaf gain and loss for 20 Viburnum species along a tropical-temperate latitudinal transect
DOI: 10.5061/dryad.k505s/4
title: climate data for field sites

description: monthly temperature and precipitation data for field sites along the phenology transect
DOI: 10.5061/dryad.p1v07/1
title: Livestock, Cattle, elephants abundance in hirola's  range_77_2011

description: This is aerial survey data from the Department of Resource Survey and Remote Sensing Kenya from 1977 to 2011 to give historical estimates wildlife and livestock abundances. We estimated the trends of livestock, hirola, elephants abundances from this data.
DOI: 10.5061/dryad.p1v07/2
title: Masalani_daily rainfall

description: The rainfall data file contains daily rainfall observations for Masalani station in the centre of hirola's geographic range for the period from 1970-2009.
DOI: 10.5061/dryad.p1v07/3
title: Hirolacollardatamay2nd 2015

description: The hirola collar data contains the telemetry data of collared hirola individuals within the hirola's geographic range. Note: due to the sensitive nature of the data, GPS location information for the critically endangered Beatragus hunteri have been removed from the dataset.
DOI: 10.5061/dryad.p1v07/4
title: Imagery analysis

description: P166R61zip contains details of the imagery analysis (1985 and 2012) for the hirola's geographic range.
DOI: 10.5061/dryad.q0s20/1
title: StacyetalEcologyEvolution2017Dryad

description: Here are the data files for Stacy, Paritosh, Johnson & Price. 2017. Incipient ecological speciation between successional varieties of a dominant tree involves intrinsic postzygotic isolating barriers (accepted for publication February 2017).  The file contains 16 sheets compiled in one Excel file.
DOI: 10.5061/dryad.rm95m/1
title: BotterillJamesetal_BES_MateFamiliarity

description: Behavioural and Reproductive Data associated with BotterillJames et al. Behavioral Ecology and Sociobiology
DOI: 10.5061/dryad.s07cg/1
title: PloidyDrive: R setup file

description: This R code file loads the required libraries and data for analysis and figures.
DOI: 10.5061/dryad.s07cg/2
title: PloidyDrive: R figures file

description: This R code file will reproduce the figures in the manuscript.
DOI: 10.5061/dryad.s07cg/3
title: PloidyDrive: R stats file

description: This R code file will reproduce the statistics in the manuscript.
DOI: 10.5061/dryad.s07cg/4
title: Flow cytometry data

description: Raw flow cytometry data used to analyze genome size change. Columns labeled enviro-evol.2 indicate the location of a secondary G1 peak when it was present. Used in the R setup file.
DOI: 10.5061/dryad.s07cg/5
title: GR_allSDC

description: Ancestral and evolved growth rate and yield data from SDC (complete medium). Used in the R setup file.
DOI: 10.5061/dryad.s07cg/6
title: GR_allSD

description: Ancestral and evolved growth rate data from SD (minimal medium). Used in the R setup file.
DOI: 10.5061/dryad.s07cg/7
title: GR_allPlim

description: Ancestral and evolved growth rate data from phosphorus depleted (Pdep) medium. Used in the R setup file.
DOI: 10.5061/dryad.s07cg/8
title: GR_allNlim

description: Ancestral and evolved growth rate data from nitrogen depleted (Ndep) medium. Used in the R setup file
DOI: 10.5061/dryad.sc0nf/1
title: Sample_information

description: Aphrocallistes vastus sample metadata including sequencing barcode identifier, full sample name, collection year, sample site, GPS coordinates, depth, and heading of the remote operated vehicle (ROV) during collection. Samples correspond to sequence data and are organized by sequencing barcode. This list include controls (samples sequenced twice as well as one Heterochone calyx control) and samples with poor sequence data which did not contribute to the analyses.
DOI: 10.5061/dryad.sc0nf/2
title: Genotypes_ID_dataset_91samples_76loci

description: Aphrocallistes vastus single nucleotide polymorphism (SNP) genotypes for full sample set (all samples with adequate sequencing coverage/quality except for interspecies control) including sequencing controls. This dataset was used to examine clonality (identity) across samples. Samples are identified by sequencing barcode with sample site identifiers in the second column. Data are organized into two columns per locus with GenAlEx format (A=1,C=2,G=3,T=4, missing=0).
DOI: 10.5061/dryad.sc0nf/3
title: POP_dataset_78samples_67loci

description: Aphrocallistes vastus single nucleotide polymorphism (SNP) genotypes for samples used in population analyses (all samples from sample sites with n &gt; 5) excluding sequencing controls. Samples are identified by sequencing barcode with sample site identifiers in the second column. Data are organized into two columns per locus with GenAlEx format (A=1,C=2,G=3,T=4, missing=0).
DOI: 10.5061/dryad.ss3r7/1
title: Raw migratory connectivity data

description: Data were extracted from the literature (see Materials & Methods), and essentially represent start and end points (i.e. breeding and non-breeding locations) of the migration routes of individual tracked migrants land-birds.Named variables are defined as follows:"system" (TEXT) - migration system; "afro" = Afro-Palearctice, "neo" = Neotropical"study" (TEXT) - data source; see Supplementary Materials for full citations"species" (TEXT) - species common name"family" (TEXT) - taxonomic family"order" (TEXT) - taxonomic order"popunique" (NUMERIC) - arbitrary code grouping individuals from the same species into unique populations separated by &lt; 100km. Typically, this means grouping individuals from the same study site into populations. "method" (NUMERIC) - tagging method; 1 = solar geolocator, 2 = GPS, 3 = satellite tag"sampledat" (NUMERIC) - sampling site; 1 = breeding site, 2 = non-breeding site"age" (NUMERIC) - age of bird; 0 = juvenile (first migration), 1 = adult, blank = unknown"country" (TEXT) - tagging country"state" (TEXT) - tagging state / province (for USA and Canada)"year" (NUMERIC) - year of tagging (2014 = 2014/15 migration period); blank if unknown"blat" (NUMERIC) - latitude of tagging site in decimal degrees"blon" (NUMERIC) - longitude of tagging site in decimal degrees"wlat1" (NUMERIC) - latitude of first winter site in decimal degrees"wlon1" (NUMERIC) - longitude of first winter site in decimal degrees"wlat2" (NUMERIC) - (if applicable) latitude of second winter site in decimal degrees "wlon2" (NUMERIC) - (if applicable) longitude of second winter site in decimal degrees"wlat3" (NUMERIC) - (if applicable) latitude of third winter site in decimal degrees "wlon3" (NUMERIC) - (if applicable) longitude of third winter site in decimal degrees"notes" (TEXT) - additional notes
DOI: 10.5061/dryad.ss3r7/2
title: Full data package

description: Includes raw migratory connectivity data & annotated, reproducible R scripts. See README.txt for more details.
DOI: 10.5061/dryad.t7m7g/10
title: Mean ocular media transmission
DOI: 10.5061/dryad.t7m7g/11
title: MSP data no unpaired DC
DOI: 10.5061/dryad.t7m7g/12
title: MSP data with unpaired DC
DOI: 10.5061/dryad.t7m7g/13
title: Raw MSP data with best matching template for Figure 2
DOI: 10.5061/dryad.t7m7g/14
title: Reflectance curves for 8 T delaisi irides
DOI: 10.5061/dryad.t7m7g/7
title: Fluorescence matrix Td ID 793-1
DOI: 10.5061/dryad.t7m7g/8
title: Fluorescence matrix Td ID 793-2
DOI: 10.5061/dryad.t7m7g/9
title: Irradiance from 6 to 36m depth STARESO
DOI: 10.5061/dryad.v444t/1
title: full_assay_dataset

description: Data from plant infections of Tomato and Arabidopsis with P.syringae lines from an experimental evolution experiment.
DOI: 10.5061/dryad.v444t/2
title: Assay and passage data, SNP calls.

description: Experimental data from the assay and evolution experiment (bacterial counts at each transfer) and SNP calls. Readme.txt file explains column info. Directory compressed as a tar file.
DOI: 10.5061/dryad.vk26r/1
title: SYLCUR data for manuscript

description: Spring arrival data
DOI: 10.5061/dryad.03mn0/1
title: Data Morphology

description: This file corresponds to the morphological data. All the variables required to perform the morphological animal models are contained in this table.
DOI: 10.5061/dryad.03mn0/2
title: Data.LHT

description: This file corresponds to the life-history trait data. All the variables required to perform the life-history animal models are contained in this table.
DOI: 10.5061/dryad.03mn0/3
title: Pedigree Morphology

description: This table contains the pedigree for the individuals used in the morphological animal models.
DOI: 10.5061/dryad.03mn0/4
title: Pedigree LHT

description: This table contains the pedigree for the individuals used in the life history animal models.
DOI: 10.5061/dryad.26h4q/13
title: Weather-PSE

description: R Script for the analysis of the effect of weather on the probability of an egg being laid (pausing analysis)
DOI: 10.5061/dryad.26h4q/14
title: Weather-CSIZE

description: R Script for the analysis of the effect of weather on clutch size
DOI: 10.5061/dryad.26h4q/15
title: Weather-INC

description: R Script for the analysis of the effect of weather on incubation
DOI: 10.5061/dryad.26h4q/16
title: Feeding-CGH-K

description: Example R script for carrying out K-fold cross-validation of the models. In this case, it is for the model of the effect of the feeding treatment on hatching time (censored Gaussian).
DOI: 10.5061/dryad.28995/1
title: Table_S1. Endosymbiont-induced parthenogenesis in haplo-diploid species (or haplo-haploid in the case of Brevipalpus), with confirmed cases highlighted in grey.

description: This dataset includes all possible haplodiploid parthenogens induced by endosymbionts. The dataset is collected from published articles, with confirmed cases highlighting in grey and others are speculative cases (no strong cause-effect relationship). The detailed information includes species taxa, species name, common name, endosymbiont name, approaches to verify, possible cellular mechanism, whether the species has reproductive polymorphism (presence of both sexual and parthenogenetic females in natural populations).
DOI: 10.5061/dryad.28995/2
title: Table_S2.  List of parthenogenetic species with gamete duplication and where parthenogenesis is due to genetic causes. For species in brackets, gamete duplication is not formally confirmed but likely.

description: This dataset is a list of parthenogenetic species with gamete duplication and where parthenogenesis is due to genetic causes. For species in brackets, gamete duplication is not formally confirmed but likely. These include information on the host order, host species name, common name and host sex determination system.
DOI: 10.5061/dryad.28995/3
title: Table_S3. Species with a firm demonstration of endosymbiont-induced parthenogenesis, and with reproductive polymorphism.

description: This dataset is a list of species with a firm demonstration of endosymbiont-induced parthenogenesis, and with reproductive polymorphism. These include information on host order, host species, host common name, sexual population distribution (with detailed locations) and asexual population distribution (with detailed locations).
DOI: 10.5061/dryad.28995/4
title: Table_S4. Haplo-diploid parthenogens in which parthenogenesis is due to genetic causes.

description: This dataset is haplo-diploid parthenogens in which parthenogenesis is due to genetic causes, and where the cellular mechanisms underlying parthenogenesis are studied (all species except the last one in the list are hymenopterans. Heliothrips haemorrhoidalis is a thrips species). These include information on species name and the cellular mechanism for parthenogenesis.
DOI: 10.5061/dryad.31v01/1
title: 3D FDTD hatchetfish nearfield scattering calculations

description: Folder containing all files and data necessary to model and plot Figure 4, the 3D nearfield scattering calculations from the hatchetfish skin using FDTD and MEEP.
DOI: 10.5061/dryad.31v01/2
title: MeepFarFieldFluxsetup_AH_March2017

description: Folder containing files for calculating and plotting figure 2c,2d and 2e, the farfield backscatter from hatchetfish skin.
DOI: 10.5061/dryad.31v01/3
title: MeepScatteringCalculationSetup_ER_march2017

description: Folder containing all files necessary to calculate and plot Figure 3b, the scattering phase functions of different types of single cells.
DOI: 10.5061/dryad.31v01/4
title: Threshold Camouflage Calculation

description: Matlab file used to calculate threshold detection for bioluminescent searchlight predator in Figure 5b
DOI: 10.5061/dryad.31v01/5
title: BRDF plot, Figure 2a

description: Matlab file for opening BRDF data called S17_grn_BRDF_around_incTheta_8.mat and plotting like Figure 2a. Requires S17_grn_BRDF_around_incTheta_8.mat.
DOI: 10.5061/dryad.40qt2/5
title: vitalRateModels

description: Executes and saves the results of a Bayesian model quantifying all vital rates using uniformed priors; illustrates basic diagnostics that can be run on the results of an MCMC run (i.e., the posterior parameter distribution) to check for model convergence and autocorrelation of the posterior samples.
DOI: 10.5061/dryad.40qt2/6
title: makeIPM

description: Demonstrates how to construct IPMs including continuous (above-ground) and discrete (seedbank) transitions for parameter means of the Bayesian models; saves IPMs for each combination of TSF (n =5) × LS (n = 2) × site (n = 8) (Part A). The code also saves IPMs for each TSF × LS averaged over sites (Part B). Site-specific and average kernel transitions for the vital rate growth (γ in main text) are also saved. The IPMs in Part A are used to calculate the stochastic population growth rate log λs, and extinction probability, Pq(t) by t = 300 years. The IPMs in parts A and B are used to calculate elasticities of log λs to changes in mean transitions across environmental states (TSF & LS) and in the standard deviation of transitions.
DOI: 10.5061/dryad.40qt2/7
title: sLambdafixedLS

description: Runs and plots results of simulations of log λs using IPMs constructed for mean parameter values. The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.
DOI: 10.5061/dryad.40qt2/8
title: sLambdaStochLS

description: Runs and plots results of simulations of log λs using IPMs constructed for mean parameter values. Here, the growth kernel transitions are also included alongside the full IPMs. The simulations consider both fire and livestock browsing as an integrated stochastic process in which transitions between combinations of TSF × LS states are based on fire return interval and browsing management efforts.
DOI: 10.5061/dryad.40qt2/9
title: elastVR

description: Runs and plots results of simulations of log λs and elasticities using IPMs constructed for lower vital rate survival (σ). The simulations consider fire as a stochastic process in which transitions between TSF states are based on fire return interval. Transitions between LS are not considered.
DOI: 10.5061/dryad.49dn0/1
title: R Script

description: This is the R Script used running the ordinations as well as creating the figures and supplementary materials for this study.
DOI: 10.5061/dryad.49dn0/2
title: OTUs in Blank

description: This is an OTU-sample table of the OTUs found in the blank sample (negative control) and removed from further analysis. The representative sequences and the BLAST matches are included.
DOI: 10.5061/dryad.49dn0/3
title: Mapping File

description: This is the barcode and primer mapping file used in this study.
DOI: 10.5061/dryad.49dn0/4
title: OTU Table

description: This is the OTU-sample table used in this study after quality filtering with raw read abundances and in presence-absence format.
DOI: 10.5061/dryad.4f775/1
title: Vaccaro et al. 2016 sleep raw data

description: Data for S2 Fig
DOI: 10.5061/dryad.4f775/2
title: Lifespan data

description: Data for S1A and S1B Figures (Prism .pzf format)
DOI: 10.5061/dryad.5v02v/1
title: Parasitism of H. manauara on L. henryi - DarwinCore

description: This dataset includes records of the parasitism of Hymenoepimecis manauara on Leucauge henryi collected in Ducke Reserve near Acará Stream in Manaus County, Amazonas state, Brazil. The dataset uses DarwinCore standard column headings, which are explained in the 'Parasitism of H. manauara on L. henryi - DarwinCore' file.
DOI: 10.5061/dryad.61mk0/1
title: Dryad_data

description: Baseline and prey tongue-flick rate, diet and foraging mode for 94 lepidosaurian species, assembled from available literature. I-C, insectivorous-carnivorous; O, omnivorous; H, herbivorous; SW, sit-and-wait foraging; AC, active foraging.
DOI: 10.5061/dryad.7126m
title: Data from: Evolutionary dynamics of hepatitis C virus in patients with mixed infection over a 13-year follow-up period
DOI: 10.5061/dryad.7126m/1
title: Patient 1 HCV alignments

description: 16 HCV sequence alignments for patient 1 - Core and NS5B regions, 8 time samples.
DOI: 10.5061/dryad.7126m/2
title: Patient 2 HVC alignments

description: 10 HCV sequence alignments for patient 2 - Core and NS5B regions, 5 time samples.
DOI: 10.5061/dryad.7126m/3
title: Patient 3 HCV alignments

description: 6 HCV sequence alignments for patient 3 - Core and NS5B regions, 3 time samples
DOI: 10.5061/dryad.f1j0s/1
title: Gonadosomatic Index in both hybrid groups

description: GSI data, taxon, gender and collection dates for all individuals used in GSI comparisons.
DOI: 10.5061/dryad.f1j0s/2
title: Liver vacuolation in both hybrid groups

description: Hepatocyte vacuolation data, taxon and gender identifiers for each individual used in the body condition analyses.
DOI: 10.5061/dryad.f1j0s/3
title: Length at age data for the C. guttatissimus group

description: Length, age and taxon identifiers for each individual used in VBGF fitting for the C. guttatissimus hybridising group
DOI: 10.5061/dryad.f1j0s/4
title: Length at age data for the C. trifasciatus group

description: Length, age and taxon identifiers for each individual used in VBGF fitting for the C. trifasciatus hybridising group
DOI: 10.5061/dryad.f6154/10
title: Scenario codes and priors for simulations Torunament#3

description: In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the third random forest tournament we carried out. This reproduces the results which are reported in the Table S8 in the supplementary materials, i.e. the tournament aimed to determine whether or not there was secondary introgression among the two Baltic lineages and whether or not there had been an expansion in the ancestral population.
DOI: 10.5061/dryad.f6154/11
title: Scenario codes and priors for simulations  Final Scenario

description: In this file we report the scenario codes and priors to reproduce, using the software DIY-ABC, the reference table (500 0000 simulations) used to estimate the final parameters and to check the final model.
DOI: 10.5061/dryad.f6154/8
title: Scenario codes and priors for simulations Torunament#1

description: In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the first random forest tournament we carried out.
This reproduces the results which are reported in the Table S6 in the supplementary materials, i.e. the tournament aimed at identifying the main divergence scenario.
DOI: 10.5061/dryad.f6154/9
title: Scenario codes and priors for simulations  Torunament#2

description: In this file we report the scenario codes to reproduce, using the software DIY-ABC, the reference table which can then be analyzed by the R package "abcrf" to produce the results from the second random forest tournament we carried out. This reproduces the results which are reported in the Table S7 in the supplementary materials, i.e. the tournament aimed to determine whether or not the two Baltic 
lineages underwent a bottleneck followed by a demographic expansion during and after the invasion of the Baltic Sea
DOI: 10.5061/dryad.fs8kv/1
title: Matrix I

description: Concatenated matrix of the genes with &gt;90% gene occupancy. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.g551v/1
title: Tree mortality data

description: Excel file containing 4 tabs: mortality data as extracted from publications, annualised mortality data used in analysis, single survey proportional data used in analysis and trait data used in analysis.
DOI: 10.5061/dryad.g7h7n/1
title: Col Broken stick

description: Col Pond plot of broken stick model results