cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.50sg7/6
title: Untrimmed multiple sequence alignments

description: This file contains MAFFT-aligned (Version 7) 28S rRNA, 18S rRNA, and ITS-1 sequences of 13 Ligophorus species as they were at the end of running MAFFT. Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53.
DOI: 10.5061/dryad.50sg7/7
title: Maximum likelihood tree of 13 Ligophorus species

description: This file contains the inferred maximum likelihood tree of 13 Ligophorus species (Figure 3 in Khang et al. (2016)). The tree was inferred using the IQ-tree pipeline. Parameters: DNA substitution model: GTR + G; 10 000 bootstrap replicates; mid-point rooting.
DOI: 10.5061/dryad.64n47/1
title: Vegeation index, SIF and VPM model results

description: The data includes PAR, air temperature, EVI, LSWI, APAR and SIF. The parameters for the VPM model are also included.
DOI: 10.5061/dryad.65k7g/1
title: Wood et al 2016 Bewick Swan breeding success paper data

description: A Microsoft Excel spreadsheet containing the raw and standardized values for all variables used in the analysis of Bewick's Swan breeding success. The data cover the period 1988-2013. A legend describing the identity of each variable is also included.  Further information on the data analysis is available in the published paper.
DOI: 10.5061/dryad.7017n/1
title: Dryad-data1-Am Nat-Guivier

description: Host life history traits
DOI: 10.5061/dryad.7017n/2
title: Dryad-data2-Am Nat-Guivier

description: Immunological data
DOI: 10.5061/dryad.734c8/1
title: Selection experiment data

description: This file contains adult survival data and juvenile population counts during the course of the selection experiment described in the associated publication. The proportion of surviving adults and juveniles numbers are given for replicate populations within each treatment.
DOI: 10.5061/dryad.734c8/2
title: Resistance bioassay data

description: This file contains survival data for the resistance bioassays conducted in the associated publication. The initial number of worms alive and dead is given for each developmental stage (adults and juveniles) and for replicate populations within each treatment from generations 0, 5 and 10 of the selection experiment. In addition, bioassays were conducted at zero, high and low doses of Ivermectin signified in the data set by dose.
DOI: 10.5061/dryad.cj375/1
title: Brapa_flr_morph_measurements

description: Floral size and shape measurements from Brassica rapa recombinant inbred lines (up to 6 replicates per line from the R500 x IMB211 RIL population) raised in AES fields at the University of Wyoming.
DOI: 10.5061/dryad.cj375/2
title: Brapa_UV_patterning_survey

description: Accession, site of origin, and UV pattern information on each Brassica rapa sample raised in the field (University of Wyoming, Laramie, WY, USA) or sampled from herbarium sheets (Rocky Mountain Herbarium; University of Wyoming).
DOI: 10.5061/dryad.d6rh9/1
title: Figure
DOI: 10.5061/dryad.g2t66/1
title: mechanisms of general practice 2016

description: An excel file containing the variables used in the study
DOI: 10.5061/dryad.gf4qj/1
title: Leroy_2015_newphytologist_dataset_969AFLP

description: our dataset: 104 strains genotyped at 969 AFLP loci (binary 0/1 character matrix, missing data = -9)
DOI: 10.5061/dryad.gv348/1
title: Hopwood-etal-male reproductive competition in burying beetles JEB-2015-00671-data

description: These data relate to "The effect of size and sex-ratio experiences on reproductive competition in Nicrophorus vespilloides burying beetles in the wild." Hopwood, Paul E., Moore, Allen J., Tregenza, Tom, Royle, Nick J.
DOI: 10.5061/dryad.h25hj/1
title: 130224_Larix_sample_info
DOI: 10.5061/dryad.h25hj/2
title: 130224_Larix_sample_info_mt_ha
DOI: 10.5061/dryad.k2k08/1
title: Environmental, taxonomic, and functional data

description: This file contains i) all regional and local environmental variables measured in the field of our 8 sites across France, ii) all taxonomic information on the plots of every site, and iii) the community-weighted mean of the functional variables used in this study. A brief metadata to describe each variable was also included. This file contains all the data necessary to reproduce the results in our study.
DOI: 10.5061/dryad.k78f6/1
title: Source pond GPS coordinates
DOI: 10.5061/dryad.k78f6/2
title: Survival_data

description: Data shown in Fig. 1. Number of starting animals and number of surviving animals after UV-B exposure and subsequent exposure to photorepair radiation (light) or no radiation (dark).
DOI: 10.5061/dryad.k78f6/3
title: Carotenoid content

description: Carotenoid data shown in figure in Supporting Information.
DOI: 10.5061/dryad.k78f6/4
title: DNA damage data

description: Data shown in Fig 2A & 2B, with statistical results shown in Table 1. Data are absorbance values from ELISA for cyclobutane pyrimidine dimers (CPDs) in DNA.
DOI: 10.5061/dryad.k78f6/6
title: DNA damage data (dark treatment)

description: Data shown in Fig 2C. Data are absorbance values from ELISA for cyclobutane pyrimidine dimers (CPDs) in DNA.
DOI: 10.5061/dryad.kf575/1
title: Precipitation, herbivory intensity and pine sapling height growth

description: The dataset contain Relative Height Growth (RHG) and age of 234 pine saplings of Pinus sylvestris and P. nigra in two native forests of Southern Europe during the period 1993-2008, both at treeline and woodland areas. Red deer (Cervus elaphus) abundance and summer (June, July and August) total precipitation data of the study area (Sierra de Baza Natural Park, SE Spain) are included, as well as herbivory intensity (percentage of saplings suffering leader browsing) recorded in sampled plots for the study period.
DOI: 10.5061/dryad.mg73v/1
title: White_et_al_Relapse_data_PRSB_2016

description: Data on relapse timings.
DOI: 10.5061/dryad.nb267/1
title: Supporting Information Table 1

description: Dietary data and references.
DOI: 10.5061/dryad.r87d6/1
title: demographic & management data
DOI: 10.5061/dryad.r95s8/1
title: Scilly_seagrass_data
DOI: 10.5061/dryad.rh97t/13
title: A250613

description: Data archive
DOI: 10.5061/dryad.rh97t/14
title: A260413

description: Data archive
DOI: 10.5061/dryad.rh97t/15
title: A290413

description: Data archive
DOI: 10.5061/dryad.rh97t/16
title: A301014

description: Data archive
DOI: 10.5061/dryad.rh97t/17
title: A300413

description: Data archive
DOI: 10.5061/dryad.rh97t/18
title: A311014

description: Data archive
DOI: 10.5061/dryad.rh97t/19
title: B071014

description: Data archive
DOI: 10.5061/dryad.rh97t/20
title: B080613

description: Data archive
DOI: 10.5061/dryad.rh97t/21
title: B081014

description: Data archive
DOI: 10.5061/dryad.sm1gt/1
title: FordSmisethJEB12797
DOI: 10.5061/dryad.v7h28/10
title: Et.Etrach_0.final

description: Manual annotation of Contig 0, E. tracheiphila reference strain BuffGH
DOI: 10.5061/dryad.v7h28/11
title: Et.Etrach_1.final

description: Manually corrected annotation of Contig 1, reference strain BuffGH
DOI: 10.5061/dryad.v7h28/12
title: Et.Etrach_2.final

description: Manually corrected annotation of E. tracheiphila BuffGH contig 2
DOI: 10.5061/dryad.v7h28/6
title: GZ4-assembly

description: E. tracheiphila strain GZ4 assembly file in fasta format, generated by a hybrid mapping + deNovo strategy
DOI: 10.5061/dryad.v7h28/7
title: core_Enterobactericeae_alignment

description: Core Enterobacteriaceae alignment used to create figure 2. Relevant methods are in the 'Methods' section of the publication
DOI: 10.5061/dryad.v7h28/8
title: core_Erwinia_Pantoea_Alignments

description: Core genome alignment of the Erwinia/Pantoea clade used to create figure 4. Relevant methods are in the 'methods' section of the publication
DOI: 10.5061/dryad.v7h28/9
title: Supplemental_File_1

description: File describing the exact parameters for the hybrid mapping + deNovo assembly using Mira 4.1, as described in the 'Methods' section of the accompanying publication
DOI: 10.5061/dryad.1kv63/1
title: Tremblay-et-al-ESM

description: Dimensions of female unionids used for infestation experiments, and the viability of their glochidia Unionid mussel and fish pairings, and total lengths of experimental fish
DOI: 10.5061/dryad.1tk3d/1
title: Datasets used in this study

description: This is a compressed zip file of all the datasets used in this study grouped by analysis.
DOI: 10.5061/dryad.231cm/1
title: Bayandala data

description: Table S1.  Environmental conditions in the forest understory and gaps beneath adults of Cornus controversa and Prunus grayana. Table S2. Causes of seedling mortality (%) during the 2011 growing season in the forest understory (FU) and gap (Gap) beneath C. controversa and P. grayana adults in the reciprocal seed-sowing experiment. Table.S3-1. Proportion (%) of leaves damaged by zonate leaf blight, number of leaves attached to a seedling, proportion of seedlings showing cell wall defence against zonate leaf blight beneath adults of Cornus controversa. Table S3-2. Proportion (%) of leaf area damaged by angular leaf spot and the number of leaves attached to a seedling for both species in the forest understorey (FU) and gaps (Gap)  beneath adults of Prunus grayana.  Table S4.  Seedling mass  (g), RGR (g g-1 day-1) and percent infection of  AMF (%) of Cornus controversa and Prunus grayana seedlings beneath the adults of each of the two species in forest understory (FU) and gaps (GAP)
DOI: 10.5061/dryad.2c506/1
title: Phylogeny

description: Phylogeny of the 25 Poaceae species. The time scale is arbitrary.
DOI: 10.5061/dryad.2c506/2
title: Plant trait data

description: Individual-level data of measured plant traits
DOI: 10.5061/dryad.2c506/3
title: Clump-scale flammability traits

description: Individual-level data for clump-scale flammability traits
DOI: 10.5061/dryad.2c506/4
title: Leaf-scale flammability traits

description: Individual-level data of leaf-scale flammmability traits
DOI: 10.5061/dryad.34dr2/1
title: Data for manuscript RSPB-2015-2988.R1

description: This file contains all of the raw data presented in the manuscript 'Finding the Gap: A brightness-based strategy for guidance in cluttered environments'.
DOI: 10.5061/dryad.4b3qn/1
title: Input files

description: This excel file contains five sheets: SNP information, individual genotypes (baseline populations), individual genotypes (to be assigned), an input file for a multinomial likelihood ratio test and an input file binomial GLM.
DOI: 10.5061/dryad.580bh/1
title: Guillaume et al 2015_Transgenerational plasticity_Fertilisation success data

description: Galeolaria caespitosa were collected from Brighton marina, Melbourne, Australia in 2013. Adults were brought back to Monash University for two weeks acclimation prior to fertilisation assays. The workbook contains three sheets: 'Fertilisation success', 'Egg measurements'; 'Sperm measurements'. The descriptions of column headings are available in the ReadMe file.
DOI: 10.5061/dryad.580bh/2
title: Guillaume et al 2015_Transgenerational plasticity_Offspring survival data

description: Galeolaria caespitosa were collected from Brighton marina, Melbourne, Australia in 2013 and 2014. Adults were brought back to Monash University for two weeks acclimation prior to larval survival experiments. The column headings are as follows: 'Run' = assay number; 'Date_start' = Starting date for adult acclimation; 'Days_acclimate' = Number of days adults were left to acclimate in their treatment conditions; 'Paternal_envt' = male treatment acclimation temperature (cold ~16.5 deg C; hot ~22.0 deg C); 'Maternal_envt' = female treatment acclimation temperature (cold ~16.5 deg C; hot ~22.0 deg C); 'Offspring_envt' = Fertilisation and incubation temperature of offspring; 'Replicate' = replicated male*female*offspring treatment temperatures A and B; 'Number_eggs in' = Number of successfully fertilised eggs selected for treatment; 'Number_larvae developed' = Number of larvae that developed from the selected eggs; 'Percent_survival' = Percent of larvae that developed from the selected eggs.
DOI: 10.5061/dryad.580bh/3
title: Guillaume et al 2015_Transgenerational plasticity_Offspring survival switched male data

description: Galeolaria caespitosa were collected from Brighton marina, Melbourne, Australia in 2014. Adults were brought back to Monash University for a total of four weeks acclimation prior to larval survival experiments. At two weeks into the acclimation period, half of the males changed acclimation treatment temperatures. The column headings are as follows: 'Run' = assay number; 'Date_start' = Starting date for adult acclimation; 'Paternal_envt1' = the male temperature treatment experienced for the first two weeks of acclimation (cold ~16.5 deg C; hot ~22.0 deg C); 'Paternal_envt2' = the male temperature treatment experienced for the final two weeks of acclimation (cold ~16.5 deg C; hot ~22.0 deg C); 'Maternal_envt' = female treatment acclimation temperature (cold ~16.5 deg C; hot ~22.0 deg C); 'Offspring_envt' = Fertilisation and incubation temperature of offspring; 'Replicate' = replicated male*female*offspring treatment temperatures A and B; 'Number_eggs in' = Number of successfully fertilised eggs selected for treatment; 'Number_larvae developed' = Number of larvae that developed from the selected eggs; 'Percent_survival' = Percent of larvae that developed from the selected eggs.
DOI: 10.5061/dryad.64482/1
title: Tetraploid Genotype dataset - Salix Cinerea

description: Example SSR allele (genotype) data from seven loci in a tetraploid, dioecious species, Salix cinerea.  From: Hopley, T (2011) Reproductive ecology and dispersal dynamics of the invasive willow, Salix cinerea, in south-eastern Australia. Ph.D. Thesis, The Australian National University, Canberra.
DOI: 10.5061/dryad.64482/2
title: Hexaploid Allelic Phenotype dataset - Eremophila glabra ssp. glabra

description: Example SSR (allelic phenotype) data from seven loci in a hexaploid, monoecious species, Eremophila glabra ssp. glabra.  From: Elliott, CP (2010) Patterns and processes: ecological and genetic function of fragmented Emu bush (Eremophila glabra ssp. glabra) populations. Ph.D. Thesis, The Australian National University, Canberra.  Formatted for use with PolyPatEx package.
DOI: 10.5061/dryad.64482/3
title: R script - PolyPatEx usage example.

description: An R script to perform the example of use of PolyPatEx in the published manuscript.  Operates on the Eremophila (allelic phenotype) dataset to obtain IDs and counts of potential fathers that remain after exclusion.
DOI: 10.5061/dryad.64482/4
title: PolyPatEx performance simulation R scripts

description: R scripts to perform the simulations assessing PolyPatEx performance in the published PolyPatEx manuscript.  Unzips to create a folder, "Simulation_scripts" with content.
DOI: 10.5061/dryad.64482/5
title: Eremophila allelic phenotype dataset in COLONY-required format

description: The Eremophila glabra spp. glabra allelic phenotype dataset recoded for use with COLONY (Jones OR, Wang J (2002) COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10(3), 551–555.).  Unzips to create a folder, 'COLONY_data_files', with content.
DOI: 10.5061/dryad.6p76c3pb.2
title: Data from: Using supermatrices for phylogenetic inquiry: an example using the sedges
DOI: 10.5061/dryad.6p76c3pb.2/1.2
title: phase1_at_nf.phy

description: Nucleotide data for Cyperaceae species from various markers, collected from GenBank using the software tool "phlawd". This alignment corresponds to the fully unfiltered alignment--labeled AT/NF in our manuscript.
DOI: 10.5061/dryad.6p76c3pb.2/2.2
title: phase2_at_rf.phy

description: Nucleotide data for Cyperaceae species from various markers, collected from GenBank using the software tool "phlawd". This alignment corresponds to the unscaffolded, rogues-filtered alignment--labeled AT/RF in our manuscript.
DOI: 10.5061/dryad.6p76c3pb.2/3.2
title: phase3_sc_nf.phy

description: Nucleotide data for Cyperaceae species from various markers, collected from GenBank using the software tool "phlawd". This alignment corresponds to the scaffolded alignment with rogues unfiltered--labeled SC/NF in our manuscript.
DOI: 10.5061/dryad.6p76c3pb.2/4.2
title: phase4_sc_rf.phy

description: Nucleotide data for Cyperaceae species from various markers, collected from GenBank using the software tool "phlawd". This alignment corresponds to the maximally filtered alignment: scaffolded and having had rogues removed--labeled SC/RF in our manuscript.
DOI: 10.5061/dryad.6p76c3pb.2/5.2
title: cyp_states

description: Latitudinal range data for all currently recognized species of Cyperaceae from Govaerts et al. (2007), World Checklist of Cyperaceae. Range data are encoded as tropical (state 1) or extratropical (state 0), and represent the position of the latitudinal midpoint of each species range, as estimated based on the geographic distribution data encoded within the World Checklist of Cyperaceae referenced above.
DOI: 10.5061/dryad.6p76c3pb.2/6.2
title: Appendix_I

description: Formulas for summary statistics used in the creation of Figure 1 from the text.
DOI: 10.5061/dryad.6p76c3pb.2/7.2
title: Appendix_II

description: ML bootstrap majority rule consensus tree topologies from 300-replicate RAxML bootstrap searches using alignments 1-3 described in the text. Branch labels are bootstrap proportions.
DOI: 10.5061/dryad.cj375/3
title: Brapa_petal_hplc

description: Concentrations of sinapoyl glucose and isorhamnetin in UV-absorbing or UV-reflecting petal blade regions from replicates of two Brassica rapa genotypes (R500 and IMB211) raised in the AES-fields at the University of Wyoming.
DOI: 10.5061/dryad.cj375/4
title: Brapa_insect_visitation_UV_exp

description: Insect visitation in 20 experimental arrays each composed of three replicate plants of the Brassica rapa genotype R500.  Within each block plants were randomly assigned to one of three treatments:  control=not manipulated; duck fat=petals painted with duck fat, allowing UV patterns to be visible (i.e., internal control); sunscreen=sunscreen compounds disolved in duck fat and applied to petals, which experimentally alters UV patterned flowers to resemble dark UV-absorbing phentoypes found in Brassica rapa weedy populations.  In each array insect visitation was recorded for a 30-minute interval between 1000-1200 MST.
DOI: 10.5061/dryad.cj375/5
title: Brapa_BLUPs_for_qtlcart

description: A QTL cartographer input file of floral size and shape traits estimated as genotypic BLUPs for recombinant inbred lines resulting from crosses between Brassica rapa genotypes, R500 and IMB211.  The genetic linkage map consists of 1273 SNPs (naming scheme: chromosome_physical.location in B. rapa genome v1.1) across 10 chromosomes, which were identified from RNA-seq reads of expanding apical meristem tissue that was collected from RILs raised in the UW-AES agricultural fields during the summer of 2011.  SNP markers were assigned to linkage groups (LG; R/QTL; Broman et al., 2003) based on recombination fractions (maximum rf= 0.32) and LOD scores (minimum LOD= 4.1).  We used R/QTL to order markers within LGs, passing the resulting best-supported positions of markers to a ripple function to explore alternative arrangements in a 5-marker sliding window.  The resulting linkage map of ten chromosomes has an average distance of 0.79 cM between adjacent markers.
DOI: 10.5061/dryad.g6f47/1
title: Balcova - raw data

description: The file structure is the same for all of .csv files.Each column represents one individiual mouse of the genotype stated in the header. Each cell of the column represents MLH1 or RAD51/DMC1 (according to the file name) count of analyzed cell of the given mouse. Strain abbreviation: D# is B6.PWD-Chr#; D7F1 is B6.PWD-Chr7 x B6 F1The data were analyzed in R 3.2.2 and using its packages as is declared in Materials and Methods of the published paper.
DOI: 10.5061/dryad.h13jv/1
title: Stacks catalog and variant files

description: All catalog and variant files produced by STACKS that formed the basis of the population genomic analyses. Note that additional individuals and populations were used to create the catalog, but were not used for this project.
DOI: 10.5061/dryad.h13jv/2
title: Variant Call Format (VCF) file

description: Data file containing the final (filtered) variants for all individuals that were used to build the site frequency spectrum and the population cluster analyses. Only one SNP per RAD-tag locus was included in this file.
DOI: 10.5061/dryad.h13jv/3
title: BayeScan results

description: Full BayeScan output and data file.
DOI: 10.5061/dryad.h13jv/4
title: Magadi morphometrics input files

description: Input data file containing the two dimensional coordinates of the twelve landmarks used in the morphometric analysis
DOI: 10.5061/dryad.h13jv/5
title: Stable_isotope_data

description: Stable isotope data file containing all relevant quantities.
DOI: 10.5061/dryad.k5b70/1
title: Ant behaviour and chemical ananlysis data

description: This file contains the behaviour data, including how ants direct different number of antennation behaviour towards different body parts of its opponents; the antennation behaviour and length of display behaviour when the ant's antennae have been amputated or washed with hexane.This file also contains chemical analysis data from GC-FID, how the cuticular hydrocarbon signals on different body parts are different, and data of antennae, legs, and abdomen collected from single ants.
DOI: 10.5061/dryad.k78f6/5
title: qPCR data for photorepair gene

description: Raw Ct (cycle threshold) values from quantitative PCR, used to calculate relative expression values for photorepair gene shown in Fig. 3. Loci abbreviations are as follows: phr = photorepair, EF1A = elongation factor 1-alpha (reference gene), ATUB = alpha-tubulin (reference gene), G3PD = glyceraldegyde-3-phosphate dehydrogenase (reference gene)
DOI: 10.5061/dryad.kb508/1
title: Alignment of the sequences and tree files upload to Dryad_WH_2015_8_7
DOI: 10.5061/dryad.r0j3s/1
title: bighornc5_counts_PatzkowskyandHolland_2016_Paleobiology

description: This file contains the collection counts for the Ordovician Horseshoe Mountain Member in the Bighorn Mountains, Wyoming.
DOI: 10.5061/dryad.r0j3s/2
title: bighornc5_factors_PatzkowskyandHolland_2016_Paleobiology

description: This file contains the sample attributes for the Horseshoe Mountain Member collection counts.
DOI: 10.5061/dryad.r0j3s/3
title: C5CincyCounts_PatzkowskyandHolland_2016_Paleobiology

description: This file contains the collection count data for the C5 sequence in the Cincinnatian type area.
DOI: 10.5061/dryad.r0j3s/4
title: sharedtaxa_ecol_param_PatzkowskyandHolland_2016_Paleobiology

description: This file contains the ecological parameters shared between the Horseshoe Mountain Member in the Bighorn Mountains, WY and the C5 sequence in the Cincinnatian type area.
DOI: 10.5061/dryad.rh97t/22
title: B160713

description: Data archive
DOI: 10.5061/dryad.rh97t/23
title: B190913

description: Data archive
DOI: 10.5061/dryad.rh97t/24
title: B230913

description: Data archive
DOI: 10.5061/dryad.rh97t/25
title: B250613

description: Data archive
DOI: 10.5061/dryad.rh97t/26
title: B311014

description: Data archive
DOI: 10.5061/dryad.rh97t/27
title: C071014

description: Data archive
DOI: 10.5061/dryad.rh97t/28
title: C160713

description: Data archive
DOI: 10.5061/dryad.rh97t/29
title: C250613

description: Data archive
DOI: 10.5061/dryad.rh97t/30
title: D180413

description: Data archive
DOI: 10.5061/dryad.sb560/1
title: Supplementary figure 1

description: Multiple alignment of ITS region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB)
DOI: 10.5061/dryad.sb560/2
title: Supplementary figure 2a

description: Multiple alignment of atpB region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB).
DOI: 10.5061/dryad.sb560/3
title: Supplementary figure 2b

description: Multiple alignment of rps16 region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB).