cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p311/1
title: Mammalian Predator-Prey Body-Mass Data

description: This data file includes data on predator body mass for 107 carnivorous mammals. Associated information on prey body mass and daily energetic expenditure are also included. All data have been extracted from the literature and the data sources have been included. All body mass and energetic data have been log10 transformed. Mass data is measured in kilograms. Energetic information is in kJ day-1. Each species has been classified by habitat type; marine or terrestrial.
DOI: 10.5061/dryad.b85pj/1
title: MtDNA concatenated dataset with outgroup

description: Fasta file generated with CLUSTALX v.2 of 79 concatenated mtDNA (CR1 and ND2) shag sequences and 2 outgroup sequences, used in phylogenetic analyses.
DOI: 10.5061/dryad.b85pj/2
title: Molecular clock analysis of the shag

description: Input file generated with BEAST v.1.8 used for the molecular clock analysis, under a relaxed clock of uncorrelated lognormal  distribution model and a “Coalescent: Constant Size” prior on rates of cladogenesis.
DOI: 10.5061/dryad.b85pj/3
title: Population structure analysis using microsatellite data

description: Input files (including microsatellite raw data, estimation parameters and population labels) used in the STRUCTURE v.2.3.4 program to estimate the genetic structure of 28 shag populations.
DOI: 10.5061/dryad.cd546/100
title: Online Appendix 5

description: Species-genotype association file in ASTRAL-II format, also used for SVDquartets and MP-EST.
DOI: 10.5061/dryad.cd546/101
title: Online Appendix 6

description: ASTRAL-II analysis performed with individual sequences treated as species to assess potential issues with uncertain species limits. Note that these results strongly resemble the concatenation topology and are highly congruent with the ASTRAL-II topology assigning multiple sequences to putative species.
DOI: 10.5061/dryad.cd546/94
title: ASTRAL optimal gene trees (in one file) and boostraps (separate files in subdirectory)
DOI: 10.5061/dryad.cd546/95
title: BUCKy gene MCMC distributions, with individual gene alignments
DOI: 10.5061/dryad.cd546/96
title: Online Appendix 1

description: Table of voucher information, collection localities, SRA accession numbers, and coverage values for nuclear, plastid, and mitochondrial contigs, as well as individual low-copy nuclear genes. A translate table for phylogenetic files in the online appendices is also provided.
DOI: 10.5061/dryad.cd546/97
title: Online Appendix 2

description: Sanger phylogeny of three plastid regions (trnL-F, rpl32-trnL, and rps16-trnK), included in order to increase outgroup sampling (n =15; added samples summarized in Methods). Bootstrap proportions are plotted on all branches of non-zero length; branch coloration follows Fig. 1.
DOI: 10.5061/dryad.cd546/98
title: Online Appendix 3

description: All 277 analyzed gene trees as inferred in RAxML. The loci are labeled and arranged by descending order of locus length. All clade bootstraps ≥ 50 are plotted on branches.
DOI: 10.5061/dryad.cd546/99
title: Online Appendix 4

description: All 277 analyzed Bayesian MCM distributions from MrBayes, summarized as 50% majority consensus trees. The loci are labeled and arranged by decreasing length. All clade posterior probabilities ≥ 50 are plotted on branches.
DOI: 10.5061/dryad.fb240/4
title: source data 4

description: CFS Interaction matrices for Load condition, pos. Tail
DOI: 10.5061/dryad.fb240/5
title: source data 5

description: Alpha-beta CFS Interaction matrices, pos. Tail
DOI: 10.5061/dryad.fb240/6
title: source data 6

description: CFS Interaction matrices for Mean condition, neg. Tail
DOI: 10.5061/dryad.fb240/7
title: source data 7

description: Effect Size/Correlation Coefficients and p-values for PAC patch-patch interactions
DOI: 10.5061/dryad.fb240/8
title: source data 2

description: Effect sizes and p-values for group statistics of recomputed cross-frequency amplitude-amplitude correlations.
DOI: 10.5061/dryad.fb240/9
title: source data 3

description: CFS Interaction matrices for Mean condition, pos. Tail
DOI: 10.5061/dryad.fp0nh/1
title: High resolution map of estimated human footprint levels across Antarctica

description: Raster file (tif.) of 30 arcsecond resolution (1x1 km in the equator) with the human footprint levels across Antarctica simulated electronically. Detailed information on the modelling process can be found in Pertierra LR, Hughes KA, Vega GC and Olalla-Tarraga MA (2016) ‘High resolution spatial mapping of human footprint across Antarctica and its implications for strategic avifauna conservation’ PlosONE.
DOI: 10.5061/dryad.ft928/1
title: Final SNP set.

description: This file contains the final SNP set (after several filtering steps detailed at manuscript) in .vcf and .fasta format. Fasta file contains ~80bp sequences of each RADtag loci. After alignment of each sequences from same loci, SNP of each sample can be accessed.
DOI: 10.5061/dryad.ft928/2
title: Minicontigs associated with RADtag loci.

description: Minicontigs associated with RADseq loci in .fasta format.
DOI: 10.5061/dryad.ft928/3
title: Microsatellites found in minicontigs.

description: This file contains a table of identified microsatellite with contig ID, motif and coordinates of each motif, and a file with parameters used in MiSA for SSR search.
DOI: 10.5061/dryad.ft928/4
title: Repetitive elements identified with RepeatMasker.

description: This file contains a table of the identified repetitive elements (.tbl),  a file with masked contigs and repetitive elements (.fasta format) and a file with contig ID, repetitive element ID and coordinates.
DOI: 10.5061/dryad.ft928/5
title: Blast2GO annotation file.

description: This .gff file contain the final annotation of minicontigs obtained using Blast2GO pipeline.
DOI: 10.5061/dryad.m8jr7/1
title: for_dryad

description: Using ribosome profiling, we identified novel translated ORFs in  annotated ncRNAs and pseudogenes in Arabidopsis thaliana. We searched other 15 plant genomes to examine if the novel protein sequences are conserved. The 19 fasta files contain amino acid sequence alignments of each novel ORF and their homologs. The distance.py file is a python script file for calculation of sequence identity among the homologs.
DOI: 10.5061/dryad.ng3bv/10
title: chalciolepis_distribution_pts

description: File containing the distribution points used for distribution modeling in Maxent. These points come from verified herbarium records and personal collections.
DOI: 10.5061/dryad.ng3bv/11
title: nova_distribution_points

description: File containing the distribution points used for distribution modeling in Maxent. These points come from verified herbarium records and personal collections.
DOI: 10.5061/dryad.ng3bv/8
title: chalciolepis_empirical_summary_stats

description: This is an example of the empirical summary statistics that must be included in the simulation folder. This file was created using arlsumstat program and the empirical dataset (see 'chal_empirical_data'). The file can be viewed and modified in a text editor. See the Arlequin/arlsumstat documentation for more information.
DOI: 10.5061/dryad.ng3bv/9
title: settings_chalciolepis_splatche

description: This is an example of a settings file for a single Splatche run. The Splatche documentation describes all of the options within the file in detail. The file can be viewed and modified in a text editor.
DOI: 10.5061/dryad.qg80q/1
title: Male sand goby egg care and anti-predator defensive behaviour

description: Data on male care (egg fanning, defensive displays and nest opening size) under high and low oxygen, out of and in the presence of egg predators (shore crabs). Also listed are data on fish length, crab carapace length and filial cannibalism.
DOI: 10.5061/dryad.qm1g8.1
title: Data from: Interspecific interactions through 2 million years: are competitive outcomes predictable?
DOI: 10.5061/dryad.qm1g8.2
title: Data from: Interspecific interactions through 2 million years: are competitive outcomes predictable?
DOI: 10.5061/dryad.qm1g8.2/1.2
title: Wanganui_Cheilostome_interactions

description: R workspace containing bryozoan data and R functions required to reproduce analyses presented in the paper.
DOI: 10.5061/dryad.qm1g8.2/2.2
title: Liow code bryozoans

description: R code to reproduce analyses presented in the paper.
DOI: 10.5061/dryad.qm1g8.2/3.2
title: Wanganui_Cheilostome_interactions

description: Plain text file containing bryozoan data.
DOI: 10.5061/dryad.v751b/1
title: Species and Spatio-temporal distribution of animal rabies

description: Data collected in daily registers of institutions dealing with rabies from 2009 to 2013. Data are coded according to the variables corresponding to the column heading as shown for each column when mouse passes.
DOI: 10.5061/dryad.1p004/1
title: Mean Cross Dataset - RI, GD, and ED

description: Dataset contains mean reproductive isolation values, genetic distance values and ecological distance values for each taxon pair cross.
DOI: 10.5061/dryad.21b04/1
title: STATA_Reporting Quality of Randomized Controlled Trial Abstracts Among High-Impact General Medical Journals: A Review and Analysis

description: The following file contains STATA data for the 2015 review and analysis of reporting quality of randomized controlled trial abstracts in five high-impact general medical journals based on adherence to the CONSORT for abstracts guidelines.
DOI: 10.5061/dryad.2973n/3
title: Selection on maturity proxy

description: Number of offspring produced by IV population in competitive monogamy and polygamy trials across ages, for both sexes.
DOI: 10.5061/dryad.319sr/10
title: Additional file 10 Figure S8

description: Additional file 10: Figure S8. Number of populations. A. Plot of Delta K (ΔK).
B. Plot of the log likelihood; internal plot corresponds to the log
likelihood (thousands) for K ranging from 1 to 9. All values were obtained
from STRUCTURE HARVESTER analysis. Fourteen populations were considered in a
data set of 18,565 SNPs (10% missing imputed genotypes) and 150 samples.
DOI: 10.5061/dryad.319sr/11
title: Additional file 11 Figure S9

description: Additional file 11: Figure S9. Number of populations. A. Plot of Delta K (ΔK).
B. Plot of the log likelihood; internal plot corresponds to the log
likelihood (thousands) for K ranging from 1 to 9. All values were obtained
from STRUCTURE HARVESTER analysis. Fourteen populations were considered in a
data set of 43,713 SNPs (30% missing imputed genotypes) and 150 samples.
DOI: 10.5061/dryad.319sr/12
title: Additional file 12 Figure S10

description: Additional file 12: Figure S10. Box plot analyses of the 23 morphological
characters examined for members of Daucus carota complex (subsp. sativus not
included) in this study. The box plot displays individual plant values for
median, 25% and 75% percentile, range, and outliers.
DOI: 10.5061/dryad.319sr/13
title: SNP data set_Daucus_0.1 missing data_Arbizu et al

description: Data set containing 164 accessions with 10%
missing imputed genotypes.
DOI: 10.5061/dryad.319sr/14
title: SNP data set_Daucus_0.3 missing data_Arbizu et al

description: Data set containing 164 accessions with 30%
missing imputed genotypes.
DOI: 10.5061/dryad.319sr/8
title: Additional file 8 Figure S6

description: Additional file 8: Figure S6. Relationships among 144 accessions of Daucus
carota complex and outgroup from an exhaustive quartet sampling inference
using 43,713 SNPs (30% missing imputed genotypes) obtained by GBS. Numbers
above branches represent bootstrap values, with only values higher than 70%
shown. Names given to clades refer to the geographic origin and improvement
status of the accessions of D. carota complex. ME & E refers to Middle East &
Europe. Accessions designated by double stars are misplaced relative to the
maximum likelihood topology of Daucus carota complex using the same number of
SNPs. The outgroup taxon is D. syrticus.
DOI: 10.5061/dryad.319sr/9
title: Additional file 9 Figure S7

description: Additional file 9: Figure S7. Species tree of the Daucus carota complex based
on a coalescent model using an exhaustive quartet sampling inference and
18,565 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers above
the branches represent bootstrap values. The outgroup taxon is D. syrticus.
DOI: 10.5061/dryad.35ks2/1
title: Public B-cell dataset
DOI: 10.5061/dryad.734v9/1
title: Cutter-Gray_PBD_simulation_output

description: This data matrix includes mean species richness values from 50 replicate runs of the R speciation simulation package protractedbirthdeath::summaryrepsim(). Each of the five input parameters were varied at 0.1 increments from 0.1 to 0.9.
DOI: 10.5061/dryad.76r00/1
title: Weekly data in MDA and non-MDA chiefdoms

description: The dataset contains weekly aggragated data in MDA and non-MDA chiefdoms. Main data elements include all-cause outpatients, all-cause admissions, outpatient malaria cases, malaria admissions, microscopically tested cases, microscopically positive cases, RDT tested cases, RDT positive cases, Slide positivity rate (mic), test positivity rate (RDT), non-malaria outpatient cases, non-malaria inpatient cases, proportion of malaria (of all outpatients), proportion of malaria admissions (of all admissions), Ebola alerts. All the above are categorized in two groups: MDA-chiefdoms and non-MDA chiefdoms.
DOI: 10.5061/dryad.780hc/1
title: Aboveground biomass data for B. eriopoda

description: Aboveground biomass (g) for B. eriopoda in every experimental pot where individuals existed at the end of the experiment. See ReadMe file for variable definitions.
DOI: 10.5061/dryad.780hc/2
title: Aboveground biomass data for B. gracilis

description: Aboveground biomass (g) for B. gracilis in every experimental pot where individuals existed at the end of the experiment. See ReadMe file for variable definitions.
DOI: 10.5061/dryad.7f91m/1
title: Body temperature data

description: Hourly body temperatures for all animals at 30LD, 30DD, 25LD, 25DD, 20LD and 20DD.
DOI: 10.5061/dryad.7f91m/2
title: Activity data

description: Per minute locomotor activity data for all animals at 30LD, 30DD, 25LD, 25DD, 20LD and 20DD
DOI: 10.5061/dryad.80th2/1
title: Read pair sequence information for buffalograss primers

description: Paired end sequence data used to design the 15 SSR loci reported in Hadle et al.
DOI: 10.5061/dryad.85s6t/1
title: Sugie_Suzuki_LO_doi_10.1002lno.10473
DOI: 10.5061/dryad.875fb/1
title: Data used in GAMs

description: Data collected during bottom trawl surveys and hydrological surveys in the central Baltic Sea, Excel file.
DOI: 10.5061/dryad.875n5/3
title: A VCF file of all whole-genome sequenced heliothine indviduals, aligned to BACs (not those containing CYP337B1, 2 or 3) available on NCBI

description: BAC descriptions are available in the supplementary document. Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (&gt;95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen), before being quantified with a Qubit 2.0. Nextera libraries were produced following the manufacturer’s instructions and sequence was generated as 100 bp PE reads (Illumina HiSeq 2000, Biological Resources Facility, Australian National University, Canberra, Australia, as well as at Beijing Genomics Institute, Hong Kong). Sample and sequencing data are included in the supplementary material (Table S2). Raw reads were aligned to BAC sequences, originally derived from H. armigera and available on NCBI (accessions in supplementary document), using BBMap. Reads were trimmed when quality in at least 2 bases fell below Q10. Only uniquely aligning reads were included in the analysis, to prevent spuriously inferring evolutionary processes occurring independently on each BAC. Outputted BAM files were sorted before duplicate reads were removed and files were annotated with read groups using Picard v. 1.138 (http://picard.sourceforge.net). BAC reference sequences were indexed using Samtools v. 1.1.0 (Li et al. 2009). UnifiedGenotyper in GATK v. 3.3-0 (McKenna et al. 2010) was used to estimate genotypes across all individuals simultaneously, implementing a heterozygosity value of 0.01. Variant call format files containing SNP calls were reformatted into Plink format using VCFtools v. 0.1.12b (Danecek et al. 2011).
DOI: 10.5061/dryad.875n5/4
title: Supplementary document containing accession codes and eigenstrat analyses of all BACs used as references for whole genome sequencing of heliothine species

description: Supplementary document containing accession codes and eigenstrat analyses of all BACs used as references for whole genome sequencing of heliothine species.
DOI: 10.5061/dryad.875n5/5
title: vcf file of all heliothine individuals that have undergone whole genome sequencing aligned to B3 and B1/B2 BAC

description: Chromosome "1" contains the B3 BAC, Chromsome "B1_B2" contains the B1/B2 BAC. Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (&gt;95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen), before being quantified with a Qubit 2.0. Nextera libraries were produced following the manufacturer’s instructions and sequence was generated as 100 bp PE reads (Illumina HiSeq 2000, Biological Resources Facility, Australian National University, Canberra, Australia, as well as at Beijing Genomics Institute, Hong Kong). Sample and sequencing data are included in the supplementary material (Table S2). Raw reads were aligned to BAC sequences, originally derived from H. armigera and available on NCBI (accessions in supplementary document), using BBMap. Reads were trimmed when quality in at least 2 bases fell below Q10. Only uniquely aligning reads were included in the analysis, to prevent spuriously inferring evolutionary processes occurring independently on each BAC. Outputted BAM files were sorted before duplicate reads were removed and files were annotated with read groups using Picard v. 1.138 (http://picard.sourceforge.net). BAC reference sequences were indexed using Samtools v. 1.1.0 (Li et al. 2009). UnifiedGenotyper in GATK v. 3.3-0 (McKenna et al. 2010) was used to estimate genotypes across all individuals simultaneously, implementing a heterozygosity value of 0.01. Variant call format files containing SNP calls were reformatted into Plink format using VCFtools v. 0.1.12b (Danecek et al. 2011). When linkage disequilibrium (LD)-based pruning was necessary, Plink v. 1.07 (Purcell et al. 2007) was used to filter one of a pair of SNPs using a pairwise LD threshold (r2=0.5) within windows of 50 SNPs, moving forwards 5 SNPs per iteration.
DOI: 10.5061/dryad.8v70v/1
title: Code for Combined Survival

description: Executes the first analysis described in the paper. Compares models with differing annual density dependent parameters.
DOI: 10.5061/dryad.8v70v/2
title: Code for Split Survival

description: Executes the second analysis described in the paper. Compares models with differing seasonal density dependent parameters.
DOI: 10.5061/dryad.8v70v/4
title: BPOP_summary

description: Black duck breeding population estimates used in the analysis.
DOI: 10.5061/dryad.9fc86/10
title: SLC38_MC_T

description: Alignment of 74 sequences of Cabrera vole tissue samples for the autossomal gene SLC38A7, intron 8.
DOI: 10.5061/dryad.9fc86/11
title: SMCY7_MC_T

description: Alignment of 39 sequences of Cabrera vole tissue samples for the sex-linked (Y-chromossome) gene SMCY, intron 7.
DOI: 10.5061/dryad.9fc86/6
title: IRBP_MC_T

description: Alignment of 78 sequences of Cabrera vole tissue samples for the autossomal gene IRBP, exon 1.
DOI: 10.5061/dryad.9fc86/7
title: OSTA5_MC_T

description: Alignment of 74 sequences of Cabrera vole tissue samples for the autossomal gene OSTA, intron 5.
DOI: 10.5061/dryad.9fc86/8
title: PNPO3_MC_T

description: Alignment of 77 sequences of Cabrera vole tissue samples for the autossomal gene PNPO, intron 3.
DOI: 10.5061/dryad.9fc86/9
title: RAG1_MC_T

description: Alignment of 70 sequences of Cabrera vole tissue samples for the autossomal gene RAG1, exon 1.
DOI: 10.5061/dryad.b1rr1/1
title: All admx for BMJ Open_v0.02

description: Dataset for analysis of all emergency department presentations in relation to the above paper, along with a key.
DOI: 10.5061/dryad.c5m0r/1
title: raw-data for Synergistic impacts by an invasive amphipod and an invasive fish explain native gammarid extinction

description: Excel file. Data collected in laboratory experiments. Tab 1: Mortality data [%] (1=size class small, 2=size class big); Tab 2: Predation data [total number]; Tab 3: Swimming behaviour [number of free swimming gammarids] (T1-T5: Replicate tanks).
DOI: 10.5061/dryad.cd546/102
title: Online Appendix 7

description: Table of results for the φ tests for recombination.
DOI: 10.5061/dryad.cd546/103
title: Online Appendix 8

description: NeighborNet split network inferred using the concatenated nuclear data, showing conflict among nuclear loci. The currently recognized sections are indicated by colored circles: orange = sect. Holochloa; blue = sect. Heuchera; green = sect. Bracteatae; pink = sect. Rhodoheuchera.
DOI: 10.5061/dryad.cd546/104
title: Online Appendix 9

description: Comparison of coalescent branch length estimates in BUCKy (with individual sequences treated as species, using all 277 loci, subsampled MCMC, and α = 1) and MP-EST (with multiple sequences assigned to putative species). Only internal branches are shown since infraspecific sampling is required to reliably estimate external branch lengths, causing these to misleadingly take on the maximum possible values when there is only one individual per species. The outgroup branch is not to scale.
DOI: 10.5061/dryad.cd546/105
title: Online Appendix 10

description: Table of thermocycler programs and PCR primers for PCR and Sanger sequencing.
DOI: 10.5061/dryad.cd546/106
title: Online Appendix 11

description: Summary of taxa included in the analysis of Sanger-sequenced loci, including voucher information and GenBank accession numbers.
DOI: 10.5061/dryad.cd546/107
title: Online Appendix 12

description: Gene trees simulated under the coalescent using the MP-EST tree.
DOI: 10.5061/dryad.cd546/108
title: Online Appendix 13

description: Summary of bipartitions in the gene trees of online Appendix 12, plotted on the MP-EST species tree estimate.
DOI: 10.5061/dryad.cd546/109
title: Online Appendix 14

description: Gene trees simulated under the coalescent using the BUCKy tree.
DOI: 10.5061/dryad.cd546/110
title: Online Appendix 15

description: Summary of bipartitions in the gene trees of online Appendix 14 using the plastid tree.
DOI: 10.5061/dryad.cf860/2
title: statistic-update
DOI: 10.5061/dryad.d0gm2/1
title: R codes

description: Zip file containing the R codes needed to run the simulations reported in this manuscript. Please see Main_simulation_starter.R  for details of the simulation setup.
DOI: 10.5061/dryad.d0gm2/2
title: Formatted_output

description: Formatted output files from our simulation run. Variable names follow the convention established in the R codes. Row IDs correspond to the number of individuals sampled.
DOI: 10.5061/dryad.d8p66/10
title: midbrain electrophysiological recordings

description: Electrophysiological data from midbrain neurons
DOI: 10.5061/dryad.d8p66/11
title: single afferent electrophysiological recordings

description: Data from single afferents. Please look at readme file first.