cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m35k6/63
title: ModelSel_GCKI_2012_Occupancy

description: AIC model selection table and associated coefficients for golden-crowned kinglet 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/64
title: ModelSel_GCKI_2013_Occupancy

description: AIC model selection table and associated coefficients for golden-crowned kinglet 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/65
title: ModelSel_HAFL_2012_Occupancy

description: AIC model selection table and associated coefficients for Hammond’s flycatcher 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/66
title: ModelSel_HAFL_2013_Occupancy

description: AIC model selection table and associated coefficients for Hammond’s flycatcher 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/67
title: ModelSel_HETH_2012_Occupancy

description: AIC model selection table and associated coefficients for hermit thrush 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/68
title: ModelSel_HETH_2013_Occupancy

description: AIC model selection table and associated coefficients for hermit thrush 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/69
title: ModelSel_HEWA_2012_Occupancy

description: AIC model selection table and associated coefficients for hermit warbler 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.mf42f/30
title: Database
DOI: 10.5061/dryad.mf42f/31
title: Examples_SQL_Queries
DOI: 10.5061/dryad.mf42f/32
title: Literature_Search
DOI: 10.5061/dryad.mf42f/33
title: Article
DOI: 10.5061/dryad.mf42f/34
title: Site
DOI: 10.5061/dryad.mf42f/35
title: Crop_Sequence_Trt
DOI: 10.5061/dryad.mf42f/36
title: Crop
DOI: 10.5061/dryad.mf42f/37
title: Tillage
DOI: 10.5061/dryad.mg0jb/1
title: SNP list of threespine stickleback

description: We selected SNPs that met the following three criteria: (1) 50-bp flanking regions on both sides of the SNP were conserved between anadromous and stream resident populations, (2) the Illumina designability rank score was one, (3) the SNP was located within coding regions if available. We chose 278 SNPs that were evenly distributed across the reference genome sequence (average distance of 1.56 Mb). Ten SNPs were chosen from the regions within or near five genes that are known to be or potentially important for freshwater adaptation.
DOI: 10.5061/dryad.mg0jb/2
title: QTL input data

description: The data sheet includes SNP information (A=anadromous, B=stream resident, H=heterozygote) with sex, body weight and plasma Na+ values.
DOI: 10.5061/dryad.mg0jb/3
title: 95%BI2

description: A list of genes located within the 95% bayesian credible intervals (95%BI) of QTL peak positions.
DOI: 10.5061/dryad.pp6k4/1
title: Sample sites, phylogenetic methods, parasite descriptions and PCR methods

description: This supplementary file contains methods and results relating to laboratory procedures and the identification and description of avian malaria parasites
DOI: 10.5061/dryad.pp6k4/2
title: R Code for statistical analyses

description: This datafile contains an R script and can be used along with the supplied raw data to replicate all of the bayesian and logistic regressions used in the manuscript.
DOI: 10.5061/dryad.pp6k4/3
title: Raw Data used for analyses

description: This datafile is a csv file of individual birds and their infection statuses with each of the focal parasites. Also included are the data used as covariates in analyses (birds' species identity, sample site, island and habitat type).
DOI: 10.5061/dryad.q03n7/1
title: Raw data package from: Subfunctionalization of Peroxisome Proliferator Response Elements Accounts for Retention of Duplicated fabp1 Genes in Zebrafish

description: Raw data package contains the following: 1) File folder titled "ClustalOmega fabp1", this file folder contains: a) PHYLIP text files (fabp1_Aminoacids_Clustal_PHYLIP.rtf, 	fabp1_mRNA_Clustal_PHYLIP.rtf, fabp1_Promoter_Clustal_PHYLIP.rtf) containing raw 	data for the multiple-sequence alignments and their associated draw tree files, and b) a multi-fasta file containing the amino acid, mRNA, and promoter sequence files for 	Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2 and Lepisosteus oculatus 	(spotted gar) fabp1 genes. 2) A GraphPad Prism 6.0 file containing the curve fitting and analyses of data presented in the associated manuscript (Laprairie et al 2016 BMC Evol Biol Analyses.pzfx). 3) A Microsoft Excel files containing the raw data values for all data presented in the associated manuscript (Laprairie et al 2016 BMC Evol Biol Raw Data.xlsx). 4) The text output file for found peroxisome proliferator-activated receptor response elements (PPREs) in the isolated Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2 and Lepisosteus oculatus (spotted gar) fabp1 promoters described in the associated manuscript. 5) The multi-fasta file containing the sequenced pGL3 promoter constructs for Danio rerio (zebrafish) fabp1a, fabp1b.1, and fabp1b.2; fabp1a 5'flanking region mutant, fabp1a direct repeat 1 region mutant, fabp1b.1 5'flanking region mutant, fabp1b.1 direct repeat 1 region mutant; Lepisosteus oculatus (spotted gar) fabp1; fabp1 PPRE-1 mutant, fabp1 PPRE-2 mutant promoters sequences from the positive strand (RVprim3 primer) and negative strand (GLprim2 primer) of the pGL3 plasmid (Laprairie et al 2016 BMC Evol Biol Plasmid Sequencing.rtf).
DOI: 10.5061/dryad.qb36g/1
title: Supplements 1-12

description: Supplemental DataSupplement 1. Reference sequences derived from vouchers collected for this study.Supplement 2. Reference sequences derived from external NCBI GenBank accessions.Supplement 3. GenBank accession numbers of the Salep tubers.Supplement 4. RAxML maximum likelihood phylogenetic tree for nrITS.Supplement 5. RAxML maximum likelihood phylogenetic tree for trnL-F spacer.Supplement 6. RAxML maximum likelihood phylogenetic tree for matK.Supplement 7. RAxML maximum likelihood phylogenetic tree for the concatenated matrix.Supplement 8. MrBayes bayesian phylogenetic tree for nrITS.Supplement 9. MrBayes bayesian phylogenetic tree for trnL-F spacer.Supplement 10. MrBayes bayesian phylogenetic tree for matK.Supplement 11. MrBayes bayesian phylogenetic tree for the concatenated matrix.Supplement 12. Molecular identifications of tubers based on similarity- and tree-based approaches.
DOI: 10.5061/dryad.qb36g/2
title: Sequence alignment files

description: Alignment matrices in FASTA format per individual marker and concatenated matrix for RAxML and MrBayes phylogenetic analyses. Matrices are labelled with the corresponding tree supplement name and number.
DOI: 10.5061/dryad.tj7k5/1
title: Genotyping of mothers and offspring

description: This table represents the genotypes of mothers and offspring used in the publication.
DOI: 10.17632/53xmnmd45n.1
title: Acoustical properties of plywood/waste tire rubber composite panels

description: This paper presents the acoustical performance of plywood/waste tire rubber (PWTR) composite panels. Beech (Fagus orientalis) and alder (Alnus glutinosa) veneers having 1.8 mm thickness were used in the preparation of panels. The wood layers were bonded using commercial urea–formaldehyde (UF) resin, and methylene diphenyl diisocyanate (MDI) was used to form the rubber layers and bond them to the wood veneers. The four variable parameters considered were WTR contents (430 and 720 g), resin contents (120 and 160 g/m2), hot pressing (one- and two-stage), and arrangements of veneer layers. Free vibration based on a free-free bar method was used to evaluate the specific modulus of elasticity, damping factor, acoustic coefficient, and acoustic converting efficiency of the experimental panels. The test results indicated that the sound insulation property of PWTR was highly dependent on the variable parameters. We found that the damping factor and acoustical coefficient of PWTR are significantly affected by the amount of WTR and UF resin content used in the composite. An increase in the usage of WTR and the dosage of UF adhesive considerably improved the soundproof property of the PWTR. An increase in the WTR content in plywood improved the composite’s damping factor. Finally, the results demonstrated that the PWTR composite has potential as an interior building material to absorb sound but requires full-scale testing on site. This approach offers an environmental friendly solution to the ongoing problem of WTR.
DOI: 10.17632/p2z6rtcf8j.2
title: Patchiness of forest landscape can predict species distribution better than abundance: the case of a forest-dwelling passerine, the short-toed treecreeper, in central Italy.

description: The two datasets have been used to perform the analysis in the paper 'Patchiness of forest landscape can predict species distribution better than abundance: the case of a forest-dwelling passerine, the short-toed treecreeper, in central Italy.' published by PeerJ journal.
DOI: 10.5061/dryad.1n1kc/1
title: Telomere and telomere expression data used in the manuscript

description: (1) Cross sectional and (2) longitudinal data on frillneck lizards telomere length in relation to sex, age, survival and temporal change in telomere length.  (3) Telomere length (TL)  in relation to telomerase expression (TE).
DOI: 10.5061/dryad.3jm7h/1
title: Expt1PastFull

description: Full data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include host offspring counts, day of death, spores per host, host species and host genotype
DOI: 10.5061/dryad.3jm7h/2
title: Expt1MetschFull

description: Full data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Metschnikowia bicuspidata. Variables include host offspring counts, day of death, spores per host, host species and host genotype
DOI: 10.5061/dryad.3jm7h/3
title: Expt1PastBST

description: Transmission data for Exp1. Hosts: Daphnia dentifera, Ceriodaphnia dubia. Parasite: Pasteuria ramosa. Variables include transmission rate (Beta), parasite growth rate (sigdeath), host species and host clone.
DOI: 10.5061/dryad.48m7c/1
title: Additional-data

description: Raw data relative to analyses in Antunes et al. 2016.
DOI: 10.5061/dryad.70j22/1
title: Data on bee colony dynamics and health used in this study "Requier et al. (2016) Pollen shortage negatively impacts bee colony survival. Journal of Applied Ecology"

description: The data available came from part of ECOBEE, a long term ecological research program set up to monitor honeybee colonies in a context of real professional beekeeping practices in the Poitou-Charentes region in central western France (46°23’N, 0°41’W). Over five consecutive years, from 2008 to 2012, the colony dynamics were monitored by measuring three core colony traits: the amount of brood in the colony (termed brood size), adult population and honey reserves, bimonthly throughout the monitoring period. This dataset also include the Varroa mite load (assessing using a sticky board placed at the bottom of the hive brood chamber, and the seasonal and witner colony survival (the criteria for the seasonal survival and the overwintering survival of the colony were whether the colony remained operational for beekeeping activity during the season or after winter arousal, respectively). All the colonies came from an A. mellifera mellifera × caucasica strain and were managed in accordance with local professional beekeeping practices, without migration, with honey collections, systematic supplemental feeding with syrup when necessary, and systematic treatment against Varroa mites. (see Odoux et al. 2014 for more details). Complete details may be found in "Requier et al. (2016) The carry-over effects of pollen shortage decrease the survival of honeybee colonies in farmlands. Journal of Applied Ecology.
DOI: 10.5061/dryad.82pm0/1
title: StartingPopulation
DOI: 10.5061/dryad.82pm0/2
title: ImmigrantPopulation
DOI: 10.5061/dryad.d875g/5
title: Sapelo natural patch expansion

description: Data on the rate of expansion of 79 patches remaining wishing Sapelo Island marsh die offs after 6, 12 and 19 months.
DOI: 10.5061/dryad.d875g/6
title: Soil water storage

description: Data on the grams of water stored per gram of soil from cores collected from inside and outside mussel mounds in a Sapelo Island, GA marsh
DOI: 10.5061/dryad.f2j00/1
title: ContigsMacra3

description: Taraxacum officinale microspecies Macranthoides accession 3 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.
DOI: 10.5061/dryad.f2j00/2
title: ContigsMacra8

description: Taraxacum officinale microspecies Macranthoides accession 8 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.
DOI: 10.5061/dryad.f2j00/3
title: ContigsMacra11

description: Taraxacum officinale microspecies Macranthoides accession 11 genomic sequences of repetitive DNA assembled following the procedure by Novak et al. 2010.
DOI: 10.5061/dryad.h32p6/1
title: Zerebeckietal_1-5

description: Zerebeckietal_1-5.zip contains 5 consecutively numbered csv files which contain the data presented in the manuscript and appendices.
DOI: 10.5061/dryad.hm55b/1
title: Supplementary information

description: Figures S1-S15 // Tables S1-S2
DOI: 10.5061/dryad.hm55b/2
title: Data and results 1

description: Part 1. tar.gz compressed folder containing: initial tree data for running R pipeline (data/) and a results folder for every analysis run (results/). References for phylogenetic trees can be found in metadata.csv. For more details, see: https://github.com/DomBennett/Project-EDBMM
DOI: 10.5061/dryad.m35k6/70
title: ModelSel_HEWA_2013_Occupancy

description: AIC model selection table and associated coefficients for hermit warbler 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/71
title: ModelSel_ORJU_2012_Occupancy

description: AIC model selection table and associated coefficients for dark-eyed (Oregon) junco 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/72
title: ModelSel_ORJU_2013_Occupancy

description: AIC model selection table and associated coefficients for dark-eyed (Oregon) junco 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/73
title: ModelSel_PAWR_2012_Occupancy

description: AIC model selection table and associated coefficients for Pacific wren 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/74
title: ModelSel_PAWR_2013_Occupancy

description: AIC model selection table and associated coefficients for Pacific wren 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/75
title: ModelSel_PSFL_2012_Occupancy

description: AIC model selection table and associated coefficients for Pacific-slope flycatcher 2012 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/76
title: ModelSel_PSFL_2013_Occupancy

description: AIC model selection table and associated coefficients for Pacific-slope flycatcher 2013 for all initial occupancy models. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.