cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6cq0n/5
title: QTLF1measurements

description: Mapping F1 measurements
DOI: 10.5061/dryad.6cq0n/6
title: QTL F2 Measurements

description: Mapping F2 measurements
DOI: 10.5061/dryad.6ff85/1
title: P_conservatio_alignment

description: Alignment of 12S and 16S sequences with ambiguous regions deleted, used to generate tree depicted in Figure 9.
DOI: 10.5061/dryad.73s36/1
title: Host populations
DOI: 10.5061/dryad.73s36/2
title: Parasite spore counts
DOI: 10.5061/dryad.7785h/2
title: aeb2 phylogenies

description: Aeb2 includes members of Bacteria, Archaea, and Eukarya.  Methods of tree inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb2 includes “Archezoan” (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) sequences; the subset “aeb2 Arch+” refers to the presence of Archezoa without Korarchaeota and Thaumarchaeota and the subset, “aeb2 KT+” refers to the presence of Korarchaeota and Thaumarchaeota without Archezoa.  Aeb2 Arch+ and KT+ attempt to mitigate long-branch attraction (LBA) artifacts due to substitution rate saturation and allow us to assess the influence of taxonomic sampling on phylogenetic outcome. Gap removal occurred after the creation of the supermatrix (resulting in 13929 positions for aeb2 Arch+ and 13941 positions for aeb2 KT+).
DOI: 10.5061/dryad.7785h/4
title: aeb1 alignment

description: aeb1 alignment in fasta format
DOI: 10.5061/dryad.7785h/6
title: aeb2 KT+ alignment
DOI: 10.5061/dryad.7785h/7
title: aeb3 alignment

description: Aeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.
DOI: 10.5061/dryad.7k5p1/1
title: Incidence of larval egg cannibalism in Formica ants

description: Incidence of larval egg cannibalism, nestmate relatedness, larvae size and larvae sex ratios in eight species of Formica ant
DOI: 10.5061/dryad.7m6kg/67
title: Fig. 11b: HK-MF-00001 (anterior) — Nectocaris ?pteryx, large morph from Chengjiang

description: Showing striated funnel infill, pervasive bioturbation in axial cavity, and projections from head
DOI: 10.5061/dryad.7m6kg/68
title: Fig. 11b: HK-MF-00001 (fin) — Nectocaris ?pteryx, large morph from Chengjiang

description: Showing relief associated with fin striations, and bars with ?shrinkage-related wrinkling
DOI: 10.5061/dryad.8q6n4/20
title: Blount et al Nat 2012 sup fig 5 set 2 transformed
DOI: 10.5061/dryad.8q6n4/21
title: Blount et al Nat 2012 sup fig 5 set 3 raw
DOI: 10.5061/dryad.8q6n4/22
title: Blount et al Nat 2012 sup fig 5 set 3 transformed
DOI: 10.5061/dryad.8q6n4/24
title: Blount et al Nat 2012 fig 7
DOI: 10.5061/dryad.9v852/7
title: SPP_Molec_Ecol_raw_allozyme_data

description: Raw allozyme data
DOI: 10.5061/dryad.b1q2n/4
title: figure1_r_script.r

description: File: figure1_r_script.rFormat: r source fileContents: reads in all growth data, calculates doubling times, calculates statistics, plots figure 1 to pdfNote: requires package nlstools
DOI: 10.5061/dryad.b1q2n/5
title: intrinsic_costs.zip

description: Files: intrinsic_costs.zip (contains files well.XXX (XXX are numbers from 001 to 096))Format: ZIP archive (contents are flow cytometry data files FCS 2.0)Contents: Flow cytometry analyses of bacterial cultures. Samples were excited at a wavelength of 488 nm, while emission was detected at 510 nm (GFP) and 560 nm (DsRed).
DOI: 10.5061/dryad.b1q2n/6
title: 120524_exp390.csv

description: File: 120524_exp390.csvFormat: text (comma separated values)Contents: Data obtained from the analysis of all flow cytometry data files in intrinsic_costs.zip using WEASEL 3.0.1. Files also contains information about the identity of every sample.
DOI: 10.5061/dryad.b1q2n/7
title: intrinsic_costs_r_script.r

description: File: intrinsic_costs_r_script.rFormat: r source fileContents: reads in all flow cytometry data and calculates statistics
DOI: 10.5061/dryad.b1q2n/8
title: 120524_1.pda

description: File: 120524_1.pda
Format: SoftMax Pro 5.42.1.0 (Molecular Devices, Sunnyvale, CA)
Contents: Measurements of optical density of bacterial cultures. Cultures in rows A, C, E, and G contain treatments without phage T4rII, cultures in rows B, D, F, and H contain treatments with phage T4rII. E. coli lambda was labelled with pDsRed in columns 1, 3, 5, 7, 9, and 11. E. coli lambda was labelled with pGFP in columns 2, 4, 6, 8, 10, and 12. The initial frequency of E. coli lambda was 99.9% in cultures in columns 1 and 2, 99% in cultures in columns 3 and 4, 95% in cultures in columns 5 and 6, 90% in cultures in columns 7 and 8, 50% in cultures in columns 9 and 10, and 10% in cultures in columns 11 and 12.
DOI: 10.5061/dryad.b1q2n/9
title: 120524_1.txt

description: File: 120524_1.txtFormat: textContents Measurements of optical density of bacterial culturesNote: Same data as in file 120524_1.pda
DOI: 10.5061/dryad.b5d6b/2
title: AriasCetal2014CO1alignment
DOI: 10.5061/dryad.b5d6b/3
title: CO1 Beast Tree File

description: mtDNA-CO1 Trees File: a subset of 1001trees from Beast analysis
DOI: 10.5061/dryad.b5d6b/4
title: AFLP structure input file

description: AFLP input file for STRUCTURE analysis
DOI: 10.5061/dryad.b5d6b/5
title: Arlequin AFLP input file

description: AFLP data: Input file for Arlequin analysis
DOI: 10.5061/dryad.b5d6b/6
title: mtDNA-CO1 Arlequin Input File

description: mtDNA-CO1 input file for Arlequin Analysis
DOI: 10.5061/dryad.b6h36/1
title: Data underlying comparisons within and among recently divergent junco populations in a novel environment: testosterone (seasonal & peak), parental care, aggression, extrapair behavior, plumage ornaments, breeding phenology

description: Excel file with mutiple worksheets, each titled to indicate contents.
DOI: 10.5061/dryad.cq376/1
title: Supplementary table 1

description: List of all taxa included in the diveristy curves, and their affinities, ranges and the countries in which they are found
DOI: 10.5061/dryad.cq376/2
title: Supplementary table 2

description: List of phylogenetic hypotheses included in the creation of the supertree, and reasons for removal of thise hypotheses not included
DOI: 10.5061/dryad.cq376/3
title: Supplementary figure 1

description: Supertree used in the creation of the Phylogenetic diversity curve. Black lineages – known ranges, Gray lineages – temporal uncertainty in the dating of localities (included in the phylogenetic diversity estimate), Red lineages – ghost lineages. Timescale representing millions of years ago appears at the bottom
DOI: 10.5061/dryad.cv86385c/5
title: eEcology_data_readme
DOI: 10.5061/dryad.fj168/1
title: Thermal games between prey and predator

description: Dataset is divided into six sheets:1. Newt+dragonfly_lab – data from laboratory experiment 2. Newt_seminatural – prey data from seminatural experiment3. Newt_seminatural_predation – prey predation data from seminatural experiments4. Dragonfly_seminatural - predator data from seminatural experiment5. Dragonfly_seminatural_2012 - predator data from seminatural experiment in 20126. Dragonfly_lab_2012 - predator data from seminatural experiment in 2012See sheet 1 for column explanations.
DOI: 10.5061/dryad.g216n/6
title: Climatic data used in species distribution modelling

description: The input layers used to make the Maxent model
DOI: 10.5061/dryad.g9s2k/3
title: Prunus_lusitanica-flow cytometry

description: 2C values obtained through FCM for a subset of individuals representing P. lusitanica subspecies
DOI: 10.5061/dryad.gf18v/1
title: Russian River 2007-2011 SNPPITinput
DOI: 10.5061/dryad.h9j67/1
title: Ksepka et al. Podicipediformes Matrix

description: Nexus file containing phylogenetic matrix.
DOI: 10.5061/dryad.hs37s/1
title: MYLU microsatellite data

description: Microsatellite loci data as coded as an input file for GENEPOP
DOI: 10.5061/dryad.k2q52/1
title: Annavi et al datafile JEB
DOI: 10.5061/dryad.qj153/2
title: Vences_Boophis_narinsi_description_TableS2

description: Distribution of haplotypes among voucher specimens, referring to haplotype networks in publication.
DOI: 10.5061/dryad.rf14r/1
title: Johnson etal. 2014 data

description: Seedling data used in this study.
DOI: 10.5061/dryad.sb432/3
title: Drought Data dec 10th 2009-1

description: Full experiment data sheet the includes all ther measurements for the drought and mhycorrhizal response treatments of the experiment.
DOI: 10.5061/dryad.16737/12
title: RAxML_COI_Richart&Hedin

description: COI RAxML gene tree in Newick tree format with bootstrap values.
DOI: 10.5061/dryad.1k1ns/2
title: Lp01 "core" genome (GenBank format)

description: GenBank formatted file derived from editing NC_002942 (Legionella pneumophila subsp. pneumophila str. Philadelphia 1). Lp01 is a common laboratory strain, a streptomycin resistant, restriction-minus derivative of the Philadelphia-1 clinical strain. This "core" sequence reflects the genome of the original Lp01 isolate, calculated based on the phylogeny between contemporary Lp01 strains and Lp02.
DOI: 10.5061/dryad.1tv93/5
title: ALLELES

description: Alleles used in simulation
DOI: 10.5061/dryad.32n76/1
title: Lemur aDNA sequence data and bait capture information
DOI: 10.5061/dryad.37n69/1
title: 2011 Soil moisture and temperature

description: Soil moisture and temperature for wet meadow grassland sampling points in 2011. Cumulative soil moisture adds together data from sampling events 3 and 4. Data was collected in the field.
DOI: 10.5061/dryad.37n69/2
title: Plant data 2011

description: Aboveground plant biomass data for wet meadows in 2011 that has been scaled up to g/m2. Separated by grass, forbs, rush, iris, and woody vegetation. Graminoid scaled up is rush and grass data added together. Data was collected in the field.
DOI: 10.5061/dryad.37n69/3
title: Plant Biomass 2012

description: Aboveground plant biomass for upland grasslands in 2012 that shows original data and data that has been scaled up to g/m2. Separated by grass, forbs, rush, sedge, iris, and woody vegetation. Graminoid scaled up is rush, sedge, and grass data added together. Grass columns include both live and dead vegetation, while alive grass columns include only live vegetation that was determined via visual estimates when spread out over white paper. Data was collected in the field.
DOI: 10.5061/dryad.37n69/4
title: 2012 arthropod biomass

description: 2012 individual and total arthropod biomass (mg) for top 6 abundant orders WITHOUT ZEROS. Length and counts for arthropods were done in the lab and then standardized equations were applied to obtain weights.
DOI: 10.5061/dryad.43534/2
title: Frog_color&contrast

description: Data collected and prepared by Beatriz Willink, Esteban Brenes-Mora, Heike Pröhl. Date of collection: 20110701-20111112. No missing data. Data includes measures of color and visual contrasts (as seen by a model bird viewer) for the dorsal and ventral skin of frogs. Contrasts were calculated against natural backgrounds and with the local irradiance (see METHODS). Calculations for color elements (Qt, Hue and Chroma) are given in Endler. 1993. Biol. J. Linn. Soc 41:315-352. Calculations for contrasts are given in Appendix 1 of Pröhl and Ostrowski. 2011. Evol Ecol 25:993-1015. Qt is the sum of reflected light across all 1 nm intervals between 400-700 nm. Chroma and Hue are objective color color space measures. Chroma is the Euclidean distance from the origin of color space to the reflectance spectra. Hue is the angle clockwise from the axis defined by the long-wavelentgh segment of the spectra (Red). Units for contrasts are jnd (just noticeable differences). In column headers, CC means Color (chromatic) contrast and BC is brightness (achromatic) contrast. TR refers to contrasts calculated against trunks (all types of tree bark), MR refers to contrasts calculated against rocks, usually covered with moss, GL indicates contrasts calculated against green leaves and LL indicates contrasts calculated against leaf-litter
DOI: 10.5061/dryad.43534/3
title: Focal_male_behavior

description: Data collected by Beatriz Willink during 20110613-20111112. No missing data. Behavioral data of focal males. Calling_time_no_fem is the total time (in seconds) a male was observed calling during all observations in which there were no females nearby. Quiet_time_no_fem is the total time (in seconds) a male was observed NOT calling during all observations in which there were no females nearby. Feeding_events is the number of feeding events in 150 min for each male. Movement is the number of minutes (out of 150) in which frogs moved over a distance of more than 5 cm. No_movement is the number of minutes (out of 150) in whichs frogs did not move. Inactivity_time is the number of minutes (out of 150) in which frogs did not move, forage or call, but were sitting still. Activity_time is the number of minutes (out of 150) in which frogs performed at least one conspicuous behavior, calling, moving or foraging. Calling_exposure is the average exposure at a distance of 1 m (and weighed by the time spent at all calling positions) of a frog's body while calling. See METHODS for details.
DOI: 10.5061/dryad.5sr48/1
title: Color data for male African starling species

description: Species average color variables of measurements from male African starlings. Variables represent the first two Principal Components calculated from the relative quantum catches of the four cones involved in color vision (PC1 and PC2), and brightness (log-transformed average reflectance) for 10 body patches.
DOI: 10.5061/dryad.62ck3/2
title: Kuehneotherium mandible CT scan video
DOI: 10.5061/dryad.6bt92/1
title: VSAO Workshop Version (OBO format)

description: This data file contains the workshop version of the Vertebrate Skeletal Anatomy Ontology described in Dahdul et al. (2012). It is a text file in OBO format (http://www.geneontology.org/GO.format.obo-1_2.shtml).
DOI: 10.5061/dryad.6bt92/2
title: VSAO Revision 2012-11-6 (OBO format)

description: This data file contains the version (2012-11-6) of the Vertebrate Skeletal Anatomy Ontology described in Dahdul et al. (2012). It is a text file in OBO format (http://www.geneontology.org/GO.format.obo-1_2.shtml).
DOI: 10.5061/dryad.6p2h0/2
title: MER-13-0064_Sequence_data

description: This file contains original sequence trace files for the manuscript MER-13-00641)	PVA  is labeled as ‘NVI’2)	Fridge and Freezer storage is labeled as ‘fresh’ in some trace file names and was changed later in Excel for data parsing3)	Please refer to Table 2 in the manuscript for experiment setup description
DOI: 10.5061/dryad.7d2g2/5
title: Supplementary Table 3

description: Supplementary Table 3
DOI: 10.5061/dryad.84dp4/1
title: RSBL-2013-0125-Behaviour

description: Behavioural profiles of Pachycondyla inversa workers obtained through scan sampling
DOI: 10.5061/dryad.88h10/1
title: Hpa1N_lib

description: Genomic DNA sequences in fasta-format
DOI: 10.5061/dryad.88h10/2
title: Hpa01N_lib
DOI: 10.5061/dryad.88h10/3
title: Hpa1S_lib
DOI: 10.5061/dryad.88h10/4
title: Hpa01S_lib
DOI: 10.5061/dryad.88h10/5
title: Hpy1N_lib
DOI: 10.5061/dryad.98c48/1
title: Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive lifespan

description: Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive lifespan have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in at presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive lifespan, and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort.
DOI: 10.5061/dryad.9v852/3
title: Nannoperca cytb data for all individuals

description: Nexus file for sequence data for cytochrome b gene for all individuals.
DOI: 10.5061/dryad.9v852/4
title: Nannoperca cytb data for all individuals grouped by lineage

description: Mega file for sequence data for cytochrome b gene for all individuals grouped by lineage.
DOI: 10.5061/dryad.b1q2n/10
title: figure2.zip

description: Files: figure2.zip (contains files well.XXX (XXX are numbers from 079 to 108 and from 301 to 396))Format: ZIP archive (contains flow cytometry data files FCS 2.0)Contents: Flow cytometry analyses of bacterial cultures. Samples were excited at a wavelength of 488 nm, while emission was detected at 510 nm (GFP) and 560 nm (DsRed).
DOI: 10.5061/dryad.b1q2n/11
title: 120525_exp391.csv

description: File: 120525_exp391.csvFormat: text (comma separated values)Contents: Data obtained from the analysis of flow cytometry data files well.301 - well.396 using WEASEL 3.0.1. File also contains information about the identity of every sample. Data are from samples taken after the competition experiment.
DOI: 10.5061/dryad.b1q2n/13
title: figure2_r_script.R

description: File: figure2_r_script.rFormat: r source fileContents: reads in all growth data, reads in all flow cytometry data, calculates statistics, plots figure 2 to pdfNote: requires package dichromat
DOI: 10.5061/dryad.b1q2n/15
title: 120525_exp392b.csv

description: File: 120525_exp392b.csvFormat: text (comma separated values)Contents: Data obtained from the analysis of flow cytometry data files well.101 - well.196 and well.201 - well.204 using WEASEL 3.0.1. File also contains information about the identity of every sample. Data are use to produce figure 3a.
DOI: 10.5061/dryad.b1q2n/17
title: figure3_r_script.r

description: File: figure3_r_script.rFormat: r source fileContents: reads in all growth data, reads in all flow cytometry data, calculates statistics, plots figure 3a and 3b to pdfNote: requires package dichromat
DOI: 10.5061/dryad.b8842/1
title: Simulation Files

description: Sims900inds_L3Thresh250i.csv is CDPOP input file.  C2C2_900Inds64PixelsIDXY.csv is file of individual locations used in CDPOP.  CD3_900Inds64Pixels_R20.csv is input file of cost distances with b1=1 and b2=20.  GDmatrix.csv is an output file from the 100th generation simulated by CDPOP.
DOI: 10.5061/dryad.bs200/1
title: Jiwa data file

description: SPSS datasets
DOI: 10.5061/dryad.cq376/4
title: Supplementary figure 2

description: Supertree in which temporal uncertainty is not taken into account, and each locality is restricted to two or fewer substages. Timescale representing millions of years ago appears at the bottom.
DOI: 10.5061/dryad.d7g00/1
title: DELCOURT_fitness_data

description: Please see README.txt
DOI: 10.5061/dryad.f7m5t/2
title: Concatenated nuclear gene alignment (Gblock)

description: Nuclear genes used in this study, Gblock data set. See Supplemental Table S2. CAD, 1, 3291; PGD, 3292, 3999; SNF, 4000, 4206; AATS, 4207, 5232; PER, 5233, 5778; SINA, 5781, 6125; TPI, 6126, 6527.
DOI: 10.5061/dryad.g08c7/4
title: Frequency_RADs

description: We present the allelic frequencies of all SNPs and  natural populations. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
DOI: 10.5061/dryad.hs37s/2
title: MYLU mtDNA Arlequin infile

description: Mitchondrial haplotypes of the Hypervariable II area of the control region for Myotis lucifugus.  Data are in the form of an Arlequin infile.
DOI: 10.5061/dryad.hs37s/3
title: STRUCTURE MYLU infile

description: Microsatellite data for Myotis lucifugus from Eastern Canada coded as an infile for the program STRUCTURE.
DOI: 10.5061/dryad.hs37s/4
title: STRUCTURE MYLU mainparams

description: Parameters used in the program STRUCTURE for the analysis of the microsatellite data.
DOI: 10.5061/dryad.j7230/5
title: Pairwise Fgp values among 8 plots in females

description: Input file for software GenAlEx.
DOI: 10.5061/dryad.j7230/6
title: Pairwise Fgp values among 8 plots in males

description: Input file for software GenAlEx.
DOI: 10.5061/dryad.jh8j7/3
title: Descriptive Statistics Coloration Measurements

description: This data file contains the descriptive statistics for all raw coloration and greyscale measurements collected from each of seven individuals from five groups of fish.
DOI: 10.5061/dryad.jk832/1
title: stabselbin3

description: Fortran 77 computer program used to generate results shown in Table 1 of paper
DOI: 10.5061/dryad.jn14d/6
title: Griffiths2013LengthMass2011ChignikLake

description: Length and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Chignik Lake, AK.
DOI: 10.5061/dryad.k37m7/3
title: ITS1_asco

description: ITS1 sequences of ascomycetous fungi in INSD databases.
DOI: 10.5061/dryad.n48cm/1
title: Supplementary Table A

description: SUPPLEMENTARY TABLE A: Allocation of reproductive function in the Animal Kingdom. The table shows the proportion of species with asexual and sexual reproduction and the proportion of sexual species that are dioecious. The proportions are given as none, rre, minority, majority, almost all or all. The table also gives the type of hermaphroditism where present (simultaneous, protandric, protogynous or alternating) and the patterns of sexual dimorphism in dioecious species. Estimates are shown separately for each animal phylum and its constituent classes.
DOI: 10.5061/dryad.nm70b/1
title: barton-jae-data

description: Data contains raw data (comma separated values and a GIS shapefile) and R code for producing the analyses and figures in the associated paper.
DOI: 10.5061/dryad.nt13m/1
title: datafecaltG1

description: oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in each of these in the first generation of test (ie alternation within a single generation).
DOI: 10.5061/dryad.nt13m/2
title: datafecaltG2

description: oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in each of these in the second generation of test (ie alternation among generations).
DOI: 10.5061/dryad.nt13m/3
title: datafecLA2G

description: oviposition rate of mites evolving in alternating vs homogeneous environments, when tested in either tomato or pepper (test for local adaptation and potential cost of generalism)
DOI: 10.5061/dryad.q1kf0/1
title: Microsatellite data file

description: Microsatellite data from green sea turtles of six Atlantic rookeries at fifteen loci.
DOI: 10.5061/dryad.q1kf0/2
title: Arlequin microsatellite input file

description: Arlequin microsatellite input file from six Chelonia mydas rookeries in the Atlantic, for 15 loci.
DOI: 10.5061/dryad.q1kf0/3
title: DNAsp compressed file

description: MtDNA haplotype data for 13 Atlantic/Mediterranean Chelonia mydas rookeries, from the published literature (see Figure 1 for references).