cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q20jf/3
title: Woodland species matrix

description: Woodland species found in the ground flora of each plot. Data collected in the field. Species names are abbreviated to the first three letters of the genus followed by the first three letters of the species. Full names can be found in the read me file. Plot information for each code can be found in the 'Plant and leaf-miner richness' file.
DOI: 10.5061/dryad.q20jf/4
title: Leaf-miner matrix

description: Leaf-miner species found on each plot. Data collected in the field. Plot information for each code can be found in the 'Plant and leaf-miner richness' file.
DOI: 10.5061/dryad.v0c77/1
title: Simulation data

description: The final generation (generation 1250) of each simulation run and replicate. Simulations are divided into no selection simulations ("Nsims"), gradient selection simulations ("Gsims"), and discrete selection simulations ("H1/H5/H9sims").
DOI: 10.5061/dryad.v0c77/2
title: Selection surfaces and sampling file

description: One of the gradient selection files ("gradient1024x1024_N0_S1.txt") and a full set of habitat configuration rasters (H1/H5/H9 with 10 replicates each). The 500 randomly sampled individuals are provided in "sample500.csv".
DOI: 10.5061/dryad.1qs85/1
title: LakeTurkana_KeyFishesIsotopeData

description: Stable isotope (15N and 13C), site of collection and standard length data for seven fish species from Lake Turkana (Oreochromis niloticus, Lates niloticus, Tilapia zillii, Labeo horie, Synodontis schall, Alestes baremose, Hydrocynus forskalli)
DOI: 10.5061/dryad.20r6d/1
title: sigloss_data

description: This file contains all of the raw data from the avida experiments.
DOI: 10.5061/dryad.26pm4/1
title: Host-parasite specialization

description: This data file contains data on bacterial resistance in two subpopulations linked by migration. Homogeneous subpopulations are linked by 1% dispersal (where treatment A gives dispersal between 0.5-0.5 M9 and B gives dispersal between 5-5 M9). Hetergeneous populations (0.5-5 M9) are linked by either 1% (C) or 50% (D) dispersal. For each subpopulation 5 bacterial clones (A1-A5 and B1-B5) where tested for resistance (1 or 0) against infectivity by 5 phage clones (A1-A5 and B1-B5) isolated from each subpopulation.
DOI: 10.5061/dryad.3bs4j/1
title: R Code for Continental-scale biogeographic variation: provinces vs. gradients

description: This is the R code used for data preparation and analysis of similarity among provinces and regions used in the paper "Continental-scale biogeographic variation: provinces versus gradients in the Late Ordovician of Laurentia". It uses Paleobiology database data or imported occurrence/abundance matrices.
DOI: 10.5061/dryad.3fj52/1
title: Concatenated

description: The matrix of ITS and trnL-F.
DOI: 10.5061/dryad.44372/23
title: Structure_137samples_4nuDNA_input

description: Structure input file based on four nuclear genes (fasta format).
DOI: 10.5061/dryad.44372/24
title: Structure_137samples_4nuDNA_input

description: Structure input file (genotype matrix format) obtained from xmfas2struct program; -9 is used for missing data.
DOI: 10.5061/dryad.44372/25
title: IMa2_137samples_5genes_input

description: IMa2 input file based on five genes.
DOI: 10.5061/dryad.4d75c/1
title: Supplementary File 8 - R Code

description: R code, requiring ape, geiger, and Claddis packages, used to run the analysis.
DOI: 10.5061/dryad.4d75c/2
title: Supplementary File 9 (Continuous PCO Changes)

description: Morphospaces of Principal Coordinates 1 and 2, for morphologies within each time bin and optimal topologies derived from the combined discrete-continuous phylogenetic analyses. Open circles represent basal eutherians with respect to the crown group, open squares more crownward non-placental eutherians, and black squares crown placentals. Abbreviations are as follows: CM = Continuous, minimum constraint; CF = Continuous, full constraint; CP = Continuous, Purgatorius constraint.
DOI: 10.5061/dryad.4d75c/3
title: Supplementary File 4 CF cal3 dated

description: Trees deriving from the continuous data and full constraint, dated using cal3.
DOI: 10.5061/dryad.583t5/7
title: Wild female and offspring genotypes
DOI: 10.5061/dryad.5s5k8/1
title: JAV 00871 R2 Whinchat tag effect data 2015 wrlc at st andrews

description: File of individual whinchats used in the study and for all analyses: capture dates, survival, biometrics and tagging details
DOI: 10.5061/dryad.6t34b/1
title: 4H_Damara_Phenotypes_BOL-16Aug2015

description: Phenotypes and ID of all animals included in analysis
DOI: 10.5061/dryad.6t34b/2
title: Damara_OV_FinalReport.txt

description: A zipped folder containing four .txt files with all the genotypes for the animals used in the analyses.
DOI: 10.5061/dryad.7nh1v/1
title: Evaporative Water Loss of Squamate Species

description: Habitat type, Mass, Evaporative Water Loss, Measurement Conditions and Measurement Code for 120 species of squamate reptiles. For Habitat Type, A = arid, M= mesic, and S = semiarid. TEWL= Total Evaporative Water Loss. Please see manuscript for the description of how the habitat types were assigned. Please see Supplementary Table S1 for the literature cited associated with each species.
DOI: 10.5061/dryad.7nh1v/2
title: Squamate Habitat Types

description: A list of the habitat types for 860 species of squamate reptiles. A = arid, S=semiarid, and M= mesic. Please see manuscript for details of how habitat type was assigned. Please see supplementary Table S2 for the literature cited associated with this data.
DOI: 10.5061/dryad.7nh1v/3
title: Habitat types bordering squamate geographic ranges

description: List of habitat types of species and both the number and types of habitats bordering the geographic range of 227 squamate reptiles from North America. A = arid, S = semiarid, and M = mesic. Please see manuscript for methodology and literature cited associated with this data.
DOI: 10.5061/dryad.7pn80/2
title: Data Figure 4

description: Data to reproduce Figure 4, showing group performanceand amount of task partitioning over subsequent generations for each of the 22 evolutionary runs. The first three fields indicate the ID of the evolutionary run, generation and repetition (respectively), the fourth and fifth fields indicate the number items retrieved in a partitioned and non-partitioned way (respectively, the sum of which row-wise corresponds to fitness), and the sixth indicates the average absolute robot speed projected along the main axis of the environment.
DOI: 10.5061/dryad.7pn80/3
title: Data Figure 5

description: Data to reproduce Figure 5, robot densities and trajectories for a typical run. The first fields indicates the timestep, the second, third, fourth and fifth fields indicate the x-axis (main environment axis) coordinate of the four robots, and the last field contains the number of items present in the cache.
DOI: 10.5061/dryad.7pn80/4
title: Data Figure 6

description: Data to reproduce Figure 6, showing the effect of the degree of task specialization and average linear speed on the fitness performance of the 22 controllers evolved from first principles. The first and second fields indicate the ID of the evolutionary run and of the repetition, the third and fourth fields indicate the number of items retrieved in a partitioned and non-partitioned way (respectively), the fifth field indicates the proportion of items retrieved in a task partitioned way, the sixth and seventh fields indicate the average linear speed and the same quantity as a proportion of the maximum theoretical speed, and the last field indicates the fitness.
DOI: 10.5061/dryad.821b5/1
title: Durka_et_al_2016_JAPPL_AFLP

description: This folder contains 7 files with AFLP data of Durka et al. (2016) Genetic differentiation among multiple common grassland plants supports seed transfer zones for ecological restoration. Journal of Applied EcologyArrhenatherum_elatius_AFLP.txtCentaurea_jacea_AFLP.txtDaucus_carota_AFLP.txtGalium_album_AFLP.txtHypochaeris_radicata_AFLP.txtKnautia_arvensis_AFLP.txtLychnis_flos-cuculi_AFLP.txtEach files contains columnsID   Individual plant IDPop  Population identifier, i.e. one of 8 accessionsn columns of AFLP data with the first line giving the primer combination + fragment length (e.g. ACA_CTGA_195)E Geographic coordinate of population in decimal degrees: EastN Geographic coordinate of population in decimal degrees: North
DOI: 10.5061/dryad.9r5v7.2
title: Data from: Deciphering the evolutionary history and developmental mechanisms of a complex sexual ornament: the abdominal appendages of Sepsidae (Diptera)
DOI: 10.5061/dryad.9r5v7.2/1.2
title: M.fasciculatus cell counts

description: Cell counts for all histoblast nests in both males and females of the species Meroplius fasciculatus.
DOI: 10.5061/dryad.9r5v7.2/2.2
title: P.dikowi cell counts

description: Cell counts for all histoblast nests in both males and females of the species Perochaeta dikowi.
DOI: 10.5061/dryad.b33q0/1
title: Candolin & Tukiainen Red area and intensity
DOI: 10.5061/dryad.b58r0/1
title: Dataset with raw phenotypes

description: Dataset with raw data, no data cleaning has been done
DOI: 10.5061/dryad.b58r0/2
title: corrected data

description: Dataset with corrected data, used for the genetic analysis
DOI: 10.5061/dryad.b58r0/3
title: pedigree file

description: Dataset with the pedigree information
DOI: 10.5061/dryad.bh276/11
title: Phylogenetic analysis of CYP719 gene candidates from twenty BIA-accumulating plant species. Rooted tree.
DOI: 10.5061/dryad.bh276/3
title: Phylogenetic analysis of aldo-keto reductase gene candidates with homology to codeinone reductase (COR) from twenty BIA-accumulating plant species. Rooted tree.
DOI: 10.5061/dryad.bh276/4
title: Phylogenetic analysis of carboxyl esterase (CXE) gene candidates from twenty BIA-accumulating plant species.
DOI: 10.5061/dryad.bh276/5
title: Phylogenetic analysis of carboxyl esterase (CXE) gene candidates from twenty BIA-accumulating plant species. Rooted tree.
DOI: 10.5061/dryad.bh276/6
title: Phylogenetic analysis of CYP80 gene candidates from twenty BIA-accumulating plant species.
DOI: 10.5061/dryad.bh276/7
title: Phylogenetic analysis of CYP80 gene candidates from twenty BIA-accumulating plant species. Rooted tree.
DOI: 10.5061/dryad.bh276/8
title: Phylogenetic analysis of CYP82 gene candidates from twenty BIA-accumulating plant species.
DOI: 10.5061/dryad.bh276/9
title: Phylogenetic analysis of CYP82 gene candidates from twenty BIA-accumulating plant species. Rooted tree,
DOI: 10.5061/dryad.br022/3
title: AmidesAndBats_FruitChoiceByFruit

description: see associated ReadMe file
DOI: 10.5061/dryad.br022/4
title: AmidesAndBats_NoChoice

description: see associated ReadMe file
DOI: 10.5061/dryad.f7t25/1
title: Genotypes at four candidate loci

description: Genotypes at four candidate loci (CLOCK1, ADCYAP1, NPAS2, CREB1) for all tree swallows sampled in this study.
DOI: 10.5061/dryad.f7t25/2
title: Data for GxE analyses

description: Data used for GxE analyses, where each line represented a  reproductive event within a nest box. Columns included year (YEAR), female identity (ID.F) and its age (AGE.F; SY=second-year, ASY=after second-year), male identity (ID.M), density of breeders	(DENSITY; % of occupied nest boxes), altitude (ALT; meters), latitude and longitude (LAT, LONG; decimal degrees), May temperature (TEMP.LD; Celcius degrees), April temperature (Celcius degree), laying date (LD; julian days), incubation duration (INC; days), and sum of alleles at the four studied loci for females (CLOCK.SUM.F, ADCYAP.SUM.F, CREB.SUM.F, NPAS.SUM.F) and males (CLOCK.SUM.M, ADCYAP.SUM.M, CREB.SUM.M, NPAS.SUM.M).
DOI: 10.5061/dryad.h3p05/1
title: OHara et al data from greenhouse study

description: These data were collected in a greenhouse study published in Evolution entitled "Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa". Column headings include (A) the plant number, (B) the temporal population including arb97, the ancestral population, and arb04, the descendant population, (C) watering treatment, (D) inoculation treatment, (E) days to flowring, (F) whether the plant was included in the flowering time analysis based on parameters described in the manuscript, (G) soil moisture, (H) health of inoculated leaf, (I) the leaf area used to calculate SLA, (J) the dry leaf weight used to calculate SLA, (K) SLA.
DOI: 10.5061/dryad.hs200/10
title: Daphnia ambigua EpiRADseq Rarefaction Raw Count Tables

description: A zipped archive containing the raw counts for each rarefacted sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.
DOI: 10.5061/dryad.hs200/3
title: Daphnia ambigua EpiRADseq Raw Count Tables

description: A zipped archive containing the raw counts for each sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.
DOI: 10.5061/dryad.hs200/4
title: Daphnia ambigua P treatment - first generation with predatory cues treatment (3 replicates) - Raw Illumina Reads

description: A zipped fastq file that contains multiplexed reads from the three replicates from the predator treatment (generation 1). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the P treatments in the manuscript and with all applicable Dryad file names and processing steps.
DOI: 10.5061/dryad.hs200/5
title: Daphnia ambigua PN treatment - second generation without predatory cues treatment (3 replicates) - Raw Illumina Reads

description: A zipped fastq file that contains multiplexed reads from the three replicates from the no predator treatment (generation 2). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the PN treatments in the manuscript and with all applicable Dryad file names and processing steps.
DOI: 10.5061/dryad.hs200/6
title: Frequency summary of Daphnia pulex genome double digest

description: A summary file that provides the number of fragments in given fragment size range. Based on an in silico digestion of the Daphnia pulex genome. The Perl script used to generate this data is contained with all other data processing scripts.
DOI: 10.5061/dryad.hs200/7
title: Daphnia ambigua EpiRADseq Data Analysis Scripts, Files, & Documentation

description: A zipped archive containing all scripts necessary to quality-trim raw reads, construct the pseudo-reference genome, and map the reads back to the psuedo-reference to infer methylation. Each script contains a proper description of function and usage and the complete pipeline (from raw reads to counts) is automated and documented in the EpiRADseq_analysis.sh script.
DOI: 10.5061/dryad.hs200/8
title: Daphnia ambigua EpiRADseq Rarefaction Raw Read Files

description: A zipped archive containing randomly subsetted read files from all replicates, which were used for rarefaction analysis.
DOI: 10.5061/dryad.hs200/9
title: Daphnia ambigua EpiRADseq Rarefaction Mapping Files

description: A zipped archive containing BAM mapping files for each rarefacted sample (3 replicates across 2 treatments) mapped to the Daphnia ambigua pseudo-reference genome.
DOI: 10.5061/dryad.js25t/2
title: Squirrel FGM concentrations

description: Fecal glucocorticoid metabolite concentrations
DOI: 10.5061/dryad.k84c3k8j.1
title: Data from: Early evolutionary trends in ammonoid embryonic development
DOI: 10.5061/dryad.k84c3k8j.2/1.2
title: Table S1: Embryonic shell measurements of Devonian ammonoids
DOI: 10.5061/dryad.k84c3k8j.2/2.2
title: Table S2: Embryonic shell measurements of Carboniferous-Cretaceous ammonoids
DOI: 10.5061/dryad.k84c3k8j.2/3.2
title: Table S3: Compilation of egg sizes and fecundities of Recent cephalopods
DOI: 10.5061/dryad.k84c3k8j.2/4.2
title: Table S4: Compilation of adult size conch measurements, calculated body chamber and egg volumes and egg number estimates
DOI: 10.5061/dryad.k84c3k8j.2/5.2
title: Figure S1: Changes in coiling and initial chamber size through time

description: (A) Diversity from the early Emsian to the late Eifelian with proportion of forms with openly coiled adult whorls and umbilical window (open + enclosed). The embryonic and post-embryonic whorls of representative taxa are shown of each category are shown (respectively Erbenoceras, Mimagoniatites and Agoniatites). (B-C) Boxplots showing the distribution and fluctuations of initial chamber size (initial chamber diameter PD in mm) within the Devonian (B) and in the Phanerozoic (C) from the Devonian until the Cretaceous (whiskers = minima and maxima excluding outliers, boxes = middle two quartiles, horizontal stripe = median value, dots = outliers). Abbreviations: E. Dev = Early Devonian, M. Dev. = Middle Devonian, L. Dev. = Late Devonian, Dev. = Devonian, Carb. = Carboniferous, Perm. = Permian, Tria = Triassic, Jura. = Jurassic, Cret. = Cretaceous. Histograms were produced in the freely available statistical environment R (http://www.r-project.org/).
DOI: 10.5061/dryad.mp0d5/1
title: IMPACT DATA

description: Plot level data from grassland surveys used for impact analyses.
DOI: 10.5061/dryad.nm722/1
title: Doctors_6

description: Questionnaire with doctors
DOI: 10.5061/dryad.nm722/2
title: Pharmacists_3_7

description: Questionnaire with pharmacists
DOI: 10.5061/dryad.q1r50/1
title: Interaction Outcome dataset

description: Data of co-occurrences (Real coex. column) and expected co-occurrences (Expected coex. column) between target species (A. herba-alba, S. vermiculata and L. spartum) and the other plant species found intransects. Data is separate in different sheets for different study sites. Species code can be found in the first sheet.
DOI: 10.5061/dryad.q1r50/2
title: ISAR dataset

description: Number of species found around each individual of target species (A. herba-alba, S. vermiculata and L. spartum)  from  d=0 to d=400cm, every 20 cm.
DOI: 10.5061/dryad.q1r50/3
title: Chao-Jaccard dataset

description: Matrix of coexistences between target species (A. herba-alba, S. vermiculata and L. spartum) and the other species found in transects. Data is separate in different sheets for different study sites. Species code can be found in the first sheet.
DOI: 10.5061/dryad.q6s1f/1
title: Concatenated alignment of nuclear and chloroplast loci of Catasetinae
DOI: 10.5061/dryad.q6s1f/2
title: Consensus chloroplast tree of Satyrium

description: Consensus tree derived from Bayesian inference
DOI: 10.5061/dryad.q6s1f/3
title: Consensus nuclear tree of Satyrium

description: Consensus tree derived from Bayesian inference
DOI: 10.5061/dryad.q6s1f/4
title: Set of chloroplast posterior probability trees of Satyrium

description: 20000 posterior probability trees of Satyrium derived from Bayesian inference and chloroplast data
DOI: 10.5061/dryad.q6s1f/5
title: Set of nuclear posterior probability trees of Satyrium

description: 20000 posterior probability trees of Satyrium derived from Bayesian inference and nuclear data
DOI: 10.5061/dryad.q6s1f/6
title: PACo-ParaFit script for outlier detection in phylogenies

description: Detailed R script for outlier detection in phylogenies using PACo and ParaFit
DOI: 10.5061/dryad.qh7k8/1
title: MsJungwirth5ProcBData

description: An excel file containing all long-term data of groups and individuals and the respective fitness estimates which are described in the manuscript
DOI: 10.5061/dryad.rq80k/1
title: Genotypes_26503SNPs

description: File with ID and genotypes for 26503 SNPs for 1285 animals (from three breeds).
DOI: 10.5061/dryad.rv766/1
title: SOS expression cip doses

description: Impacts of ciprofloxacin on SOS expression. Mean relative expression (+/- s.e.m; n≥3) of a bioluminescent SOS reporter construct across a gradient of ciprofloxacin (ug/L) in a WTpLex:Lux reporter strain and a WT control lacking the reporter construct
DOI: 10.5061/dryad.rv766/2
title: Cell density cip doses

description: Impacts of ciprofloxacin on bacterial population density. Mean (+/- sem; n≥3) density of viable cells in cultures of the WT strain that were grown overnight across a gradient of ciprofloxacin (ug/L).
DOI: 10.5061/dryad.rv766/3
title: Fitness wt-lex cip-no ratios

description: Short-term fitness effects of the SOS response. Competitive fitness of the WT strain relative to the LexA mutant, as measured using overnight competition experiments in the presence of ciprofloxacin or not. Values are the average of 20 independent replicates starting from different WT:LexA frequencies and error bars are SEM.
DOI: 10.5061/dryad.rv766/4
title: 5-days competition lex-wt

description: Short-term fitness effects of the SOS response. Frequency of the WT strain in competition with the LexA strain across multiple cycles of competition, in the presence of ciprofloxacin or not. After 16 generations, the WT strain had achieved such a high frequency that it could no longer be accurately measured.
DOI: 10.5061/dryad.rv766/5
title: Mutation rate wt-lex with cip

description: Mutation rate of WT and LexA in the absence or presence of ciprofloxacin, as calculated using a fluctuation test that measures the rate of mutation to rifampicin resistance.  Estimation of mutation rate values (and 95 % confidence intervals) was done using MSS maximum likelihood method from eight independent replicates.
DOI: 10.5061/dryad.rv766/6
title: Fitness lex-wt time-evolvability

description: Fitness changes of WT and LexA populations that evolved in the presence and absence of ciprofloxacin. Fitness was measured relative to the ancestral WT strain in 10 replication populations for each treatment.
DOI: 10.5061/dryad.rv766/7
title: MIC wt-lex time

description: MIC scores (ciprofloxacin concentration in ug/L) in WT and LexA populations that were allowed to evolve for 200 generations in the presence and absence of ciprofloxacin. We also present the date from the ancestor (T0) populations.
DOI: 10.5061/dryad.1f734/1
title: Experiment data

description: Contains all data from the experiment used in analyses in the manuscript. The "notes" tab contains column title descriptions.
DOI: 10.5061/dryad.33fq5/1
title: Apis provider Apis colonies

description: SPSS data file
DOI: 10.5061/dryad.33fq5/2
title: Apis provider Bombus colonies

description: SPSS data file
DOI: 10.5061/dryad.33fq5/3
title: Apis Provider_All flowers

description: SPSS data file
DOI: 10.5061/dryad.3bs4j/2
title: Appendix 1

description: Paleobiology Database collection numbers for collectionsused in the continental-scale study
DOI: 10.5061/dryad.3f355/1
title: RADseq_Loci_in_all_individuals

description: Sequences and hamming distance from assembled mitochondrial sequences in RAD sequencing
DOI: 10.5061/dryad.3f355/2
title: Nucleotide alignment_CO1

description: Fasta file of partial sequences. Description of samples can be obtained from Excel spreadsheet provided. See Column G of "Sample_details_updated.xlsx".
DOI: 10.5061/dryad.3f355/3
title: Nucleotide alignment_ND4

description: Partial ND4 sequences. Labels match column B of "Sample_details_updated.xlsx". See comments in cell H1 for explanation of sequences labelled "...Assembly..."
DOI: 10.5061/dryad.3f355/4
title: Nucleotide alignment_ND5

description: Partial ND5 sequences. See column F of "Sample_details_updated.xlsx" to trace back actual sample details.
DOI: 10.5061/dryad.3f355/5
title: Primer1

description: Sequence from region amplified by primer pair 1 (see Behura et al. 2011). Labels match column B of "Sample_details_updated.xlsx". See comments in cell H1 for explanation of sequences labelled "...Assembly..."