cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0nm8t/8
title: Season1_Closed_Results

description: The results from the autumn 2013 closed-population analysis.
DOI: 10.5061/dryad.0nm8t/9
title: Season2_Closed_Results

description: The results from the spring 2014 closed-population analysis.
DOI: 10.5061/dryad.3qs21/1
title: Trioza microsatellite data

description: An excel file containing Trioza barrettae genotypes at 14 microsatellite loci.
DOI: 10.5061/dryad.3qs21/2
title: Trioza CO1 data

description: An excel file containing Trioza barrettae haplotype frequencies for the mitochondrial COI gene
DOI: 10.5061/dryad.4ff04/1
title: StudyDataDryas

description: The data contains species names and used explanatory variables in the study published in Oikos. For further information, please contact Janne Alahuhta.
DOI: 10.5061/dryad.5j354/1
title: Lopez-Uribe-etal_Genepop-Peponapis-Genotypes

description: Genotype data for the 942 individuals included in the analysis. File is in genepop format.
DOI: 10.5061/dryad.5j354/2
title: Lopez-Uribe_Peponapis-Geographic-Information

description: This excel file contains detailed geographic information for all individuals used in the genetic analysis.
DOI: 10.5061/dryad.6226d/10
title: MAE mutation counts

description: This file describes, for each sequenced clone of the MAE, the counts of each mutation types recovered. It is produced by the program ComputeMutationThroughTimeDryad.pl and is used to produce figures using the MAE as a reference.
DOI: 10.5061/dryad.6226d/11
title: LTEE point mutation matrix for phylogeny

description: This file contains an array in which the presence and absence of point mutations recovered in the LTEE sequenced clones is stored as 0 or 1 respectively for each clone. It is produced by ComputeMutationThroughTimeDryad.pl and is used to produce figure 2.
DOI: 10.5061/dryad.6226d/12
title: REL606 ancestral genome composition

description: This file, produced by GenomeCompositionComputer.pl, reports the composition of the ancestral genome (synonymous, nonsynonymous, intergenic) for each type of point mutations (AT to CG, AT to GC ...). It is used to compute the expected number of nonsynonymous mutations based on the observed number of synonymous.
DOI: 10.5061/dryad.6226d/13
title: ComputeMutation command file LTEE

description: This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking for all mutations of the LTEE to be reported.
DOI: 10.5061/dryad.6226d/14
title: ComputeMutation command file MAE

description: This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking for all mutations of the MAE to be reported.
DOI: 10.5061/dryad.6226d/6
title: MAE fitness

description: This files contains the fitness estimates of the MAE clones sequenced.
DOI: 10.5061/dryad.6226d/7
title: LTEE spectrum counts

description: This file describes the spectrum of mutations that have accumulated through time in each population of the LTEE
DOI: 10.5061/dryad.6226d/8
title: LTEE mutation counts (1)

description: This file describes, for each sequenced clone of the LTEE, the counts of each mutation types recovered. It is used for the genome size figure.
DOI: 10.5061/dryad.6226d/9
title: LTEE mutation counts (2)

description: This file describes, for each sequenced clone of the LTEE, the counts of each mutation types recovered. It is produced by the program ComputeMutationThroughTimeDryad.pl and is used to produce most figures.
DOI: 10.5061/dryad.68mc8/1
title: digital Fragment Analysis Histograms

description: Histograms (in text files) of each microsatellite locus from Ondatra zibethicus (muskrat). These histograms were created with a custom Python script from Illumina MiSeq paired-end sequencing reads that were merged, quality filtered, and de-replicated. A file to map the sample to the specimen ID (and its sampling population) is in the ReadMe file.
DOI: 10.5061/dryad.68mc8/2
title: digital Fragment Analysis Final Genotypes

description: Final microsatellite genotypes for each muskrat specimen, including muskrat ID, location, allele (0,1), and eleven micorsatellite loci. A text file that maps alleles to their sequence is in the ReadMe file.
DOI: 10.5061/dryad.8m6j3/1
title: Thome.fsc

description: Genetic data analysis files.
DOI: 10.5061/dryad.8mj19/1
title: Second (group) level activation analysis

description: Second level spm models. One modelling the interaction (between relatedness and proportion), used to provide t-maps for the interaction and main effect of relatedness, and one modelling the main effect of proportion, used to provide t-maps for the main effect of proportion and the word-pairs versus baseline.
DOI: 10.5061/dryad.8mj19/2
title: Second (group) level connectivity analysis

description: Second level SPM/gPPI models for the connectivity analyses from seeds in left inferior frontal gyrus (LIFG) and left anterior cingulate cortex (LACC). The main effect of proportion is modelled.
DOI: 10.5061/dryad.bt4vj.2/10.2
title: Posterior_sequence_ratios

description: Summary posterior molar proprtion data (m2-4) for Macropodoid taxa exported from R. Summary statistics (mean, sample size; n, standard deviation;sd) for m3/m2 and m4/m2.
DOI: 10.5061/dryad.bt4vj.2/11.2
title: R_scripts

description: R script files compiled in the program TinnR.
DOI: 10.5061/dryad.bt4vj.2/12.2
title: READ_ME
DOI: 10.5061/dryad.bt4vj.2/4.2
title: Morphological_tree_states

description: Character states for the modified morphological phylogeny originally produced by Prideaux and Warburton (2010; see in paper text for full citation). "1"= Posthypocrstid presemy, "0"= posthypocristid absent. Data was originally compiled in excel and exported as a text file.
DOI: 10.5061/dryad.bt4vj.2/41.2
title: SurfaceFiles

description: Surface files exported from MeshLab v1.3.3 64bit. Naming convention is "Institution_SpecimenNumber_Species_Element.ply". Institutional abbreviations:Australian Museum (AM), Australian National Wildlife collection (ANWC), Flinders University Vertebrate Palaeontology Laboratory (FU), Northern Territory MuseumAlice Springs (NTM), Queensland Museum (QM), South Australian Museum (SAM), University of California Musuem of Paleontology (UCMP), Wesetern Australian Museum (WAM). Element abbreviations:LRMX= Lower right (or left;L) molar (X denotes tooth number (1-4); X if unknown), OES= Outer enamel surface, EDJ= Enamel-dentine junction, ENAM= Enamel cap, DENT= Dentine, RMAND= Right (or left;L) mandible.
DOI: 10.5061/dryad.bt4vj.2/5.2
title: Morphological phylogeny

description: Modified (see paper text) most parsimonious morphological input tree from Prideaux and Warburton (2010).
DOI: 10.5061/dryad.bt4vj.2/6.2
title: Timescaled morphological phylogeny of Macropodoidea

description: Output timescaled morphological phylogeny from R in Newick tree file.
DOI: 10.5061/dryad.bt4vj.2/7.2
title: Posthypocrstid_relief_data

description: Posthypocristid relief data based on CT scan measurements in Avizo 8. PHCvert=vertical posthypocristid relief, PHCwdith= width across the talonid fossa at its point of maximum relief, Relief_Ratio = the quotient of PHCvert by PHCwidth. Comment= describes whether the crest is a homologue or analogue of the posthypocristid.
DOI: 10.5061/dryad.bt4vj.2/8.2
title: Tooth_dimensions

description: Tooth dimension data based on museum collection specimens."ID"= Specimen number,  "Side"= specimen is left ("L") or right ("R") dentary, "Origin"= collection holding specimen (AM= Australian Museum Sydney, BMNH= British Museum of Natural History, SAM= South Australian Museum Adelaide, UCMP= University of California Museum of Paleontology, QVM= Queen Victoria Museum, Inveresk, Tasmania, WAM= Western Australian Museum Perth, FU= Flinders University Vertebrate Palaeontology Laboratory Adelaide , ANWC= Australian National Wildlife Collection Canberra, NTM= Northern Territory Museum, Alice Springs, QM=Queensland Museum, Brisbane), "AW"= maximum anterior molar width, "PW"= maximum posterior width, "L"= maximum molar length, "Tooth_id" = molar tooth position, "Collector"= observer responsible for measurement (AC= Aidan Couzens, GJP= Gavin J. Prideaux).
DOI: 10.5061/dryad.bt4vj.2/9.2
title: Sum_m3HI_byW

description: Summary Crown heigh data for living macropodoids exported from R. Taxa= Species, MeanPhyb= Hypsodonty index calculated as mean hypoconid crown height divided by max talonid width, sePhyb= bootstrap estimate of standard error.
DOI: 10.5061/dryad.cq4td/1
title: Sequence mtDNA COII

description: mtDNA sequences for COII to Cryptotermes
DOI: 10.5061/dryad.gm465/1
title: Castillo and Delph isofemale data

description: For each mating replicate data is provided for the length of the male and female, the interaction latency, and copulation latency
DOI: 10.5061/dryad.k43t2/1
title: Lp_phyloseq_database

description: Sequence IDs, information on data source (e.g. genbank accession number) and species identities for sequences used in making the large opsin phylogeny.
DOI: 10.5061/dryad.k43t2/2
title: Lp_ALLOPS

description: Phylip file of all sequences used in large opsin dataset
DOI: 10.5061/dryad.k43t2/3
title: Lp_ALLOPS_newick

description: Newick tree file for large opsin dataset phylogeny
DOI: 10.5061/dryad.k43t2/4
title: LpONLY.phy

description: Phylip formatted file of Limulus opsin ONLY dataset.
DOI: 10.5061/dryad.k43t2/5
title: LpONLY_newick

description: Newick tree file of Limulus opsin only phylogeny
DOI: 10.5061/dryad.kj7p2/1
title: Data accompanying Seebacher et al RSOS ms160316

description: Data used in this manuscript. Each measured response is given in a different sheet of the Excel file, with a brief summary of metadata in the first sheet.
DOI: 10.5061/dryad.mb2gb/1
title: Vega-Trejo et.al. 2016.BMC Evol Biol.Data
DOI: 10.5061/dryad.nt269/1
title: Neotropical Miliuseae_concatenated aligment

description: This Nexus file is a concatenated alignment containing chloroplast (ndhF, matK, psbA-trnH, rbcL, rps16-trnQ and trnL-F) sequences of the Neotropical Miliuseae (Annonaceae) used in this study.
DOI: 10.5061/dryad.q8h75/1
title: all_cleaned_unique_cep_genomic_clone_sequence_new_names

description: coding sequence for all unique CEP genomic clones from R. reniformis.
DOI: 10.5061/dryad.rb7h0/1
title: README

description: ReadMe file describing the data package
DOI: 10.5061/dryad.1q8p3/1
title: species-codes

description: Guide to species codes in alignment files. All species are in the genus Penstemon. See our manuscript for accession information
DOI: 10.5061/dryad.1q8p3/2
title: full-s80t15

description: Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 15. A key to species codes is given in the separate file entitled species-codes.txt.
DOI: 10.5061/dryad.1q8p3/3
title: full-s80t20

description: Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 20. A key to species codes is given in the separate file entitled species-codes.txt.
DOI: 10.5061/dryad.1q8p3/4
title: full-s80t30

description: Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 30. A key to species codes is given in the separate file entitled species-codes.txt.
DOI: 10.5061/dryad.1q8p3/5
title: full-s90t15

description: Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 15. A key to species codes is given in the separate file entitled species-codes.txt.
DOI: 10.5061/dryad.1q8p3/6
title: full-s90t20

description: Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 20. A key to species codes is given in the separate file entitled species-codes.txt.
DOI: 10.5061/dryad.39d23/1
title: Brandolini - dataset - Einkorn Europe

description: SNP DaRT data of 148 diploid wheat accessions (136 T. monococcum, 9 T. boeoticum and 3 T. urartu)
DOI: 10.5061/dryad.3k713/1
title: Dryad_ECOG_E02209_Nunes et al._2016

description: Phenotypic data of brown boobies from six colonies along the South Atlantic Ocean; plus latitude, air temperature, and sea surface temperature data.
DOI: 10.5061/dryad.4h76d/1
title: SI-Draft-6Apr16

description: Sections S1 to S4 and Figures S1 to S10
DOI: 10.5061/dryad.4h76d/2
title: SI-Movies

description: Movies M1 to M7
DOI: 10.5061/dryad.6226d/15
title: ComputeMutation command file LTEE mutator

description: This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking to report only mutations occurring in point mutator clones of the LTEE
DOI: 10.5061/dryad.6226d/16
title: ComputeMutation command file LTEE non mutator

description: This file is the command file used by ComputeMutationThroughTimeDryad.pl to compute the mutation counts, the mutation matrix. This version is asking to report only mutations occurring in non point mutator clones of the LTEE
DOI: 10.5061/dryad.6226d/17
title: Compute genome composition perl script

description: This perl script computes the GenomeComposition.txt file that reports the number of synonymous, nonsynonymous and intergenic mutations for each of the 6 types of possible point mutations. See ReadMe.pdf for usage.
DOI: 10.5061/dryad.6226d/18
title: Compute mutation through time perl script

description: This perl script computes the spectrum of mutations found in each clone as well as the matrix used for the phylogeny. See ReadMe.pdf for usage.
DOI: 10.5061/dryad.6226d/19
title: Figures R script

description: This R script is used to create all figures and extended data figures. See ReadMe.pdf for usage.
DOI: 10.5061/dryad.6226d/20
title: Gstat perl script

description: This perl script computes the G stastics of convergence and the randomisation of point mutations used to estimate the p-value of the G estimated. See ReadMe.pdf for usage.
DOI: 10.5061/dryad.7nf43/1
title: SBW25 density and richness
DOI: 10.5061/dryad.7t18j/1
title: Local adaptation study
DOI: 10.5061/dryad.809v4/1
title: Behavioural data for F0F2 guppies
DOI: 10.5061/dryad.8bb66/1
title: Solidago_FINAL_HERBARIUM

description: Spreadsheet of historical and experimental counts.
DOI: 10.5061/dryad.8mj19/3
title: Regions of Interests

description: Regions of interests (5mm radius spheres in left anterior temporal, left posterior middle/superior temporal and left inferior frontal gyrus) used for small volume correction (SVC)
DOI: 10.5061/dryad.8mj19/4
title: SeedsForConnectivity

description: Seeds in left inferior frontal gyrus (LIFG) and left anterior cingulate cortex (LACC) used for the connectivity (gPPI) analysis.
DOI: 10.5061/dryad.8mj19/5
title: Behavioural Task Performance

description: Percentage correct on task in the higher and lower proportion blocks in the experiment (clicking a button whenever a word for an animal was displayed).
DOI: 10.5061/dryad.8s75g/1
title: Dataset

description: The effects of diet on parental life-history traits, the effects of mating partner on resource allocation and the effects of parental diet on offspring life-history traits, are organized in four worksheets. Please, note that the shortcuts H and L in the dataset, denote the high and low diet, respectively.
DOI: 10.5061/dryad.8s835/1
title: Kaiser et al. - Climatic data

description: Climatic data collected during the field experiment
DOI: 10.5061/dryad.8s835/2
title: Kaiser et al. - Larval survival

description: Sheet 1 and 2 includes data on larval survival of Pararge aegeria and Lasiommata megera, respectively
DOI: 10.5061/dryad.8s835/3
title: Kaiser et al. - Adult body mass

description: Sheet 1 and 2 includes data on adult body mass of Pararge aegeria and Lasiommata megera, respectively
DOI: 10.5061/dryad.bt4vj.1
title: Data from: The role of inhibitory dynamics in the loss and re-emergence of macropodoid tooth traits
DOI: 10.5061/dryad.fs798/1
title: Distribution of aquatic organisms across freshwater along the Azores Archipelago

description: Data consists of presence/absences of aquatic organisms in freshwater lakes. The dataset consists of a single table that was generated by combining survey data from the Springs of 2011 and 2012.
DOI: 10.5061/dryad.h6s5j/1
title: Nuclear and mtDNA loci

description: Sequence data files in NEXUS format for all four nuclear and two mtDNA loci used in this study. These files contain the sequence data analyzed in Weisrock et al. (2010) as well as new sequence data from this study.
DOI: 10.5061/dryad.h6s5j/2
title: Lemur Map Localities

description: A list of coordinate information for the localities presented in Figure 1.
DOI: 10.5061/dryad.h6s5j/3
title: STRUCTURE Analyses

description: A folder containing all input and results files for STRUCTURE analyses performed in this study.
DOI: 10.5061/dryad.h6s5j/4
title: BPP Analyses

description: A folder containing all input and results files from BPP analyses. Also included are .xlsx files summarizing the full set of BPP runs.
DOI: 10.5061/dryad.h6s5j/5
title: Bayes Factor Analyses

description: This folder contains all input and result files associated with *BEAST-based Bayes factor analyses performed in this study. Also included is an .xlsx file summarizing results across all analyses, including HME, sHME, Path Sampling, and Stepping Stone sampling calculations.
DOI: 10.5061/dryad.n654g/1
title: Durinskia baltica peptides

description: The file in fasta format contains 125,805 peptides predicted by Trinity TransDecoder from the assembled Durinskia baltica transcriptome, clustered at 98% similarity using CDHIT.
DOI: 10.5061/dryad.n654g/2
title: Phylogenetic Trees for Dinoflagellate-associated genes from Supplementary Table 2

description: FastTree-constructed phylogenetic trees in NEXUS format of dinoflagellate-associated genes in Durinskia baltica summarized in Supplementary Table 2. Blue texts indicate diatom transcripts, yellow/brown texts indicate dinoflagellate transcripts, green texts indicate dinotom transcripts, red texts indicate the query sequence used to query the respective database and black texts indicate all other taxa.
DOI: 10.5061/dryad.n654g/3
title: Phylogenetic Trees for Diatom-associated genes in Supplementary Table 2

description: FastTree-constructed phylogenetic trees in NEXUS format of diatom-associated genes in Durinskia baltica summarized in Supplementary Table 2. Blue texts indicate diatom transcripts, yellow/brown texts indicate dinoflagellate transcripts, green texts indicate dinotom transcripts, red texts indicate the query sequence used to query the respective database and black texts indicate all other taxa.
DOI: 10.5061/dryad.n654g/4
title: Phylogenetic Trees Cell division

description: FastTree-constructed trees in NEXUS format of diatom-associated genes in Durinskia baltica homologous to Phaeodactylum tricornutum cell division components as listed in Supplementary Table 5. Blue texts indicate diatom transcripts, yellow texts indicate dinoflagellate transcripts, green texts indicate dinotom transcripts, red texts indicate the query sequence used to query the respective database and black texts indicate all other taxa.
DOI: 10.5061/dryad.q8h75/2
title: all_cleaned_unique_cep_genomic_clone_sequence_new_names

description: genomic nucleotide sequence for all unique CEP genomic clones from R. reniformis.
DOI: 10.5061/dryad.q8h75/3
title: all_cleaned_unique_cep_genomic_clone_sequence_new_names

description: Protein sequence for all unique CEP genomic clones from R. reniformis.
DOI: 10.5061/dryad.q8h75/4
title: Unique_genomic_CEPs_cleaned_basian_new_names

description: Bayesian phylogenetic tree of cloned genomic CEP sequences.
DOI: 10.5061/dryad.q8h75/5
title: All_transcripts_from_the_same_comp_as_those_containing_cep-like_sequences_in_transcriptome

description: All transcripts from the same comp as those containing cep-like sequences in transcriptome.
DOI: 10.5061/dryad.q8n0v/1
title: Dryad

description: Data matrices and scripts to repeat all analyses presented in the paper.
DOI: 10.5061/dryad.rb7h0/4
title: GCF_000004515.3_V1.1_genomic

description: The script "BLAST_to_Coding_SSR.R”  (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS").This file is the gff file needed for the script.
DOI: 10.5061/dryad.rb7h0/5
title: G_R_0764-0510-HitTable

description: The script "BLAST_to_Coding_SSR.R”  (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS").This is the second of three files needed to run the script.
DOI: 10.5061/dryad.rb7h0/6
title: G_R_0803-0253-HitTable

description: The script "BLAST_to_Coding_SSR.R”  (https://github.com/soltislab/transcriptome_microsats/blob/master/BLAST_to_Coding_SSR.R) uses a .gff file (annotated Glycine max genome from NCBI), and a BLAST report for SSR Loci blasted against the Glycine max genome to prepare two files, which will be used in a subsequent script (Coding_SSR.py -- https://github.com/soltislab/transcriptome_microsats/blob/master/Coding_SSR.py) to determine which loci are in translated regions of the genome (i.e., regions that are annotated as "CDS"). The output of this script is two files (one contains the SSR loci identified from the BLAST search, with some unncessary columns and duplicates removed, and the other contains the regions of the Glycine max genome that are annotated as "CDS").This is the third of three files needed to run the script.
DOI: 10.5061/dryad.rb7h0/7
title: glycine_max_454_raw_all

description: A fasta file is necessary to run pal_finder.  The file included here is a fasta file of raw 454 genomic reads from Glycine max (NCBI Trace Archive (TI 1732557604-1733276192; Swaminathan et al., 2007)).
DOI: 10.5061/dryad.v677p/1
title: Archivio_dati_perimask

description: Data of the Time frequency analysis time locked to the onset of the visual feedback. 12 subjects (numbered from 1 to 12): each subject contributes 2 files relative to the High and Low error condition. Data were generated with the EEGLAB program.
DOI: 10.5061/dryad.v677p/2
title: Archivio_dati_periEC

description: Data relative to the timefrequency analysis time locked to the onset of error correction. 12 subjects. Each subject contributes 2 files relative to the High and Low error condition. Data were generated with the EEGLAB program.