cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8807/1
title: Table_S1_online

description: Frequencies of M. m. musculus alleles for each locus and sampling site. Distance along the transect and effective number of alleles (Ne) are also given. h = hybrid index expressed as the frequency of musculus alleles averaged across the six diagnostic allozyme loci.
DOI: 10.5061/dryad.8257/1
title: Panhuisetal_Supplementary Table 1_Evalueranges_sub

description: This is a supplementary table of the BLASTX results presented as the number of unique transcripts represented in a specific E-value range. The total number of P. turneri and P. presidionis unique sequences was 1956 and 924, respectively.
DOI: 10.5061/dryad.8779/1
title: Fig1AB

description: Fig1AB.xls provides the raw data used in the figure 1, A and B. A: These data were obtained in Puerto Viejo (location 1), Uruguay and describe the weight (in g) of the P. integrifolia capsules obtained after having covered the flowers either during the day or night.B: These data were obtained in Rivera (location 2), Uruguay and describe the weight (in g) of the P. integrifolia capsules obtained after having covered the flowers either during the day or night.
DOI: 10.5061/dryad.8787/1
title: MHCFreqAgudo

description: Haplotypes and frequencies of MHC class II B genes observed in three populations of Egyptian vulture
DOI: 10.5061/dryad.8790/2
title: big_plants.tar

description: The 55473 tip phylogenetic dataset including the extended phylip format alignment and the model file identifying the gene and partitions.
DOI: 10.5061/dryad.8795/1
title: cDNA_Dactylorhiza

description: cDNA-AFLP data on diploid and polyploid individuals of Dactylorhiza
DOI: 10.5061/dryad.qq877/1
title: Multiple sequence alignment

description: Nexus file containing multiple sequence alignment for phylogenetic analysis of Flectonotus and Fritziana, with character sets defined for mitochondrial 16S ribosomal RNA and proopiomelanocortin A (POMC) genes.
DOI: 10.5061/dryad.1321/1
title: Alignment of DNA sequences of Phrynobatrachus species

description: Alignment generated using ClustalX (gap cost = 15) of mitochondrial DNA sequences.
DOI: 10.5061/dryad.1926/8
title: 28S.3.2.may4.compress

description: 28S rDNA segment
DOI: 10.5061/dryad.8809/1
title: Boncoraglio et al database Dryad file

description: Original data collected in the lab. File created with Excel 2003. No abbreviations used for column headings.
DOI: 10.5061/dryad.q318s/1
title: Theba pisana Bold Park data

description: Shell morph frequencies in annual censuses of 5m x 5m quadrats along transect across ecotone between dense Acacia thicket and low, open vegetation in coastal dunes at Bold Park, Perth, Western Australia. Only adults and subadults (at least 10mm diameter) are included.
DOI: 10.5061/dryad.1267/1
title: microsatellite alleles sizes of mothers and brood, and of the population sample.xls

description: The table contains microsatellite allele sizes of mothers and their broods, and of the population sample. The data were used to reconstruct the number of sires per brood. Offspring sample IDs are prefixed by a 'C'.
DOI: 10.5061/dryad.8826/1
title: CRISPR spacer database

description: This data file consists of a FASTA file containing all spacers in the CRISPR spacer database used for this publication. The name of each sequence describes the NC number of the species in which the CRISPR spacer is found, the number of the CRISPR locus in which it is found, and the number of the spacer within that CRISPR locus. The manuscript describes how this database was created.
DOI: 10.5061/dryad.8826/2
title: Supplementary Table 2

description: This file, designated Supplementary Table 2 in the manuscript, consists of a resemblance matrix used to compare the set of all CRISPR spacers in each genome in the NCBI database against the set of CRISPR spacers in every other genome. X- and Y- axes of the matrix list all sequenced strains in the NCBI database as of April 20th, 2010. Numbers corresponding to each pair indicate the number of CRISPR spacers shared between the two strains, divided by the sum total of all CRISPR spacers between the two strains."Shared" here indicates an alignment of 100% identity  across at least 20 base pairs.
DOI: 10.5061/dryad.8837/1
title: Papallacta females

description: Data collected for Papallacta female choice trails.  Used excel to create the file and then used R software for analysis.  Decoy is the live male decoy used for each trial. Song_name is the treatment: PAPA=Papallacta, PIN= Pintag, BA= Buenos Aires, CON=Control.   Playback is the song variation of the treatment used.
DOI: 10.5061/dryad.8487/2
title: Variance-covariance matrix

description: Variance-covariance matrix of the phylogeny to the tip names in AgamidDataTip.xls. Branch lengths are set to 1 but polytomies resolved with a branch length of 0.0001.
DOI: 10.5061/dryad.8608/1
title: LandmarkDatabase

description: Two dimensional coordinates (consensus for each caviomorph genera) for landmarks dataset (L). Data file was generated using tpsDig 2.12 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/).
DOI: 10.5061/dryad.8608/2
title: LandmarkSemilandmarkDatabase

description: two-dimensional coordinates (consensus for each caviomorph genera) for landmarks plus semilandmarks dataset (SL). Data file was generated using tpsDig 2.12 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)
DOI: 10.5061/dryad.8835/1
title: Hoban_J_cinerea_Mol_Ecol_2010_Microsat_Data_Dryad

description: This file contains the microsatellite genotypes for 11 loci and 904 individuals, in 29 natural populations (forest) of butternut (J cinerea L) across eastern North America.  These are the data referred to in the first sentence of the Results.  They are data AFTER removal of hybrid individuals, identical genotypes, or individuals with too much missing data.  These data are therefore the data used to calculate all statistics in the paper. The data are in GENEPOP format.  The names of individuals are unique identification numbers used in our lab.  The names of the loci correspond to those from Robichaud et al, and Hoban et al, as described in the Materials and Methods of the paper.
DOI: 10.5061/dryad.8837/2
title: Papallacta Males

description: Papallacta male simulated territorial intrusions.  Collected data in the field. Used excel for spreadsheet. Used JMP and SAS for data analysis. Treatment= song origin. PAP:Papallacta, Pin: Pintag, lp: La Paz, Ba: Buenos Aires, Con: Control song. Songs= number of songs sung during trial. Approach= closest approach to the playback speaker.
DOI: 10.5061/dryad.8837/3
title: Pintag Males

description: Pintag male simulated territorial intrusions.  Collected data in the field. Used excel for spreadsheet. Used JMP and SAS for data analysis. Treatment= song origin. PAP:Papallacta, Pin: Pintag, lp: La Paz, Ba: Buenos Aires, Con: Control song. Songs= number of songs sung during trial. Approach= closest approach to the playback speaker.
DOI: 10.5061/dryad.8837/4
title: Pintag Females

description: Data collected for Pintag female choice trails.  Used excel to create the file and then used R software for analysis.  Decoy is the live male decoy used for each trial. Song_name is the treatment: PAPA=Papallacta, PIN= Pintag, BA= Buenos Aires, CON=Control.   Playback is the song variation of the treatment used.
DOI: 10.5061/dryad.8845/1
title: Summary data for the studies used in the meta-analysis of local adaptation (Table 1 from the publication)

description: This table contains the data used in this published meta-analysis. The data were originally extracted from the publications listed in the table. The file corresponds to Table 1 in the original publication.
DOI: 10.5061/dryad.8265/1
title: Chemical interest trial data Runemark et al.
DOI: 10.5061/dryad.8265/2
title: Pheromone composition data Runemark et al.
DOI: 10.5061/dryad.8490/1
title: supplemental_MEC-10-1246.R1

description: The zipped file contains the alignments and tree files from the Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V) used in the study Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota.
DOI: 10.5061/dryad.8608/3
title: RWLandmark

description: RW scores (for each caviomorph genera) obtained through a Generalized Procrustes Analysis of the landmark dataset (L). Archive format: .nts. Data generated using tpsRelW 1.46 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)
DOI: 10.5061/dryad.8608/4
title: RWLandmarkSemilandmark

description: RW scores (for each caviomorph genera) obtained through a Generalized Procrustes Analysis of the landmarks plus semilandmarks dataset (SL). Archive format: .nts. Semilandmarks were slid using a minimum bending energy criterion with 5 iterations. Data generated using tpsRelW 1.46 (Rohlf, 2008. Available at: http://life.bio.sunysb.edu/morph/)
DOI: 10.5061/dryad.8845/2
title: SAS script used to perform meta-analyses

description: This file contains the essential elements of the SAS script used to perform meta-analyses published in Hoeksema & Forde 2008. Multi-factor models were fit to the data using weighted maximum likelihood estimation of parameters in a mixed model framework, using SAS PROC MIXED, in which the species traits and experimental design factors were considered fixed effects, and a random between-studies variance component was estimated. Significance (at alpha = 0.05) of individual factors in these models was determined using randomization procedures with 10,000 iterations (performed with a combination of macros in SAS), in which effect sizes and their weights were randomly permuted among levels of the independent variables.
DOI: 10.5061/dryad.8861/1
title: Data trajectories after a kill

description: These data describe the movements of 8 lions after some identified kills. Data are from GPS-collars.
DOI: 10.5061/dryad.8849/1
title: PacSNP chum data for MER

description: The file is formatted for GenAlEx software, but can easily be converted to Genepop or similar formats.  Genotypes are in two-column format with missing data designated with a “0”.   Population code and locus code worksheets follow the rawdata.  The population order differs between the rawdata which is in numeric order and Table 1 of the manuscript which is ordered geographically.  This is particularly noticeable in the order of the Western Alaska populations including the Yukon River.  The rawdata includes laboratory names for the SNPs; a key to published names is in the locus code worksheet. The mtDNA SNPs are listed independently and have not been combined into composite haplotypes.
DOI: 10.5061/dryad.8856/1
title: data for dryad

description: This file contains three tables. Two tables include all primary data for the response variables at regional and local scales of the experiment. The last table explains all variables.
DOI: 10.5061/dryad.8858/1
title: Epistasis_KB

description: Epistasis data for 14 rifampicin-resistant double mutants of Pseudomonas aeruginosa in nutrient-rich KB growth media. Column headers described in the readme file.
DOI: 10.5061/dryad.8858/2
title: Epistasis_BIOLOG

description: Epistasis data for 14 rifampicin-resistant double mutants of Pseudomonas aeruginosa in 41 different single-carbon source (BIOLOG) environments. Column headers described in the readme file.
DOI: 10.5061/dryad.8437/1
title: Genbank HQ540559

description: DNA sequence of mitochondrial NADH2 gene from golden cownose ray
DOI: 10.5061/dryad.8437/2
title: Genbank HQ540560

description: DNA sequence of mitochodnial NADH2 gene from golden cownose ray
DOI: 10.5061/dryad.8437/3
title: Genbank HQ540561

description: DNA sequence of mitochondrial NADH2 gene from golden cownose ray
DOI: 10.5061/dryad.8866/2
title: Metamorphs body weight

description: 143 metamorphs (four to five per tank) were used for analyses. Formalin fixed metamorphs were weighed with a digital balance.
DOI: 10.5061/dryad.8437/4
title: Genbank HQ540562

description: DNA sequence of mitochondrial NADH2 gene from golden cownose ray
DOI: 10.5061/dryad.8861/2
title: Data random trajectories

description: These data correspond to 48-hour trajectories after a random location that did not correspond to a kill site. There are data from the same 8 GPS-collared lions monitored for trajectories after a kill.
DOI: 10.5061/dryad.8866/1
title: metamorph brains

description: Experimental treatments included low and high larval density, crossed with the presence and absence of a caged predator. 100 tadpoles from each of the 12 clutches were pooled into a bucket and allocated to each tank (high density = 50 tadpoles/tank; low density = 10 tadpoles/tank). In tanks with the predator treatments, one dragonfly larva (Aeshna sp.) was placed in a cylindrical cage (diameter 8 cm; height 21 cm) made of transparent plastic film with a double net bottom (mesh size 1.5 mm) and hung 6 cm over the tank bottom. This allowed tadpoles to receive both visual and chemical cues from the predator, while the predator was unable to actually prey on tadpoles. In the no-predator treatment, the cage was left empty. During the experiment, tadpoles relied on the initial resources provided (leaves, rabbit pellets), as well as subsequent algal growth. Each treatment combination was replicated eight times, resulting in a total of 32 experimental units.  143 metamorphs (four to five per tank) were used for analyses. Formalin fixed metamorphs were weighed with a digital balance. After dissection, dorsal and right lateral views of brains were photographed with a digital camera connected to a dissecting microscope. We could only measure two dimensions for each brain part (length and width of telencephalon, diencephalon and optic tectum, and height and width of medulla oblongata) because some of the borders of the brain parts could not be identified accurately. Measurements were taken from digital photographs using tpsDig 1.37 software, and were defined as the greatest distance enclosed by the given structure in the given direction. All brains were photographed and measured three times. Repeatability of different brain measurements was high (R = 0.71 – 0.96 [mean = 0.86]).
DOI: 10.5061/dryad.8869/1
title: Mature Tree Data

description: Contains all the data related to the merged
DOI: 10.5061/dryad.8869/2
title: Facilitation Experiment Data

description: Data from the seedling experiment.
DOI: 10.5061/dryad.2025/1
title: dataset
DOI: 10.5061/dryad.8384/1
title: Wu_2011_Data

description: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes.Dongying Wu, Martin Wu, Aaron Halpern, Doug Rusch, Shibu Yooseph, Marvin Frazier, J. Craig Venter, Jonathan A. Eisen.Supplementary Data: (1) recA data: recA.tgz. recA.tgz contains the following files:recA_GOS.pep -- Amino acid sequences for GOS RecAs, recA_ref.pep -- Amino acid sequences for RecAs from NRAA and genome sequences, recA_cluster.txt -- Lek clusters of RecA sequences (Table 1), recA.ali -- Original alignment for the RecA tree (Figure 1), recA.trim.ali -- Trimmed RecA alignment that the RecA tree is built upon (Figure 1), recA.tre -- RecA tree in Newick format (Figure 1), recA_GOS_pepID_assemblyID.map -- The assembly IDs of the recA encoding GOS assemblies (Table 2), recA_linked.pep -- The Amino Acid sequences of the genes that share assemblies with the GOS novel recA (Table 2). (2) rpoB data: rpoB.tgz. rpoB.tgz contains the following files: rpoB_GOS.pep -- Amino acid sequences for GOS RpoBs, rpoB_ref.pep -- Amino acid sequences for RpoBs from NRAA and genome sequences, rpoB_cluster.txt -- Lek clusters of RpoB sequences (Table 3), rpoB.tre.ali -- Original alignment for the RpoB tree (Figure 3), rpoB.tre.trim -- Trimmed RpoB alignment that the RpoB tree is built upon (Figure 3), rpoB.tre -- RpoB tree in Newick format (Figure 3). (3) ss-rRNA data: ssu.tgz. ssu.tgz contains the following files: SSU_GOSreads.fa -- GOS ss-rRNA sequences, SSU_GOSreads_deepbrach.fa -- Potential GOS deep-branching ss-rRNA. (4) Lek Clustering Program: lek.tgz. lek.tgz contains scripts for the Lek clustering protocol. Instructions can be found in the included README file.
DOI: 10.5061/dryad.8887/1
title: Pfeiffer et al_JOH-2010-168.R1_Mercurialis_01matrices

description: Primary data: 01 matrices (3 scoring routines) for the SSR fingerprinting (8 loci) in polyploid Mercurialis perennis; see sheet "Description" for further details
DOI: 10.5061/dryad.8891/6
title: Colletotrichum_gloesporioides_combined_matrix

description: Colletotrichum agg. gloeosporioides - Nexus file, aligned, concatenated datasets:complete ITS, tef-1, and gpd loci.
DOI: 10.5061/dryad.8891/7
title: Pestalotiopsis_microspora_combined_matrix

description: Pestalotiopsis agg. microspora - Nexus file, aligned, concatenated datasets: ITS, tef-1, and gpd loci.
DOI: 10.5061/dryad.17rc2f69/1
title: Lupinus.online.FigureS1.04.26.11

description: SUPPLEMENTARY FIGURE S1. Ancestral geographic ranges of Lupinus inferred under a dispersal–extinction cladogenesis (DEC) model in lagrange, based on the maximum clade credibility tree in Figure 2 of the main text. Circles correspond to the maximum likelihood estimate of ancestral ranges, with divided circles indicating ancestral ranges split by dispersal and/or extinction on subtending branches. The DEC estimates are very similar to the BEAST continuous-time Markov chain (CTMC) phylogeographic results shown in the main text, with the main difference being that DEC tends to reconstruct widespread ancestral ranges at nodes with uncertain posterior distributions in the CTMC analysis. We obtained similar estimates for DEC analyses based on 1000 trees randomly selected from the posterior distribution of Bayesian MCMC tree searches in BEAST (results not shown), indicating that the DEC analyses were robust to phylogenetic uncertainty.
DOI: 10.5061/dryad.17rc2f69/2
title: Lupinus.online.FigureS2.04.26.11

description: SUPPLEMENTARY FIGURE S2. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model. MEDUSA analyses were conducted using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Histograms show the frequency (ƒ) of estimates from replicate MEDUSA likelihood runs: a) ΔAIC scores for pure–birth versus birth–death models; b) background rates of net diversification in Lupinus; c) ΔAIC scores for a rate shift in eastern South America; d) net diversification rates in eastern South America; e) ΔAIC scores for a rate shift in western North America; f) net diversification rates in western North America; g) ΔAIC scores for a rate shift in Mexico/Andes; h) net diversification rates in Mexico/Andes. ΔAIC scores indicated that a pure–birth model was strongly favored over a model incorporating extinction (Fig. S2a). The strongest support for a primary rate shift was recovered in western North America (Fig. S2e), although the fastest rates were estimated in the Mexican/Andean clade (Fig. S2h).
DOI: 10.5061/dryad.17rc2f69/3
title: Lupinus.online.FigureS3.04.26.11

description: SUPPLEMENTARY FIGURE S3. Net diversification rates (r = lineages/million years) in Lupinus estimated under the MEDUSA birth–death likelihood model, including relative extinction (ε = birth/death) as a free parameter. MEDUSA analyses were conducted using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Surface plots show the frequency (ƒ) of estimates from replicate MEDUSA likelihood runs, including the joint relationship between r and ε: a) background rates in Lupinus; b) eastern South America; c) western North America; d) Mexico/Andes. Estimates of net diversification were generally similar to estimates obtained under a pure–birth MEDUSA model, with the primary differences including lower r and high ε in the eastern South American clade (Fig. S3b), and a bimodal distribution of ε in the Mexican/Andean clade (Fig. S3d). However, ΔAIC scores shown in Figure S2a indicate that the pure–birth model was strongly favored over the birth–death results shown here. We obtained similar results for pure–birth and birth–death MEDUSA analyses based on the posterior distribution of trees from birth–death Bayesian MCMC tree searches in BEAST (results not shown), indicating that the MEDUSA analyses were robust to the choice of tree prior used for phylogenetic inference. Note that estimates of ε for eastern South America should be considered unreliable, since unresolved terminal clades do not contain sufficient information to infer this parameter (Rabosky et al. 2007; Alfaro et al. 2009).
DOI: 10.5061/dryad.17rc2f69/4
title: Lupinus.online.FigureS4.04.26.11

description: SUPPLEMENTARY FIGURE S4. BiSSE analyses of correlated rates of net diversification (r = lineages/million years) for life history (annual versus perennial) and habitat (lowland versus montane) in Lupinus. BiSSE analyses were conducted under a pure–birth model using 1000 trees randomly selected from the posterior distribution of constrained pure–birth Bayesian MCMC tree searches in BEAST, pruned to the infrageneric skeleton topology in Figure 3 of the main text. Histograms show the frequency (ƒ) of estimates from replicate BiSSE likelihood runs: a) ΔAIC scores for unconstrained versus constrained life history rate models; b) rates of net diversification in annual species; c) rates of net diversification in perennial species; d) ΔAIC scores for unconstrained versus constrained habitat rate models; (e) rates of net diversification in lowland species; (f) rates of net diversification in montane species. The weight of evidence indicates strong support for higher rates of net diversification in perennial and montane lineages.
DOI: 10.5061/dryad.17rc2f69/5
title: Lupinus.online.Appendix1.15.08.11

description: Supplementary methods and Identities, botanical vouchers, GenBank numbers and sources of DNA sequence data
DOI: 10.5061/dryad.17rc2f69/6
title: Lupinus.online.Appendix2.04.26.11

description: DNA sequence alignment
DOI: 10.5061/dryad.17rc2f69/7
title: Lupinus.online.Appendix3.04.26.11

description: Classification and assignment of extant diversities to infrageneric groups in Lupinus. The lettered notations below correspond to monophyletic terminal clades shown in Figure 3 of the main text.
DOI: 10.5061/dryad.8877/1
title: Cayetano-et-al-C-maculatus-data

description: Morphometric data for Callosobruchus maculatus beetles from 16 replicate artificial evolution lines.
DOI: 10.5061/dryad.17rc2f69/8
title: Lupinus.online.Appendix4.04.26.11

description: Life history and habitat data for ancestral state reconstructions of character states in Lupinus.
DOI: 10.5061/dryad.4930/1
title: small PEBP analysis

description: “small PEBP analysis.zip” file is consisted of 4 files derived from a small PEBP phylogenetic analysis. Two multiple sequence alignment (protein) files in .fas (fasta) and .nex (nexus) are enclosed. This latter can be visualized using Mesquite software (Maddison and Maddison, 1992). The .mts (MEGA4) file corresponds to the phylogenetic tree analysis using the MEGA4 software (Tamura et al., 2007). The .emf file is an output picture file corresponding to the obtained phylogenetic tree.
DOI: 10.5061/dryad.4930/2
title: large PEBP analysis

description: “large PEBP analysis.zip” file is consisted of 4 files derived from a large PEBP phylogenetic analysis. Two multiple sequence alignment (protein) files in .fas (fasta) and .nex (nexus) are enclosed. This latter can be visualized using Mesquite software (Maddison and Maddison, 1992). The .mts (MEGA4) file corresponds to the phylogenetic tree analysis using the MEGA4 software (Tamura et al., 2007). The .emf file is an output picture file corresponding to the obtained phylogenetic tree.