cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.85q50/3
title: Cladogram (analysis #1)

description: Cladogram used for MCMCtree analysis #1 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85q50/4
title: Cladogram (analysis #2)

description: Cladogram used for MCMCtree analysis #2 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85q50/5
title: Cladogram (analysis #4)

description: Cladogram used for MCMCtree analysis #4 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85qd6/2
title: Sperm transfer experiment

description: This data has been used for sperm transfer experiment and production of figure 2.
DOI: 10.5061/dryad.85qd6/3
title: Figure 3 data

description: % hatching success per sperm has been calculated and figure 3 has been produced.
DOI: 10.5061/dryad.9g7d8/1
title: Historical Bee Data

description: This data comprise museum collection records with Date of collection, Latitude and Longitude for all species used in the analysis. It also contains the asynchrony value with apple peak bloom (see article for details).
DOI: 10.5061/dryad.b9m853tp/1
title: ITS_MATK_datamatrix_Eriogonoideae.phy

description: Phylip format; data matrix of 61 species; 2829 characters
DOI: 10.5061/dryad.bt51g/4
title: ReadMe_new

description: A Readme file.
DOI: 10.5061/dryad.cv39v/5
title: Li et al. Supplemental File 5: Table 5. Expression changes in Ptbp2-NesKO mice.

description: Genes showing overall expression changes were identified by Cuffdiff analysis.
DOI: 10.5061/dryad.cv39v/6
title: Li et al. Supplemental File 6: Table 6. Gene Ontology analysis of genes up-regulated in Ptbp2-NesKO mice.

description: Genes showing a two-fold or greater increase in expression in the KO relative to WT were analyzed for functional or process enrichment relative to all genes expressed in wildtype brain.
DOI: 10.5061/dryad.cv39v/7
title: Li et al. Supplemental File 7: Table 7. Gene Ontology analysis of genes down-regulated in Ptbp2-NesKO mice.

description: Genes showing two-fold or greater reduced expression in the KO relative to WT were analyzed for functional or process enrichment relative to all genes expressed in wildtype brain.
DOI: 10.5061/dryad.cv39v/8
title: Li et al. Supplemental File 8: Table 8. Splicing Changes Identified by RNAseq analysis in Ptbp2-EmxKO mice.

description: RNAseq reads from P1 WT and EmxKO mice were subjected to Splicetrap analysis (see Methods). Events with a change in PSI of greater than 10% are shown with genome coordinates, read numbers, and coverage statistics.
DOI: 10.5061/dryad.dc1r2/1
title: Coccinellidae nucleic acid and morphological data matrix

description: Partitioned nexus file containing molecular and morphological data, used for Bayesian inference of coccinellid phylogeny. Includes the loci COI, COII, and 28S.
DOI: 10.5061/dryad.dc1r2/2
title: Coccinellidae combined dataset: consensus tree

description: Consensus of 50K trees from Bayesian analysis, excluding 3k burnin.
DOI: 10.5061/dryad.fg868/1
title: Evolution_data

description: All simulation data: Fitness and parameters and matlab source code.
DOI: 10.5061/dryad.hb7j1/1
title: Supplemental Data Set 1. Read Statistics of RNA-Seq Data and Computational Analysis of Transcriptome-Wide AS and Gene Expression.

description: (A) Alignment statistics of all RNA-seq reads derived from Illumina sequencing.(B) - (E) Event based alternative splicing analysis based on comparisons of WT vs. lba1 upf3-1 double mutant (B), WT vs. lba1 (C) and WT vs. upf3-1 (D) single mutants, and Mock vs. CHX treatment (E) datasets. For each AS event and comparison, p and Q values from testing AS variant ratio changes in either one (up) or the other (down) direction as well as the minimum (min) values are provided. Furthermore, rankings within each list according to the p values are provided.(F) Combined list of alternative splicing analyses (based on single comparisons displayed in (B) - (E)) allowing comparison of different datasets on a single event basis. Use matrix in columns R-U to analyze differential gene expression (GE) or AS pattern changes (TE) for the indicated comparisons by changing thresholds for FDR or p values. The matrix allows considering single tests as well as combinations, and both maximum (MAX THRESHOLDS) and minimum (MIN THRESHOLDS) cut-off values can be set. Number of significant changes with given settings are displayed under “SIGNIFICANCE COUNTS”. Results for single events can be viewed and sorted using columns A-P, with values “1” and “0” indicating “FALSE” and “TRUE”, respectively, for fulfilling the criteria set in the matrix shown in columns R-U. Note that the logic provided in this spreadsheet only works if sorting in sheets (B) - (E) is unchanged.(G) Splice Index Score (Percent spliced in, PSI) of all tested alternative splicing events in all samples and replicates (R) analyzed.(H) Table for internal lookup to compute differential gene expression data. Sorting of this table must not be changed. For analyzing differential gene expression use sheet (I).(I) Differential gene expression analysis for all genes and samples. Numbers provide p values. Matrix in columns P-AB can be used to enter gene types and cut-off values for the individual samples, displaying the total number of genes (“COUNT”) fulfilling the set criteria.Further information and a detailed description of the computational pipeline are provided in Supplemental Methods.
DOI: 10.5061/dryad.hb7j1/2
title: Supplemental Data Set 2. Analysis of NMD Target Features for All Events.

description: (A) General information on mapping of all and the significantly changed alternative splicing events. (B) AS event positions relative to the cds of the representative transcript model annotated in TAIR10 for all AS events and those significantly changed in the different samples. Subsets as described in Figure 3B.(C) Analysis of NMD target feature frequencies for the AS events significantly changed in the indicated samples. For each AS event and dependent on the direction of the AS ratio change, one of the two corresponding splicing variants was assigned to the control sample (WT or Mock treatment), whereas the other was assigned to the NMD-impaired sample (“Δ NMD”). This splicing variant assignment then allowed counting how many of those contained classical NMD features, separately analyzing events mapping to the 5’ UTR, cds, and 3’ UTR. NMD feature inspection included upstream open reading frames (uORFs), translation initiation site (TIS) overlapping uORFs, occurrence of PTCs leading to 3’ UTRs &gt; 347 nts, splice junctions more than 50 nts downstream of a stop codon, and PTC-independent, long 3’ UTRs &gt; 347 nts.(D) Frequency patterns of NMD-eliciting features in different datasets. Occurrence of NMD features described in (C) were analyzed considering the following categories: splicing variant assigned to the control, but not to the NMD impairment has NMD feature (1,0), splicing variant assigned to the NMD impairment, but not to the control has NMD feature (0,1), both splicing variants have NMD feature (1,1), and none splicing variant has NMD feature (0,0).(E) 3’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (C).(F) 5’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (C).(G) Numbers of genes containing single or multiple significantly changed AS events for the indicated subsets. For the genes with multiple events, transcripts with all possible combinations were assembled and analyzed for the rescue of a PTC introduced by a single event.Further details on data analysis are provided in Supplemental Methods.
DOI: 10.5061/dryad.hb7j1/3
title: Supplemental Data Set 3. Analysis of NMD Target Features for Genes Containing Single Events.

description: (A) AS event positions relative to the cds of the representative transcript model annotated in TAIR10 for all AS events and those significantly changed in the different samples. Subsets as described in Figure 3B.(B) Analysis of NMD target feature frequencies for the AS events significantly changed in the indicated samples. For each AS event and dependent on the direction of the AS ratio change, one of the two corresponding splicing variants was assigned to the control sample (WT or Mock treatment), whereas the other was assigned to the NMD-impaired sample (“Δ NMD”). This splicing variant assignment then allowed counting how many of those contained classical NMD features, separately analyzing events mapping to the 5’ UTR, cds, and 3’ UTR. NMD feature inspection included upstream open reading frames (uORFs), translation initiation site (TIS) overlapping uORFs, occurrence of PTCs leading to 3’ UTRs &gt; 347 nts, splice junctions more than 50 nts downstream of a stop codon, and PTC-independent, long 3’ UTRs &gt; 347 nts.(C) Frequency patterns of NMD-eliciting features in different datasets. Occurrence of NMD features described in (B) were analyzed considering the following categories: splicing variant assigned to the control, but not to the NMD impairment has NMD feature (1,0), splicing variant assigned to the NMD impairment, but not to the control has NMD feature (0,1), both splicing variants have NMD feature (1,1), and none splicing variant has NMD feature (0,0).(D) 3’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (B).(E) 5’ UTR length distribution for transcripts assigned to the control or NMD-impaired samples for the indicated subsets. Assignments of two splicing variants for each event as described in (B).Further details on data analysis are provided in Supplemental Methods.
DOI: 10.5061/dryad.hb7j1/4
title: Supplemental Data Set 4. Categorization of NMD-Regulated and Reference Gene Sets into Functional Subgroups.

description: (A) Functional categorization of genes derived from the different subsets described in Figure 3B as well as all annotated genes based on the TAIR10 release and all genes displaying AS evidence based on our data (“all AS”). Furthermore, indicated subsets of cassette exon (CE)-containing genes were analyzed. Category bin and names and corresponding counts are listed.(B) Combination of MapMan based functional classifications into different functional subgroups as shown in table on the left side. Numbers of genes falling into these combined categories for the indicated subsets are shown. Below each set, data are also displayed in pie charts. Hypergeometrical test for differential representation of the combined categories are provided for the individual subsets.(C) Differential gene expression data for annotated splicing factors in NMD-impaired samples versus their respective controls based on the analysis described in Supplemental Dataset 1I. Furthermore, expression of the annotated, representative isoforms was analyzed in WT and lba1 upf3-1 using rQuant as described in Supplemental Methods.
DOI: 10.5061/dryad.hb7j1/5
title: Supplemental Data Set 5. Expressed Intergenic Regions and NMD Impairment-Responsive ncRNAs and Pseudogenes.

description: (A) Differential gene expression data for all annotated ncRNAs based on the analysis described in Supplemental Dataset 1I. Separate display of ncRNAs differentially expressed (either up- or downregulated) in the indicated samples.(B) Differential gene expression of annotated pseudogenic transcripts based on the analysis described in Supplemental Dataset 1I. The matrix provides counts for genes and pseudogenes differentially expressed (p &lt; 0.01) in the indicated NMD-impaired samples relative to their corresponding controls.(C) Expression of identified intergenic regions; listed are total read counts for the indicated subsets and regions. Significantly expressed intergenic regions are marked by an asterisk, colored in green are the regions analyzed in Figure 7D. Furthermore, information on the numbers of intergenic regions, which are more than twofold up- or downregulated in the indicated types of NMD impairments versus their corresponding controls, is indicated below the table. For more detailed information on data analysis see Supplemental Methods.
DOI: 10.5061/dryad.hk45m/10
title: 25442 locus phased alignment

description: 25442 locus phased alignment in fasta format
DOI: 10.5061/dryad.hk45m/11
title: 25613 locus phased alignment

description: 25613 locus phased alignment in fasta format
DOI: 10.5061/dryad.hk45m/12
title: 27331 locus phased alignment

description: 27331 locus phased alignment in fasta format
DOI: 10.5061/dryad.hk45m/13
title: 27818 locus phased alignment

description: 27818 locus phased alignment in fasta format
DOI: 10.5061/dryad.hk45m/14
title: MUSK locus phased alignment

description: MUSK locus phased alignment in fasta format
DOI: 10.5061/dryad.hk45m/15
title: ND2 locus alignment

description: ND2 locus alignment in fasta format
DOI: 10.5061/dryad.hk45m/16
title: ND2 locus alignment-trimmed

description: ND2 locus alignment that has been trimmed to include only the 25 individuals sequenced for nuclear introns. The full (1041 bp) ND2 gene was sequenced for these individuals.
DOI: 10.5061/dryad.hk45m/17
title: Morphological data matrix

description: A table described the four observed plumage character states for all scored individuals.
DOI: 10.5061/dryad.hk45m/9
title: 24972 locus phased alignment

description: 24972 locus phased alignment in fasta format
DOI: 10.5061/dryad.jm858/1
title: XML for input into BEAST with increasing temporal sampling range

description: XML were created in BEAUti v1.5.4 for analysis in BEAST v1.7.4, as described in Hedge et al. 2013 (Drummond & Rambaut, 2007, Drummond et al. 2012). Each file specifies the EpiFlu accession numbers of the segments concatenated into the whole-genome sequences and used as input data for the analysis (http://platform.gisaid.org/). Each file is labelled with the name of the last month during which sequences included in the analysis were sampled and the growth modelled employed. For example, June.exp.xml comprises EpiFlu accession numbers of sequences sampled from the start of the pandemic until June 2009 and specifies the use of an exponential growth model. Details of the substitution, clock and coalescent models are provided along with the priors placed on the model parameters. An additional block implementing the estimation of the marginal likelihood of the model using path-sampling is given after the Markov chain Monte Carlo (MCMC) block (Baele et al. 2012).
DOI: 10.5061/dryad.jt2b5/1
title: Absorbance data

description: Raw data of absorbances of culture relating to Fig 2 in main text
DOI: 10.5061/dryad.jt2b5/2
title: count data

description: Cell count raw data for Fig 2 in main text
DOI: 10.5061/dryad.kf251/1
title: Supplementary Figures and Tables
DOI: 10.5061/dryad.m1fp77jg/1
title: Runemark_and_Svensson_MatingData

description: Please see the readme file
DOI: 10.5061/dryad.m1fp77jg/2
title: Geographic_locals_Runemark_and_Svensson

description: Please see the readme file
DOI: 10.5061/dryad.n7m28/1
title: humanGenome_Results.part01

description: hg19 predictions (part 1)
DOI: 10.5061/dryad.n7m28/2
title: humanGenome_Results.part02

description: hg19 predictions (part 2)
DOI: 10.5061/dryad.n7m28/3
title: humanGenome_Results.part03

description: hg19 predictions (part 3)
DOI: 10.5061/dryad.n7m28/4
title: humanGenome_Results.part04

description: hg19 predictions (part 4)
DOI: 10.5061/dryad.pk85d/1
title: Tungara frog multimodal choice test data

description: Results from two-choice experiments where female tungara frogs were allowed to choose among combinations of acoustic and visual components of male mating signals.  All frogs were wild-collected from the field in the Republic of Panama.
DOI: 10.5061/dryad.pn7t4/1
title: Phenotype cladistic matrix

description: Cladistic matrix based on phenotypic characters
DOI: 10.5061/dryad.pn7t4/2
title: microRNA cladistic character matrix

description: Cladistic character matrix for the repertoire of microRNAs in the taxa considered in the analysis
DOI: 10.5061/dryad.qj3sb/1
title: Kronauer et al. 2013 Beh Ecol Microsatellite Data

description: Microsatellite genotype raw data
DOI: 10.5061/dryad.r6ng71d4/1
title: Predel_SystBiol_supplMat1
DOI: 10.5061/dryad.t1b051ph/2
title: Microsatellite_scores-67cheetahs

description: Scores of 67 cheetahs screened at 18 microsatellite loci
DOI: 10.5061/dryad.t7qm4/1
title: FemaleBodyMass

description: Individual raw data for female body mass of species used in analyses
DOI: 10.5061/dryad.t7qm4/2
title: 28SD1

description: Previously unpublished 28SD1 sequences
DOI: 10.5061/dryad.t7qm4/3
title: 28SD2

description: Previously unpublished 28SD2 sequences
DOI: 10.5061/dryad.t7qm4/4
title: COI

description: Previously unpublished COI sequences
DOI: 10.5061/dryad.t7qm4/5
title: Ef1a

description: Previously unpublished EF1a sequences
DOI: 10.5061/dryad.t7qm4/6
title: GAPDH

description: Previously unpublished GAPDH sequences
DOI: 10.5061/dryad.t7qm4/7
title: IDH

description: Previously unpublished IDH sequences
DOI: 10.5061/dryad.t7qm4/8
title: RpS5

description: Previously unpublished RpS5 sequences
DOI: 10.5061/dryad.t7qm4/9
title: WGL

description: Previously unpublished WGL sequences
DOI: 10.5061/dryad.110nt/2
title: Mitochondrial traits
DOI: 10.5061/dryad.110nt/3
title: Spain flight metabolism
DOI: 10.5061/dryad.110nt/4
title: French males flight metabolism etc
DOI: 10.5061/dryad.110nt/5
title: Nrv2 and Phd expression in new adults
DOI: 10.5061/dryad.110nt/6
title: Phd_Noc_Nrv2_Hif1a in pupae
DOI: 10.5061/dryad.122sv/1
title: Dandekar_Biolog_data

description: Biolog Phenotype Microarray data
DOI: 10.5061/dryad.18nk2/1
title: SL of original species

description: This file includes original data for our Fig. 1-B. Standard length (mm) of each individuals of each species at 14, 28 and 56 days post hatch are listed.
DOI: 10.5061/dryad.18nk2/2
title: genetic map

description: Includes 4 files (.qtx) that were used to create genetic map (Fig S2-A, S2-B).
DOI: 10.5061/dryad.18nk2/3
title: QTL

description: There are 2 files (.qtx) that were used for QTL analysis (Fig 2, and Fig S3).
DOI: 10.5061/dryad.18nk2/4
title: Allelic effect

description: Original data for Table_2. Individuals were divided into 4 groups according to their genotypes at f198, and SL (mm) for each specimen were listed.
DOI: 10.5061/dryad.2k9j0/1
title: Complete Simulation Results

description: This excel spreadsheet gives the complete simulation results for all methods and parameter settings described in the main simulation.
DOI: 10.5061/dryad.2k9j0/2
title: Squangle Python Code

description: This zip files includes the python implementation of the squangles method, the files that define the squangle polynomials, an example input file, and example output file and a README file that describes how to use the code.
DOI: 10.5061/dryad.3n977/1
title: InputFiles

description: Input files for simulations run. See "ReadMe.txt" for more information
DOI: 10.5061/dryad.3nc54/1
title: Python scripts - File formatting - Sequence Capture

description: All relevant scripts used to format files, analyse data and obtain results from sequence capture experiment on two sympatric populations of whitefish ecotypes in the process of speciation.
DOI: 10.5061/dryad.3nc54/2
title: Whitefish sequence capture assembly

description: Fasta file containing 2,228 genes de novo assembled after conducting a targeted enrichment and re-sequencing experiment on two sympatric populations of whitefish (Coregonus clupeaformis) currently in the process of speciation.
DOI: 10.5061/dryad.3rn6c/1
title: TabS2

description: microsatellite genotypes (number of nucleotides per STR allele) for 167 individual wolves and dogs from Georgia (genotypes of wolves from the eastern and from the western Georgia shown separately). Microsoft Exel file, single spreadsheet.
DOI: 10.5061/dryad.4dv78/1
title: VisModelsMimicryData

description: This dataset includes the reflectance spectra for all salamanders in the study, as well as the background spectra used in analyses.
DOI: 10.5061/dryad.4jf42ct4/1
title: DalGrande et al_2012

description: Multilocus genotypes and coordinates for each thallus of Lobaria pulmonaria in 64 populations
DOI: 10.5061/dryad.519bm/1
title: Phenotype_forGenABEL2011111.txt

description: Compressed phenotype file in text format for the R GenABEL library
DOI: 10.5061/dryad.5248s/62
title: catechol 2,3-dioxygenase C-terminal domain with intra-domain region original MUSCLE alignment.txt
DOI: 10.5061/dryad.5248s/63
title: catechol 2,3-dioxygenase N-terminal domain original MUSCLE alignment.txt
DOI: 10.5061/dryad.5248s/64
title: catechol 2,3-dioxygenase N-terminal domain with extra-domain region original MUSCLE alignment.txt
DOI: 10.5061/dryad.5248s/65
title: catechol 2,3-dioxygenase N-terminal domain with intra-domain region original MUSCLE alignment.txt
DOI: 10.5061/dryad.5248s/66
title: catechol 2,3-dioxygenase original MUSCLE alignment.txt
DOI: 10.5061/dryad.5248s/67
title: ferredoxin-like peptide original MUSCLE alignment.txt
DOI: 10.5061/dryad.5f4d8/1
title: 11-2052 data

description: MS Excel spreadsheet containing data obtained under natural (field) and controlled (laboratory) conditions. Individual S. canicula were electronically tracked in the natural environment, whilst in the laboratory the movements of individuals were tracked using video tracking techniques. Observations made under both natural and controlled conditions are also included. See manuscript materials and methods for further details.
DOI: 10.5061/dryad.5h45c/1
title: EALdata

description: Genera used in analyses, with ranges from Webster (2003) and expected arm loss calculated here.
DOI: 10.5061/dryad.5h45c/2
title: infestation-regeneration

description: Data on genera found infested with parasitic platyceratid snails and those found with regenerating arms (compiled from papers by Baumiller and Gahn), along with EAL values calculated herein.
DOI: 10.5061/dryad.6gr7t/10
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff

description: Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/11
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_as_aa

description: FASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/12
title: Car_ign_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed

description: Parsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI.