cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ps4r/3
title: 3. Relative rates sister-clades analysis

description: This folder contains the input and output files used in and obtained from the program Phyltest (Phyltest v.2.0, http://www.kumarlab.net/publications) for the sister-clade relative rates analysis. This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Transitions are identified by the set# in the file name (e.g. “Set1” or “S1” = transition #1, transitions as described in the Supplementary Material). All transitions were analysed with separate input and output files except for the transitions within the source study folder Cunha et al. 2011 where each transition was run from the same file per gene. Within the input files the abbreviations FL=flightless, F=flight-capable, OG=outgroup, and the number after these identifiers signifies the transition. Each gene folder (except where just described) contains 2 files per transition: 1 input file (nucleotide - “.dat”) and 1 output file.
DOI: 10.5061/dryad.46kv1/1
title: Supplementary Information

description: Number of occurrences for each species and species sampling; Fossil calibration; AUC and CI for niche models; Relative input of variables into niche models; Test for normality of PC variances;  Kurtosis for PC scores distributions; Geographical range for each species; Mean latitude and centroid-based latitude estimates for each species; Evolutionary models comparison for niche position and breadth
DOI: 10.5061/dryad.49j7t/1
title: Koala behaviour, microclimate and tree temperature data

description: Koala behaviour, microclimate and tree temperature data collected in the field (French Island, Victoria, Australia). See ReadMe file for details.
DOI: 10.5061/dryad.57ms3/1
title: array_25mer

description: Database containing intensities and probe calibration information for 25-mer array.
DOI: 10.5061/dryad.57ms3/2
title: array_60mer

description: Database containing signal intensities and probe calibration information for 60-mer array.
DOI: 10.5061/dryad.57ms3/3
title: CNV_ProbeInAllExpts_ap

description: Gene copy number values calculated based on hybridization with the calibrated 60-mer array.
DOI: 10.5061/dryad.5q3b3/1
title: Banff Bear DNA Data

description: Microsatellite data for 105 black bears and 134 grizzly bears detected in Banff National Park.  Excel file contains 3 worksheets (description, black bear data, grizzly bear data)
DOI: 10.5061/dryad.6mh29/1
title: log file from *BEAST analysis
DOI: 10.5061/dryad.6mh29/2
title: tree file from *BEAST analysis
DOI: 10.5061/dryad.6mh29/3
title: xml input file for *BEAST analysis
DOI: 10.5061/dryad.708j7/1
title: North Pacific humpback whale haplotype sequences and tables
DOI: 10.5061/dryad.79bt8/1
title: Data_file_for_Hopwood_et_al_Func_Ecol
DOI: 10.5061/dryad.863s0/1
title: Dryad

description: File shows segregations of sex phenotypes from crosses between two species and a hybrid zone
DOI: 10.5061/dryad.8dh7r/1
title: BEAST tree files

description: BEAST MCC tree files of analyses [A]-[D].
DOI: 10.5061/dryad.b5j25/1
title: breeding values in fitness-linked traits in the Houbara bustard captive breeding

description: The ZIP file consists in 5 files referring to 5 traits (NBJ: display rate, NBO: number of eggs, SPZ: number of spermatozoa, PoidsM: male body mass, PoidsF: female body mass). Each file contains the breeding values (and other fixed and random effects) estimated with MCMCglmm (R). NonInf in the file name to the non informative prior used, and Gauss or Poi to the distribution of errors (Normal or Poisson). 1000 iterations have been simulated for each individual.
DOI: 10.5061/dryad.g1h6b/1
title: Hunting returns data

description: Delimited plain text file with the following columns: date, age_cat, sex, foraging_activity, total_foraging_time, total_kcal. These correspond to: (1) date of focal follow, (2) age category of focal forager, (3) sex of focal forager, (4) type of hunt, (5) total hunt time in min, (6) total energetic returns in kcal.
DOI: 10.5061/dryad.g3375/10
title: 10 - Structure_input

description: Structure input file
DOI: 10.5061/dryad.g3375/11
title: 11 - BAPS_Structure_output

description: The BAPS and Structure output
DOI: 10.5061/dryad.g3375/12
title: 12 - NewHybrids_input

description: NewHybrids input file
DOI: 10.5061/dryad.g3375/13
title: 13 - Alle_proportion

description: Table with distribution of T. ivanbureschi and T. macedonicus alleles in newts from the T. arntzeni type locality
DOI: 10.5061/dryad.g3375/9
title: 9 - BAPS_input

description: BAPS input file (GENEPOP format)
DOI: 10.5061/dryad.gd905/1
title: leaf and root data

description: Includes %N, %C, d15N and d13C of foliar samples.
DOI: 10.5061/dryad.gd905/2
title: lma data

description: data used to calculate leaf mass per area: area of scanned leaves in cm2 and dry weight of leaf sample
DOI: 10.5061/dryad.gd905/3
title: soil data

description: Includes %C, %N, d15N, and d13C of soils sampled to 90cm depth.
DOI: 10.5061/dryad.j18g0/4
title: Full_pedigree

description: The full pedigree of all individuals (females and males) considered in the study, along with their genotype and the identity of both maternal and paternal chromosomes.
DOI: 10.5061/dryad.jm4d5/5
title: combined_BEAST
DOI: 10.5061/dryad.jm4d5/6
title: Testing_Dispersals_R Source Code
DOI: 10.5061/dryad.jm4d5/7
title: Figure S1_Dated Phylogeny with taxon names_accepted
DOI: 10.5061/dryad.jt683/1
title: Modified BOTTLESIM source code

description: Source code from BOTTLESIM program, modified slightly to report A50 (allelic richness from 50 individuals), to work for population sizes &gt;1000, and to compile under Mac OS X 10.8.4 with XCode. The code only allows use of the "Diploid singlelocus, constant population size" simulation module. For original source code, see Kuo, C.-H. & Janzen, F.J. (2003). BOTTLESIM: a Bottleneck Simulation Program for Long-Lived Species With Overlapping Generations. Molecular Ecology Notes, 3, 669–673, available from http://chkuo.name/software/BottleSim.html.
DOI: 10.5061/dryad.jt683/2
title: R code for bottlenecks in stepping-stone populations

description: Script written for R to simulate a bottleneck in a set of populations connected by stepping-stone migration. Assumes diploid individuals and calculates the number of immigrants from each population as a Poisson random number with mean m*Ne2 (for a total of 2*m*Ne2 alleles). We use Ne2 from the focal population (the one receiving the immigrants). Returns a list with two vectors: 1) meanA (allelic richness for each generation, where the first entry is the pre-bottleneck value); and 2) meanHe (expected heterozygosity for each generation, where the first entry is the pre-bottleneck value).
DOI: 10.5061/dryad.jt683/3
title: Genetic diversity database

description: This CSV (comma-separated) file contains microsatellite diversity data from marine fishes that was compiled from published papers, theses, and white papers. See our published paper for the criteria we used to select data. The readme file explains the columns.
DOI: 10.5061/dryad.kf490/1
title: Lagisz_DATATABLE

description: General description : the table contains genetic and phenotypic data for 47 Nematoda species and 2 outgroup species.Table columns:ord - numerical ordering of the table in order of data collection.animal - specie's full latin name.Refseq - specie's Refseq code.NCBItaxID - specie's taxonomic ID from NCBI.genus - specie's genus name.species - species name.host - main definitive host or habitat.host_code - main definitive host code: 0 = free-living or plant-parasitic, 1 = parasite of endotherms, -1 = parasite of ectotherms.class - specie's taxonomic class.reproduction - specie's reprodactive mode: dioecy, hermaphroditism, androdioecy.max_male_length - maximum length of males [mm].av_male_width - average male width [mm].av_female_length - average female length [mm].max_female_width - maximum female width [mm].size_sources - literature sources for body size measurements.volume_male - calculated male body volume [mm3].volume_female - calculated female body volume [mm3].log_volume_male- logarithm of male body volume.log_volume_female- logarithm of female body volume.genome_length - species mitogenome sequence length [bp].p_GC_content - percent of GC base content of the mitogenomic sequence.p_prot_coding - percent of protein-coding bases in the mitogenomic sequence.p_coding - percent coding bases in the mitogenomic sequence.N_cDNAs - number of protein-coding genes in the mitogenome.N_tRNAs - number of tRNA-coding genes in the mitogenome.N_rRNAs - number of rRNA-coding genes in the mitogenome.bp_cDNAs - length of protein-coding sequence in the mitogenome [bp].bp_tRNAs - length of tRNA-coding sequence in the mitogenome [bp].bp_rRNAs - length of rRNA-coding sequence in the mitogenome [bp].bp_noncoding - length of non-coding sequence in the mitogenome [bp].N_repeats - number of repeats in the mitogenome.bp_repeats - length of repeat sequence in the mitogenome [bp].p_repeats - percent of repeat sequence in the mitogenome.go_dist_anc - rearrangement distance from the estimated most recent ancestror of Nematoda, estimated with MGR software.subs_rate - species amino-acid substitution rate in the mitogenome, estimated with BEAST.
DOI: 10.5061/dryad.kf490/2
title: Lagisz_tree_PHYML

description: Maximum Likelihood phylogenetic tree of 47 Nematoda species and 2 outgroup species created with PHYML software and based on concatenated aa sequences of mitochondrial protein-coding genes.
DOI: 10.5061/dryad.kf490/3
title: Lagisz_tree_BEAST

description: Bayesian phylogenetic tree of 47 Nematoda species and 2 outgroup species created with BEAST software and based on concatenated aa sequences of mitochondrial protein-coding genes.
DOI: 10.5061/dryad.kf490/4
title: Lagisz_tree_NCBI

description: Ultrametric topological phylogenetic tree of 47 Nematoda species created from NCBI taxonomy with polytomies resolved at random.
DOI: 10.5061/dryad.n3c2f/1
title: Beauchesne Jaeger and St-Laurent_PLoS ONE datasets

description: Characteristics of observed and random steps of female Woodland caribou inhabiting a highly disturbed landscape in eastern Canada.
DOI: 10.5061/dryad.n40hc/15
title: Supplemental Dataset 15. Stresses-responsive lincRNAs
DOI: 10.5061/dryad.n40hc/16
title: Supplemental Dataset 16. LincRNAs associated with smRNAs
DOI: 10.5061/dryad.n40hc/17
title: Supplemental Dataset 17. LincRNAs regulated by SERRATE and CBPs
DOI: 10.5061/dryad.n40hc/18
title: Supplemental Dataset 18. Verfication of SE and CBPs regulated lincRNAs by  qRT-PCR
DOI: 10.5061/dryad.n40hc/19
title: Supplemental Dataset 19. Summary of expression evidence of lincRNA
DOI: 10.5061/dryad.nc0gc/1
title: TRAGUST_Correlation-Removal-FungalOutgrowth_data
DOI: 10.5061/dryad.nc0gc/2
title: TRAGUST_Daily-Brood-intake_data
DOI: 10.5061/dryad.nc0gc/3
title: TRAGUST_Daily-Brood-removal_data
DOI: 10.5061/dryad.nc0gc/4
title: TRAGUST_GroomingFrequency_data
DOI: 10.5061/dryad.nc0gc/5
title: TRAGUST_NrBrood_Presentation_Intake_Removal_FungalOutgrowth_data
DOI: 10.5061/dryad.nq38s/1
title: Dryad raw data microarrays

description: Firsts Sheet -- Column A : gene number ; Column B : Mira River/Grande Riviere Blanche fold change at the river mouth ; Column C : Mira River/Grande Riviere Blanche fold change after 3 months in fresh water ; Column D : Mira River/Grande Riviere Blanche fold change after 3 months in brackish water ; Column E : Grande Rivière Blanche in brackish water vs fresh water fold change after 3 months ; Column F : Mira River in brackish water vs fresh water fold change after 3 months ; Column G : Gene name and basic annotation.  Second Sheet -- Column A : Gene name ; Column B : sequence length ; Column C : Consensus sequence ; Column D to G : blast result.
DOI: 10.5061/dryad.ns135/1
title: C. compressirostris electric organ contigs (Velvet/Oases)

description: Set of contigs assembled from the electric organ reads using Velvet/Oases.
DOI: 10.5061/dryad.ns135/2
title: C. compressirostris skeletal muscle contigs (Velvet/Oases)

description: Set of contigs assembled from the skeletaal muscle reads using Velvet/Oases.
DOI: 10.5061/dryad.ns135/3
title: Gene Ontology annotation (electric organ)

description: List of electric organ contig names with the corresponding annotated GO code.
DOI: 10.5061/dryad.ns135/4
title: Gene Ontology annotation (skeletal muscle)

description: List of skeletal muscle contig names with the corresponding annotated GO code.
DOI: 10.5061/dryad.ns135/5
title: C. compressirostris reads mapping vs C.numenius mt genome.

description: Result of C. compressirostris transcriptome reads mapping against the mitochondrial genome of C.numenius.
DOI: 10.5061/dryad.p7507/1
title: Data from the infection assay and feeding rate assay in the first experiment.

description: The transmission model (equ. S1 and S2) and foraging model (equ. S4) were simultaneously fit to these data from the infection and feeding rate assays, respectively.  For more details on how these data were used to estimate components of transmission potential, see 'Statistical methods for estimating parameters' in Appendix S1.
DOI: 10.5061/dryad.p7507/2
title: Data from the infection assay in the second experiment.

description: The transmission model (equ. S1 and S2) was fit to these data to estimate infection risk.  For more details on how these data were used to estimate components of transmission potential, see 'Statistical methods for estimating parameters' in Appendix S1.
DOI: 10.5061/dryad.rq412/1
title: ApoB alignment

description: Ninety-two samples of sequence data from the ApoB gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies).
DOI: 10.5061/dryad.rq412/2
title: BRCA alignment

description: Ninety-two samples of sequence data from the BRCA gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies).
DOI: 10.5061/dryad.rq412/3
title: GBA alignment

description: Ninety-two samples of sequence data from the GBA gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies).
DOI: 10.5061/dryad.rq412/4
title: MYH6 alignment

description: Ninety-two samples of sequence data from the MYH6 gene across jumping mice including N. insignis (5 subspecies), Z. hudsonius (12 subspecies), Z. princeps (10 subspecies), and Z. trinotatus (4 subspecies).
DOI: 10.5061/dryad.rq412/5
title: SDM_records

description: High-quality, natural history museum-based samples obtained from MANIS (Jan-2011) and down-sampled (aka thinned) to 10km radius to offset sampling bias.  Taxa are lineage-based assignments for each species used in niche modeling.
DOI: 10.5061/dryad.ss548/10
title: Starkey_WeatherStation_Data

description: This file contains all of the raw weather station data used to parameterize the microclimate model during our study for landscape-scale simulations at the Starkey Experimental Forest and Range (Starkey).
DOI: 10.5061/dryad.ss548/11
title: Mass_Condition_Change_Data

description: This file contains all of the data and equations used to estimate weekly changes in body mass and nutritional condition (percent ingesta-free body fat) of elk during each year of our study at both study sites (Starkey and the INL).
DOI: 10.5061/dryad.ss548/12
title: Piecewise_SAS_Code

description: This file contains the SAS code and one example dataset for running the iterative piecewise regression described in the manuscript.
DOI: 10.5061/dryad.ss548/13
title: GIS Layers

description: This zipped folder contains a variety of GIS layers used in our study, and is divided into two subfolders, one for the Idaho National Laboratory Site (INL) and one for the Starkey Experimental Forest and Range (Starkey).
DOI: 10.5061/dryad.ss548/14
title: Niche Mapper Inputs

description: This zipped folder contains the key input files for running both single-site and landscape-scale simulations in Niche Mapper for each of our study sites.
DOI: 10.5061/dryad.ss548/15
title: ReadMe

description: This file contains detailed metadata that describe the contents of each individual data file associated with this paper.
DOI: 10.5061/dryad.tm1k0/1
title: OTU_best_rep_97_similarity

description: Best representative sequences from each OTU based on 97% similarity.
DOI: 10.5061/dryad.tm1k0/2
title: OTU_best_rep_98_similarity

description: Best representative sequences from each OTU based on 98% similarity.
DOI: 10.5061/dryad.tm1k0/3
title: OTU_best_rep_99_similarity

description: Best representative sequences from each OTU based on 99% similarity.
DOI: 10.5061/dryad.tm1k0/4
title: OTU_matrix_97_similarity

description: A presence absence matrix for each OTU and specimen using 97% similarity to assign OTUs
DOI: 10.5061/dryad.tm1k0/5
title: OTU_matrix_98_similarity

description: A presence absence matrix for each OTU and specimen using 98% similarity to assign OTUs. See read me file in 'OTU_matrix_97_similarity.tab'
DOI: 10.5061/dryad.tp5g2/1
title: DNA alignment for the genus Leucadendron

description: This alignment is the concatenation of eight markers that were designed and described in the paper cited above. Those markers were amplified for 42 species collected in natural populations in the South-African fynbos, except for two external groups which were collected in the Kirstenbosch Botanical Garden. A detailed map of the alignment is given below: Positions 1 - 428 : PPR_like marker which contains an exon of 233bp and a 3'-UTR of 195bp. Positions 429 - 1182 : SVR7 marker which contains an exon of 652bp and a 3'-UTR of 102bp. Positions 1183 - 1563 : CAF1-6 marker which only contains an exon of 381bp. Positions 1564 - 2177 : the classical ITS marker. Positions 2178 - 2973 : ATINT1 marker which contains an exon of 665bp and a 3'-UTR of 131bp. Positions 2974 - 3250 : APO2 marker which contains only an exon of 277bp. Positions 3251 - 3908 : ATPHAN marker which contains only an exon of 658bp. Positions 3909 - 4247 : APG6 marker which contains only an exon of 339bp
DOI: 10.5061/dryad.266h9/21
title: rawvar_rmdup.ind21

description: Raw SNP data from Index 20 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/22
title: rawvar_rmdup.ind22

description: Raw SNP data from Index 22 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/23
title: rawvar_rmdup.ind23

description: Raw SNP data from Index 23 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/24
title: rawvar_rmdup.ind24

description: Raw SNP data from Index 24 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/3
title: rawvar_rmdup.ind3

description: Raw SNP data from Index 3 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/4
title: rawvar_rmdup.ind4

description: Raw SNP data from Index 4 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/5
title: rawvar_rmdup.ind5

description: Raw SNP data from Index 5 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/6
title: rawvar_rmdup.ind6

description: Raw SNP data from Index 6 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.274b1/1
title: Microsatellite genotypes of Alpine ibex demes in the Swiss Alps

description: This file contains raw data (genotypes of 37 microsatellites) of 954 individuals sampled in 31 Alpine ibex demes in the Swiss Alps. These data were collected and processed between 2005 and 2008 by Iris Biebach (iris.biebach@ieu.uzh.ch) and collaborators in the lab of Lukas Keller (lukas.keller@ieu.uzh.ch) at the University of Zurich, Switzerland. The content of this file has the following format: First line: number of loci (37). Lines 2 to n-1 (one line per individual): deme_id	allele1_of_locus1; allele2_of_locus1; allele1_of_locus2; allele2_of_locus2. Names of demes (deme_id; first column in lines 2 to n-1) correspond to those given in Table S1 in the Supporting Information.
DOI: 10.5061/dryad.2m65j/1
title: Uca beebei fight-1(NTS15)

description: Recorded in the field, west bank of the Pacific entrance to the Panama Canal, 1 km north of the Bridge of the Americas.
DOI: 10.5061/dryad.2m65j/2
title: Uca beebei fight-2(NTS15)

description: Fight between male Uca beebei recorded in the field, west bank of the Pacific entrance to the Panama Canal, 1 km north of the Bridge of the Americas.
DOI: 10.5061/dryad.3074s/1
title: Online  supplementary Figure 1

description: Online Supplementary Figure 1. Concatenation of the 26 haplotypes found in the 16 multimeric clones analyzed in this paper. Note that chimeric types appear shorter than interior non-chimeric types. As explained in methods, chimerics are constructed using the closest complementary part of the interior 5S gene but this part is not represented in order to clarify the scheme.
DOI: 10.5061/dryad.3074s/2
title: Online Supplementary Figure 2

description: Online Supplementary Figure 2. Secondary structures of the predicted 5S rRNA transcripts for 26 Medicago haplotypes. Variable positions differing from the consensus sequence (haplotype 1) are identified with arrow heads.
DOI: 10.5061/dryad.3np1m/1
title: Symbiodinium species in Clade D microsatellite alleles

description: This data file is an excel file that contains the allele scores for 8 independently sorting microsatellite loci.
DOI: 10.5061/dryad.3np1m/2
title: Clade D microsatellite flanking region sequences

description: Example flanking sequences of loci 88 and 93 (sensu Wham et al. 2011) for Symbiodinium trenchii, S. boreum, and S. eurythalpos.
DOI: 10.5061/dryad.53vs3/1
title: Raw ostracode census data

description: Ostracode count data of the core EW9302 23GGC.
DOI: 10.5061/dryad.53vs3/2
title: 3-point moving sum ostracode census dataset

description: 3-point moving sum ostracode census dataset of the core EW9302 23GGC.
DOI: 10.5061/dryad.53vs3/3
title: 3-point moving sum ostracode census dataset for R modeling

description: 3-point moving sum ostracode census dataset of the core EW9302 23GGC for R modeling. Shallow-water and non-benthic species are removed. See the paper for the full details.
DOI: 10.5061/dryad.53vs3/4
title: Table S1

description: Table S1 in MS Excel format
DOI: 10.5061/dryad.53vs3/5
title: Table S2

description: Table S2 in MS Excel format
DOI: 10.5061/dryad.53vs3/6
title: Table S5

description: Table S5 in MS Excel format
DOI: 10.5061/dryad.53vs3/7
title: Table S6

description: Table S6 in MS Excel format
DOI: 10.5061/dryad.5sv39/1
title: Supplementary file 1-SRSF1 translational targets

description: Data containing list of 1576 mRNAs that showed a 1.85-fold increase in polysomal-association in response to SRSF1 overexpression (translational targets tab). Data are supplied as an excel spreadsheet. Descriptions of columns are included in additional tab (descriptions of columns). Negative controls tab contains information on cellular abundance of mRNAs used as negative controls in all validation experiments.
DOI: 10.5061/dryad.5sv39/2
title: Supplementary file 2-SILAC analysis following SRSF1 overexpression

description: List of proteins identified in SILAC experiment (SILAC tab).  Data are supplied as an excel spreadsheet. Descriptions of columns are included in the additional tab (description of columns tab).
DOI: 10.5061/dryad.5sv39/3
title: Supplementary file 3-Alternative splicing changes following SRSF1 overexpression

description: List of 382 SRSF1-regulated cassette exons determined by exon arrays (cassette exons tab) and list of SRSF1-regulated cassette exons with SRSF1-clip-tags CLIP tag over casette exon (clip tag over cassette exon tab).  Data are supplied as an excel spreadsheet.