cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.060b1/8
title: file 8 - R code for simulations based on allele frequencies in experimental populations

description: This code runs simulations based on observed allele frequencies in experimental populations. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. Instructions on the first line detail how to change the input for the desired population. This code links to the following files, which must be in the working directory: files 1 - 3, and file 23 - 25.
DOI: 10.5061/dryad.060b1/9
title: file 9 - R code for simulations based on allele frequencies in experimental populations (linkage taken into account)
DOI: 10.5061/dryad.17f8v/16
title: batchPulse3_22

description: batch file for generating prior sample for estimates in Table S4 (data Table S3)
DOI: 10.5061/dryad.17f8v/17
title: BirdCOI R scripts_psi3

description: R scripts for generating estimates in table S4
DOI: 10.5061/dryad.1q389/1
title: Changes in temperature-specific growth rates across ontogeny in damselfly larvae

description: Growth rates ("gr") of larvae of six species of damselflies reared in the laboratory at three or four temperatures ("temp"). Growth rates represent size-corrected relative growth rates (in the unit off mm increase in headwidth/day; the size-correction was done using Equation 8 in the corresponding article) estimated during early (day 0-42), intermediate (day 42-84) and late ontogeny (day 84-126)("period").
DOI: 10.5061/dryad.1q389/2
title: Phenological data on the start and end of the flight season of European damselflies

description: Data on the day of the year when the flight season of 15 European species of damselfies start ("Spring") and end ("Fall") based on literature records. Literature refererence IDs ("Ref") correspond to numbers used in Appendix B of the corresponding article and the records are graded from 1 to 4 based on their quality ("Quality"), with 4 being the most reliable.
DOI: 10.5061/dryad.2nk64/1
title: RADseq data and ACD6 genotype for Costa Brava accessions

description: Genotypic information obtained by RADseq for 1688 accessions collected in the Costa Brava region of Spain in Spring 2012. Reads were processed with SHORE (ver. 0.9) and mapped to the reference sequence, Col-0, with BWA, using the default parameters and allowing 5% mismatches. All mapped reads were converted into BAM format by Samtools (ver. 0.1.18) for further analysis. Single nucleotide polymorphism (SNP) genotypes were generated using the subprogram UnifiedGenotyper implemented in GATK (ver. 2.3-6). The genotype at the ACD6 locus is reported for each individual as well, as determined by direct Sanger sequencing of the transmembrane domain of ACD6.
DOI: 10.5061/dryad.2qf2f/1
title: Simulation files as used in paper

description: README.TXT FOR SIMULATION FILES: These files are the source code for the one-dimensional and two-dimensional population simulations used in the Hartfield et al 2012 paper "The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation". Simulations are written in C and need to be compiled prior to execution. See blurb at start of each program for description and how to execute. Please also note that simulations use routines that are part of the GNU Scientific Library (GSL). Since GSL is distributed under the GNU General Public License(http://www.gnu.org/copyleft/gpl.html), you must download it separately from these files. Note that we have also uploaded a Mathematica file, outlining the study into obtaining confidence intervals, as described in the manuscript. Comments should be sent to Matthew Hartfield (matthew.hartfield@ird.fr)
DOI: 10.5061/dryad.4b0sr/1
title: Data for Figures 5, 9 and 10

description: Please see the ReadMe file for a full description.
DOI: 10.5061/dryad.4q2f3/1
title: Summary data for leaf N studies in meta-analysis

description: This file contains summary information and calculated effect sizes extracted from studies that measured leaf Nmass and/or Narea along an elevational gradient. Column titles: study, author and year published, see online appendix S1; r, untransformed correlation coefficient (effect size); n. sites, number of sites sampled; indiv.per.site, number of plants sampled per site; n. indiv., total number of plants sampled; n. reg., n used for the regression where r was estimated; by.mass.or.area, which of Nmass or Narea was measured; within.or.among, whether interspecific or intraspecific variation was sampled; pft, plant functional type; biome, which of temperate/tropical/boreal; grad.min, minimum elevation; grad.max, maximum elevation; lat.mean, mean latitude; species, 1 or more species measured; details, notes if necessary.
DOI: 10.5061/dryad.4q2f3/2
title: Summary data for LMA studies in meta-analysis

description: This file contains summary information and calculated effect sizes extracted from studies that measured SLA or LMA along an elevational gradient. Column titles: study, author and year published, see online appendix S1; r, untransformed correlation coefficient (effect size); n. sites, number of sites sampled; indiv.per.site, number of plants sampled per site; n. indiv., total number of plants sampled; n. reg., n used for the regression where r was estimated; sla.or.lma; which of SLA or LMA was given in paper (SLA = 1/LMA); within.or.among, whether interspecific or intraspecific variation was sampled; pft, plant functional type; biome, which of temperate/tropical/boreal; grad.min, minimum elevation; grad.max, maximum elevation; lat.mean, mean latitude; species, 1 or more species measured; details, notes if necessary.
DOI: 10.5061/dryad.4t157/1
title: All code & scripts

description: This zipped tarball contains all the code & scripts necessary (combined with R packages available through CRAN) to reproduce the analyses of this study. All files are plain text and contain a short description of the specific analysis or analyses that will be generated by the script.
DOI: 10.5061/dryad.5d6p6/1
title: Actin Salgado

description: Alpha actin gene sequence alignment.
DOI: 10.5061/dryad.5f95s/1
title: Inoculation matrix
DOI: 10.5061/dryad.5f95s/2
title: Genetic data
DOI: 10.5061/dryad.611310kt/1
title: Analysed DNA sequences

description: All the sequences analysed in the study in FASTA format. The name includes the MOTU number, the sequence identification number and the species or genus level identification.
DOI: 10.5061/dryad.64380/1
title: Turtle Encounter Histories

description: Mark-recapture data for adult female painted turtles from 1995-2012 for the Thomson Causeway population on the Mississippi River.
DOI: 10.5061/dryad.6b2t6/2
title: AFLP_LJaponica

description: AFLP data for 194 L. japonica plants collected in summer 2006 across the northern range margin and within the core of the range. Population locations are given in the readme file.
DOI: 10.5061/dryad.6hs29/2
title: input and output files DAMBEdating

description: Alignement, input tree, and dated tree of dating analysis carried out in DAMBE
DOI: 10.5061/dryad.6jh51/5
title: Genetic input of Dipterxy odorata

description: This file consists of the genetic input  for running the simulations on Ecogene program. The file contains the number of individuals, coordinates (2 columns), dbh (diameter at breast height) and genotypes of 7 microsatellite markers
DOI: 10.5061/dryad.6jh51/6
title: Mortality data of Dipteryx odorata

description: This file consists of the mortality data of Jacaranda copaia, the file contains: first line is the header, second line is the number of dbh (diameter at breast height) classes, third line onwards the dbh class and the frequency in the population (number of individuals)
DOI: 10.5061/dryad.6jh51/7
title: Demography data of the species

description: In this file contains data of 15 species, including Jacaranda copaia and Dipteryx odorata. The input contais the species name, Mean diameter, SD diameter, Diameter temp. correlation, Max Diameter, Max height
DOI: 10.5061/dryad.6mv07/1
title: Microsatellite genotyping of Botrytis cinerea grey mold and noble rot populations in France

description: Microsatellite genotyping using 8 markers. Populations of B. cinerea collected in the field, in 3 wine-producing French regions, from grey mold and nobel rot symptoms. Data are given in allele size in bp (haploid data). 0 indicate missing values.
DOI: 10.5061/dryad.6s5pn/1
title: AAEL004226 sequences

description: Fasta file of the sequences for the gene AAEL004226. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/2
title: AAEL004738 sequences

description: Fasta file of the sequences for the gene AAEL004738. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/3
title: AAEL007488 sequences

description: Fasta file of the sequences for the gene AAEL007488. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/4
title: AAEL007892 sequences

description: Fasta file of the sequences for the gene AAEL007892. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/5
title: AAEL008155 sequences

description: Fasta file of the sequences for the gene AAEL008155. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/6
title: AAEL009077 sequences

description: Fasta file of the sequences for the gene AAEL009077. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.6s5pn/7
title: AAEL012778 sequences

description: Fasta file of the sequences for the gene AAEL012778. AE samples corespond to the susceptible Aedes aegypti Bora-Bora strain. LiTOX samples corespond to the Bti resistant strain.
DOI: 10.5061/dryad.7gs24/1
title: Fecundity data

description: development, selective environment, population, isofemale line, centroid size, fecundity at 14C, 16C, 20.5C, 25C, 28C, 320C, 32C, 36C.
DOI: 10.5061/dryad.c62gg/1
title: Plasmodium mexicanum sex ratios and genotypes from Experiment II (Vardo-Zalik)

description: Compiled data on experimentally initiated infections of the lizard malaria parasite Plasmodium mexicanum in its natural host, the lizard Sceloporus occidentalis, including sex ratio and parasitemia counts and alleles observed at 4 microsatellite loci. Data was collected for the current study ("Testing sex ratio theory with the malaria parasite Plasmodium mexicanum in natural and experimental infections") from samples generated for a previous study conducted by Joseph Schall and Anne Vardo-Zalik (see ReadMe file for citation and more detailed information).
DOI: 10.5061/dryad.c62gg/2
title: Plasmodium mexicanum sex ratios and genotypes from Experiment I (Osgood)

description: Compiled data on experimentally initiated infections of the lizard malaria parasite Plasmodium mexicanum in its natural host, the lizard Sceloporus occidentalis, including sex ratio and parasitemia counts and alleles observed at 4 microsatellite loci. Data was collected for the current study (Testing sex ratio theory with the malaria parasite Plasmodium mexicanum in natural and experimental infections) from samples generated for a previous study conducted by Joseph Schall and Sarah Osgood (see ReadMe file for citation and more detailed information).
DOI: 10.5061/dryad.c62gg/3
title: Plasmodium mexicanum sex ratios and genotypes from natural infections collected 2007-2009

description: Compiled data on naturally-occuring infections of the lizard malaria parasite Plasmodium mexicanum in its host, the lizard Sceloporus occidentalis, including sex ratio and parasitemia counts and alleles observed at 4 microsatellite loci. Data was collected for the current study (Testing sex ratio theory with the malaria parasite Plasmodium mexicanum in natural and experimental infections) from samples collected by Allison Neal, Jennifer Fricke, and Anne Vardo-Zalik. Contribution of other dataset authors is outlined in ReadMe file, as well as more detailed inforamtion about the study and data set.
DOI: 10.5061/dryad.fc02f/1
title: Data_Kerschbaumer_et_al_2013

description: Cartesian coordinates of 18 landmarks; genotypes for 6 microsatellite markers:  UNH130 (Lee and Kocher, 1996), Pzep2, Pzep3 (van Oppen et al., 1997), UME003, UME002 (Parker and Kornfield, 1996) and TmoM27 (Zardoya et al., 1996);723 individuals of two color morphs and two species of the genus Tropheus, collected from eight locations at the eastern coast of Lake Tanganyika
DOI: 10.5061/dryad.g6r70/3
title: Monotropoideae_Arbutoideae_BEAST

description: XML file for BEAST. This was used to get tree in Monotropoideae_Arbutoideae_chrono.tre.
DOI: 10.5061/dryad.g6r70/4
title: BoraginaceaeML_SH

description: Boraginaceae phylogeny in newick format with local SH nodal supports. Tree estimated with RAxML from multilocus DNA sequence dataset.
DOI: 10.5061/dryad.g6r70/6
title: Ericales

description: Ericales DNA sequence data in relaxed phylip format used by RAxML.
DOI: 10.5061/dryad.h0228/10
title: DarwinTunes-medley-at-1125-generations

description: A medley of audio loops selected manually from a particular point in the evolution of experimental population 1 (EP1).
DOI: 10.5061/dryad.h65f4/1
title: Data for compositional analysis of caribou

description: Data used to characterize the land cover type of node of network for caribou. Used proportions of various land cover types are estimated based on the observed GPS locations. Available proportions of various land cover types are calculated based on the 100% minimum convex polygon.
DOI: 10.5061/dryad.j81r0/1
title: crow fledging success

description: Success of parasitized and non-parastized broods
DOI: 10.5061/dryad.j81r0/2
title: cuckoo translocation experiment

description: cuckoo translocation experiment. Variable "treatment": ADD=cuckoo added, REM=cuckoo removed, PAR=unmanipulated parasitized, NON PAR=unmanipulated non-parasitized
DOI: 10.5061/dryad.j81r0/3
title: crow translocation experiment

description: crow translocation experiment. Variable "treatment": Variable "treatment": ADD=crowadded, REM=crow removed, CONT=control
DOI: 10.5061/dryad.j81r0/4
title: Repellence experiment with crows

description: Repellence experiment with crows. Variable "treatment": NS=Natural cuckoo secretion; C=control
DOI: 10.5061/dryad.j81r0/5
title: Repellence experiment with raptors

description: Repellence experiment with raptors. Variable "treat": NS=Natural cuckoo secretion; C=control
DOI: 10.5061/dryad.k7t50/1
title: delineation matrix

description: delineation matrix (LxS), 24 loci (columns), ~78,000 species units (rows). tab delimited, unix line breaks. spaces separate individual members of a single gene motu. members are representated by their originally designated taxonomy which is converted to species strings according to Hunt and Vogler (2008, MPE 47:289), followed by underscore and NCBI accession.
DOI: 10.5061/dryad.k7t50/2
title: insecta.taxkey

description: table giving full taxonomic information for each taxonomic string used later in the results files. taxonomic string is the first string in each row. strings are built from full heirachy up to given node, according to Hunt and Vogler (2008, MPE 47:289). 2nd column is full taxonomic name for that node, 3rd column is NCBI taxonomy number for that node.
DOI: 10.5061/dryad.k7t50/3
title: insecta.fas

description: processed insect fasta database. file is compressed. entries are represented by taxonomic string followed by NCBI accession number. some duplicate data is removed from original insect db. and some particularly long DNA sequences are also ommited.
DOI: 10.5061/dryad.k7t50/4
title: Supplemental figure 1

description: Supplementary Fig. 1: Assessment of the protocol. A: Contrasting estimates of species numbers for assigned names (x axis) and clusters based on sequence similarity (y axis). ~20 of the species dense homologs are plotted, based on species counts made only for the 26 model genera given in the methods. Upper gray point indicates COI locus, lower gray 18S. B: Contrasting the number of MOTU for each family in the dataset, where the species clustering parameters are inferred insect-wide (x-axis), or locally for each family (y-axis). Linear regression line is shown on A and B.
DOI: 10.5061/dryad.nm4bn/1
title: Microsatellite data of European tortoises, Testudo hermanni

description: This file contains microsatellite data of Testudo hermanni in Europe.
DOI: 10.5061/dryad.pm136/1
title: Python radiolocations

description: This file includes Burmese python capture locations, release locations, and radiolocations collected in the field.
DOI: 10.5061/dryad.s5s3s/1
title: IngramKai2014SebastesData

description: Contains three data files: one with raw individual-level morphological data for Sebastes rockfishes, one with species mean size-corrected data, and one with the phylogenetic principal component scores used to construct the morphospace. Each file is accompanied by a README .txt file.
DOI: 10.5061/dryad.s7q3c/25
title: Data from Fig. S4bc
DOI: 10.5061/dryad.s7q3c/27
title: Data from Fig. S6abc
DOI: 10.5061/dryad.s7q3c/28
title: Data from Fig. S7bc
DOI: 10.5061/dryad.s7q3c/29
title: Data from Fig. S8b
DOI: 10.5061/dryad.s7q3c/30
title: Data from Fig. S9
DOI: 10.5061/dryad.s7q3c/31
title: Data from Fig. S10bc
DOI: 10.5061/dryad.s7q3c/32
title: Data from Fig. S10d
DOI: 10.5061/dryad.s7q3c/33
title: Data from Fig. S11b
DOI: 10.5061/dryad.s7q3c/35
title: Data from Fig. S12
DOI: 10.5061/dryad.sg546/1
title: Microsatellite data for Fennoscandian Pungitius pungitius

description: This data set covers 183 individuals from 4 local populations genotyped for 12 microsatellite loci. The genotypes refer to sequence lengths.
DOI: 10.5061/dryad.sg546/2
title: Morphological and behavioral measurements from Pungitius pungitius

description: This data set involves 92 individuals from four local populations. The entry for each individual covers data needed for animal-model type analyses (parents, sex, origin of parents), behavioral and morphometric measurements. The behavioral variables involve number of attacks against stimulus conspecific, time to orient and time to 'full out' in seconds and feeding behavior recorded as a binary variable. All morphometric measurements are given in millimetres. SL refers to standard length.
DOI: 10.5061/dryad.v82jf/1
title: Figure S1

description: Map of collecting sites in the states of Washington and Oregon for Rhagoletis pomonella flies behaviorally analyzed in the study.
DOI: 10.5061/dryad.vq6mp/1
title: Molecular sequence data for Euphorbia sections Goniostema, Denisophorbia, and Deuterocalli.

description: Aligned sequence data for ITS, ETS, atpI-atpH, psbA-trnH, matK, ndhA, trnQ-rps16, and rbcL for 279 samples in Euphorbia sections Goniostema, Denisophorbia, and Deuterocalli (ingroup) and appropriate outgroup samples in the genus Euphorbia.
DOI: 10.5061/dryad.02qv3/1
title: data_matrices_for_Bazinet_et_al_PLOS_ONE_2013

description: The zip archive (data_matrices_for_Bazinet_et_al_PLOS_ONE_2013.zip) contains the following files:lep_16_taxa_19_genes_degen1.nexlep_16_taxa_741_genes_CONSENSUS_degen1.fastalep_16_taxa_741_genes_REPRESENTATIVE_degen1.fastalep_38_taxa_19_genes_degen1.nexlep_38_taxa_741_genes_CONSENSUS_degen1.fastalep_38_taxa_741_genes_REPRESENTATIVE_degen1.fastalep_45_taxa_19_genes_degen1.nexlep_46_taxa_741_genes_CONSENSUS_degen1.fastalep_46_taxa_741_genes_REPRESENTATIVE_degen1.fastaThese are the data matrices associated with the publication:Can RNA-Seq resolve the rapid radiation of advanced moths (Lepidoptera: Apoditrysia)? An exploratory study,Bazinet, Adam L., Cummings, Michael P., Mitter, Kim T., Mitter, Charles,to appear in PLOS ONE, 2013.
DOI: 10.5061/dryad.060b1/11
title: file 11 - R code for simulated bottleneck in the N=10 x5 population

description: This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Once the bottleneck is simulated, only the allele frequencies are used to generate the subsequent pedigree so variance in individual IBD generated during the bottleneck is not retained. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17, files 23 – 26 and file 28.
DOI: 10.5061/dryad.060b1/12
title: file 12 - R code for simulated bottleneck in the N=10 x1 population with variance in individual IBD retained

description: This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x1 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17 and files 24 – 27.
DOI: 10.5061/dryad.060b1/13
title: file 13 - R code for simulated bottleneck in the N=10 x5 population with variance in individual IBD retained

description: This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 – 17, files 24 – 26 and file 28.
DOI: 10.5061/dryad.060b1/14
title: file 14 - R code for simulations with null alleles introduced to all loci with frequency = 0.05

description: This code runs simulations based on observed allele frequencies in the control population but with null alleles artificially introduced to all loci at a frequency of 0.05. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. This code links to the following files, which must be in the working directory: files 22 – 25.
DOI: 10.5061/dryad.060b1/15
title: file 15 - R code for simulations with null alleles introduced to three loci or three loci removed

description: This code runs simulations based on observed allele frequencies in the control population but with null alleles artificially introduced to three randomly selected loci at a frequency of 0.05 or these same three loci removed from the data set. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. This code links to the following files, which must be in the working directory: file 1 and files 22 – 25.
DOI: 10.5061/dryad.060b1/16
title: file 16 - x0 data for MasterBayes cr2 only

description: Microsatellite genotypes for markers residing on chromosome two observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.
DOI: 10.5061/dryad.060b1/17
title: file 17 - x0 data for MasterBayes cr3 only

description: Microsatellite genotypes for markers residing on chromosome three observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.