cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7b56k/2
title: F2ACdominantgenotypes

description: Dominant marker genotypes for an F2 S. aethnensis x S. chrysanthemifolius mapping family
DOI: 10.5061/dryad.7b56k/3
title: F2ACgenotypesnotes

description: Notes explaining the F2ACcodominantgenotypes and F2ACdominantgenotypes data files
DOI: 10.5061/dryad.7b56k/4
title: F2ACjoinmap

description: Joinmap formatted input file for an F2 S. aethnensis x S. chrysanthemifolius mapping family
DOI: 10.5061/dryad.7b56k/5
title: F2ACjoinmapnotes

description: Notes for F2ACjoinmap data file
DOI: 10.5061/dryad.7b56k/6
title: F2ACmap

description: Genetic linkage map for an F2 S. aethnensis x S. chrysanthemifolius mapping family
DOI: 10.5061/dryad.7b56k/7
title: F2ACmapnotes

description: Notes for F2ACmap data file
DOI: 10.5061/dryad.7pc00/1
title: Alignments of expressed VSG sequences

description: Please see Hall2013_ReadMe.txt for details.
DOI: 10.5061/dryad.7pc00/2
title: Basic copy VSG sequences associated with expressed VSGs

description: Please see Hall2013_ReadMe.txt for details.
DOI: 10.5061/dryad.7pc00/3
title: Details of expressed VSG sequences

description: Please see Hall2013_ReadMe.txt for details.
DOI: 10.5061/dryad.7pc00/4
title: Hall2013_ReadMe.txt

description: ReadMe file for associated data files.
DOI: 10.5061/dryad.82gg4/1
title: autocorrelation

description: To quantify larval swimming, still images were extracted every 2.5 s for the entire 60-min video recording, and larval positions (x, z co-ordinates) were measured using ImageJ. To obtain w and s for each replicate, all individuals in focus from 20 pairs of frames (frames in a pair were 2.5 s apart) were used, each pair being separated by 3-min intervals.To analyze the temporal covariance of vertical swimming velocities, the position of 20 randomly selected larvae (1 every 3 min) was recorded over time (t) for as long as possible (i.e. until it crossed paths with another larva, or moved out of frame or out of focus). The covariance of each larva's vertical swimming velocity was calculated for time lags from 0 to 60 s.  Data set includes larval rearing temperature (°C), experimental temperature (°C), replicate number, larvae number, x (horizontal) and z (vertical) positions within the frame (mm), time since introduction of larvae (min:s:ms or decimal s), and vertical swimming velocities (mm s-1)
DOI: 10.5061/dryad.8nb7v/1
title: Amborella-Maxent-data

description: Amborella localities and corresponding environmental information used for Maxent modelling. Localities are in decimal degrees (UTM58S and WGS84 Coordinate System). Description, abbreviations and source of environmental variables is given in the paper and in Table S7
DOI: 10.5061/dryad.8nb7v/2
title: Amborella-nSSR-data-dryad

description: Microsatellite genotypes for 12 Amborella trichopodia populations sampled across New Caledonia and genotyped at 10 SSR loci
DOI: 10.5061/dryad.8r6jp/1
title: GOT1_6a_align

description: Alignment of sequences from the GOT1_6a gene from Tigriopus californicus populations. The population from which sequence was obtained is indicated by the SD, AB, SCN, or LJS label. The GOT1_6A_mRNA_SD sequence was obtained from cDNA sequence from the SD population and spans a larger region than the remaining sequences. Other sequences were obtained by direct sequencing of PCR products from a single copepod. The two alleles of a single individual are indicated with a and b designations. Phase of multiple mutations in a single individual was not determined experimentally.
DOI: 10.5061/dryad.b5r86/2
title: Sequencher file of processed and assembled ITS2 chromatograms

description: In this Sequencher 4.1.4 file, the forward and reverse ITS2 chromatograms of each individual were assembled into contigs. For each homozygote, the contig was checked and cleaned then received the name of the individual sequenced. For length-variant heterozygotes, the double peaks were called either manually or using Sequencher's "Call Secondary Peak..." function, then the two haplotypes were reconstructed by combining the information carried by the forward and reverse chromatograms using the program Champuru (see http://dx.doi.org/10.1111/j.1471-8286.2006.01355.x, http://dx.doi.org/10.1111/j.1471-8286.2007.01857.x, available online at http://jfflot.mnhn.fr/champuru/ and http://seqphase.mpg.de/champuru); the contig and reconstructed haplotypes of each such individual received the name of this individual followed with "H", "a" and "b", respectively. For heterozygotes having two alleles of equal lengths, we used SeqPHASE (http://dx.doi.org/10.1111/j.1755-0998.2009.02732.x, available online at http://seqphase.mpg.de/seqphase) and PHASE to infer their haplotypes; the contig of each such individual received the name of this individual followed with "H" then the number of heterozygous SNPs observed (i.e., the number of double peaks in the contig), whereas its two inferred haplotypes received its name followed with "a" or "b", respectively. Finally, some individuals had double peaks but their chromatograms were two noisy to reconstruct accurately the two sequences: rather than risking to reconstruct one erroneous haplotype, for each such individual we only kept the haplotype that could be reconstructed unambiguously; these contigs were named by appending "h" to the names of the individuals concerned.
DOI: 10.5061/dryad.b5r86/3
title: Microsatellites

description: Genotypes of all 427 specimens analysed (in a Genetix file)
DOI: 10.5061/dryad.c6q65/1
title: Dataset_Progredi

description: Pre, post and follow-up data for the participants in the RCT.
DOI: 10.5061/dryad.c6q65/2
title: R Syntax

description: Syntax made in R showing the data-analysis.
DOI: 10.5061/dryad.c70gv/1
title: Hydnobolites_sporemat_measurements
DOI: 10.5061/dryad.c70gv/10
title: Pezizaceae_LSU_alnmnt

description: Pezizaceae LSU alignment in FASTA format, missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM")
DOI: 10.5061/dryad.c70gv/11
title: PezizalesExclPezizaceaeLSU

description: Pezizales exclusive of Pezizaceae LSU alignment in FASTA format, missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM")
DOI: 10.5061/dryad.c70gv/12
title: Hydnobolites_ITS_alignment

description: This is an alignment of ITS sequences (ITS1, 5.8s, ITS2) from fruit bodies, ectomycorrhizal roots and mitotic spore mats.
DOI: 10.5061/dryad.c70gv/13
title: Pachyphloeus_alignment_ITS

description: Pachyphloeus ITS alignment in FASTA format, Ambiguously aligned regions were excluded in GBlocks using the least stringent setting (Castresana, 2000; Talavera & Castresana, 2007), missing data is represented by "?" Sources of sequences include ascocarps, mitospore mats (taxon name preceded by "AM")and ectomycorrhizal roots (taxon name preceded by "EM").
DOI: 10.5061/dryad.c70gv/2
title: Pachyphloeus_sporemat_measurements
DOI: 10.5061/dryad.c70gv/3
title: terfezia_peziza_depressa_sporemat_measurements
DOI: 10.5061/dryad.c70gv/4
title: Pezizales_mitospore_measurements

description: This file has mitospore measurements taken from 1 mm square of sporemat and counted on a hemocytometer under bright field microscopy at 1000x. Genus of Pezizales is in the field header to the left of rows, and the header over the  collector number in the header for each column of spore measurements, which are in micrometers. At the top of the sheet are averages calculated for the 1 mm square of sporemat from which the spores were taken.
DOI: 10.5061/dryad.c70gv/5
title: Ectomycorrhizal contaminants on experimental roots

description: These ectomycorrhizal roots were selected and sequenced by ME Smith, RA Healy and GM Bonito in May of 2011. They come from sequenced root tips from axenically grown seedlings that were inoculated with mitospores, and then transferred to a growth chamber including other inoculated plants. None of the mitospore phylotypes were recovered from root tips, but three contaminant ectomycorrhizal species were sequenced from the roots. We think they came from water splash during watering of adjacent pots that had been purposely inoculated with Tuber borchii. Identifications were from ITS sequence similarity at 97%.
DOI: 10.5061/dryad.ct40s/15
title: Carduelis 241809
DOI: 10.5061/dryad.ct40s/16
title: Cyanocitta femur 242057
DOI: 10.5061/dryad.ct40s/17
title: Colaptes humerus 241887
DOI: 10.5061/dryad.ct40s/18
title: Cyanocitta 241803
DOI: 10.5061/dryad.ct40s/19
title: Dendroica 240871
DOI: 10.5061/dryad.ct40s/20
title: Dendroica 241982
DOI: 10.5061/dryad.ct40s/21
title: Diomedea 210390
DOI: 10.5061/dryad.ct40s/22
title: Grus 116250
DOI: 10.5061/dryad.d8n64/1
title: BpopOD600nm

description: Bacterial population density data
DOI: 10.5061/dryad.d8n64/2
title: TpopCellsmL

description: Protist population densities
DOI: 10.5061/dryad.d8n64/3
title: BfrequenciesCFU

description: F113 frequencies
DOI: 10.5061/dryad.d8n64/4
title: EvolDefence

description: Defence evolution data
DOI: 10.5061/dryad.d8n64/5
title: EvolGrowth

description: Evolution of bacterial growth
DOI: 10.5061/dryad.d8n64/6
title: AncDefGrowth

description: Ancestral strains' defence and growth
DOI: 10.5061/dryad.f3h72/1
title: ENCODE_micFFL

description: List of micFFL circuits obtained from ENCODE data
DOI: 10.5061/dryad.f3h72/2
title: Jaspar_micFFL

description: LIst of micFFL circuits obtained from Jaspar PWM
DOI: 10.5061/dryad.jt440/1
title: Archive containing data from aculeate phylogeny by Johnson et al.; Current Biology

description: This zip file contains data associated with this publication. For detailed description of contents please see ReadMe file.
DOI: 10.5061/dryad.np597/1
title: Ribosomal phylogeny alignment

description: MUSCLE alignment of concatenated protein sequences from 48 ribosomal proteins from species of the family Chlamydiaceae. File is in nexus format.
DOI: 10.5061/dryad.np597/2
title: Ribosomal tree file

description: Maximum-likelihood (PhyML) phylogenetic tree calculated using JTT+G substitution model with the concatenated sequences of 48 ribosomal proteins from species of the family Chlamydiaceae using PhyML. File is in Newick tree file format.
DOI: 10.5061/dryad.np597/3
title: PMP AT domain alignment

description: MUSCLE alignment of the autotransporter (AT) domain of polymorphic membrane proteins (PMP) originating from Chlamydia species. File is in nexus format.
DOI: 10.5061/dryad.np597/4
title: PMP AT domain tree file

description: Phylogenetic tree of the autotransporter domain of polymorphic membrane proteins originating from Chlamydia species. Distances were calculated using a JTT+I+G substitution model and trees generated using PhyML. File is in Newick tree file format.
DOI: 10.5061/dryad.np597/5
title: Chlamydial cytotoxins alignment

description: MUSCLE alignment of chlamydial cytotoxoin proteins. GBlocks v 0.91 was used to eliminate regions that could not be unambiguously aligned resulting in an alignment of 2845 amino acids (75% of the original 3766 positions). File is in nexus format.
DOI: 10.5061/dryad.pd383/1
title: Dryad_BahamasFemales

description: Within this file are two worksheets. The first lists all the life history variables for each individual female used in the published study including the number of aborted embryos. The second worksheet lists the embryonic dry weight per developmental stage per population, which were used for the Matrotrophy Index analyses.
DOI: 10.5061/dryad.pq143/8
title: R script for Tassel analysis

description: R script called by PBS shell script to analyse results of Tassel
DOI: 10.5061/dryad.pq143/9
title: R functions for Tassel analysis

description: Functions required by R for analysis of Tassel results
DOI: 10.5061/dryad.pq608/1
title: Gamble_Zarkower_Supp_File1

description: Supplementary File 1. RADtools output – full dataset
DOI: 10.5061/dryad.pq608/2
title: Gamble_Zarkower_Supp_File2

description: Supplementary File 2. Fasta file with male-specific RAD loci
DOI: 10.5061/dryad.06g5v/1
title: MicrosatGuanacosFalkland24-7-09b

description: Microsatellities data
DOI: 10.5061/dryad.0mq69/1
title: PaleoDB raw occurrence data downloaded 25-09-2010

description: The data used for our study were downloaded from the Paleobiology Database (PaleoDB) on 25 September 2010. The download included all occurrences entered by the Marine Invertebrate Working Group, excluding vertebrates and genera listed in quotation marks or qualified as "?", "cf.", or "aff." were excluded from the subsequent analysis. The following data associated with each occurrence were also downloaded: paleolatitude, paleolongitude, paleoenvironment, primary lithology, and taxon abundance. Please see the PaleoDB (http://http://paleodb.org) for additional details regarding data fields.
DOI: 10.5061/dryad.0mq69/2
title: Harnik et al - Phanerozoic rarity and extinction data
DOI: 10.5061/dryad.1fs7c/1
title: Concatenated Alignment File

description: This file contains the concatenated sequence data used in this study.  A character block is provided at the bottom outlining character sets within the alignment.
DOI: 10.5061/dryad.1fs7c/2
title: AppendixS1

description: This Appendix S1 provides the locality data for samples used in the study as well as coordinate data for samples used for ecological modeling procedures.  GenBank numbers are provided in a complete Appendix S1 published with the study, and correspond to sequences found within the concatenated alignment file submitted with this appendix to Dryad.
DOI: 10.5061/dryad.1fs7c/3
title: Maximum Likelihood Bootstrap Topology

description: Bootstrap topology resulting from partitioned Maximum Likelihood Analyses.
DOI: 10.5061/dryad.1g9g7/1
title: Data Alignment

description: This is the alignment file for the molecular dataset used in the study.  A character set is listed at the bottom of the alignment providing gene and tRNA information.
DOI: 10.5061/dryad.1g9g7/2
title: Bayesian Consensus

description: Tree file containing the consensus results of Bayesian analyses.
DOI: 10.5061/dryad.1g9g7/3
title: RAxML Bootstrap Topology

description: This is the tree file containing the results of Maximum Likelihood analyses in the program RAxML
DOI: 10.5061/dryad.1g9g7/4
title: Pseudogekko Voucher ID File

description: This is an excel file that provides the field number and corresponding museum catalog numbers for the Pseudogekko samples used in phylogenetic analyses.
DOI: 10.5061/dryad.27q3r/1
title: Traits of the 334 specimens

description: A list of all 334 specimens of Periophthalmus argentilineatus, Periophthalmus kalolo and of the outgroup P. malaccensis. For each call number that is used in the nexus files, the species, the sample locality and the population in which the specimen was included by the AMOVA in the paper, are indicated.
DOI: 10.5061/dryad.27q3r/2
title: 16S sequences to be combined with dloop

description: These are the 26 16S sequences that were combined in BEAST with the 26 d-loop sequences to reconstruct the combined tree.
DOI: 10.5061/dryad.27q3r/3
title: 16S sequences for calibration

description: The 16S fish sequences used in the 16S molecular clock
DOI: 10.5061/dryad.27q3r/4
title: dloop-sequences to be combined with 16s

description: The 26 d-loop sequences used to build the combined tree in BEAST.
DOI: 10.5061/dryad.27q3r/5
title: d-loop dataset

description: The complete D-loop dataset (334 sequences)
DOI: 10.5061/dryad.27q3r/6
title: rag1 dataset

description: The complete rag1 dataset (22 sequences)
DOI: 10.5061/dryad.28kd1/1
title: SexRatioFINAL_GLMApril2012

description: Life history traits and sex ratio data used in the GEE phylogenetic comparative analysis and GLM.
DOI: 10.5061/dryad.28kd1/2
title: Phylo6_247_April2012

description: Original nexus file containing the phylogenetic data. This is not the final data analysed as it contains an additional 4 species removed prior to analysis due to failing quality criteria (see manuscript). Moreover, this is the base tree from which 200 further trees were created (see next file).
DOI: 10.5061/dryad.28kd1/3
title: 200treesNoiseBL&PolyResolv

description: Actually phylogenies used in the final GEE analyses. 200 tree were generated using Mesquite to randomly resolve polytomies and to add noise to branch lengths.
DOI: 10.5061/dryad.38m4p/1
title: mam60_4genes

description: Concatenation of two mitochondrial (MT-RNR1 and MT-ND1) and two nuclear (BRCA1 and VWF) genes for 60 mammalian taxa. Ambiguously aligned sites have been excluded using Gblocks on each individual gene dataset prior to concatenation.
DOI: 10.5061/dryad.38m4p/2
title: mam60_all_gb_paup_gtrg8_midroot

description: Maximum likelihood phylogram for 60 mammalian taxa obtained from the concatenation of the four genes under the GTR+G8 model using PAUP with TBR branch-swapping on a NJ starting tree.
DOI: 10.5061/dryad.4bh26/1
title: Data for Composite Iron Mountain (CIM) M. guttatus linkage map

description: Excel files with the individual x marker genotype matrices for three F2 mapping populations. See readme file for more info on the mapping populations and linkage map generation.
DOI: 10.5061/dryad.4bh26/2
title: Individual x genotype matrices for BG4 and BN4 nearly isogenic line (NIL) populations

description: Both NIL populations were derived from the inbred line cross of Sherar's Falls (SF) Mimulus nasutus and Iron Mountain 62 (IM62) M. guttatus. The BG4 and BN4 lines started with IM62 x SF and SF x IM62 F1 hybrids, respectively, underwent 4 generations of backcrossing with the recurrent parent as pollen donor, and were made with single seed descent and no intentional selection. In both files, b = IM62 homozygote, a = SF homozygote, and H = heterozygote.
DOI: 10.5061/dryad.4bh26/3
title: Individual x genotype matrix for NIM2 F2 mapping population (SF M. nasutus x IM62 M. guttatus)

description: Matrix of genotypes for second SF x IM62 F2 mapping population. b = IM62 homozygote, a = M. nasutus homozygote, h = heterozygote. Some markers with extreme transmission ratio distortion relative to flanking markers are included in dataset, but were removed during mapping.Plant growth conditionsSeeds were planted in 2.25-in pots filled with Fafard 4P potting mix, watered, and stratified in the dark at 4°C for one week.  Pots were then moved to the Duke University greenhouses and maintained under long-day photoperiod conditions (16 h light at 24°C / 8 h dark at 16°C) using supplemental high-intensity sodium lights (daytime PPFD  &gt;750 mmol m-1 s-1).  Light response curves indicate that this light level was near saturating for the plants (data not shown).  We sowed approximately five seeds per pot, and thinned to the centermost individual after most seeds had germinated, two weeks after planting.  While in the greenhouses, plants received weekly treatment with Peter’s Professional Blossom Booster 10-30-20 fertilizer.
DOI: 10.5061/dryad.60699/1
title: mass_conv_indiv_measurements

description: The file titled "mass_conv_indiv_measurements" contains data on the size of tapeworm individuals from 8 species. Four species grow in the final host (G) whereas the remaining four do not (NG). Some of these worms were from the Liverpool museum and their reference number is given. Worms were either measured live or preserved in formalin or ethanol. The worms were collected from either the intermediate host as plerocercoids or from definitive hosts as adults. Length, width, and mass are listed for all worms. Depth was also recorded for some worms. Area was calculated by multiplying length and width.
DOI: 10.5061/dryad.60699/2
title: mass_conv_species_avgs

description: For each of the species measured, the average length (mm), area (mm2), and mass (mg) were calculated. Additionally, this file contains data taken from the literature (see Online Table B1). Averages from our measurements are designated (orig), whereas the values from the literature are noted (lit).
DOI: 10.5061/dryad.60699/3
title: Larval_adult_size

description: The file titled "Larval_adult_size" contains data on the larval and adult size of tapeworms that grow in their piscivorous bird final host (G species). Lengths, widths, and areas (length x width) are given for each species. Areas were also converted to mass using relationships described in Online Appendix B. Finally, the source from which larval size was taken is listed (author, journal, volume, page numbers). Adult size was taken from Ryzhikov et al. (1985).
DOI: 10.5061/dryad.60699/4
title: Host_masses_mammals

description: Two files contain information about the mass of cestode definitive hosts, "Host_masses_birds" and "Host_masses_mammals". For each cestode species, known hosts are listed with their mass. The mass of birds was taken from Dunning (1992). The mass of mammals from Smith et al. (2003) The average host size for each cestode is calculated. The host lists for cestodes in piscivorous birds were given by Ryzhikov et al. (1985). The host lists for cestodes in mammals were taken from the references from which size data were collected (see file "Host_size_regression.csv").
DOI: 10.5061/dryad.60699/5
title: Host_masses_birds
DOI: 10.5061/dryad.60699/6
title: Host_size_regression

description: The file "Host_size_regression" includes the size (length, width, area) of growing (G) and non-growing (NG) adult tapeworms in piscivorous birds and mammals. Log cestode area was also converted to log cestode mass as described in Online Appendix B. Data for cestodes of piscivorous birds were taken from Ryzhikov et al. (1985), whereas data for cestodes of mammals were taken from the primary literature (references are given for these tapeworms). The average host mass for a given cestode species is the average mass of known definitive hosts (see files "Host_masses_birds.csv" and "Host_masses_mammals.csv").
DOI: 10.5061/dryad.65t6n/1
title: Concatened_MrB

description: Nexus file of concatenated mitochondrial partitions used to perform the Bayesian phylogenetic analysis of Alcelaphini. Five partitions were considered: tRNAs (1-1512 nucleotide positions), rRNA (1513-4039), and first, second and third codon sites of the protein coding genes (4040-15439). The Bayesian inference consisted of ten million generations analysis (sampled every 1,000 generations), and a 50% burn-in.
DOI: 10.5061/dryad.65t6n/2
title: Chromosome_MP

description: Nexus files of 23 chromosome characters used to perform maximum parsimony phylogenetic analysis of Alcelaphini. The data matrix was established by assigning 0 or 1 values for the absence or presence of characters. MP trees were generated using a heuristic search option and phylogenetic support for each node was assessed using 1000 bootstrap replicates.
DOI: 10.5061/dryad.65t6n/3
title: ChraALL

description: Nexus file of 5 ambiguous chromosomal characters used to estimate ancestral states and chromosome evolution in  Alcelaphini via SIMMAP.
DOI: 10.5061/dryad.65t6n/4
title: BurninMrB

description: Nexus file containing the 4999 post-burning Bayesian trees used to estimated the posterior probability distribution of the rate of change of 5 ambiguous chromosome characters in Alcelaphini. SIMMAP estimated ancestral states by averaging the posterior distribution over multiple trees. The number of changes is proportional to branch lengths.
DOI: 10.5061/dryad.82gg4/2
title: velocity

description: To quantify larval swimming, still images were extracted every 2.5 s for the entire 60-min video recording, and larval positions (x, z co-ordinates) were measured using ImageJ. To obtain w and s for each replicate, all individuals in focus from 20 pairs of frames (frames in a pair were 2.5 s apart) were used, each pair being separated by 3-min intervals. Data set includes larval rearing temperature (°C), experimental temperature (°C), replicate number, time since introduction of larvae (min:s:ms or decimal s), larvae number, x (horizontal) and z (vertical) positions within the frame (mm), and vertical swimming velocities (mm s-1)