cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.61s1n/1
title: Stubbs et al. Morphological analysis - Raw Landmark Data

description: This is a tps. file containing 2-D digitized landmarks for the mandibles (lower jaws) of 107 Mesozoic crurotarsans, in lateral view. The file describes the landmark coordinates for all 74 landmark points taken on each specimen. Together with the associated NTS. sliders file this is used to compute aligned, Procrustes transformed, coordinates. The file can be read by notepad, PAST and a number of geometric morphometrics software packages, including tps software, MorphoJ, or IMP software.
DOI: 10.5061/dryad.61s1n/2
title: Stubbs et al. Morphological analysis - Semi-Landmark Data (sliders file)

description: This simple NTS. file describes which of the 74 landmarks used in this study are sliding (semi-landmarks). The file is required to compute aligned, Procrustes transformed, coordinates; together with the associated raw landmark data file. The file was created in TPSUTIL. To create aligned coordinates both this file and the raw landmark data should be input in TPSRELW using the chord – min d2 sliding method.
DOI: 10.5061/dryad.61s1n/3
title: Stubbs et al. Morphological analysis - Procrustes Aligned Coordinates

description: This data file contains the Procrustes transformed aligned 2-D landmark coordinates for 107 Mesozoic crurotarsan mandibles. The file contains taxonomic labels in the first column. The file can be opened in PAST (Palaeontological Statistics). Using the PCA function on all the data will produce a 2-D lateral lower jaw morphospace for Mesozoic crurotarsans.
DOI: 10.5061/dryad.61s1n/4
title: Stubbs et al. Morphological analysis - PCA axes 1-15

description: File contains 15 PC scores from the principal component analysis on the Procrustes transformed aligned landmarks. Plotting axes 1 and 2 as an XY plot produces a 2-D lateral mandibular morphospace for Mesozoic crurotarsans. In our main analyses the first 10 axes were used to calculate morphological disparity, together with binary occurrence and groups files using the MDA add-on for MATLAB. Data regarding the stratigraphic occurrences and groupings for each taxon can be found in the electronic supplementary material accompanying our article (Table S1).
DOI: 10.5061/dryad.61s1n/5
title: Stubbs et al. Biomechanical analysis - Raw biomehanical character data

description: This file contains the raw data from 14 biomechanical measurements, taken from the mandibles of 107 Mesozoic crurotarsans. To produce a biomechanical morphospace the data should be z-transformed and entered into PAST. Using the PCO (principle coordinates) function and the Gower similarity index will produce a biomechanical mandibular morphospace. Abbreviations for characters: Total mandibular length (TOTL), Quadrate/articular offset (QUADOFF), Relative length of the mandibular symphysis (SYMPH), Relative length of dental row (%DENT), Relative area of the fenestrae (%FEN), Anterior mechanical advantage (AMA), Posterior Mechanical Advantage (PMA), Opening mechanical advantage (OMA), Maximum Second Moment of Area (MAXI), Average Second Moment of Area (AVRI), Max polar moment of inertia (MAXJ), Average polar moment of inertia (AVRJ), Slenderness of the largest tooth (CUSPMAX), The curvature of largest tooth (CURVEMAX). Full descriptions of each character can be found in the electronic supplementary material accompanying the main article.
DOI: 10.5061/dryad.61s1n/6
title: Stubbs et al. Biomechanical analysis - PCO axes 1-15

description: File contains 15 PC scores from a principal coordinates analysis of the z-transformed biomechanical data, from 107 Mesozoic crurotarsan mandibles. Plotting axes 1 and 2 as an XY plot produces a biomechanical mandibular morphospace. In our main analyses the first 10 axes were used to calculate biomechanical disparity, together with binary occurrence and groups files using the MDA add-on for MATLAB. Data regarding the stratigraphic occurrences and groupings for each taxon can be found in the electronic supplementary material accompanying our article (Table S1).
DOI: 10.5061/dryad.69329/19
title: Supplementary Figure S5

description: Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
DOI: 10.5061/dryad.69329/20
title: Tutorial

description: Tutorial on how to set up and modify a species tree diffusion analysis
DOI: 10.5061/dryad.69329/21
title: Appendix - Specimens list

description: Full list of specimens used for species tree inference with additional information on collection localities in decimal grades
DOI: 10.5061/dryad.6fd1n/1
title: COI sequence alignment

description: DNA sequence alignment containing all 3165 individuals. Sequence labels contain genus, species, drainage system, country of origin, field or museum ID, and sample ID.
DOI: 10.5061/dryad.6mh29/29
title: Cognettia 16S run2 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/30
title: Cognettia COI run1 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/31
title: Cognettia COI run2 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/32
title: Cognettia H3 run1 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/33
title: Cognettia H3 run2 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/34
title: Cognettia ITS run1 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/35
title: Cognettia ITS run2 t file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/36
title: Cognettia 16S trprobs file from MrBayes analysis
DOI: 10.5061/dryad.74j06/1
title: annotationScripts

description: This compressed directory contains perl scripts to retrieve gene annotation information for focal loci, an R script for an annotation-based randomization test, example files, and a README file.
DOI: 10.5061/dryad.74j06/2
title: bgsr.tar

description: C++ source code to analyze the transplant experimetns. This program analyzes allele frequency changes in experimental populations. The model assumes a set of experimental populations were founded from a single source population and that a sample of individuals from the source population exist. Further, the model assumes that individuals are sampled from each experimental population after a single generation. This software requires the GSL and HDF5. To compile the software try: h5c++ -O3 -o bgsr main.C mcmc.C func.C -lm -lgsl -lgslcblas
DOI: 10.5061/dryad.74j06/3
title: fstanalysis

description: R code to calculate SNP-specific Fst.
DOI: 10.5061/dryad.74j06/4
title: fitHmm

description: R code to fit and summarize the HMM for divergence state based on SNP Fst estimates.
DOI: 10.5061/dryad.785sr/1
title: Key To FIles Used For Analysis

description: Key to sequence titles
DOI: 10.5061/dryad.785sr/2
title: Morph and call data_Island Bat Diets 2013
DOI: 10.5061/dryad.785sr/3
title: Unique Haplotypes wtih bat ID
DOI: 10.5061/dryad.785sr/4
title: Unique Haplotypes with bat ID redued to those 157bp
DOI: 10.5061/dryad.81q1v/1
title: Fecundity data

description: Spreadsheet "Fecundity" contains the results of the fecundity assay. The aphids used in this experiment either contained no known secondary symbionts or were artificially infected with different complements of symbiont species.  We counted the number of offspring produced by single wingless aphids, representing one of five genotypes and hosting one of seven symbiont complements, during three (grain aphids) or four (pea aphids) consecutive three-day intervals. In the spreadsheet, rows contain offspring counts for individual aphids. Columns are as follows: &gt;&gt;&gt;Species - Aphid species, two levels (A. pisum, S. avenae). &gt;&gt;&gt;Gen - Aphid genotype, five levels (145, J68, J102, Co23, Co26). &gt;&gt;&gt;Sym - Symbiont infection status. Ha / Ri / Sp represent Hamiltonella defensa, Rickettsia sp. or Spiroplasma sp., and the value after underscore represents the genotype of original pea aphid host. &gt;&gt;&gt;Block - The ID number of experimental block. In all cases, lines of a given genotype were tested at the same time (and so have the same block ID number), separately from lines of other genotypes. The fecundity assay for genotype 145 was conducted in two blocks. &gt;&gt;&gt;D10 - number of offspring produced by single wingless aphids before its 10th day of life. &gt;&gt;&gt;D13, D16, D19 - numbers of offspring produced by single aphids during consecutive three-day intervals. &gt;&gt;&gt;Fec_total - total number of offspring produced during 16 days (S. avenae) or 19 days (A. pisum). Missing data are indicated by “NA”.
DOI: 10.5061/dryad.8m67m/1
title: Factors

description: This file contains the data associated with this manuscript on a per field basis including each factor included in the analyses presented.
DOI: 10.5061/dryad.948j3/1
title: Sturgeon polyploid microsatellite genotypes

description: multi-locus microsatllite genotypes for non-mendelian loci scored for lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan
DOI: 10.5061/dryad.b2k47/2
title: MACH Script

description: MACH.pl =&gt; This script will extract the sequences of the major alleles from a popoolation2 .sync file
DOI: 10.5061/dryad.bv188/1
title: 2006 COMPETITION DATA SET

description: Samples were taken from mice infected with either one or a pair of Plasmodium chabaudi clones of differing virulence. Daily samples were taken on red blood cell density, weight and asexual parasite density (by qPCR).
DOI: 10.5061/dryad.ck0mp/1
title: Schueth et al Supplementary Materials

description: Supplementary appendices for the Probable Datum Method manuscript.  Included are: positive control appendix, sensitivity analysis, comparison with other methods, etc.
DOI: 10.5061/dryad.d43j8/1
title: List of Flatidae species known from Madagascar
DOI: 10.5061/dryad.gk880/2
title: Mukherjee_Ray_AppendixS2-R1
DOI: 10.5061/dryad.gk880/3
title: Mukherjee_Ray_AppendixS3-R2
DOI: 10.5061/dryad.gk880/4
title: Mukherjee_Ray_AppendixS4_R2
DOI: 10.5061/dryad.j8kp5/1
title: Supplementary file 1
DOI: 10.5061/dryad.m2m1b/1
title: δ13C related to the origin of Calanus spp.. A Canadian Healthy Oceans Network Population Connectivity project, PC-08

description: Deep-dwelling stage V copepodites (CVs) were collected in the Marine Park as well as in putative source regions in the St. Lawrence system using a vertical tow initiated near the bottom to 100 m with a 75 cm diameter, 202 μm Nitex plankton net equipped with an opening-closing device. The dataset include variables used to perform the QDFAs: Percent lipid content of individuals (%Lipids),dry weight before (DW) and after lipid extraction (DWLE), δ13C, δ14N, %C.
DOI: 10.5061/dryad.m81b5/10
title: 21k_MIROC_Patagonia

description: Bioclimatic layers for past conditions (21 kya, MIROC model) obtained from WorldClim used in species-distribution modeling with Maxent
DOI: 10.5061/dryad.m81b5/11
title: 120k_Patagonia

description: Bioclimatic layers for past conditions (120 kya) obtained from WorldClim used in species-distribution modeling with Maxent
DOI: 10.5061/dryad.m81b5/12
title: Georeferenced localities

description: Geographic coordinates of sampled localities used in species-distribution modeling with Maxent
DOI: 10.5061/dryad.m81b5/3
title: TCS_files

description: Compressed zip file containing the output log files of TCS analyses for cyt b and for phased alleles of 14 anonymous nuclear loci
DOI: 10.5061/dryad.m81b5/6
title: Geneland_files

description: Compressed zip file containing the input and output files of GENELAND analyses for all loci.
DOI: 10.5061/dryad.m81b5/7
title: Beast_strict_clock_files

description: Compressed zip file containing the input files of Extended Bayesian Skyline Plot (EBSP), Standard Random Walk (SRW), and Relaxed Random Walk (RRW) analyses in BEAST using a strict molecular clock for the substitution rate of cyt b. Log files for marginal likelihood estimation (MLE), the maximum credibility tree (MCC), and the KML file for visualization in Google Earth are also included for SRW and RRW analyses.
DOI: 10.5061/dryad.m81b5/8
title: 0k_patagonia

description: Bioclimatic layers for current conditions obtained from WorldClim used in species-distribution modeling with Maxent
DOI: 10.5061/dryad.m81b5/9
title: 21k_CCSM_Patagonia

description: Bioclimatic layers for past conditions (21 kya, CCSM model) obtained from WorldClim used in species-distribution modeling with Maxent
DOI: 10.5061/dryad.rf0bh/1
title: Ma et al._female_copulationpropensity

description: cross_F_M: cross between females and males. SS_S: sexual females (SS) cross with sexual males (S). A_SS: pure sexual females (SS), here A is used to rank the groups in an alphabet order. mating1: successful mating (with daughter produced) is scored as 1. mating 0.5: unsuccessful mating (no daughter produced) is scored as 0.5
DOI: 10.5061/dryad.rf0bh/2
title: Ma et al._broodsize_comparison

description: SS_S: cross between sexual females and sexual males. SA_S: cross between F1 hybrid females and sexual males. total: brood size per family
DOI: 10.5061/dryad.rf0bh/3
title: Ma et al._offspringsexratio

description: ASS_S: sexual female "SS" cross with sexual male "S", A is the alphabet to indicate the order, does not have special meaning. total: brood size.  sex ratio: proportions of male offspring per family
DOI: 10.5061/dryad.rf0bh/4
title: Ma et al._localmatecompetition

description: SS_S: cross between sexual females "SS" and sexual males "S". total: brood size per family. sex ratio: the proportions of male offspring per family. foundress: the number of parental females per patch
DOI: 10.5061/dryad.sp0ks/1
title: Individual genotypes

description: Allelic profile of otolith and tag extracts for each of the four amplified microsatellite loci : Gmo-C18, PGmo38, Tch11 and Tch14.For each extract two PCR replicates were provided.
DOI: 10.5061/dryad.vb5pj/1
title: Stable isotopes dynamics of diapausing Calanus spp.. A Canadian Healthy Oceans Network Population Connectivity project, PC-08

description: These data were collected at a fixed station near Rimouski located in the middle of the Laurentian Channel (340 m) of the St. Lawrence Estuary (Québec, Canada). Deep-dwelling zooplankton (100–320 m) were collected with a vertical plankton tow using a 0.75-m diameter plankton net, 202-mm Nitex net equipped with an opening-closing device. Diapausin stages CVs were monitored for 4 months under controlled laboratory conditions. CVs and newly moulted adults were analyzed for d13C and d15N signatures as well as lipid, carbon and nitrogen content. Lipids were extracted in half of the samples to compare d13C of individuals with and without lipids and to evaluate the accuracy of mass balance correction models for d13C under lipid influence.This study was the first part of a MSc project aiming at using stable isotope signatures as markers of origins for Calanus spp. in a Marine Protected Area, the Saguenay-St. Lawrence Marine Park (SSLMP), Canada (Perrin et al., doi:10.3354/meps10651).
DOI: 10.5061/dryad.2018h/1
title: Counts of petite and grande colonies for spontaneous and evolved petites.

description: Three spreadsheets are included: "spontaneous" gives the counts of petite and grande colonies for spontaneous petite mutants; "spont.posteriors" gives the MCMC estimates for the spontaneous mutants; "evolved" gives the counts of petite and grande colonies for the three ancestors (X, Y, and Z) selected at each of five effective population sizes (1, 3, 10, 32, 100). The mip1-deleted control is also included on the "evolved" and "spontaneous" spreadsheets.
DOI: 10.5061/dryad.2215v/1
title: Bib area measurements from two sets of annotators

description: Based on photos from male house sparrows at 5 times of year, photographed with a ruler for reference, and measured using ImageJ software.
DOI: 10.5061/dryad.2215v/2
title: Receptor concentrations (MR and GR) in bib skin and belly skin

description: Receptor concentrations measured via radioligand binding assays in bib skin and belly skin of male house sparrows at 5 different times of year. All binding was standardized to fmol/mg protein as measured using Bradford assays.
DOI: 10.5061/dryad.2qs35/1
title: SNPs and genotypes identified in H. rufescens, Fort Ross 2011.

description: tab-delimited text file containing all SNPs passing the GATK VQSR algorithm found in Fort Ross abalone in 2011, and genotypes in all individuals assigned with Q20 as cutoff. The standard GATK best practise protocol v2 was followed, using an initial call set with Q30 as cutoff to train the VQSR. Raw data files are accessible at the NCBI Short Read Archive (SRA), project accession # SRP037568.
DOI: 10.5061/dryad.36077/9
title: directly sequenced COII

description: Fasta files of the directly sequenced partial COII genes.
DOI: 10.5061/dryad.3639h/1
title: Jasus edwardsii microsatellite analysis
DOI: 10.5061/dryad.36c10/1
title: DNA seq alignments for BEAST

description: DNA sequence alignments for divergence time analysis; COI, 16S and 28S. Including the sequences of Cavernacmella spp. and outgroup species.
DOI: 10.5061/dryad.36c10/2
title: DNA seq alignments for phylogenetic tree

description: DNA sequence alignments for phylogenetic trees; COI, 16S, 28S and ITS. Including the sequences of Cavernacmella spp.
DOI: 10.5061/dryad.36c10/3
title: Morphological measurements of Cavernacmella spp. in Ogasawara.

description: Raw data of morphological measurements of Cavernacmella spp. in Ogasawara. Site nos. and abbreviation for each measurements refer to manuscript.
DOI: 10.5061/dryad.37b28/1
title: Data on voluntary wheel running

description: Data on voluntary wheel running from the base population up to generation 31 of the artificial selection experiment. See ReadMe.txt
DOI: 10.5061/dryad.37b28/2
title: Descriptive statistics

description: Descriptive statistics (N=number of individuals, mean, variance, sd=standard deviation, range, CV=coefficient of variation) of voluntary wheel running (in revolutions per day) for four control lines (linetype=C) and four selected lines (linetype=HR) as a whole and for the subset of individuals that were selected for reproduction in each generation. These statistics were used to calculate the selection differential (s), the standardized selection differential (s’), the cumulative standardized selection differential (acc s’), the average of the four control lines at each generation (Mean controls), and the selective gain relative to the average of the four control lines at each generation (gain vs. control).
DOI: 10.5061/dryad.37b28/3
title: Pedigree

description: Pedigree of the population from the base population up to generation 31 of the selection experiment
DOI: 10.5061/dryad.3mm06/1
title: parsite genetic diversity and genetransfer

description: The first data sheet includes the processed data, i.e. gene diversity within and among replicate populations, calculated for the chromosomal marker as for the combination of chromosomal and toxin gene marker, as well as the mean toxin gene gain and loss per replicate population. The second data sheet includesthe raw data. For this, the genetic background of 10 clones per replicate population was determined as well as the presence of three toxin genes.
DOI: 10.5061/dryad.3t30n/1
title: Segoli & Rosenheim 2013

description: Data for egg loads of newly emerged females collected as pupae from the field (potential fitness), estimated number of eggs laid by females collected dead from the field (realized fitness), hind tibia length, and relative Wolbachia density in the body individual females (estimated as -ddCt).
DOI: 10.5061/dryad.4cj42/1
title: Lake trout genotypes

description: The raw genotype of all individuals used in this study.
DOI: 10.5061/dryad.4cj42/2
title: Ancient lake trout genotypes

description: The subset of historical genotypes compared to contemporary ones.
DOI: 10.5061/dryad.61g42/1
title: Viburnum.tre

description: phylogenetic tree from Chatelet et al. 2013; pruned to include only taxa from this analysis
DOI: 10.5061/dryad.61g42/2
title: alltrait_raw

description: raw data for all variables analysed in this study. tab-delineated text. for variable abbreviations and units please see publication.
DOI: 10.5061/dryad.61g42/3
title: alltrait_means

description: species mean values, standard deviation, and standard error for all variables analysed in this study. tab-delineated text. for variable abbreviations and units please see publication.
DOI: 10.5061/dryad.6mh29/37
title: Cognettia COI trprobs file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/38
title: Cognettia H3 trprobs file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/39
title: Cognettia ITS trprobs file from MrBayes analysis
DOI: 10.5061/dryad.785sr/5
title: R_virgo_BLAST
DOI: 10.5061/dryad.785sr/6
title: R_inops_BLAST
DOI: 10.5061/dryad.785sr/7
title: R_arcuatus_BLAST

description: Please see the read me file for details.
DOI: 10.5061/dryad.785sr/8
title: H_pygmaeus_BLAST

description: Please see read me file for instructions.
DOI: 10.5061/dryad.81q1v/2
title: Pathogen susceptibility data

description: Spreadsheet "Susceptibility" contains the results of the pathogen susceptibility assay. The aphids used in this experiment either contained no known secondary symbionts or were artificially infected with different complements of symbiont species.  Groups of 20 aphids, representing one of five genotypes and hosting one of seven symbiont complements, were exposed to spores of the pathogenic fungus Pandora neoaphidis. After six days all aphids were scored as a) sporulating; b) dead but not sporulating; or c) alive. In the spreadsheet, each row represents a replicate with 20 aphids. Columns are as follows: &gt;&gt;&gt;Species - Aphid species, two levels (A. pisum, S. avenae). &gt;&gt;&gt;Gen - Aphid genotype, five levels (145, J68, J102, Co23, Co26)&gt;&gt;&gt;Sym - Symbiont infection status. Ha / Ri / Sp represent Hamiltonella defensa, Rickettsia sp. or Spiroplasma sp., and the value after underscore represents the genotype of original pea aphid host. &gt;&gt;&gt;Fung_D6 - The number of aphids in a replicate which were classified as sporulating six days after the exposure. &gt;&gt;&gt;Dead_D6 - The number of aphids in a replicate which were classified as dead but not sporulating. &gt;&gt;&gt;Alive_D6 - The number of aphids in a replicate which were alive six days after the exposure. &gt;&gt;&gt;Total - The total number of aphids in the three previous categories. Note that in some cases the total is different than 20 – occasionally not all aphids were found six days after the exposure, or the number of the exposed aphids in a replicate may have been miscalculated by 1 or 2.
DOI: 10.5061/dryad.8hf1c/1
title: Data mast
DOI: 10.5061/dryad.98c81/1
title: Biomass data Experiment 1

description: Biomass data Experiment 1
DOI: 10.5061/dryad.98c81/2
title: Biomass data Experiment 2

description: Biomass data Experiment 2
DOI: 10.5061/dryad.b6428/1
title: Laying order, sex and paternity of blue tit hatchlings in 2009

description: Laying order, sex and paternity of 743 blue tit hatchlings in 2009, from 68 broods.
DOI: 10.5061/dryad.bc8pc/1
title: Canadian benthos Fasta files

description: Fasta files for the benthos insect datasets from Fredericton, New Brunswick, Canada: 1) ~ 100 bp fragments (454), 2) ~ 200 bp fragments (454), 3) ~ 600 bp reference (Sanger) sequences.
DOI: 10.5061/dryad.bc8pc/2
title: Training the naive Bayesian classifier

description: Contains the Fasta and taxonomy files needed to train the Ribosomal Database Project naive Bayesian classifier three different ways: 1) GenBank-genus, 2) GenBank-barcode, 3) GenBank-family.
DOI: 10.5061/dryad.bc8pc/3
title: Customizing the Insecta taxonomy used with the classifier

description: Contains three tab-delimited taxonomy files that can be used to help customize the taxonomic scheme used by the naive Bayesian classifier: 1) GenBank-genus, 2) GenBank-barcode, 3) GenBank-family.  One of these files, should be used with one of the two provided Perl scripts to generate a taxonomy file in the format required by the Ribosomal Database Project naive Bayesian classifier during training: 1) make_NBC_taxonomy.plx, 2) make_NBC_taconomy_family.plx.
DOI: 10.5061/dryad.bc8pc/4
title: Malaise insect dataset

description: Fasta file of Malaise insect data set, see also Gibson et al. (in prep).