cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4h462/6
title: dfoil simulation script

description: use --help for full options
DOI: 10.5061/dryad.4h462/7
title: DFOIL post-analysis summarization script

description: summarizes introgression window statistics, use --help for full options
DOI: 10.5061/dryad.59h51/1
title: Phylogenetic alignment data
DOI: 10.5061/dryad.5cb7r/1
title: Maguire Lize Price 2015 Plos One Assessment of rival males through the use of multiple sensory cues in the fruitfly Drosophila pseudoobscura data

description: This is the data for Maguire et al 2015 PlosOne "Assessment of rival males through the use of multiple sensory cues in the fruitfly Drosophila pseudoobscura". The key data is the time to mating (mating latency) and duration of mating (copulation latency) of male flies, who had had a variety of sensory modes (vision, hearing, smell and touch) removed in various combinations, to see whether they responded to the presence of a rival male.
DOI: 10.5061/dryad.6h88s/1
title: Global nucleotide tree
DOI: 10.5061/dryad.b7156/11
title: 500 Sim-Matching simulated alignments

description: Fasta files for Sim-Matching simulation
DOI: 10.5061/dryad.b7156/12
title: 500 Sim-Multi-Individual simulated alignments

description: Fasta files for Sim-Multi-Individual simulation
DOI: 10.5061/dryad.b7156/13
title: 500 Sim-3x-Rate simulated alignments

description: Fasta files for Sim-3x-Rate simulation
DOI: 10.5061/dryad.b7156/14
title: SNP Data

description: Nexus file containing data for 1,170 SNPs genotyped for all 19 individuals.
DOI: 10.5061/dryad.b7156/15
title: All 919 Empirical Gene Trees

description: All 919 PhyML gene trees inferred using CloudForest. After collapsing short branches into polytomies, these trees were used to infer the species tree topologies used in MulRF and ASTRAL.
DOI: 10.5061/dryad.b7156/16
title: All Empirical Bootstrap Gene Trees

description: 100 bootstrap replicates for 919 loci. Bootstrap replicates were made in CloudForest. Each of the 100 bootstrap sets were used to infer species trees. These pseudoreplicates were used to add nodal support metrics to empirical MulRF and ASTRAL trees.
DOI: 10.5061/dryad.b7156/17
title: Whole Mitochondrial Genomes and MrBayes Block

description: Nexus file containing sequences for 19 whole mitochondrial genomes and a MrBayes block with MrBayes settings.
DOI: 10.5061/dryad.b7156/9
title: Figure S6 Sim-3x-Rate StarBEAST

description: Figure S6. All 10 Sim-3x-Rate *BEAST subsets.Each species tree is based on analysis of a differentsubset of 50 simulated loci. Numbers at nodesdenote Bayesian PPs.
DOI: 10.5061/dryad.h00mt/1
title: Marron microsatellite data

description: Excel file containing microsatellite genotypes for Cherax cainii and Cherax  tenuimanus sampled from the south-west of Western Australia
DOI: 10.5061/dryad.j4h5f/1
title: 01_Flow Cytometry RF Values

description: Flow cytometry relative fluorescence values used to assess hybrid occurrence at contact zones.
DOI: 10.5061/dryad.j4h5f/2
title: 02_Geographic Isolation Data

description: Data used to calculate the extent of geographic isolation between E. albidum and E. mesochoreum using floral visitors' intertegular spans.
DOI: 10.5061/dryad.j4h5f/3
title: 035_herb records

description: Herbarium records used in the analysis of phenological differences between E. albidum and E. mesochoreum
DOI: 10.5061/dryad.j4h5f/4
title: herbarium analyses

description: R code for the herbarium analyses
DOI: 10.5061/dryad.j4h5f/5
title: FL Phenology Null Model

description: R code for the field-based phenology model
DOI: 10.5061/dryad.m498n/1
title: piquero_bayes.dat

description: piquero_bayes.dat is the ADMB data file for running Bayesian analysis of habitat selection by Peruvian Boobies as presented in Boyd et al. "Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey".
DOI: 10.5061/dryad.m498n/2
title: piquero_bayes.tpl

description: piquero_bayes.tpl is the ADMB source code for running Bayesian analysis of habitat selection by Peruvian Boobies as presented in Boyd et al. "Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey".
DOI: 10.5061/dryad.m498n/3
title: guanay_bayes.dat

description: guanay_bayes.dat is the ADMB data file for running Bayesian analysis of habitat selection by Guanay Cormorants as presented in Boyd et al. "Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey".
DOI: 10.5061/dryad.nt18c/10
title: LDBS10_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 11th, 2012
DOI: 10.5061/dryad.nt18c/11
title: LDBS11_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 24th, 2012
DOI: 10.5061/dryad.nt18c/5
title: LDBS5_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 18th, 2011
DOI: 10.5061/dryad.nt18c/6
title: LDBS6_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 27th, 2011
DOI: 10.5061/dryad.nt18c/7
title: LDBS7_All_ST.csv

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on July 28th, 2012.
DOI: 10.5061/dryad.nt18c/8
title: LDBS8_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 2nd, 2012
DOI: 10.5061/dryad.nt18c/9
title: LDBS9_All_ST

description: Acoustic survey data (exported single target detections) from Lac du Bonnet, Manitoba, on August 8th, 2012
DOI: 10.5061/dryad.pr11m/2
title: Breast arterial calcifications and CAD, data
DOI: 10.5061/dryad.q018v/3
title: FileS5 revisedAssemblyUnmasked.fa.zip

description: Fasta file containing revised genome assembly based on consensus scaffold order and orientation as described in File S4 in the Glazer et al. manuscript. File is zipped.
DOI: 10.5061/dryad.q018v/4
title: FileS6 revisedAssemblyMasked.fa.zip

description: Repeat masked fasta file containing revised genome assembly based on consensus scaffold order and orientation as described in File S4 in the Glazer et al. manuscript. Repeat masked fasta file is based off the repeat masked version of the original genome assembly, which was masked with RepeatMasker. File is zipped.
DOI: 10.5061/dryad.q018v/5
title: FileS7 ensGene_revised.gtf

description: Revised .gtf file of Ensembl gene predictions. Coordinates of gene predictions were converted to the revised assembly coordinates. All Ensembl-predicted genes were included, except ENSGACT00000019430, which spans two scaffolds (11 and 79) that are not adjacent in the revised genome assembly. File is zipped.
DOI: 10.5061/dryad.q018v/6
title: ScafKeyForNewFasta.csv

description: Key for scaffold order in fasta files
DOI: 10.5061/dryad.q018v/7
title: SampleList.csv

description: List of all samples and barcodes in the GBS F2s.
DOI: 10.5061/dryad.q018v/8
title: convertCoordinate.R

description: This R function converts between the 'old' and 'new' stickleback assembly coordinate systems. The 'old' coordinate system is the assembly described in the Jones et al 2012 stickleback genome paper. It requires access to the FileS4 NewScaffoldOrder.csv file. It has 4 inputs: chr, pos, direction, and scafFile. It returns a list of [chromosome, position]. See README or comments in convertCoordinate.R for further details.
DOI: 10.5061/dryad.r22h4/131
title: file format Description
DOI: 10.5061/dryad.r22h4/2
title: MRI_subject_10
DOI: 10.5061/dryad.r22h4/3
title: MRI_subject_11
DOI: 10.5061/dryad.r22h4/5
title: MRI_subject_12
DOI: 10.5061/dryad.r22h4/6
title: MRI _subject_13
DOI: 10.5061/dryad.t40f2/1
title: Hutchinson et al data

description: This file contains the data used in the empirical case study of our manuscript.  The first three tabs contain site occupancy, survey-specific covariates, and site-specific covariates for our full (656 sites, 3 surveys) survey effort.  The last three tabs contain site occupancy, survey-specific covariates, and site-specific covariates for the first 2 surveys from 55 randomly-selected sites (the reduced data set in the paper).  Further information is available in the attached "ReadMe" file.
DOI: 10.5061/dryad.1s445/2
title: LSSI model code 15Apr15

description: Source code for the Larval Slope Source Index model
DOI: 10.5061/dryad.2bm41/1
title: Simmons 2015

description: Raw peak areas of the compounds identified in hexane washes of individual bees
DOI: 10.5061/dryad.34t55/2
title: Challands2015Analysis2

description: Challands 2015 matrix - Friedman 2007 Dipnoan matrix with Rhinodipterus kimberleyensis i.e. the matrix of Clement updated for Dipterus valenciennesi.
DOI: 10.5061/dryad.361gs/1
title: Data
DOI: 10.5061/dryad.417kf/1
title: PIRI_metab_Dryad

description: sex 1:male 2=female; age=years; PIRI&gt;25 0=no 1=yes; metabolic syndrome, smoker, alcohol, lack of exercise 0=no 1=yes; lack of sleep 1=no, 2=yes; hypercolesterolemia hypertrygliceridemia hypertension diabetes obesity 0=no 1=yes; PIRI standardized score
DOI: 10.5061/dryad.59h51/2
title: sequence data code
DOI: 10.5061/dryad.59h51/3
title: NJ_Phylogenetic tree
DOI: 10.5061/dryad.650cn/1
title: Larval Dissections

description: This file contains the dissection data for Agalychnis callidryas larvae reared at 5, 25, or 45 individuals per mesocosm at the Smithsonian Tropical Research Institute in Gamboa, Panama. The file provides the density, tank number and larval ID for each individual.  There are total body lengths and body masses for each individual, as well as  liver masses, fat body masses, and total gut masses.  There are also measures of length and projected area for each section of the gut including the manicotto, small intestine, and large intestine.  These values were obtained by photographing the gut and a ruler from above and analyzing the photo using ImageJ software from the National Institute of Health.  The area represents the area of each gut section as seen in the photo, not the surface area of the gut.
DOI: 10.5061/dryad.650cn/2
title: Metamorph external morphology

description: This file contains morphometric data for Agalychnis callidryas metamorphs on the day they emerged from the mesocosm in which they were reared as larvae. They were reared at either 5, 25, or 50 individuals per mesocosm.  The file contains the date of emergence, the tank (mesocosm) number, rearing density, and metamorph ID for each individual.  The measurements include snout-vent length, belly width and tail length, as well as body mass.  The linear measurements were made when the metamorph was asleep in its water conservation posture on the side of a small, clear cup.  We used dial calipers to make each measurement through the cup wall.  Snout vent length was the distance from the tip of the snout on the most anterior end of the animal to the vent (cloaca).  The belly was measured at its widest part, and the tail was measured from its base to its tip.
DOI: 10.5061/dryad.650cn/3
title: Froglet dissections

description: This file contains the dissection data for Agalychnis callidryas froglets reared as larvae at 5, 25, or 45 individuals per mesocosm at the Smithsonian Tropical Research Institute in Gamboa, Panama.  We dissected froglets one after they had completed tail resorption.  The file provides the rearing density, tank number and froglet ID for each individual.  There are snout vent lengths and body masses for each individual, as well as liver masses, fat body masses, and total gut masses.  There are also measures of length and projected area for each section of the gut including the stomach, small intestine, and large intestine.  These values were obtained by photographing the gut and a ruler from above and analyzing the photo using ImageJ software from the National Institute of Health.  The area represents the area of each gut section as seen in the photo, not the surface area of the gut.
DOI: 10.5061/dryad.68b3g/1
title: R code for simulations and analysis

description: This file contains R code for running the simulations described in the manuscript and some functions that were written to analyse the data.
DOI: 10.5061/dryad.6h88s/2
title: Global sequence alignment
DOI: 10.5061/dryad.6h88s/3
title: Hediste diversicolor nucleotide tree
DOI: 10.5061/dryad.6h88s/4
title: Hediste diversicolor sequence alignment
DOI: 10.5061/dryad.977p1/1
title: Data for condition dependence analysis

description: Data included in the attached file were collected from a series of mosquitofish on Abaco island in The Bahamas. The data are untransformed, raw phenotypic data from adult male fish collected from populations experiencing variable predation pressure.
DOI: 10.5061/dryad.bk8p4/1
title: Mist-netting data - six species, five primary sessions

description: This dataset has eight columns: These are named, and represent: (1) session: the primary session for sampling under the capture-recapture modelling framework; (2) season - categorical - whether breeding or post-breeding; (3) plot - nominal - name of the sampling plot (A, B, C, D, F, H, J); (4) tree density per hectare - continuous, and at the plot level; (5 & 6) quality of the buffer around the plot relative to plot quality in terms of vegetation - (5) represents this value for a buffer width of 300 metres around the plot, and (6) this value for a buffer width of 1000m around the plot; (7) a code representing the identity of each individual (the ring number of the ring used to ring each bird); and (8) the scientific name of the six species, with the genus and species names separated by a period.
DOI: 10.5061/dryad.c5m42.2
title: Data from: Accelerated rate of molecular evolution for vittarioid ferns is strong and not due to selection
DOI: 10.5061/dryad.gg47h/1
title: IUI Survey response spreadsheet- Dryad

description: Survey responses from Fertility clinics in the United Kingdom- Excel spreadsheet
DOI: 10.5061/dryad.h06r3/1
title: Data underpinning the results in TGG Steane et al. 2015

description: This excel file comprises five sheets of data (relating to Eucalyptus salubris population differentiation), each with an accompanying page of explanatory notes.  The information contained herein includes: (1) population level climate data from ANUCLIM; (2) population level soil data; (3) population level isotope data relating to physiological measurements; (4) morphological measurements from ten individuals of each population; and (5) dominant DArT marker data from each of about 30 trees per population.
DOI: 10.5061/dryad.hv500/1
title: Female Vg1 qRTPCR

description: Datafile containing qRT-PCR data on vg expression from whole head samples, females, from 5 social conditions.
DOI: 10.5061/dryad.hv500/2
title: Female Vg2 qRTPCR

description: Datafile containing qRT-PCR data on vg2 expression from whole head samples, females, from 5 social conditions.
DOI: 10.5061/dryad.hv500/3
title: Male Vg1 qRTPCR

description: Datafile containing qRT-PCR data on vg1 expression from whole head samples, males, from 5 social conditions.
DOI: 10.5061/dryad.hv500/4
title: Male Vg2 qRTPCR

description: Datafile containing qRT-PCR data on vg2 expression from whole head samples, females, from 5 social conditions.
DOI: 10.5061/dryad.hv500/5
title: VgR male female Brain Head Compare

description: vg receptor expression data, qRT-PCR, from whole head samples and just brain samples, males and females.
DOI: 10.5061/dryad.hv500/6
title: VgR_FemaleHeads qRTPCR

description: Datafile containing qRT-PCR data on vg receptor expression from whole head samples, females, from 5 social conditions.
DOI: 10.5061/dryad.hv500/7
title: VgR_MaleHeads qRTPCR

description: Datafile containing qRT-PCR data on vg receptor expression from whole head samples, males, from 5 social conditions.
DOI: 10.5061/dryad.j4h5f/10
title: Code for sd set sd mass and SI

description: R code for analyses of seed set, seed mass, and SI release
DOI: 10.5061/dryad.j4h5f/11
title: pollination spreadsheet 2010 2011

description: spreadsheet of hand-pollination data for analyses of seed set, seed mass, and SI release
DOI: 10.5061/dryad.j4h5f/12
title: 06_Pollen viability counts spreadsheet_for ms

description: Data used for calculations of E. mesochoreum and hybrid pollen viability
DOI: 10.5061/dryad.j4h5f/6
title: phenology2010

description: 2010 phenology data (see description in R script)
DOI: 10.5061/dryad.j4h5f/7
title: phenology2010edit

description: edited 2010 phenology data (see R script for description)
DOI: 10.5061/dryad.j4h5f/8
title: phenology2011

description: 2011 phenology data (see R script for additional info)
DOI: 10.5061/dryad.j4h5f/9
title: phenology2011edit

description: edited 2011 phenology file (see R script for details)
DOI: 10.5061/dryad.jc3ht/1
title: snpsLaskySciAdv_dryad.tar
DOI: 10.5061/dryad.m498n/4
title: guanay_bayes.tpl

description: guanay_bayes.tpl is the ADMB source code for running Bayesian analysis of habitat selection by Guanay Cormorants as presented in Boyd et al. "Predictive modelling of habitat selection by marine predators with respect to the abundance and depth distribution of pelagic prey".
DOI: 10.5061/dryad.m498n/5
title: ReadMe
DOI: 10.5061/dryad.mk44c/1
title: CMR Data

description: Detail of the capture recapture data and covariates.
DOI: 10.5061/dryad.mv13v/1
title: Fraaije et al. field experiments

description: Eight worksheets with data on experimentally studied recruitment processes (germination, seedling survival, and seedling growth: worksheet 1-3), re-structured for multivariate analyses (worksheet 4-6), soil parameters (worksheet 7) and description of column headers (worksheet 8).
DOI: 10.5061/dryad.mv13v/2
title: Fraaije et al. mesh bags control experiment

description: Two worksheets containing data on a control experiment which tested the effect of mesh bags on germination, with the data in worksheet 1, and description of column headers in worksheet 2.
DOI: 10.5061/dryad.p3b3f/1
title: Oyster Data

description: Archive containing data for P. maxima analysis with NetView P, including wild (n = 83, SNPs = 999), captive (n = 684, SNPs = 834) and simulated (n = 3000, SNPs = 1271) genotypes, as well as input files (PED/MAP), node attributes and networks for visualization in Cytoscape.
DOI: 10.5061/dryad.pg126/1
title: Kuan et al. for Plos One 2015

description: The raw data for all the analyzes in this study was collected from Tri-Service General Hospital. Patient baseline characteristics, including sex, age at surgery, stage (I, II, III, and IV), recurrence, mortality status, and gene promoter region methylation status in the candidate genes (p16, hMLH1, and MGMT), were compared.
DOI: 10.5061/dryad.q3r3k/2
title: Model data files

description: Data files from all experiments used to generate figures in the paper
DOI: 10.5061/dryad.sc6bp/1
title: DeconSeq vertebrate rRNA database

description: This is a fasta file containing the custom vertebrate ribosomal RNA database to be used with DeconSeq to remove rRNA contaminants from sequencing data.  It was created by extracting vertebrate rRNA sequences from NCBI using the query "(ribosomal RNA) AND "vertebrates"[porgn:_txid7742]", checking the sequence descriptions by eye (removing undesired sequences), and then following the procedure to create a custom database from the DeconSeq manual (http://deconseq.sourceforge.net/manual.html). Briefly, long stretches of ambiguous bases (Ns) were removed, and then the sequences were filtered (using PRINSEQ) to remove short sequences (&lt; 200 bp), those with &gt;10 ambiguous bases (Ns), and duplicate sequences.  Finally, the fasta file was indexed using BWA and used as the database for all DeconSeq filtering in this project.
DOI: 10.5061/dryad.sc6bp/2
title: spleen/buffy coat combined trinity assembly

description: RNA was extracted from the spleen and buffy coat (white blood cell portion of a blood sample) of one and two individuals from the San Diego Zoo koala colony, respectively, via TRIzol (Life Technologies) and Direct-zol (Zymo Research) according to manufacturer's instructions.  ~5 ug of RNA was used to create cDNA libraries for each sample according to the Illumina TruSeq RNA sample preparation manual and using random hexamer priming.  The buffy coat libraries were barcoded, pooled, and sequenced on one lane of the Illumina HiSeq 2000 platform while the spleen library was sequenced on one lane of the Illumina HiSeq 2500 platform.  The raw reads were then filtered for quality (PHRED Q score &gt; 20) and length ( &gt; 30 bp).  Ribosomal RNA reads were reduced using DeconSeq (version 0.4.2) and a custom vertebrate rRNA database.  The remaining reads were then assembled using Trinity (version r2013-02-25) and the assembled sequences are contained within.
DOI: 10.5061/dryad.sc6bp/3
title: trinotate annotation report of spleen/buffy coat trinity transcripts

description: The Trinity transcripts (contained within spleen/buffy coat combined trinity assembly) were annotated using the Trinotate pipeline (part of the Trinity package version r2013-02-25).  Briefly this pipeline searches the transcripts for open reading frames, BLASTs the resulting protein sequences to the NCBI's SwissProt database, and assigns GO terms off of the best hit.  It also searches the transcripts for conserved PFAM domains.
DOI: 10.5061/dryad.sc6bp/4
title: alignments of target protein sequences

description: The target gene open reading frame protein sequences (MHC, TLR, RLR, KoRV) from the Trinotate analysis were first aligned with eutherian, marsupial, and other vertebrate sequences using Jalview 2.8.0b1 and MUSCLE using default parameters.  An intital neighbor joining tree was created (using MEGA 5.2.2) and used to guide the alignments of each individual gene clade via Jalview and MUSCLE (with the exception of MHC sequences which were aligned using HMMER 3.1b and PFAM seed alignments).  These gene group alignments were then combined using COACH (version 11/21/2002 Linux) and additional sequences were added as needed.  The ends of the alignments were trimmed, when necessary, and both the full and trimmed alignments (.fas format) are included in this file package.  For more detailed methods please refer to the associated publication.
DOI: 10.5061/dryad.sc6bp/5
title: bootstrap trees (maximum likelihood and neighbor joining) for target protein sequences

description: The target protein alignments (MHC, TLR, RLR, KoRV) were used to build both maximum likelihood and neighbor joining trees using MEGA 5.2.2.  The alignments and PROTEST 3.2 were used to determine the most appropriate substitution model to use while building the tree.  For more detailed methods, please refer to the associated publication.  Each tree is presented here in Newick format.  The trees were run with 1,000 replicates and the branch lengths represent the bootstrap values.  The accession numbers for the sequences used in these trees can be found in "Online Resource 1" of the associated publication.
DOI: 10.5061/dryad.vg97f/1
title: SA1 archive file containing all supplementary materials mentioned in the text.
DOI: 10.5061/dryad.23hs1/1
title: Amphiacusta_5558SNPs_StructureFile.txt

description: A structure format file containing 5,558 single bi-allelic SNPs that were used for assessing population structure and genetic differentiation (for STRUCTURE, PCA and procrustes analyses, IBD and estimation of genetic diversity statistics).
DOI: 10.5061/dryad.23hs1/2
title: Amphiacusta_82443SNPs_ForQuartets.txt

description: A phylip file containing 82,443 single bi-allelic SNPs that were used for the quartet analysis (in SVDquartets).
DOI: 10.5061/dryad.23hs1/3
title: sampleDownMSFS.py

description: Python script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Includes an example vcf input file and population map.
DOI: 10.5061/dryad.443g2/1
title: Datafile

description: File contains individual-based behavioral assay scores as well as covariates