cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.86sk5/7
title: GrasonAmNat2016OcenebraData

description: Tables 1-7. Observed behavior of Ocenebra inornata in response to cues from Cancer productus from 1 of 7 experiments.
	Fields: 
	1. Date - Date of observation
	2. bin - replicate
	3. tmt - Cue Treatment (as described and abbreviated in table 1 of Grason AmNat, 		with the exception that the letter “P” is used in the manuscript to stand for Predator cues, while in these files “C” is used to stand in for Crab, thus “CxIC” here is the Crab consuming conspecific prey)
	4. crab - Presence of crab/predator cues in cue treatment (Y/N)
	5. ic - presence of chemical cues from injured conspecifics in cue treatment (Y/N)
	6. hide/hiding - how many snails were “hiding” under structure in bin on that observation date, total number of snails in bin is 1 unless otherwise listed in Table 2 of manuscript
	7. run/running - how many snails were attempting to “flee” by emersing on that date
	8. both - sum of “run” and “hide” 
	9. cum.hide - cumulative number of “hide” observations for that bin to date, used for calculating best metric of avoidance.
	10. cum. run - as above for emersion behavior
	11. cum.both - as above for sum of run and hide
	12. no.snails (in some tables) - total number of snails in bin on which behavioral obs were made
	13. #notes (in some tables) - detailed related to removal of snails due to death.
DOI: 10.5061/dryad.86sk5/8
title: GrasonAmNat2016UrosalpinxData

description: Tables 1-7. Observed behavior of Urosalpinx cinerea in response to cues from Cancer productus from 1 of 7 experiments.

	Fields: 
	1. Date - Date of observation
	2. bin - replicate
	3. tmt - Cue Treatment (as described and abbreviated in table 1 of Grason AmNat, 		with the exception that the letter “P” is used in the manuscript to stand for Predator cues, while in these files “C” is used to stand in for Crab, thus “CxIC” here is the Crab consuming conspecific prey)
	4. crab - Presence of crab/predator cues in cue treatment (Y/N)
	5. ic - presence of chemical cues from injured conspecifics in cue treatment (Y/N)
	6. hide/hiding - how many snails were “hiding” under structure in bin on that observation date, total number of snails in bin is 1 unless otherwise listed in Table 2 of manuscript
	7. run/running - how many snails were attempting to “flee” by emersing on that date
	8. both - sum of “run” and “hide” 
	9. cum.hide - cumulative number of “hide” observations for that bin to date, used for calculating best metric of avoidance.
	10. cum. run - as above for emersion behavior
	11. cum.both - as above for sum of run and hide
	12. no.snails (in some tables) - total number of snails in bin on which behavioral obs were made
	13. #notes (in some tables) - detailed related to removal of snails due to death.
	14. cum.obs (in Alia only) - total number of snail*observations for a given bin
DOI: 10.5061/dryad.9n42p/1
title: data_for_dryad

description: This zip archive contains parameter files, model output files, driver files, model structure files, an R script, keys to the files used to make the figures and tables, and a ReadMe file.
DOI: 10.5061/dryad.9rt50/1
title: Software for computing the ARG consensus

description: This is a tar gzip archive of all programs needed to compute the ARG consensus as described in our paper, and a documentation file explaining how they are used.  In order to use this archive you will need access to a Python interpreter and a C++ compiler.  A shell script linking the steps is included, but is optional.
DOI: 10.5061/dryad.b4s20/2
title: Covariate data juvenile Placid Greenbul - Van de Loock et al. 2017 Ecol&Evol

description: Covariate data used in analysis on juvenile mortality of Placid greenbuls. Collected at Taita Hills, SE Kenya.
DOI: 10.5061/dryad.b9482/4
title: Raw reads
DOI: 10.5061/dryad.cv4r7/1
title: Daucus_plastid_references

description: Fasta files of plastid reference sequences. These references contains only 1 inverted repeat. The full sequences have been submitted to GenBank (KX832299-KX832335).
DOI: 10.5061/dryad.cv4r7/2
title: Caucalis_platycarpos_649446

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/3
title: Daucus_aureus_319403

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/4
title: Daucus_bicolor_652321

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/5
title: Daucus_bicolor_Ames_25830

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/6
title: Daucus_carota_subsp._capillifolius_279764

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/7
title: Daucus_carota_subsp._carota_274297

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv853/1
title: Gardner et al.data.PhilTransB

description: Raw data
DOI: 10.5061/dryad.gk87k/1
title: Hudson_Toad Morphology

description: Body size measures from Wild caught and Common Garden reared cane toads.Time since colonisation (TSC group) indicates how long toad populations had been established at the time morphological measurements were made
DOI: 10.5061/dryad.gq3fk/1
title: Compiled Lipidomics Data_NCOMMS-16-13893-A

description: Raw data of MS lipidomics datasets used in Fig. 5a and Supplementary Fig. 4c. Data are from HEK cells treated with non-targeting (Control) or HS1BP3 siRNA starved for 2 hrs (mean +/- SEM., n = 6). See the Methods section for a full description of the Methods used.
DOI: 10.5061/dryad.h5g60/3
title: Illumina Fastq files from Acanthoxyla geisovi

description: A compressed file for the Illumina short read sequences from the Acanthoxyla geisovii used in the analysis.
DOI: 10.5061/dryad.h5g60/4
title: Illumina Fastq files from Clitarchus hookeri

description: A compressed file for the Illumina short read sequences from the Clitarchus hookeri used in the analysis.
DOI: 10.5061/dryad.jh843/1
title: Frog Resource Partitioning Data 072316

description: Species partitioning data for 5 species of Anurans in Kentucky, USA. This includes data on carbon and nitrogen stable isotopes, morphology, habitat, and the Chesson's alpha for stomach contents of each frog.
DOI: 10.5061/dryad.k7t20/10
title: Transcripts_Bombyx_Locations

description: Summary file of prediction locations of transcripts on the Z chromosome using blastn against Bombyx mori.
DOI: 10.5061/dryad.k7t20/11
title: PIXY_RS_amplicons

description: PIXY statistic for Rock Springs E and Z using amplicon reference.
DOI: 10.5061/dryad.k7t20/12
title: PIXY_LandEZ_amplicons

description: PIXY statistic for Landisville E and Z using amplicon reference.
DOI: 10.5061/dryad.k7t20/4
title: longestReadsDip

description: Diapausing larval tissue de novo transcriptome. Longest transcript for each component selected.
DOI: 10.5061/dryad.k7t20/5
title: longestReadsMHP

description: Male hairpencil tissues de novo transcriptome. Longest transcript for each component selected.
DOI: 10.5061/dryad.k7t20/6
title: RS_amplicons

description: FST values for Rock Springs E and Z using the amplicon reference.
DOI: 10.5061/dryad.k7t20/7
title: Land_amplicons

description: FST values for Landisville E and Z using the amplicon reference.
DOI: 10.5061/dryad.k7t20/8
title: RS_transcripts

description: FST values for Rock Springs E and Z using the Z chromosome transcript reference.
DOI: 10.5061/dryad.k7t20/9
title: Land_transcripts

description: FST values for Landisville E and Z using the Z chromosome transcript reference.
DOI: 10.5061/dryad.mf6h7/1
title: largemammalrecords_VPSP_Ferreira et al 2017_Biotropica

description: Camera trap records of large mammals in Veredas do Peruaçu State Park, Minas Gerais, Brazil. Each sheet refers to one large mammal species recorded in VPSP.  Species codes composed of first letter of the genus and first three letters of the specific name (refer to Table S1 of the paper for species names). Within sheet, each row is a camera trap site and each column is a 7-day survey occasion.
DOI: 10.5061/dryad.mf6h7/2
title: covariates_VPSP_Ferreira et al 2017_Biotropica

description: Site covariates used for occupancy modelling of large mammals in Veredas do Peruaçu State Park, Minas Gerais, Brazil. Values of covariates 'Dist Peruaçu River' and 'Dist water source' have been standardized for analysis. See methods and table 1 of the paper for details on covariates.
DOI: 10.5061/dryad.p236p/1
title: Egyptian_familial_breast_cancer_exome_variants

description: Exome variants from five breast cancer families collected in Gharbiah disctrict, Egypt. DNA was extracted from blood cells using a FlexiGene DNA kit. Exome sequencing was done with TrueSeq Exome Enrichment Kit and on HiSeq2500, paired-end 2x150 at 100X coverage. Exome sequences were mapped to hg19 using Burrows-Wheeler Aligner and pre-processed with Picard Toolkit. Variants were called using Freebayes and annotated with ANNOVAR.
DOI: 10.5061/dryad.r4g3g/1
title: Python ARG-comparison programs

description: Tar gzip archive of Python programs used to implement the ARG comparison framework and to perform the simulations in the paper.
DOI: 10.5061/dryad.s1v34/1
title: Supplementary File 1 - DNA orthologs Initial Assessment Subset

description: Supplementary File 1. Concatenated alignment of nucleotide sequence data for the ‘initial assessment subset’ of 151 orthologous loci. See character set partitions at end of matrix for the gene-specific breakdown of putative orthologs. See Supplementary File 4 for taxon abbreviations.
DOI: 10.5061/dryad.s1v34/2
title: Supplementary File 2 - AA orthologs Initial Assessment Subset

description: Supplementary File 2. Concatenated alignment of amino acid sequence data for the ‘initial assessment subset’ of 151 orthologous loci. See character set partitions at end of matrix for the gene-specific breakdown of putative orthologs. See Supplementary File 4 for taxon abbreviations.
DOI: 10.5061/dryad.s1v34/3
title: Supplementary File 3 - Comparison of phylogenetic informativeness measures

description: Supplementary File 3. Comparison of phylogenetic informativeness measures across three epochs (deep = Epoch 3; taxonomy = Epoch 2; species = Epoch 1; see Fig. 2, Supplementary File 4), using the 'initial assessment' subset of 151 orthologous loci (Supplementary Files 1-2).
DOI: 10.5061/dryad.s1v34/4
title: Supplementary File 4 - PhyDesign Informativeness Quantitation IA Subset

description: Supplementary File 4. Phylogenetic informativeness quantitation outputs from PhyDesign (López-Giráldez and Townsend, 2011) for nucleotide (Tab 1) and amino acid (Tab 2) data, using the ‘initial assessment’ subset of 151 orthologous loci (Supplementary Files 1-2). Loci are listed and ranked according to their per-site informativeness over three epochs (0-25 Ma; 25-160 Ma; 160-294.965 Ma); the top-10 ranked loci for each epoch are highlighted in red.
DOI: 10.5061/dryad.v5p11/1
title: Gress.Pitnick.AB.data

description: Raw copula durations for pomace males (m1.cop.dur) and dung males (m2.cop.dur) were recorded in the field, as was ambient temperature (temp1 = temperature during pomace mating, temp2 = temperature during dung mating); Portion of offspring sired by male 1 and 2 (P1 and P2); m1.progeny and m2.progeny represent the absolute number of offspring sired by male 1 and 2 in the subsequent female clutch; male hind tibia length was measured in the lab (m1.ru and m2.ru raw values, m1.htl.mm and m2.htl.mm are divided by 32 to convert to mm); sperm1 and sperm2 are estimates of the number of sperm transferred per ejaculate using known relationships between male htl and sperm transfer rate (0.0018 (htl^3) - 0.003) * 826.85
DOI: 10.5061/dryad.vq4f5/1
title: Crawford_MSG_data

description: MSG data sued to estimate phylogeny for Macaronesian Tolpis.
DOI: 10.17632/p3ts9p2gc8.1
title: Metal Transmission Calculator

description: Tool for calculate metal transmission in mass cytometry instruments (CyTOF)
DOI: 10.5061/dryad.1g304/1
title: CombinedAnnotation_alewife_nr

description: Alewife gill transcriptome annotations
DOI: 10.5061/dryad.1ns7n/1
title: Raw annual and perennial abundance data

description: This data set contains annual abundances for all sites and all years (2008-2012) as well as perennial heights in cms (2009-2012) and perennial ground covers as percentages (2008-2012). It also contains a column called "relationship" which shows the type of relationship found between annual abundances and perennial heights (one of positive, negative or quadratic) according to the method described in the paper. This data was used to produce figures 4, 5, 6, B2 and B4.
DOI: 10.5061/dryad.1ns7n/2
title: Environmental data along the latitudinal gradient

description: This file contains data on the abiotic and biotic conditions experienced by both annual and perennial guilds along the sampled latitudinal gradient. Variables include mean rainfall in mm, temperatures in degree celcius (mean monthly maximum, mean monthly minimum, mean daily), mean sunshine hours in autumn, spring and winter, mean number of rabbit faecal pellets (a proxy for grazing intensity), mean soil nitrogen concentration, as well as mean bryophyte ground cover and mat thickness, and mean correlation between annual abundances and bryophyte ground cover. This data was used to produce figures 3, B1 and B3.
DOI: 10.5061/dryad.1vb0h/1
title: Raccoon genotypes

description: This text file contains all information on MHC-II genotypes, sex, and social role played in our population, such as offspring, mother, father, or candidate father.
DOI: 10.5061/dryad.40qd3/1
title: Databases used for the analyses.

description: We provide three databases: the database we used for the analyses (16 loci), the database with the original annealing temperature (10 loci), and the database with the new annealing temperature (10 loci).
DOI: 10.5061/dryad.44bm6/1
title: Grandcour Wildflower strip vegetation data

description: The first datasheet contains the metadata explaining the abbreviations in the main datasheet. It contains information about species richness, above-ground biomass and species cover, that was visually estimated.
DOI: 10.5061/dryad.54c43/2
title: Filtered_log_counts_per_million

description: Final filtered log counts per million estimates of gene expression for all stickleback individuals.
DOI: 10.5061/dryad.577q1/1
title: Database with biogeographic and mating system information

description: The datafile contains all of the data on biogeography and outcrossing rates. The column heading definitions are as follows: year: Year in which the study was published
reference: Reference containing estimates of outcrossing rate
family: Plant family name of the species studied
genus: Genus-level name of the species studied
species: species-level name of the species studied
m.d.g: Broad taxonomic category; m = monocot, d = dicot, g = gymnosperm
latitude: Degree of latitude (range from 0 – 90) for the population in which outcrossing rate was measured. If multiple populations were studied for a given species this value is the average of the population-level latitudes.  Latitudes are expressed as decimal degrees and the absolute value from the equator.
hemisphere: N = northern hemisphere; S = southern hemisphere
biome: Biome categories ordered by net ecosystem productivity: 1 = Desert/arid scrub; 2 = Temperate grasslands; 3 = Shrubland/chaparral; 4 = Taiga; 5 = Tropical savannah; 6 = Temperate deciduous forest and rainforest; 7 = Tropical seasonal forest; 8 = Tropical rainforest
growth: Growth form categories: 1 = Herbaceous; 2 = Vine; 3 = Schrub; 4 = Tree; 5 = Varies
life.history: Life history categories: 1 = Annual; 2 = Biennial; 3 = Semelparous perennial; 4 = Iteroparous perennial; 5 = Varies
si: 0 = Self-incompatible; 1 = Self-compatible
mean.tm: Outcrossing rate. If multiple populations were studied for a given species this value is the average of the population-level outcrossing rates.
References: A list of references used to gather biological data on species.
DOI: 10.5061/dryad.5b5d0/1
title: Data 'Timing of breeding in an ecologically trapped bird'

description: Data in different sheets depending on the analyses presented in Materials & Methods
DOI: 10.5061/dryad.5j415
title: Dryad Item 10.5061/DRYAD.5J415
DOI: 10.5061/dryad.60k68.1/5.1
title: BF15.sync

description: Synchronized pileup file created with PoPoolation2 containing the allelic information of all populations used in the analysis of the comparison between Base and generation 15. P-Values of the Cochran Mantel Haenzel Test are attached to each SNP in the last column. The order of the population is as follows: BR1,BR3,BR2,F15R4,F15R5,F23R1,F27R5,F37R4,F37R5,F37R1
DOI: 10.5061/dryad.60nc3/1
title: Whole_fly_temperature

description: Images showing not only wings (as in the published version), but whole whiteflies stained with Eosin Y.
DOI: 10.5061/dryad.60nc3/2
title: Whole_fly_doublebarrier

description: Images showing whole animals stained with Eosin Y.
DOI: 10.5061/dryad.60nc3/3
title: chitosan&chitinEosinY

description: Chitosan and chitin stain equally with Eoisn Y at room temperature.
DOI: 10.5061/dryad.60nc3/4
title: Chitin_unstained
DOI: 10.5061/dryad.60nc3/5
title: Chitosan_unstained
DOI: 10.5061/dryad.80724/1
title: Low abundant soil bacteria can be metabolically versatile and fast growing

description: Measurement data on bacterial isolates; further description see metasheet
DOI: 10.5061/dryad.80r64/3
title: IndividualConsistencyRepeatErrorKvmDataFile3

description: This file contains information to measure the ‘on the bird’ measurement error (mean and SE) for the same logger when estimating the longitude and latitude for the same site (the breeding site Kvismaren) in two consecutive years (autumn year 1 versus spring year 2). In the excel file, ‘Sheet 1’ contains data, and the ‘info’ sheet contains explanations for the column headings of the data sheet.
DOI: 10.5061/dryad.8467g/1
title: elevation

description: A spatial layer of the elevation in the study area used for analysing of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
DOI: 10.5061/dryad.8467g/10
title: Rainfall_Jan

description: A spatial layer of the average rainfall in January in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
DOI: 10.5061/dryad.8467g/11
title: terrain_ruggedness_index

description: A spatial layer of the terrain ruggedness index in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
DOI: 10.5061/dryad.8467g/12
title: wetness_index

description: A spatial layer of the wetness index in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
DOI: 10.5061/dryad.8467g/13
title: visible_sky

description: A spatial layer of the proportion of the hemisphere visible from the location in the study area used in the analysis of yellow-bellied glider data. Description of all the covariates can be found in chapter 4 of the SI
DOI: 10.5061/dryad.8467g/14
title: SO-data

description: Site occupancy data. The archive contains the values of the covariates at the survey sites used in the analysis of yellow-bellied glider data (so_occupancy.csv and so_detection) and results of the two repeated surveys (yb-so.csv)
DOI: 10.5061/dryad.8467g/15
title: yb-pb-location

description: List of locations of sightings of yellow-bellied glider in opportunistic surveys