cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.76d82/18
title: ENO1.tbs

description: tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for ENO1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs &lt; ALTE-ENO1.tbs.ms &gt; ALTE-ENO1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
DOI: 10.5061/dryad.76d82/9
title: mtDNA control region.nex

description: FASTA file containing 199 mtDNA control region sequences (987 aligned sites) sampled from Common (Green-winged) Teal (Anas crecca). Populations (OW, Old World; NW, New World; Attu, Aleutian Islands; Shemya, Aleutian Islands; Adak, Aleutian Islands; Ugamak, Aleutian Islands) are defined within the file.
DOI: 10.5061/dryad.8654d/1
title: Codes and data for "Using genomic tools to maintain diversity and fitness in conservation programmes"

description: Files included in file DryaData.tar.gz : BigPopMSD.f90, genotiposCGD.dat, OCgen_ranmat.f90, OCroh_ranmat.f90, DistFreqsSeg_overReps.f90, genotiposMukai.dat, OCmol_ranmat.f90. Genotype data: genotiposCGD.dat and genotiposMukai.dat are obtained after 10000 generations of mutation-selection-drift  with BigPopMSD.f90 for the CGD and the Mukai scenarios, respectively. Population size is kept constant at 1000 diploid individuals (500 females and 500 males), and the genome is assumed to have 20 chromosomes of 1 Morgan each. Every chromosome includes 2000 neutral loci, 1000 selected loci and 1000 marker loci, all of thembiallelic. For the CGD scenario, the parameters used are lambda is 0.03, beta is 2.3, mean s is 0.264, and mean h is 0.2. For the Mukai scenario, the parameters used are lambda equals 0.5, beta 1, mean s is 0.05, and mean h equals 0.3. BigPopMSD.f90 generates the base population. OCgen_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise genealogical coancestry, which is calculated assuming the founder individuals are unrelated. The number of replicates is 100, but can be varied, as well as the population size during management. OCmol_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise molecular coancestry, calculated as identity by state (see Toro et al 2002, Conservation Genetics). The number of replicates is 100, but can be varied, as well as the population size during management. OCroh_ranmat.f90 performs 10 generations of optimal contributions for population management with random matings between the individuals who contribute. Contributions are calculated to optimise IBD-based coancestry, calculated as the proportion of the genome that is identical by descent between individuals. It is calculated by looking only at marker loci, and it requires a minimum length of a segment for it to be considered identical by descent. The number of replicates is 100, but can be varied, as well as the population size during management. DistFreqsSeg_overReps.f90 analyses replicates from the base population to calculate the average number of markers segregating and the average number of runs of homozygosity in the base population. Note that the codes sometimes assume reading from a file not in the same directory. OC...f90 all read from file ../genotipos_1.dat but that can be easily changed to whichever genotypes you want to read. Should you have any issues, contact angeles.decara AT gmail
DOI: 10.5061/dryad.95mt02sb/2
title: Illumina reads from the "A" lineage of macrophage-adapted L. pneumophila

description: Illumina fastq files from genomic libraries prepared from L. pneumophila passaged through macrophages. "A" lineage clones. Quality scores are standard Sanger format.
DOI: 10.5061/dryad.95mt02sb/4
title: Illumina reads from the "C" lineage of macrophage-adapted L. pneumophila

description: Illumina fastq files from genomic libraries prepared from L. pneumophila passaged through macrophages. "A" lineage clones. Quality scores are standard Sanger format.
DOI: 10.5061/dryad.95mt02sb/5
title: Illumina reads from the "D" lineage of macrophage-adapted L. pneumophila

description: Illumina fastq files from genomic libraries prepared from L. pneumophila passaged through macrophages. "D" lineage clones. Quality scores are standard Sanger format.
DOI: 10.5061/dryad.95mt02sb/6
title: Illumina reads from the progenitor strain used for generating macrophage-adapted L. pneumophila

description: Illumina fastq files from genomic libraries prepared from an LP01 strain of L. pneumophila, with the integrated pAhpC::lux plasmid. This is the progenitor, day 0, strain used during experimental adaptation of L. pneumophila to mouse macrophages. Quality scores are standard Sanger format.
DOI: 10.5061/dryad.d034g/1
title: Siepielski et al selection experiment data

description: This data file contains the treatments and results of the experiment to quantify phenotypic selection by Anax dragonflies on Ischnura cervula damselflies. Treatments refer to no dragonfly, a free-ranging dragonfly, or a caged dragonfly.
DOI: 10.5061/dryad.d034g/2
title: Siepielski et al plasticity experiment data

description: This data file contains the results of an experiment to assess whether or not Ischnura cervula damselflies exhibit phenotypic plasticity in response to Anax dragonfly predators. Treatment refers to an Anax being present or absent. Values are the number of each behavior over a 15 minute time frame.
DOI: 10.5061/dryad.gd031k26/31
title: Supplemental Dataset 31
DOI: 10.5061/dryad.gd031k26/32
title: Supplemental Dataset 32
DOI: 10.5061/dryad.gd031k26/33
title: Supplemental Dataset 33
DOI: 10.5061/dryad.gd031k26/34
title: Supplemental Dataset 34
DOI: 10.5061/dryad.gd031k26/35
title: Supplemental Dataset 35
DOI: 10.5061/dryad.hn11m/1
title: DISTLM_input_files

description: DISTLM input files
DOI: 10.5061/dryad.hn11m/2
title: DISTLM_Forward_input_files

description: DISTLM Forward input files
DOI: 10.5061/dryad.hn11m/3
title: Sex-linked_markers_-_alignment

description: Alignment files for sex-linked markers: ZFX gene intron 9; concatenated sequences of SRY, DBY4 and DBY8
DOI: 10.5061/dryad.hn11m/4
title: mtDNA_-_alignment_and_tree_files

description: Alignment files for mtDNA: Control Region, cytochrome b and concatenated sequences of CR and cytb. Tree files are provided with additional Supporting information.
DOI: 10.5061/dryad.k70h6/1
title: sample code of populus pruinosa and populus euphratica

description: including all detailed locations of populations mentioned in this manuscript
DOI: 10.5061/dryad.k70h6/2
title: Populus euphratica sequence

description: including all Populus euphratica sequence analyzed in this manuscript
DOI: 10.5061/dryad.kq5q3/6
title: Reference Sequences 16S long
DOI: 10.5061/dryad.ms6c2/1
title: Lacuna Grazing Distribution. A Canadian Healthy Oceans Network Ecosystem Function Project, EF-11

description: File contains data on the extent of grazing damage in the basal, middle, and distal sections of kelp blades. Headings are: Proportion grazed, Location on blade (as basal, middle, and distal 1/3 of each blade), Site name, Sampling date, Species name (Saccharina latissima or Laminaria digitata), and Individual (unique identifying #)
DOI: 10.5061/dryad.ms6c2/2
title: Lacuna experiment. A Canadian Healthy Oceans Network Ecosystem Function Project, EF-11

description: Data are from two separate experimental run where holes were punched in the distal ends of kelp blades to mimic different levels of grazing intensity by Lacuna vincta. Data headings include: Individual (unique identifying #), Experimental run (1 or 2), Start Date of the experiment, End Date of the experiment, Treatment (0, 10, 30, or 60 punched holes), Stipe Length Initial (cm), Blade Length Initial (cm), Total Length Initial (cm), Growth Rate (cm/day), Erosion Rate (cm/day), Productivity (g/day), Erosion (g/day)
DOI: 10.5061/dryad.n11d4/2
title: Mean daily temperature (C) at the Kagoshima tea station in Japan

description: Mean daily temperature (C) at the Kagoshima tea station in Japan
DOI: 10.5061/dryad.s2878/2
title: Commelinaceae Data

description: Trait data compiled from primary literature regarding breeding system and inflorescence condensation for the Tradescantia alliance
DOI: 10.5061/dryad.s584c/1
title: Pyura_doppelgangera_COI_sequences

description: Aligned mitochondrial dna cytochrome c oxidase subunit I (COI) sequences for the ascidian Pyura doppelgangera
DOI: 10.5061/dryad.s584c/2
title: Pyura_doppelgangera_ANT_sequences

description: Aligned nuclear DNA Adenine Nucleotide Transporter (ANT, also known as ADP/ATP translocase) sequences for the ascidian Pyura doppelgangera
DOI: 10.5061/dryad.s584c/3
title: Pyura_doppelgangera_Microsats_10populations

description: Complete microsatellite data set in Genepop format.
DOI: 10.5061/dryad.s584c/4
title: Pyura_doppelgangera_Microsats_10populations_Reduced
DOI: 10.5061/dryad.vg885/1
title: SD1_AllUnmappedScaffoldLocalizations

description: SD1_AllUnmappedScaffoldLocalizations.txt: The first column contains the contig/scaffold ID number from the HuRef Assembly. Columns 2 to 25 contain the marginal probabilities of localization to each of the 24 chromosomes given the available WCS data. That is, a probability of 1 indicates certainty that the scaffold localizes to that particular chromosome according to our model (specified in SOM). The list is limited to the 9950 scaffolds with a marginal localization probability of at least 0.9 on at least 1 chromosome.
DOI: 10.5061/dryad.14n6g/4
title: Malpica&Ornelas_morphology_info

description: Four body measurements measurement obtained from 324 adult broad-tailed hummingbirds (281 with data for all variables were used in statistical analyses).
DOI: 10.5061/dryad.14n6g/5
title: Malpica&Ornelas_localities_information

description: The file contains the collection localities for the Selasphorus platycercus samples examined in this study.
DOI: 10.5061/dryad.20cf2/2
title: DATA2

description: Genotypes of both the anadromous parents and the precocious parr identified by Colony. Genotypes of precocious parr have been inferred by Colony.
DOI: 10.5061/dryad.2236n/1
title: Arboreal NTS Photos: Before vs After Leaf Removal

description: These data were used to perform the analysis (paired t-test) comparing the number of non-target stimulus (NTS) photographs take by seven cameras before and after leaves were removed within 1.5 meters from in front of them.
DOI: 10.5061/dryad.2236n/2
title: NTS Photographs: Canopy vs Ground

description: These are the data used to perform the analysis (paired t-test) of the number of non-target camera stimuli in camera traps placed on the ground versus in the canopy.
DOI: 10.5061/dryad.2f1k3/4
title: Anas crecca ENO1 alleles.fas

description: FASTA file containing 100 resolved alleles from intron 8 of the alpha enolase (ENO1) gene sampled from 50 Common (Green-winged) Teal (Anas crecca). The first 50 alleles were sampled from Eurasia, and the next 50 were sampled from North America.
DOI: 10.5061/dryad.36775/16
title: Script associated with the bioinformatics pipeline

description: Script associated with the bioinformatics pipeline. The first script strings the programs together (used in Linux environment). The second script determines the SNPs and allelic variants. The third script creates the consensus sequences.
DOI: 10.5061/dryad.3tc7s/1
title: In situ observation data for dorid nudibranch predators of glass sponges

description: Spatial distribution data of dorid nudibranchs found to eat glass sponges in reefs in the Strait of Georgia.  A Canadian Healthy Oceans Network (CHONe) Marine Biodiversity project, MB-18.
DOI: 10.5061/dryad.4k887/1
title: Supplementary Figure 1

description: Plots of axis 1 versus axis 2 of correspondence analyses, using RSCU values and raw codon counts, respectively. Blue points indicate non­‐highly expressed genes. Red points indicate highly expressed genes.
DOI: 10.5061/dryad.4k887/2
title: Supplementary Table 1

description: Correspondence analysis of RSCU values and raw codon counts. The “Axis 0 inertia” column is the amount of inertia that is explained by the principal axis. The “Axis 1 inertia” column is the amount of interia that is explained by the next biggest CA axis. These results demonstrate that there is a single major trend that determines synonymous codon usage in vertebrates.
DOI: 10.5061/dryad.4k887/3
title: Supplementary Table 2

description: Spearman correlations. Spearman correlation comparing Axis 1 versus GC3 , and axis 1 versus expression level.
DOI: 10.5061/dryad.5086f/1
title: babysitting data

description: indivdiualSessions: number of sessions individual babysat for the litter,	totalGroupSessions: number of sessions the group babysat for that litter, lnAge: natural log of the individual's age in days,	condition: relative mass of the individual for its age, groupSize: the average group size of the group for the babysitting period,	individualID: code for individual,	group: code for group, litter: code for babysat litter, dominanceStatus: whether the individual was dominant during the babysitting period, everDominant: whether the individual became dominant in its lifetime
DOI: 10.5061/dryad.5086f/2
title: provisioning data

description: indivdiualFeeds: number of pup times individual fed to the litter, totalGroupFeeds: number of times the group fed to that litter,	lnAge: natural log of the individual's age in days,	condition: relative mass of the individual for its age, groupSize: the average group size of the group for the provisioning period,	totalObservationTime: total time the group was observed for the provisioning period, individualID: code for individual, group: code for group, litter: code for litter, dominanceStatus: whether the individual was dominant during the babysitting period, everDominant: whether the individual became dominant in its lifetime
DOI: 10.5061/dryad.5086f/3
title: guarding data

description: individualBouts: number of times the individual went on raised guard during the month,	totalGroupBouts: total number of times any group member went on raised guard during the month,	lnAge: the natural log of the individuals age, condition: the relative mass of the individual for its age,	groupSize: the average group size of the group for the month, proportionPregnant: the proportion of the month the individual was pregnant, totalObservationTime: the total time the group was observed for that month,	individualID: code for the individual, group: code for the group, monthYear: code for the month within the year, dominanceStatus: the proportion of days an individual was dominant during the month, everDominant: whether the individual ever became dominant within its lifetime
DOI: 10.5061/dryad.587ms/1
title: formica_genotypes
DOI: 10.5061/dryad.58ss8/37
title: E13-S

description: echovirus 13 - structural gene
DOI: 10.5061/dryad.58ss8/38
title: E30-S

description: echovirus 30 - structural gene
DOI: 10.5061/dryad.58ss8/39
title: E30-NS

description: echovirus 30 - non-structural gene
DOI: 10.5061/dryad.58ss8/40
title: E33-S

description: echovirus 33 - structural gene
DOI: 10.5061/dryad.58ss8/41
title: SVDV-S

description: swine vesicular disease virus - structural gene
DOI: 10.5061/dryad.58ss8/42
title: CVA24-S

description: coxsackievirus A24 - structural gene
DOI: 10.5061/dryad.58ss8/43
title: CVA24-NS

description: coxsackievirus A24 - non-structural gene
DOI: 10.5061/dryad.58ss8/44
title: PV1-S

description: poliovirus type 1 - structural gene
DOI: 10.5061/dryad.58ss8/45
title: PV1-NS

description: poliovirus type 1 - non-structural gene
DOI: 10.5061/dryad.5b79m/1
title: Heterospecific interactions

description: The dataset underlying the analysis of heterospecific reproductive isolation between Leptidea sinapis, L. reali and L. juvernica.
DOI: 10.5061/dryad.5b79m/2
title: Conspecific interactions among L. sinapis and L. juvernica

description: Outcome of mating interactions between conspecific populations of Leptidea sinapis and Leptidea juvernica, respectively.
DOI: 10.5061/dryad.5dn48/1
title: Pre-mange data
DOI: 10.5061/dryad.5dn48/2
title: Post-mange data
DOI: 10.5061/dryad.5gs1v/1
title: Beta-fibrinogen alignment

description: Beta-fibrinogen DNA sequence alignment for all individuals included. Includes two alleles per individual determined either by TA cloning, or computationally in PHASE.
DOI: 10.5061/dryad.5gs1v/2
title: Cytochrome-b alignment

description: Cytochrome-b DNA sequence alignment for all individuals included.
DOI: 10.5061/dryad.5gs1v/3
title: GHR alignment

description: GHR DNA sequence alignment for all individuals included. Includes two alleles per individual determined either by TA cloning, or computationally in PHASE.
DOI: 10.5061/dryad.5gs1v/4
title: Specimen numbers

description: Field collection numbers and associated museum collection specimen numbers for a subset of individuals that are referred to by both numbers.
DOI: 10.5061/dryad.5gs1v/5
title: BEAST infile for continuous diffusion model analysis

description: Infile generated by BEAUTi 1.7.5 for analysis in BEAST 1.7.5 of Eliurus myoxinus data of under a continuous diffusion model. Cytochrome-b sequences and locality data for each individual are included in this XML.
DOI: 10.5061/dryad.5j5r0/1
title: Biomass, bSi, and dSi data used to calculate silicon cycling budget in 3 glass sponge reefs

description: Raw field data for biomass, bSi and dSi sampling of glass sponges in 3 reefs from the Strait of Georgia. A Canadian Healthy Oceans Network  (CHONe) Marine Biodiversity Project, MB-18.
DOI: 10.5061/dryad.5j5r0/2
title: Calculations used to determine silicon cycling budget in 3 glass sponge reefs.

description: Outline of calculations used to determine silicon cycling budget in 3 glass sponge reefs in the Strait of Georgia. A Canadian Healthy Oceans Network  (CHONe) Marine Biodiversity Project, MB-18.
DOI: 10.5061/dryad.61t9h/1
title: Tribolium Larval Mass Data

description: The file gives mass measurements for individuals who are listed in rows. The first three columns list identifying information for each larva; the first column gives the ID number, the second gives the sire number, and the third gives the dam number. The fourth column gives the hatch date, from which each 'age' is measured. From here, each data entry takes three columns: one for date of measurement, one for days since hatch (or, age at measurement), and one for the actual mass measurement (which is in grams).  The numbers following the headings in this column represent the number of each measurement (i.e. 'mass5' indicates the fifth mass measure). Data concerning the pupal stage begin at the 44th column. The first three columns are the date of pupation, pupation age, and pupal mass. The 47th column indicates the sex of the individual, with 1 representing a male and 0 representing a female. The last two columns indicate the date and age of eclosion to the adult stage, respectively. Any blank entries represent a lack of data points either for that measurement or for that identifying information.
DOI: 10.5061/dryad.654sh/2
title: Supplementary Information.zip

description: Supplementary Information (images used for microwear quantification).
DOI: 10.5061/dryad.6gc6h/10
title: variant pileup for sample 10 reads mapping

description: Paired end reads from sample 10 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/11
title: variant pileup for sample 11 reads mapping

description: Paired end reads from sample 11 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/12
title: variant pileup for sample 12 reads mapping

description: Paired end reads from sample 12 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/13
title: variant pileup for sample 13 reads mapping

description: Paired end reads from sample 13 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/14
title: variant pileup for sample 14 reads mapping

description: Paired end reads from sample 14 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/15
title: variant pileup for sample 15 reads mapping

description: Paired end reads from sample 15 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/7
title: variant pileup for sample 7 reads mapping

description: Paired end reads from sample 7 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/8
title: variant pileup for sample 8 reads mapping

description: Paired end reads from sample 8 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.6gc6h/9
title: variant pileup for sample 9 reads mapping

description: Paired end reads from sample 9 genomic sequencing were mapped on Arabis alpina contigs with BWA. Variant pileup was obtanied with samtools from bam file.
DOI: 10.5061/dryad.76d82/19
title: PCK1.tbs

description: tbs (to be specified) file defining population-level parameters for simulating neutral genetic diversity in the program MS for PCK1 in green-winged teal. MS command line: ./ms 210 1000 -t tbs -r tbs tbs -I 3 50 50 110 -n 2 tbs -n 3 tbs -ej tbs 3 2 -en tbs 2 tbs -ej tbs 2 1 -en tbs 1 tbs -m 1 2 tbs -m 1 3 tbs -m 2 1 tbs -m 2 3 tbs -m 3 1 tbs -m 3 2 tbs -em tbs 1 2 tbs -em tbs 2 1 tbs &lt; ALTE-PCK1.tbs.ms &gt; ALTE-PCK1.ms.out [See the manual for MS for an explanation of the terms; http://home.uchicago.edu/rhudson1/source/mksamples.html]
DOI: 10.5061/dryad.76d82/20
title: Teal.structure.infile

description: Input file for the program STRUCTURE containing genotypic data at 8 nuclear loci for 105 individuals of green-winged teal (Anas crecca).
DOI: 10.5061/dryad.7tq37/1
title: Community-genetic effect size estimates and predictor variables

description: This file contains effect sizes describing the relationship between population-level genetic diversity in plant species and measures of the structure and functioning of associated communities and ecosystems. Each effect size is accompanied by a measurement error variance estimate describing the precision of the corresponding effect size. The remaining data in these tables comprise sources of heterogeneity (predictor variables) used in the meta-analyses, and other descriptive information relating to the studies used in the review. There are two effect size datasets, one for adaptive (genotypic) measures of genetic diversity (sheet "d"), and one for neutral molecular measures of genetic diversity (sheet "z(r)").
DOI: 10.5061/dryad.83t3c/3
title: Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa

description: All analysis was carried out in R. W.cheat was used as our response variable in our competition experiment. This is taken as the cheat malthusian parameter/ wild type malthusian parameter. If W&gt;1 cheats are said to 'invade' the population
DOI: 10.5061/dryad.9c6q0/1
title: EM Mating Pairs
DOI: 10.5061/dryad.9c6q0/2
title: Female Multiple Mating Data