cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m48tr/2
title: Single locus heterozygosity

description: Single locus heterozygosity for all individual nestlings. 0=homozygous, 1=heterozygous.
DOI: 10.5061/dryad.mm11q/1
title: cten_16s

description: Alignment of sequences for the 16S gene across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.mm11q/2
title: cten_BACH1

description: Alignment of BACH1 sequences from across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.n136c/1
title: oviposition

description: This file contains the oviposition preference data. The file includes the following fields: population name (pop), individual number (indnum), individual id (indid), sex, number of eggs laid on Astragalus miser (nast), and the number of eggs laid on Medicago sativa (nmed).
DOI: 10.5061/dryad.n136c/2
title: morphology

description: This file contains the male genitalic morphology measurements. The file includes fields for species, population (Pop), individual id (Ind), whether the left or right side of the genitalia was measured (Meas), and for each of the nine measurments. These measurements are described in the manuscript.
DOI: 10.5061/dryad.n136c/3
title: afsource.tar

description: This file contains source code for computer software that implements the allele frequency model described in the manuscript. Please e-mail zgompert@gmail.com for additional details, and full documentation will likely be released on-line in the future. 1. The software depend on the Gnu Scientific Library. The software can be compiled using the g++ compiler as follows (this assumes the GSL was isntalled in a standard location), g++ -o af main.C func.C -lm -lgsl -lgslcblas 2. You can view command line arguments to the software by typing the name of the compiled binary. The infile format is similar to the infile format for bgc. 3. Three output files are produced. One contains the posterior probabilities for the genotype at each locus for each individual (gprob). A second file contains a matrix with samples from the posterior probability distribution for the allele frequencies (afreq) with each row corresponding to an mcmc iteration and each column corresponding to a locus. The final file (alpha) contains samples from the posterior probability distribution of the genetic diversity parameter.
DOI: 10.5061/dryad.n136c/4
title: allele counts

description: This zipped file contains the number of reads matching each of two alternative allels for each indvidual and locus. Loci are delineated by a 'contig' line that gives the fragment number, position of the SNP on the pseudo-reference genome, and the estimated average error probability for the SNP. The other lines begin with an individual id, which is follwed by the number of read of each allele.
DOI: 10.5061/dryad.pn73j/1
title: Network

description: Haplotype network
DOI: 10.5061/dryad.qr0rn/1
title: C++ source code for numerical simulations

description: The freestanding C++ program that was used to run numerical simulations and generate figures for the manuscript. Must be compiled with a C++11-compatible compiler.
DOI: 10.5061/dryad.r0056/10
title: Tu.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample Tu.
DOI: 10.5061/dryad.r0056/2
title: BaB.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample BaB.
DOI: 10.5061/dryad.r0056/3
title: BaBRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample BaBRE.
DOI: 10.5061/dryad.r0056/4
title: OS.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample OS.
DOI: 10.5061/dryad.r0056/5
title: OSRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample OSRE.
DOI: 10.5061/dryad.r0056/6
title: Ta.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample Ta.
DOI: 10.5061/dryad.r0056/7
title: TaRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample TaRE.
DOI: 10.5061/dryad.r0056/8
title: TP3.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample TP3.
DOI: 10.5061/dryad.r0056/9
title: TP3RE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample TP3RE.
DOI: 10.5061/dryad.r7nt4/1
title: DNA sequence alignment of Ha-a1 gene

description: Alignment of cDNA sequences of the Ha-a1 HD1 MAT gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/2
title: DNA sequence alignment of Ha-a2 gene

description: Alignment of cDNA sequences of the Ha-a1 HD2 MAT gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/3
title: DNA sequence alignment of Ha-b1 gene

description: Alignment of DNA sequences of the Ha-b1 HD1 MAT gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/4
title: DNA sequence alignment of Ha-b2 gene

description: Alignment of DNA sequences of the Ha-b2 HD2 MAT gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/5
title: DNA sequence alignment of EFA gene

description: Alignment of DNA sequences of the elongation factor 1-alpha gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/6
title: DNA sequence alignment of G3P gene

description: Alignment of coding DNA sequences of the elongation factor 1-alpha gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/7
title: DNA sequence alignment of Gst1 gene

description: Alignment of coding DNA sequences of the glutathione-S-transferase 1 (GST1) gene, created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/8
title: DNA sequence alignment of TF gene

description: Alignment of coding DNA sequences of the transcription factor gene (TF), created in MacClade 4.08.
DOI: 10.5061/dryad.r7nt4/9
title: DNA sequence alignment of MIP gene

description: Alignment of coding DNA sequences of the mitochondrial intermediate peptidase gene (MIP), created in MacClade 4.08.
DOI: 10.5061/dryad.rk204/11
title: Haplotypes

description: Contains haplotypes for the heterozygous loci for all the samples. The homozygous loci and the haploid mitochondrial genes can be recovered from the references.
DOI: 10.5061/dryad.1cd96t8p/1
title: Seamons_ForksCreek_steelhead_Evol_Apps_DRYAD
DOI: 10.5061/dryad.1m7sm/3
title: Chimpanzee pestle-pounding data
DOI: 10.5061/dryad.26mv3f6d/1
title: Aykanat et al_JEB

description: The zip file contains raw data within several text files (trait measurement, family and stock information) as well as an r script (.r extension executable in notepad) by which the results in the MS can be replicated using raw data files. More information can be found within the r script.
DOI: 10.5061/dryad.5k76c/1
title: 7273-AD-1-Author provisional

description: Description of Eiseniona gerardoi n. sp.
DOI: 10.5061/dryad.618fv/2
title: Trees

description: This text file contains all the trees used for the PAML analyses in newick format. As mentioned in the file, the PAML annotation (#1) was used to annotate SELF branches.
DOI: 10.5061/dryad.6bp470fn/1
title: Data_AUDPC

description: This file contains: the AUDPC (Area under the disease progress curve) calculated on the sporulation percentage of the most infected leaf of each replicate. Percentage of leaf showing sporulation was scored visually at 14, 21 and 28 days after inoculation. Cross pathogenicity tests were done in a quarantine controlled climate chamber. Forty isolates from five populations were inoculated onto three Malus species ('Tested_species') with two to four accessions ('Tested_accession') per Malus species. Population names indicate the geographic origin (Asia or EU:Europe), the environment of origin (Wild or Agro: Agro-ecosystem) and the host of origin of the isolates (Malus sieversii, M. x domestica or M. sylevstris). Inoculations were done in 10 experiments.
DOI: 10.5061/dryad.6k7gh/1
title: msshellmigration

description: script to simulate expected divergence under an allopatric speciation model with limited migration using the msHOT program. Usage: perl msshellmigration.pl
DOI: 10.5061/dryad.6k7gh/2
title: msshelladmix

description: script to simulate expected divergence under a hybrid speciation model using the msHOT program. Usage: perl msshelladmix.pl
DOI: 10.5061/dryad.6k7gh/3
title: msshell_largetheta

description: script to simulate expected divergence under an allopatric speciation model with a large ancestral theta using the msHOT program. Usage: perl msshell_largetheta.pl
DOI: 10.5061/dryad.6k7gh/4
title: mspositionswindows

description: Companion script to simulation scripts msshell_largetheta.pl msshelladmix.pl and msshellmigration.pl which takes the output of ms or msHOT and calculates divergence between simulated sequences.
DOI: 10.5061/dryad.7j504/2
title: GLMM code

description: R code used for GLMM analysis
DOI: 10.5061/dryad.9412sq70/1
title: Data for genotypic diversity and invasion
DOI: 10.5061/dryad.94ms3/6
title: VCF_files
DOI: 10.5061/dryad.94ms3/7
title: Genotype data

description: Genotype data for Lissotriton montandoni from Eastern Carpathians region, provided in GENEPOP format for tests of Hardy-Weinberg equilibrium.
DOI: 10.5061/dryad.9cf75/15
title: STRUCTURE data Class3Rep3

description: STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA.  Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields.  Columns in each dataset are:  CloneID, Marker1, Marker2, Marker3, Marker4, Marker5.  All markers are unlinked.  To findthe markers on the map,  use the ID codes in the file called "MarkerIDcodes.txt"
DOI: 10.5061/dryad.9cf75/16
title: STRUCTURE data Class3Rep4

description: STRUCTURE input file for the 196 pea aphids from the wild populations from Tompkins County, New York, USA.  Clones beginning with ABR and AFR were collected from alfalfa fields.Clones beginning with CBR and CFR were collected from clover fields.  Columns in each dataset are:  CloneID, Marker1, Marker2, Marker3, Marker4, Marker5.  All markers are unlinked.  To findthe markers on the map,  use the ID codes in the file called "MarkerIDcodes.txt"
DOI: 10.5061/dryad.9m63g/1
title: Phenotypes, pedigrees & genotypes for experiment E970

description: See README (also in archive)
DOI: 10.5061/dryad.b00f2/3
title: Avila_et_al_2014_Evolution

description: Output files from simulations.
DOI: 10.5061/dryad.c3gh6/3
title: Mean Outcrossing Rates

description: Figure 3 data
DOI: 10.5061/dryad.cp2vn740/1
title: PredatorExpInitial

description: Time spent shoaling for families before predator treatment (initially as juveniles, mean for two individuals per family per tank)
DOI: 10.5061/dryad.cp2vn740/2
title: PredatorExpFinal

description: Time spent shoaling for families after predator treatment (as adults, mean for two individuals per family per tank)
DOI: 10.5061/dryad.g8010/1
title: coleoptera.trees

description: This file contains 2 nexus files each with 100 trees.
DOI: 10.5061/dryad.gm354/10
title: File 9 Dryad Adult Insectivore Morphology
DOI: 10.5061/dryad.gm354/11
title: File 10 Dryad AI
DOI: 10.5061/dryad.gm354/12
title: File 11 Dryad Flight speeds
DOI: 10.5061/dryad.gm354/13
title: File 12 Call Parameters
DOI: 10.5061/dryad.gm354/14
title: Dryad Read Me File
DOI: 10.5061/dryad.gm354/7
title: File 6 Dryad P macleayi reps BLAST
DOI: 10.5061/dryad.gm354/8
title: File 7 Dryad P parnellii reps BLAST
DOI: 10.5061/dryad.gm354/9
title: File 8 Dryad T brasiliensis reps BLAST
DOI: 10.5061/dryad.h02h0/1
title: Lyp_2002-2007-GENEPOP

description: Microsatellite genotypes for a sample of Iberian lynx individuals born in Doñana (first pop) and Andujar (second pop) between the years 2002-2007. Indivdiuals are identified by their year of birth. Data is in GenePop format.
DOI: 10.5061/dryad.h02h0/2
title: Lyp_1995-2007_UR-GENEPOP

description: Microsatellite genotypes for a sample of Iberian lynx individuals in which known pairs of closely related individuals were avoided. Individuals are identified by an internal lab code and were born in Doñana (first pop) and Andujar (second pop). Data is GenePop format.
DOI: 10.5061/dryad.h02h0/3
title: Lynx pardinus ATP8 haplotypes

description: Fasta file reporting the two partial ATP8 sequences found in Iberian lynx populations. The sequence was obtained by dideoxi sequencing of PCR products. Hapotype 1 was observed in all 23 individuals from Doñana population, while haplotype 2 was found in all 36 lynxes from Andújar population. Haplotypes 1 and 2 differ at a single site (site 42).
DOI: 10.5061/dryad.h02h0/4
title: Iberian lynx cytochrome b, partial sequence

description: The sequence was obtained by dideoxi sequencing of PCR products. All samples analysed (23 from Doñana and 36 from Andújar) yielded this same sequence.
DOI: 10.5061/dryad.h02h0/5
title: Iberian lynx control region, partial sequence

description: The sequence was obtained by dideoxi sequencing of PCR products. All samples analysed (23 from Doñana and 36 from Andújar) yielded this same sequence.
DOI: 10.5061/dryad.h02h0/6
title: Concatenated mitochondrial haplotypes

description: Fasta file with the two mitochondrial haplotypes found for Iberian lynx. Here haplotypes are defined by the concatenation of the three mitochondrial fragments: partial mitochondrial control region (1-602), partial cytochrome b (603-1299) and partial APT8 (1300-1488). Haplotype 1 was found in all 23 samples from Doñana and haplotype 2 was found in all 36 samples from Andújar.
DOI: 10.5061/dryad.h16ss/2
title: data-MolEcol-2803511MEC-12-0681.R1

description: Data file for manuscript MolEcol-2803511MEC-12-0681.R1
DOI: 10.5061/dryad.h3jv23cb/1
title: Flinders msat scoring.

description: Microsatellite data for MS
DOI: 10.5061/dryad.jr421/1
title: Circuitscape input

description: The files in this folder were used as input for Circuitscape.
DOI: 10.5061/dryad.jr421/2
title: structure_files.tar

description: This folder contains all input and output from the Structure analysis, as well as downstream analyses (Structure harvester, Clumpp, and Distruct).
DOI: 10.5061/dryad.jr421/3
title: Mantel_tests.tar

description: This folder contains all distance matrices used for Mantel tests, as well as R code used to run the Mantel tests.
DOI: 10.5061/dryad.jr421/4
title: f.insipida.tar

description: This folder contains raw AFLP chromatograms for F. insipida. AFLP profiles are split between two files: Files containing the word "all" contain the first three selective primer pairs. Fam profiles correspond to primer 2c in "aflp_profiles_by_species_genalex.xlsx"; Hex profiles correspond to primer 2b; and Ned profiles correspond to primer 1a. Files containing the digits "1-4" contain the last two selective primer pairs, 1-ned and 4-fam.
DOI: 10.5061/dryad.jr421/5
title: b.alicastrum.tar

description: This folder contains raw chromatograms of AFLP profiles of  B. alicastrum. AFLP profiles are split between two files:  Files containing the word "all" contain the first two selective primer pairs, and files containing "all2" contain the second 2.
DOI: 10.5061/dryad.jr421/6
title: b.simaruba.tar

description: This folder contains raw chromatograms of AFLP profiles of B. simaruba. AFLP profiles from all three selective primers are in one .fsa file.
DOI: 10.5061/dryad.kq72j/1
title: Linear floral traits

description: Include data from 17 floral traits measured in 125 plants of  Morrenia brachystephana
DOI: 10.5061/dryad.kq72j/2
title: empirical and hypothetical correlation matrices

description: include the Pearson’s correlation coefficients for 17 Morrenia brachystephana floral traits and the three hypothetical matrices used to explore patterns of modularity.
DOI: 10.5061/dryad.kq72j/3
title: variation on floral traits

description: include a subsample of 10 individuals of  Morrenia brachystephana for which traits in three pollinaria and three guide rails per flower in three flowers per individual were measured to explore the variation how much of the total variation is attributed to variation within flowers, among flowers in an individual, and among individuals in the population
DOI: 10.5061/dryad.kq72j/4
title: Fitnnes measured

description: include measure reproductive success in 125 plants of Morrenia brachystephana
DOI: 10.5061/dryad.kq72j/5
title: Phenotipic selection analysis

description: Include morphological and reproductive success data from 125  Morrenia brachystephana plants used to estimate phenotypic selection
DOI: 10.5061/dryad.mm11q/10
title: male_all_morph

description: Morphological and continuous meristic character data collected from male specimens across the Ctenophorus maculatus complex.
DOI: 10.5061/dryad.mm11q/3
title: cten_GAPD

description: Alignment of GAPD sequences from across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.mm11q/4
title: cten_nd2

description: Alignment of ND2 sequences from across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.mm11q/5
title: cten_NTF3

description: Alignment of NTF3 sequences from across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.mm11q/6
title: cten_PRLR

description: Alignment of PRLR sequences from across the Ctenophorus maculatus species complex.
DOI: 10.5061/dryad.mm11q/7
title: females_all_meristic

description: Meristic character data collected from female specimens across the Ctenophorus maculatus complex.
DOI: 10.5061/dryad.mm11q/8
title: females_all_morph

description: Morphological and continuous meristic character data collected from female specimens across the Ctenophorus maculatus complex.
DOI: 10.5061/dryad.mm11q/9
title: male_all_meristic

description: Meristic character data collected from male specimens across the Ctenophorus maculatus complex.
DOI: 10.5061/dryad.q30rt/1
title: Bear microsats for Paper For Dryad Archive

description: The file contains diploid genotypes for eight microsatellite DNA locifor three species of bears that were first reported in previous publications.
DOI: 10.5061/dryad.r0056/11
title: TuRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample TuRE.
DOI: 10.5061/dryad.r0056/12
title: Ty.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample Ty.
DOI: 10.5061/dryad.r0056/13
title: TyRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample TyRE.
DOI: 10.5061/dryad.r0056/14
title: Ya.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample Ya.
DOI: 10.5061/dryad.r0056/15
title: YaRE.Equus_cab_mito

description: Alignment to the Equus caballus mitochondrial reference genome for sample YaRE.
DOI: 10.5061/dryad.r0056/16
title: BaARE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample BaARE.
DOI: 10.5061/dryad.r0056/17
title: BaB.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample BaB.
DOI: 10.5061/dryad.r0056/18
title: BaBRE.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample BaBRE.
DOI: 10.5061/dryad.r0056/19
title: OS.Equus_cab_nucl

description: Alignment to the Equus caballus nuclear reference genome for sample OS.
DOI: 10.5061/dryad.rm5v5/1
title: Supplemental Figure 1: S. pennellii introgression summary for all 76 ILs.

description: Supplemental Figure 1: S. pennellii introgression summary for all 76 ILs. Graphical representation of introgression boundaries from Supplemental Table 2 online. Gridlines represent 10Mb intervals on each chromosome.
DOI: 10.5061/dryad.rm5v5/2
title: Supplemental Figure 2: RNAseq-based genotyping of all chromosomes.

description: Supplemental Figure 2: RNAseq-based genotyping of all chromosomes. Shown are the S. pennellii introgression regions for ILs covering chromosomes 1 to 12 (A-L) as determined by RNA-Seq. The depth of coverage (distance from midpoint on y-axis) and genotype (color and direction on y-axis) of each SNP/indel is plotted against chromosomal position (x-axis). Polymorphisms that match S. pennellii are colored green and plotted on the top half of each IL panel, while polymorphisms matching cv. M82 are plotted in magenta in the bottom halves. The coloring is on a continuum such that the color approaches black as a position’s genotype approaches heterozygosity. The y-axis tick marks indicate depths of coverage ranging from 0 to 100. Subsequent to genotyping, introgression boundaries consistent between the RNA-Seq and RESCAN analyses were delineated. Using these breakpoints, S. pennellii and cv. M82 regions are summarized by horizontal lines at the top and bottom of each IL panel, respectively.
DOI: 10.5061/dryad.rm5v5/3
title: Supplemental Figure 3: RESCAN-based genotyping of all chromosomes.

description: Supplemental Figure 3: RESCAN-based genotyping of all chromosomes. Shown are the S. pennellii introgression regions for ILs covering chromosomes 1 to 12 (A-L) as determined by RESCAN. The depth of coverage (distance from midpoint on y-axis) and genotype (color and direction on y-axis) of each SNP/indel is plotted against chromosomal position (x-axis). Polymorphisms that match S. pennellii are colored green and plotted on the top half of each IL panel, while polymorphisms matching cv. M82 are plotted in magenta in the bottom halves. The coloring is on a continuum such that the color approaches black as a position’s genotype approaches heterozygosity. The y-axis tick marks indicate depths of coverage ranging from 0 to 20. Subsequent to genotyping, introgression boundaries consistent between the RNA-Seq and RESCAN analyses were delineated. Using these breakpoints, S. pennellii and cv. M82 regions are summarized by horizontal lines at the top and bottom of each IL panel, respectively.
DOI: 10.5061/dryad.rm5v5/4
title: Supplemental Figure 4: Map of S. pennellii introgression lines, chromosomes 1-6.

description: Supplemental Figure 4: Map of S. pennellii introgression lines, chromosomes 1-6: A map showing the architecture of ILs based on precisely defined introgression boundaries determined from the sequenced tomato genome and next-generation sequencing data. IL size is proportional to the number of annotated genes harbored in each introgression. Bins, or intervals defined by unique combinations of IL overlap, are indicated with a “d-” prefix, indicating “Davis, CA,” to avoid confusion with previously designated bins. Regions of the genome not represented in the ILs are indicated by purple bars. Note that ILs can be non-contiguous (indicated by orange or yellow) as well as bins (indicated above graphs with arrowheads and lines). Only chromosomes 1-6 are shown for legibility. Chromosomes 7-12 are depicted in Supplemental Figure 5 online.
DOI: 10.5061/dryad.rm5v5/5
title: Supplemental Figure 5: Map of S. pennellii introgression lines, chromosomes 7-12.

description: Supplemental Figure 5: Map of S. pennellii introgression lines, chromosomes 7-12: A map showing the architecture of ILs based on precisely defined introgression boundaries determined from the sequenced tomato genome and next-generation sequencing data. IL size is proportional to the number of annotated genes harbored in each introgression. Bins, or intervals defined by unique combinations of IL overlap, are indicated with a “d-” prefix, indicating “Davis, CA,” to avoid confusion with previously designated bins. Regions of the genome not represented in the ILs are indicated by purple bars. Note that ILs can be non-contiguous (indicated by orange or yellow) as well as bins (indicated above graphs with arrowheads and lines). IL9-3-1 posses introgressions on chromosomes 9 and 12, indicated by dashed double arrow. Only chromosomes 7-12 are shown for legibility. Chromosomes 1-6 are depicted in Supplemental Figure 4 online.
DOI: 10.5061/dryad.rm5v5/6
title: Supplemental Figure 6: Distribution of genes per bin.

description: Supplemental Figure 6: Distribution of genes per bin. Histogram of the number of annotated genes per bin. A few bins possess over &gt;1000 annotated genes, but a majority possess much less than 500. The mean bin size (in terms of annotated genes) is 177 genes, and the median size is 295.03 genes.