cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rm5v5/14
title: Supplemental Figure 14: Bin mapping and gene candidates.

description: Supplemental Figure 14: Bin mapping and gene candidates. A-D) Graphs showing select bin and IL mapping results for traits as indicated. Below the graph is an IL map for the region and trait. The size of ILs is proportional to the number of annotated genes that they possess. Colors indicate significance of detected QTL for trait values less than cv. M82 (blue) or greater than cv. M82 (yellow; see key, upper righthand corner). Above the IL map is indicated significance values from bin mapping. The height of a column within the bin region indicates the -log10(p-value) of the bin significance, and like ILs, the columns are appropriately colored. A) shows results for FlowTime, d-5E, B) LftAR, d-9B, C) LftAR, d-8F, D) CompAll, d-8A. See text for discussion of candidate genes regulating these traits. E) Annotated genes present in bin-5E. Chromosome position is indicated, as well as predicted genes and their orientation (red, forward; black, reverse orientation). On this short interval lies SP5G, a strong candidate regulating the flowering time QTL detected for this bin and perhaps a regulator of leaf morphology as well.
DOI: 10.5061/dryad.rm5v5/15
title: Supplemental Figure 15: Bin mapping result legend.

description: Supplemental Figure 15: Bin mapping result legend. For each trait, bin and IL mapping results are visualized (Supplemental Figures 16–47 online). Below each graph is an IL map, the color of the ILs indicating the direction and significance of the QTL. Above this map is a graph, the height of the columns indicating the significance of the bin from the bin mapping results. Bin columns are colored based on their significance values. The y-axis indicates -log10(p-value). For both the IL map and bin mapping results graph, the size of bins and ILs is proportional to the number of annotated genes that they harbor.
DOI: 10.5061/dryad.rm5v5/16
title: Supplemental Figure 16: Bin mapping results for CompAll.

description: Supplemental Figure 16: Bin mapping results for CompAll. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/17
title: Supplemental Figure 17: Bin mapping results for CompInt.

description: Supplemental Figure 17: Bin mapping results for CompInt. See Supplemental Dataset 7 online for trait details and Supplemental Figure 15 online for legend.
DOI: 10.5061/dryad.rm5v5/9
title: Supplemental Figure 9: Broad-sense heritability for leaf developmental traits.

description: Supplemental Figure 9: Broad-sense heritability for leaf developmental traits: Colors denote traits with very high (red, H2 &gt; 0.6), high (orange, 0.4 ≤ H2 &lt; 0.6), intermediate (yellow, 0.2 ≤ H2 &lt; 0.4), and low (green, H2 &lt; 0.2) heritability values. All traits were measured under 2010 Davis, CA field conditions, unless otherwise noted (* denotes 2011 field data and § denotes cumulative data from 2010 – 2011). Generally, measures of leaflet serration, length-to-width ratio, and measures of shape (PCs 1 and 4) have high heritability, as does flowering time. Leaf complexity, other leaflet shape traits, and measures of leaflet size have intermediate heritability, whereas cellular and stomata traits have intermediate to low heritability.
DOI: 10.5061/dryad.s1q0h/1
title: Sexual selection in a hermaphroditic plant through female reproductive success
DOI: 10.5061/dryad.sh811k0h/1
title: Motivation-Agression-Moral

description: Raw self-determined motivation, aggressive behaviors and sportspersonship orientation data, collected in the field with Brazilian volleyball players.
DOI: 10.5061/dryad.sh811k0h/2
title: Todos os Dados
DOI: 10.5061/dryad.t1m2q/1
title: PAR fixation probability program

description: Text file  of Fortran program that calculates fixation probabilities for sexually antagonistic mutations in a pseudoautosomal region of a sex chromosome
DOI: 10.5061/dryad.t91v2/1
title: muscledataset

description: Raw data for muscle analysis
DOI: 10.5061/dryad.t91v2/2
title: springdataset

description: Data for spring analysis
DOI: 10.5061/dryad.t91v2/3
title: Analyses in R

description: R analyses used in study
DOI: 10.5061/dryad.v7m3q/1
title: Fig.2. Oyster larval settlement rates on adult oysters in an open estuary, field experiment.

description: Data collected in the field, in an experiment established in an estuary. Excel software was used to create the data file. A)Monospecific Bags: data represent the rate of larval settlement on 9 of each adult oyster: conspecific Sydney rock oysters and native Pacific oysters, deployed in single-species mesh bags. Status indicates oysters that were deployed live or dead. B) Mixed basket: 20 of each Sydney rock oyster and Pacific, live and dead (total 80 oysters) were deployed in one basket. Summary indicates means and standard errors of the means of raw data.
DOI: 10.5061/dryad.v7m3q/2
title: Fig.3. Larval settlement rates in response to densities of adult oyster substrate.

description: Data collected in a controlled laboratory experiment, in 8 L replicate buckets. Excel software used to create the data. The number of Sydney rock  oyster larvae settled per adult oyster is recorded. Adult oysters used as substrate were either A) Live or B) Dead.  Two species of oyster were used; Sydney rock oyster and Pacific oyster. Oysters were placed in buckets in three densities; 1 oyster, 2 oysters and 3 oysters. Summary indicates the mean, and standard error of the mean.
DOI: 10.5061/dryad.vn541ms8/1
title: brown
DOI: 10.5061/dryad.vn541ms8/2
title: sepia
DOI: 10.5061/dryad.vn541ms8/3
title: plexus
DOI: 10.5061/dryad.222vq/1
title: Karaiskou et al

description: Microsatellite data file of Parntitha red deer
DOI: 10.5061/dryad.257b9/1
title: GFEresorption

description: Data were collected in the field during the 13th year of fertilization on the Gigante Fertilization Experiment in the Barro Colorado National Monument, Republic of Panama.
Abbreviated headlines are as follows: "Blk" = Block; "Rx" = treatment; "N" = N addition; "P" = P addition; "Species" = tree species sampled; "Leaf C" = mg/g of C in dried green leaves; "Leaf N" = mg/g of N in dried green leaves; "Leaf P" = mg/g of Total P in dried green leaves; "Leaf Pi" = mg/g of Inorganic P in dried green leaves; "Leaf Po" = mg/g of Po – Pi in dried green leaves; "%Pi" = proportion of total P comprised of inorganic P; "Leaf 13C" = delta 13C values from green leaves;  "Leaf 15C" = delta 15N values from green leaves; "Litter 15N" = delta 15N values from senesced leaf litter; "Litter N corr" = mass loss based correction of litter N concentration (mg/g); "litter C" = mg/g of carbon from senesced leaf litter; "litter 13C" = delta 13C values from senesced leaf litter; "litter P" = mg/g of P from senesced leaf litter; "litter P corr" = mass loss based correction of litter P concentration (mg/g); "leaf – litter 15N" = difference among green leaf and senesced litter delta 15N values; "leaf – litter N" = difference among green leaf and senesced litter N concentration (mg/g); "leaf C:N" = ratio of carbon to nitrogen in green leaves; "litter C:N" = "leaf – litter fall P" = difference among green leaf and senesced litter P concentration (mg/g); "leaf N:P" = ratio of nitrogen to phosphorus in green leaves; "litter N:P" = ratio of nitrogen to phosphorus in senesced leaves; "litter organic P" = mg/g of Po – Pi in senesced leaves; "N res" = resorption efficiency of N; "N_res_corr" = resorption efficiency of N based on mass loss corrected leaf litter N; logN_res_corr" = log transformation; "P res" = phosphorous resorption efficiency; "P_res_corr" = resorption efficiency of P based on mass loss corrected leaf litter P; "logP_res_corr" = log transformation; "N:P res" = ratio of N to P resorption efficiencies; "logN:P_res_cor" = log transformation of mass loss corrected resorption efficiency ratios; "N:P_res_corr" = mass loss corrected resorption efficiency ratios; "transformed_P" = log transformed P concentrations; "N_resorp" = N resorption efficiency with negatives removed; "P_resorp" = P resorption efficiency with negatives removed; and, "N:P_resorp" = ratio of N and P resorption efficiencies.
DOI: 10.5061/dryad.2m667/1
title: Pontomyia phylogenetic datasets and trees

description: NEXUS file for Mesquite: A Modular System for Evolutionary Analysis (Maddison and Maddison 2011), containing the datasets subjected to phylogenetic analyses and the resulting trees.
DOI: 10.5061/dryad.2v4hv/1
title: repository_data

description: data for all experiments
DOI: 10.5061/dryad.2vk43/1
title: FebPt 2010 OVX experiment

description: Data describing SVL, mass, treatment group, growth, and fat mass for wild females at February point. Survival and recapture rates are also calculated from these data.
DOI: 10.5061/dryad.2vk43/2
title: Plasma estradiol levels and associated data

description: Plasma estradiol, treatment groups, SVL, mass, fat, and condition data for captive and wild anoles.
DOI: 10.5061/dryad.2vk43/3
title: Unilateral fecundity

description: Number of offspring produced for each pair of females assigned to 1OVX or SHAM treatments, used to determine effects of manipulation on reproductive investment.
DOI: 10.5061/dryad.2vm70/1
title: Labeled RandTag Widefield Images (Unlabeled Subset)

description: This datasets consists of fluorescent microscope images of GFP-tagged proteins locating to different organelles. The organelles were annotated by visual inspection. For each organelle, multiple proteins locating to it were identified; and for each protein, multiple images were acquired. Images contain two channels: GFP tagged protein and a nuclear marker (Hoechst). NIH 3T3 cells were tagged using CD tagging. This data was acquired on a widefield microscope
DOI: 10.5061/dryad.2vm70/2
title: Labeled RandTag Confocal Images

description: This datasets consists of fluorescent microscope images of GFP-tagged proteins locating to different organelles. The organelles were annotated by visual inspection. For each organelle, multiple proteins locating to it were identified; and for each protein, multiple images were acquired. Images contain two channels: GFP tagged protein and a nuclear marker (Hoechst). NIH 3T3 cells were tagged using CD tagging. This data was acquired on a confocal microscope.
DOI: 10.5061/dryad.2vm70/3
title: Labeled RandTag Widefield Images (Nuclear Subset)

description: Part of widefield labeled dataset
DOI: 10.5061/dryad.30vn6/1
title: Monro & Marshall 2014 AmNat

description: Estimates of relative growth rates and fecundity for 20 focal colonies replicated across 3 stages of succession in the field.
DOI: 10.5061/dryad.4298p/1
title: Offspring data

description: Data for offspring production and extinction of the inbred and hybrid populations.
DOI: 10.5061/dryad.4298p/2
title: Microsatellite data

description: Genetic data for the control and inbred populations.
DOI: 10.5061/dryad.465v3/10
title: bol_exi_fst_map_cluster_nonoverlapping_windows

description: Contains list for H. exilis - H. bolanderi of all unique positions in the genetic map, linkage groups, associated fst valuse, and other various statistics (not used in this study, but part of the original script).
DOI: 10.5061/dryad.465v3/11
title: deb_pet_fst_map_cluster_nonoverlapping_windows

description: Contains list for H. debilis - H. petiolaris of all unique positions in the genetic map, linkage groups, associated fst valuse, and other various statistics (not used in this study, but part of the original script).
DOI: 10.5061/dryad.465v3/2
title: bol_exi_fst_map

description: Contains: all SNPs kept in the H. exilis - H. bolanderi comparison, name of reference gene, position of SNP in gene, genotypes of all individuals, Fst, Fit, Fis, name, linkage group, position in centimorgan, unique position on map, number of nucleotides in gene, boolean value whether SNP is in the top5% most divergent.
DOI: 10.5061/dryad.465v3/3
title: deb_pet_fst_map

description: Contains: all SNPs kept in the H. debilis - H. petiolaris comparison, name of reference gene, position of SNP in gene, genotypes of all individuals, Fst, Fit, Fis, name, linkage group, position in centimorgan, unique position on map, number of nucleotides in gene, boolean value whether SNP is in the top5% most divergent.
DOI: 10.5061/dryad.465v3/4
title: unique_SNP

description: Contains a list of all SNPs found in either one of the three species pairs. List contains unique name (gene name and position concatenated) and the fst value for all three species pairs.
DOI: 10.5061/dryad.465v3/5
title: unique_genes

description: Contains list of all unique polymorphic genes found in either of the three species pairs, and the fst value for all three species pairs.
DOI: 10.5061/dryad.465v3/6
title: ann_arg_fst_map_dnds.out

description: Contains list of all polymorphic genes in H. annuus - H. argophyllus species pairs and dn, ds, dn/ds values.
DOI: 10.5061/dryad.465v3/7
title: bol_exi_fst_map_dnds

description: Contains list of all polymorphic genes in H. exilis - H. bolanderi species pairs and dn, ds, dn/ds values.
DOI: 10.5061/dryad.465v3/8
title: deb_pet_fst_map_dnds

description: Contains list of all polymorphic genes in H. debilis - H. petiolaris species pairs and dn, ds, dn/ds values.
DOI: 10.5061/dryad.465v3/9
title: ann_arg_fst_map_cluster_nonoverlapping_windows

description: Contains list for H. annuus - H. argophyllus of all unique positions in the genetic map, linkage groups, associated fst valuse, and other various statistics (not used in this study, but part of the original script).
DOI: 10.5061/dryad.73675/1
title: DNA sequences in IMa2 format of marbled newts from the Iberian Peninsula

description: IMa2 input files for four different areas of the T. marmoratus / T. pygmaeus hybrid zone (Coastal Portugal, Tejo river, Idanha-a-Nova and Sierra da Gata). BF = beta-Fibrinogen intron 7 ; CALC = Calreticulin intron 3 ; PDGFRA = Platelet-derived growth factor receptor alpha intron 11 and ND4 = mitochondrial NADH dehydrogenase subunit 4.
DOI: 10.5061/dryad.73675/2
title: Locality data of sampling location of Triturus marmoratus and T. pygmaeus

description: Locality data of sampled populations of T. marmoratus and T. pygmaeus, including Locality name and order number, country, hybrid zone area as described in the paper, and GPS coordinates.
DOI: 10.5061/dryad.7dp5v/11
title: Appendix 11

description: Apomorphies separating specimens assigned to Strotopora and Cliotrypa. Labeled nodes in the cladogram are referred to in the apomorphies listed below. Character abbreviations are described in Table 1 and codes are listed in Appendix 10.
DOI: 10.5061/dryad.846nj.3
title: Data from: Recombination in the threespine stickleback genome – patterns and consequences
DOI: 10.5061/dryad.8n776/5
title: Identified transposable elements

description: A list of 2,439 predicted transposable elements.
DOI: 10.5061/dryad.b4783/1
title: Museum_sample_Table

description: Sample Table includes metadata associated with the historic specimens.
DOI: 10.5061/dryad.b4783/2
title: Fasta files containing museum data

description: There are three fasta files for the 30 museum samples.  Two fasta files for non-continuous ND2 partial gene sections and one fasta file for COI partial gene sequences.
DOI: 10.5061/dryad.b4783/3
title: ND2COI_unique_430bp_HapNet

description: Nexus formatted sequence file containing unique haplotypes used to generate the parsimony haplotype newtwork shown in Figure 4.  The sequence data includes a concatenation of two non-continuous portions of the ND2 gene and one section of COI gene.
DOI: 10.5061/dryad.b4783/4
title: AMOVA_subsample_scripts

description: "AMOVA_subsample_scripts.zip" - custom scripts for subsampling modern data set to match the number of samples in each drainage in the historic data set.  3 files.
DOI: 10.5061/dryad.cj36j/1
title: Steelhead Size Data

description: This file contains length and weight time series for individual steelhead trout raised in tanks in Santa Cruz California during 2006. Individual fish were measured on a series of days starting in spring 2006 to spring 2007. The fish were derived from two hatcheries (Scott Creek Hatchery and Coleman National Fish Hatchery, denoted as "Scott" and "Coleman" respectively) and raised in set of tanks. The tank number in which each fish grew is noted in the file. The fish were fed two rations levels (high or low) and the ration associated with each time is noted in the column labeled "Ration." The sequence of feeding treatments determine the "Treatment" column which has four levels (1,2,3, or 4). See the publication for more detailed information.
DOI: 10.5061/dryad.cj36j/2
title: Steelhead Ration Schedule

description: This file shows the sequence of high and low ration treatments for each tank and the date at which changes in ration occurred.
DOI: 10.5061/dryad.d71c1/1
title: Alignment and Tree

description: Alignment of DNA sequences and tree. Nexus format.
DOI: 10.5061/dryad.ds2gp/1
title: Picea abies needle transcripts

description: de novo assembly of Picea abies needle transcripts sequenced using mRNA-seq technology
DOI: 10.5061/dryad.ds2gp/2
title: SNP file

description: This file describes the single nucleotide polymorphism position, reference and alternative phases in each transcripts.
DOI: 10.5061/dryad.ds2gp/3
title: PAML tables

description: It includes six tables that describe information of orthologous sequences used in pairwise PAML analysis when calculating Ka/Ks ratios.
DOI: 10.5061/dryad.f0b2f083/1
title: Sequence allele counts

description: Allele counts form indiviudal-based Illumina sequence data for Lycaeides butterflies. This file contains counts of the number of times each allele was observed for each locus and individual. Each locus begins with a line with the contig number and location (in bp) in the reference genome. This is followed by a single line per individual with the individuals name, the number of times the reference allele was observed (i.e., how many reads included the reference allele), and the number of times the alternative allele (i.e., nucleotide) was observed. This file contains 119,677 loci.
DOI: 10.5061/dryad.f0b2f083/2
title: Reference sequence

description: This is the fasta formatted reference sequence used for the reference-based assembly. This reference was generated by concatenating short (~92 bp) contigs from a de novo assembly and separating these sequences with 30 'N' characters.
DOI: 10.5061/dryad.f0b2f083/3
title: Source code for allele frequency estimation with genotype uncertainty

description: This compressed directory contains the source code for the allele frequency model described in the publication. Please contact the Zach Gompert (zgompert@uwyo.edu) to inquire about updates to the software, usage, and whether a manual or example files exist.
DOI: 10.5061/dryad.jd8vg.2/1.1
title: scc_examples

description: Examples of the resampling test for sister clade comparison. Needs data files from the archive data.tar.gz.
DOI: 10.5061/dryad.jd8vg.2/2.1
title: data.tar.gz

description: Examples of data found in the literature that can be analysed with the resampling test for sister clade comparisons: 1) viviparity in actinopterygian fishes (from Slowinski and Guyer, 1993, dataset from Lydeard, 1993), 2) dioecy in angiosperms (updated dataset from Heilbuth, 2000)
DOI: 10.5061/dryad.jd8vg.2/3
title: scc_test

description: R source code for the resampling test for sister clade comparisons proposed in the manuscript
DOI: 10.5061/dryad.mg606/1
title: Bayes_phylogram_Ligia_oceanica_CO1

description: Bayesian tree by MrBayes 3.2.1 (Ronquist et al., 2012) for the 61 CO1 haplotypes of Ligia oceanica. The most appropriate model was determined beforehand using the Bayesian information criterion (BIC) as implemented in jModeltest 2.1.1 (Darriba et al., 2012), indicating TPM1uf+I+G to be the optimal nucleotide substitution model with the following parameters: nucleotide frequencies A: 0.27, C: 0.19, G: 0.17, T: 0.37; substitution rates RAC: 1, RAG: 13.33, RAT: 4.63, RCG: 4.63, RCT: 13.33, RGT: 1; gamma distribution shape = 0.48; and proportion of invariable sites = 0.38. The Bayesian analysis employed 10,000,000 Markov chain Monte Carlo (MCMC) generations in two parallel runs, each with three cold chains and one hot chain. Trees were sampled every 500th generation, with the number of burn-in generations being determined using the likelihood scores over all generations in Tracer 1.5 (Rambaut & Drummond, 2007). The determination of the split frequencies in both independent runs (&lt; 0.01) with 2 x 20,001 tree samples showed good convergence after 5,000 sampled trees (split frequency &lt; 0.01), which was therefore set as the burn-in.
DOI: 10.5061/dryad.mp924433/1
title: geneTrees

description: 1878 gene trees used in our study
DOI: 10.5061/dryad.n2645/1
title: Data_Combined

description: Data files for the article: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1.Sean Michael Carroll*, Ming-Chun Lee*, Christopher J. Marx*These authors contributed equally to this workAccepted for publication in Evolution. October, 2013
DOI: 10.5061/dryad.n5q05/2
title: ARS phenotype data
DOI: 10.5061/dryad.n5q05/3
title: LRS phenotype data
DOI: 10.5061/dryad.n8234tb1/1
title: Pmac2011

description: Mitochondrial control region sequences from this study as well as those from Chenoweth SF and Hughes JM (2003) Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish, Polynemus sheridani. Mol Ecol 12: 2387-2397. In arlequin format.
DOI: 10.5061/dryad.q0k1m/1
title: dataforRSPB_PatelFlemingKilner

description: Data for the mean observation and executed movement times and confidence ratings for all subjects and actors.
DOI: 10.5061/dryad.q7ht7/1
title: Krabbenhoft_&_Turner_2014_Clock_microsat_genotypes

description: MIcrosatellite genotypes (allele lengths, in bp) for Clock1a.
DOI: 10.5061/dryad.qh113/1
title: Screening for male-killing variation among Drosophila melanogaster and Spiroplasma strains

description: This file contains 5 spreadsheets with experimental data of screening for male-killing variation among Drosophila melanogaster and Spiroplasma strains, at 18.5 and 23ºC.
DOI: 10.5061/dryad.r0056/29
title: BaARE.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaARE.
DOI: 10.5061/dryad.r0056/30
title: BaB.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaB.
DOI: 10.5061/dryad.r0056/31
title: BaBRE.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaBRE.
DOI: 10.5061/dryad.r0056/32
title: OS.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OS.
DOI: 10.5061/dryad.r0056/33
title: OSRE.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OSRE.
DOI: 10.5061/dryad.r0056/34
title: Ta.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ta.
DOI: 10.5061/dryad.r0056/35
title: TaRE.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TaRE.
DOI: 10.5061/dryad.r0056/36
title: TP3.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3.
DOI: 10.5061/dryad.r0056/37
title: TP3RE.Homo_sapiens_nucl

description: Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3RE.
DOI: 10.5061/dryad.r84n5/2
title: Aiptasia_Sym_B_MicSat_Fla2

description: Nucleotide alignment of DNA sequences from microsatellite flanking region loci CA4.86 and Si15. The alignment includes Symbiodinium minutum associated with Aiptasia from field collected and cultured specimens as well as Symbiodinium samples collected from other hosts.