cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9gg30
title: Data from: Sensitivity of the distribution of mutational fitness effects to environment, genetic background, and adaptedness: a case study with Drosophila

description: Heterogeneity in the fitness effects of individual mutations has been
 found across different environmental and genetic contexts. Going beyond
 effects on individual mutations, how is the distribution of selective
 effects, f(s), altered by changes in genetic and environmental context? In
 this study, we examined changes in the major features of f(s) by
 estimating viability selection on 36 individual mutations in Drosophila
 melanogaster across two different environments in two different genetic
 backgrounds that were either adapted or nonadapted to the two test
 environments. Both environment and genetic background affected selection
 on individual mutations. However, the overall distribution f(s) appeared
 robust to changes in genetic background but both the mean, E(s), and the
 variance, V(s) were dependent on the environment. Between these two
 properties, V(s) was more sensitive to environmental change. Contrary to
 predictions of fitness landscape theory, the match between genetic
 background and assay environment (i.e., adaptedness) had little effect on
 f(s).
description: SANE DATA for
 uploadExcel file with raw data
 used in paper.
DOI: 10.5061/dryad.b5s47
title: Data from: Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae)

description: Recent studies utilizing transcriptome sequences generated by next
 generation sequencing (NGS) technologies have demonstrated the ability to
 rapidly detect and characterize thousands of gene-based microsatellites
 from different plants. However, these simple sequence repeats (SSRs) were
 seldom used directly to test interspecific transferability in the
 populations of closely related species. Aspidistra Ker-Gawl. is a monocot
 genus with high species richness and diversity in flower structure but its
 fresh floral materials are not easy to obtain. Until now, little is known
 about genetic background in the species of Aspidistra, quite apart from
 the fearful reduction of their natural habitats. In this study, the floral
 transcriptome of Aspidistra saxicola was obtained by using NGS. Based on
 these data, a total of 5,527 SSRs were identified in the unigenes. Among
 these SSRs, the proportions of di- and tri-nucleotide repeats were quite
 close (49.6% verse 46.8%), and the most tri-nucleotide repeats were
 AGG/CCT followed by AAG/CTT and AGC/GCT in A. saxicola, showing distinct
 differences with other angiosperm species. To assess genetic diversity in
 the species of Aspidistra, 48 SSR loci were tested in four available
 populations of A. elatior. The results revealed that more than a third of
 the loci were polymorphic. The majority of these primers could be
 amplified in 24 species representing the main clades of Aspidistra. The
 primer subsets from transcriptome data proved highly useful for detecting
 polymorphisms in the related species, supporting the finding that NGS is
 an efficient approach to molecular marker development at both intra- and
 inter- species levels, especially in endangered non-model species.
description: The assembled contigs
 and unigenes, the GO annotations and the microsatellite genotypes from
 tested individualsAspidistra saxicola
 As011-annotation.xls, Aspidistra saxicola As011-Contig.fa, Aspidistra
 saxicola As011-Unigene.fa. The microsatellite genotypes from tested
 individuals in Aspidistra elatior.xlsxDryad.zip
DOI: 10.5061/dryad.1775k
title: Data from: Chromatin signature of widespread monoallelic expression

description: In mammals, numerous autosomal genes are subject to mitotically stable
 monoallelic expression (MAE), including genes that play critical roles in
 a variety of human diseases. Due to challenges posed by the clonal nature
 of MAE, very little is known about its regulation; in particular, no
 molecular features have been specifically linked to MAE. Here we report an
 approach that distinguishes MAE genes in human cells with great accuracy:
 a chromatin signature consisting of chromatin marks associated with active
 transcription (H3K36me3) and silencing (H3K27me3) simultaneously occurring
 in the gene body. The MAE signature is present in ~20% of ubiquitously
 expressed genes and over 30% of tissue-specific genes across cell types.
 Notably, it is enriched among key developmental genes that have bivalent
 chromatin structure in pluripotent cells. Our results open a new approach
 to the study of MAE that is independent of polymorphisms, and suggest that
 MAE is linked to cell differentiation.
description: MAE predictions for cell
 linesChromatin-based
 predictions of monoallelic expression in ENCODE cell lines in Open Office
 FormatNag_Savova_et_al_Dataset_S1_Dec2013.odsResult of whole RNA-seq on clones of GM12878 lymphoblastoid clones DF1 and DF2Result of whole RNA-seq on clones of GM12878 lymphoblastoid clones DF1 and DF2 in Open Office FormatNag_Savova_et_al_Dataset_S2_Dec2013.odsAST-seq dataTable in open office format listing targeted RNA-seq data on GM12878, DF1,DF2, H0 (GM13130 polyclonal), H2, H7, H14 and H16 cell lines. Results of statistical test and MAE calling is included.Nag_Savova_et_al_Dataset_S3_Dec2013.odsResults of the experiment with padlock probeThis table in open office format lists all the data for SNPs that passed QC for predicted and not-predicted genesNag_Savova_et_al_Dataset_S4_Dec2013.ods
DOI: 10.5061/dryad.1q9r8
title: Data from: Two decades of genetic profiling yields first evidence of natal philopatry and long-term fidelity to parturition sites in sharks

description: Sharks are a globally threatened group of marine fishes that often breed
 in their natal region of origin. There has even been speculation that
 female sharks return to their exact birthplace to breed (“natal
 philopatry”), which would have important conservation implications.
 Genetic profiling of lemon sharks (Negaprion brevirostris) from 20
 consecutive cohorts (1993-2012) at Bimini, Bahamas showed that certain
 females faithfully gave birth at this site for nearly two decades. At
 least six females born in the 1993-1997 cohorts returned to give birth
 14-17 years later, providing the first direct evidence of natal philopatry
 in the chondrichthyans. Long-term fidelity to specific nursery sites
 coupled with natal philopatry highlights the merits of emerging spatial
 and local conservation efforts for these threatened predators.
description: Feldheim et al. lemon
 shark morphological and catch data Bimini, Bahamas
 1995-2012The first worksheet of
 the excel file is entitled "explanation of data." This sheet
 contains a key for abbreviations and explanations of each subsequent
 sheet.Feldheim et al. lemon
 shark.xls
DOI: 10.5061/dryad.70254
title: Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013

description: Tree-roosting bats in the genus Lasiurus are widespread, migratory species
 that have not been well characterized for population genetic diversity and
 structure due to a lack of genetic resources. Generating genetic resources
 in Lasiurus is made pressing by the need for conservation genetic
 assessments of demographic trends in this genus, which comprise a large
 percentage of bat mortalities at wind turbine sites across North America.
 We report on marker development from whole-genome Illumina sequencing of
 the red bat (Lasirus borealis) and the hoary bat (L. cinereus). We
 generated paired-end libraries for a single individual of each species,
 sequenced on the Illumina HiSeq platform. We mapped a total of 46.6
 million reads to the Myotis lucifigus reference genome, and used
 bioinformatics searches to identify tends of thousands of simple sequence
 repeats (SSRs) distributed across the bat genome. We selected 48 candidate
 microsatellite loci to develop cross-species primer sequences for
 Lasiurus, assembled these into multiplex combinations, and tested for
 amplification and polymorphism levels in a sample of 23 individuals from
 each of L. borealis and L. cinereus. In total, we identified 42 highly
 polymorphic loci that could be robustly amplified and scored, the majority
 of which (39) were also combinable into highly multiplexed assays of 4-8
 loci each. The combination of new genomic sequence assemblies, a large set
 of highly polymorphic microsatellite loci, and the ability to efficiently
 multiplex represents a significant contribution to the genetic resources
 available for population and comparative genetic studies of bats.
description: Keller_etal_2013MER_MSATCOMMANDER_microsatsMicrosoft Excel file containing the results of the MSATCOMMANDER searches for simple sequence repeats (SSR's) in the genomic sequence of two bat species: Lasirus borealis and L. cinereus (Vespertilionidae).Keller_etal_2013MER_MSATCOMMANDER_primersMicrosoft Excel file of primers developed by MSATCOMMANDER for SSR loci from genomic sequencing of two bats species: Lasirus borealis and L. cinereus.Keller_etal_MER2013_Lasiurus_pipelineUNIX bash script containing the informatics pipeline used to align sequence reads for Lasiurus borealis and L. cinereus against the reference genome and determine consensus sequences.
DOI: 10.5061/dryad.cr3p6
title: Data from: Intraspecific scaling of the resting and maximum metabolic rates of the crucian carp (Carassius auratus)

description: The question of how the scaling of metabolic rate with body mass (M) is
 achieved in animals is unresolved. Here, we tested the cell metabolism
 hypothesis and the organ size hypothesis by assessing the mass scaling of
 the resting metabolic rate (RMR), maximum metabolic rate (MMR),
 erythrocyte size, and the masses of metabolically active organs in the
 crucian carp (Carassius auratus). The M of the crucian carp ranged from
 4.5 to 323.9 g, representing an approximately 72-fold difference. The RMR
 and MMR increased with M according to the allometric equations RMR =
 0.212M0.776 and MMR = 0.753M0.785. The scaling exponents for RMR (br) and
 MMR (bm) obtained in crucian carp were close to each other. Thus, the
 factorial aerobic scope remained almost constant with increasing M.
 Although erythrocyte size was negatively correlated with both
 mass-specific RMR and absolute RMR adjusted to M, it and all other
 hematological parameters showed no significant relationship with M. These
 data demonstrate that the cell metabolism hypothesis does not describe
 metabolic scaling in the crucian carp, suggesting that erythrocyte size
 may not represent the general size of other cell types in this fish and
 the metabolic activity of cells may decrease as fish grows. The mass
 scaling exponents of active organs was lower than 1 while that of inactive
 organs was greater than 1, which suggests that the mass scaling of the RMR
 can be partly due to variance in the proportion of active/inactive organs
 in crucian carp. Furthermore, our results provide additional evidence
 supporting the correlation between locomotor capacity and metabolic
 scaling.
description: Metabolic rates, blood
 cell size, and organ sizes of crucian carps with different
 sizesData
 reposition.xls
DOI: 10.5061/dryad.461nc
title: Data from: Relatedness severely impacts accuracy of marker- assisted selection for disease resistance in hybrid wheat

description: The accuracy of genomic selection depends on the relatedness between the
 members of the set in which marker effects are estimated based on
 evaluation data and the types for which performance is predicted. Here, we
 investigate the impact of relatedness on the performance of
 marker-assisted selection for fungal disease resistance in hybrid wheat. A
 large and diverse mapping population of 1,739 elite European winter wheat
 inbred lines and hybrids was evaluated for powdery mildew, leaf rust, and
 stripe rust resistance in multi-location field trials and fingerprinted
 with 9k and 90k SNP arrays. Comparison of the accuracies of prediction
 achieved with data sets from the two marker arrays revealed a crucial role
 for a sufficiently high marker density in genome-wide association mapping.
 Cross- validation studies using test sets with varying degrees of
 relationship to the corresponding estimation sets unraveled that close
 relatedness leads to a substantial increase in the proportion of total
 genotypic variance explained by the identified QTL and, consequently, to
 an overoptimistic judgment of the prospected precision of marker-assisted
 selection.
description: Genomic and Phenotypic
 dataThe excel sheet contains
 the genomic data and the phenotypic dataSupplementary_Tables.xlsx
DOI: 10.5061/dryad.db521
title: Data from: Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits

description: Association mapping has become a widely applied genomic approach to
 identify quantitative trait loci (QTL) and dissect the genetic
 architecture of complex traits. However, approaches to assess the quality
 of the obtained QTL results are lacking. We therefore evaluated the
 potential of cross-validation in association mapping based on a large
 sugar beet data set. Our results show that the proportion of the
 population that should be used as estimation and validation sets,
 respectively, depends on the size of the mapping population. Generally, a
 fivefold cross-validation, that is, 20% of the lines as independent
 validation set, appears appropriate for commonly used population sizes.
 The predictive power for the proportion of genotypic variance explained by
 QTL was overestimated by on average 38% indicating a strong bias in the
 estimated QTL effects. The cross-validated predictive power ranged between
 4 and 50%, which are more realistic estimates of this parameter for
 complex traits. In addition, QTL frequency distributions can be used to
 assess the precision of QTL position estimates and the robustness of the
 detected QTL. In summary, cross-validation can be a valuable tool to
 assess the quality of QTL parameters in association mapping.
description: Wuerschum_and_Kraft_DataPhenotypic and genotypic data underlying this studyWuerschum_and_Kraft_raw_data.txtWuerschum_and_Kraft_genetic_mapGenetic linkage map underlying this study
DOI: 10.7910/dvn/aqipi0
title: Replication Data for: Financing Multinationals

description: Review of Economics and Statistics: Forthcoming
description: Volume XX, Issue X
DOI: 10.5061/dryad.b64b4
title: Data from: Bayesian clustering analyses for genetic assignment and study of hybridization in oaks: effects of asymmetric phylogenies and asymmetric sampling schemes

description: Bayesian clustering methods have been widely used for studying species
 delimitation and genetic introgression. In order to test the effect of
 phylogenetic relationships and sampling scheme on the inferred clustering
 solution and on the performance of Bayesian clustering analysis, I
 simulated genotypes of the interfertile oak species Quercus robur, Quercus
 petraea, and Quercus pubescens and I run analyses using two popular
 software programs, STRUCTURE and BAPS. First, based on purebred
 simulations, I compared clustering solutions resulting from different
 sample size configurations. While clustering solution generally reflected
 the taxonomic relationships when equal samples of each species were
 included, spurious partition was inferred by STRUCTURE when some species
 were represented by larger and others by smaller samples. In very
 unbalanced configurations, STRUCTURE failed to identify the three species,
 even if three subpopulations were assumed. By contrast, BAPS could
 properly identify the three species under any sampling scheme. Second,
 based on simulations of purebreds and hybrids, I tested the performance of
 individual assignments with variable number of loci. This analysis showed
 that STRUCTURE can detect introgressed individuals more efficiently than
 BAPS. However, BAPS could assign purebreds more efficiently with a lower
 number of loci. Method performance also depended on phylogenetic
 relationships. In the case of Q. petraea, Q. pubescens, and their hybrids,
 method performance was lower due to their phylogenetic affinity. Inclusion
 of three instead of two species into the analysis led to reduction of
 performance, and to misclassification of hybrids, which often reflected
 the phylogenetic affinity between Q. petraea and Q. pubescens.
description: Neophytou_Bayesian_clustering_Quercus_Tree_Genetics_Genomes_DataSheet 1: Identification of tree individuals sampled in the field, assignment to sample stands, geographic coordinates, genotypic data and species assignmnent after Bayesian clustering analyses using the softwares BAPS and STRUCTURE. Sheet 2: Genotypic data of simulated individuals of the three species, first generation hybrids and backcrossings. The sampled individuals used for producing simulations are marked in the last column of the first sheet.
DOI: 10.5061/dryad.51rf8
title: Data from: Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity

description: The Kingdom Fungi adds substantially to the diversity of life, but due to
 their cryptic morphology and lifestyle, tremendous diversity, paucity of
 formally described specimens, and the difficulty in isolating
 environmental strains into culture, fungal communities are difficult to
 characterize. This is especially true for endophytic communities of fungi
 living in healthy plant tissue. The developments in next generation
 sequencing technologies are, however, starting to reveal the true extent
 of fungal diversity. One of the promising new technologies, namely
 semiconductor sequencing, has thus far not been used in fungal diversity
 assessments. In this study we sequenced the internal transcribed spacer 1
 (ITS1) nuclear encoded ribosomal RNA of the endophytic community of the
 economically important tree, Eucalyptus grandis, from South Africa using
 the Ion Torrent Personal Genome Machine (PGM). We determined the impact of
 various analysis parameters on the interpretation of the results, namely
 different sequence quality parameter settings, different sequence
 similarity cutoffs for clustering and filtering of databases for removal
 of sequences with insufficient taxonomy. Sequence similarity cutoff values
 only had a marginal effect on the identified family numbers, whereas
 different sequence quality filters had a large effect (89 vs. 48 families
 between least and most stringent filters). Database filtering had a small,
 but statistically significant, effect on the assignment of sequences to
 reference sequences. The community was dominated by Ascomycota, and
 particularly by families in the Dothidiomycetes that harbor well-known
 plant pathogens. The study demonstrates that semiconductor sequencing is
 an ideal strategy for environmental sequencing of fungal communities. It
 also highlights some potential pitfalls in subsequent data analyses when
 using a technology with relatively short read lengths.
description: seq.fna.zipSequences obtained from Ion Torrent Amplicon sequencing of the fungal community of Eucalyptus grandis in South Africa.seqs.fna.zip
DOI: 10.5061/dryad.cp8t9
title: Data from: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

description: We develop a model based on the Dirichlet-compound multinomial
 distribution (CMD) and Ewens sampling formula to predict the fraction of
 SNP loci that will appear fixed for alternate alleles between two pooled
 samples drawn from the same underlying population. We apply this model to
 next-generation sequencing (NGS) data from Baltic Sea herring recently
 published by (Corander et al., , Molecular Ecology, 2931–2940), and show
 that there are many more fixed loci than expected in the absence of
 genetic structure. However, we show through coalescent simulations that
 the degree of population structure required to explain the fraction of
 alternatively fixed SNPs is extraordinarily high and that the surplus of
 fixed loci is more likely a consequence of limited representation of
 individual gene copies in the pooled samples, than it is of population
 structure. Our analysis signals that the use of NGS on pooled samples to
 identify divergent SNPs warrants caution. With pooled samples, it is hard
 to diagnose when an NGS experiment has gone awry; especially when NGS data
 on pooled samples are of low read depth with a limited number of
 individuals, it may be worthwhile to temper claims of unexpected
 population differentiation from pooled samples, pending verification with
 more reliable methods or stricter adherence to recommended sampling
 designs for pooled sequencing e.g. Futschik & Schlötterer ,
 Genetics, 186, 207; Gautier et al., , Molecular Ecology, 3766–3779).
 Analysis of the data and diagnosis of problems is easier and more reliable
 (and can be less costly) with individually barcoded samples. Consequently,
 for some scenarios, individual barcoding may be preferable to pooling of
 samples.
description: All Data And
 ScriptsThis archive contains
 all the scripts and data used in the analyses for the
 paper.herring-analysis-distrib.tar.gz
DOI: 10.5061/dryad.564
title: Data from: Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences

description: Following (1) the large scale molecular phylogeny of seed plants based on
 plastid rbcL gene sequences (published in 1993 by Chase et al., Ann.
 Missouri Bot. Gard. 80: 528-580) and (2) the 18S nuclear phylogeny of
 flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot.
 Gard. 84: 1-49), we present a phylogenetic analysis of flowering plants
 based upon a second plastid gene, atpB, analyzed separately and in
 combination with rbcL sequences for 357 taxa. Despite some discrepancies,
 the atpB-based phylogenetic trees were highly congruent with those derived
 from the analysis of rbcL and 18S rDNA, and the combination of atpB and
 rbcL DNA sequences (comprising ca. 3000 base pairs) produced increased
 bootstrap support for many major sets of taxa. The angiosperms are divided
 into two major groups: noneudicots with inaperturate or uniaperturate
 pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales,
 and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with
 triaperturate pollen (particularly asterids and rosids). Based on rbcL
 alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum)
 are monophyletic, whereas they form a grade in the atpB trees.
 Ceratophyllum is sister to the rest of angiosperms whith rbcL alone and in
 the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae,
 Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of
 the angiosperms. The phylogenetic information at each codon position and
 the different types of substitutions (observed transitions and
 transversions in the trees versus pairwise comparisons) were examined;
 taking into account their respective consistency and retention indices, we
 demonstrate that third codon positions and transitions are the most useful
 characters in these phylogenetic reconstructions. This study further
 demonstrates that phylogenetic analysis of large matrices is feasible.
description: Savolainen et al Data
 SetatpB/rbcL combined
 matrixsavolainen.nexus