cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.443t4m1q
title: Data from: Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

description: Diet analysis is a prerequisite to fully understand the biology of a
 species and the functioning of ecosystems. For carnivores, traditional
 diet analyses mostly rely upon the morphological identification of
 undigested remains in the feces. Here, we developed a methodology for
 carnivore diet analyses based on next generation sequencing. We applied
 this approach to the analysis of the vertebrate component of leopard cat
 diet in two ecologically distinct regions in northern Pakistan. Despite
 being a relatively common species with a wide distribution in Asia, little
 is known about this elusive predator. We analyzed a total of 38 leopard
 cat feces. After a classical DNA extraction, the DNA extracts were
 amplified using primers for vertebrates targeting about 100 bp of the
 mitochondrial 12S rRNA gene, with and without a blocking oligonucleotide
 specific to the predator sequence. The amplification products were then
 sequenced on a next generation sequencer. We identified a total of 18 prey
 taxa, including eight mammals, eight birds, one amphibian, and one fish.
 In general, our results confirmed that the leopard cat has a very eclectic
 diet, and feeds mainly on rodents, and particularly on the Muridae family.
 The DNA-based approach we propose here represents a valuable complement to
 current conventional methods. It can be applied to other carnivore species
 with only a slight adjustment relating to the design of the blocking
 oligonucleotide. It is robust, simple to implement, and allows the
 possibility of very large-scale analyses.
description: pb_bk_sequence_datapb_bk_filtered_dataFiltered data obtained with blocking oligonucleotide.pb_sequence_dataFile containing all unique sequences obtained with blocking oligonucleotide.pb_filtered_dataFiltered data obtained with blocking oligonucleotide.
DOI: 10.5061/dryad.275kv81m
title: Data from: Different gene families in Arabidopsis thaliana transposed in different epochs and at different frequencies throughout the rosids

description: Certain types of gene families, such as those encoding most families of
 transcription factors, maintain their chromosomal syntenic positions
 throughout Angiosperm evolutionary time. Other, non-syntenic gene families
 are prone to deletion, tandem duplication, and transposition. Here we
 describe the chromosomal positional history of all genes in Arabidopsis
 thaliana (A. thaliana) throughout the rosid superorder. We introduce a
 public database where researchers can look up the positional history of
 their favorite A. thaliana gene or gene family. Finally, we show that
 specific gene families transposed at specific points in evolutionary time,
 particularly after whole-genome duplication events in the Brassicales, and
 suggest that genes in mobile gene families are under different selection
 pressure than syntenic genes.
description: Arabidopsis Positional
 History DatasetInformation includes
 chromosome start/stop, strand, duplicate state (parent=P, duplicate=AT
 number, or interrupter=I), TAIR9 gene description, the chromosomal
 position for each outgroup (-, S, G, FN, FB, F), the numerical synteny
 value for each chromosomal position (1=S except for grape, where 2=S;
 0.2=FB or FN, 0.1=G or -, and 0=F), total synteny value (the average of
 all synteny values for all outgroups), whether or not the gene had any
 exons (TAIR9 data), TAIR8 chromosome start/stop, functional gene space,
 the difference between gene space and functional gene space. Functional
 gene space, CNS data, GO terms, and homeolog data is from Version 2 as
 annotated by S. Subramaniam in this lab, unpublished. The CNS data was
 originally from TAIR8 but has been merged with TAIR9. Following this are
 TAIR9 GEvo link, and best hit data in A. lyrata and poplar for all
 transposed genes.Supplemental Dataset
 1.xls
DOI: 10.5061/dryad.11vq033v
title: Data from: Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life

description: The first analyses of gene sequence data indicated that the eukaryotic
 tree of life consisted of a long stem of microbial groups ‘topped’ by a
 crown containing plants, animals, and fungi and their microbial relatives.
 While more recent multigene concatenated analyses have refined the
 relationships among the many branches of eukaryotes, the root of the
 eukaryotic tree of life has remained elusive. Inferring the root of extant
 eukaryotes is challenging because of the age of the group (∼1.7-2.1
 billion years old), tremendous heterogeneity in rates of evolution among
 lineages, and lack of obvious outgroups for many genes. Here we
 reconstruct a rooted phylogeny of extant eukaryotes based on minimizing
 the number of duplications and losses among a collection of gene trees.
 This approach does not require outgroup sequences or assumptions of
 orthology among sequences. We also explore the impact of taxon and gene
 sampling, and assess support for alternative hypotheses for the root.
 Using 20 gene trees from 84 diverse eukaryotic lineages, this approach
 recovers robust eukaryotic clades and reveals evidence for a eukaryotic
 root that lies between the Opisthokonta (animals, fungi and their
 microbial relatives) and all remaining eukaryotes.
description: DryadEukaryoteData.tar
DOI: 10.5061/dryad.5r2f1n05
title: Data from: Ecological drift and local exposures drive gastrointestinal bacterial community differences among Galápagos iguana populations

description: Diet strongly influences the intestinal microbial communities through
 species sorting. Alternatively, these communicates may differ because of
 chance variation in local microbial exposures or species losses among
 allopatric host populations (i.e. ecological drift). We investigated how
 these forces shape enteric communities of Galápagos marine and land
 iguanas. Geographically proximate populations shared more similar
 communities within a host ecotype, suggesting a role for ecological drift
 during host colonization of the islands. Additionally, evidence of taxa
 sharing between proximate heterospecific host populations suggests that
 contemporary local exposures also influence the gut community assembly.
 While selective forces such as host-bacterial interactions or dietary
 differences are dominant drivers of intestinal community differences among
 hosts, historical and contemporary processes of ecological drift may lead
 to differences in bacterial composition within a host species. Whether
 such differences in community structure translate into geographic
 variation in benefits derived from these intimate microbial communities
 remains to be explored.
description: Land Iguana
 SequencesContains bacterial
 community 454 pyrosequencing reads obtained from fecal samples of land
 iguanas (LI) living on Isla Fernandina (F), Isla Plaza Sur (P) and Isla
 Santa Fe (S) in the Galápagos Islands, Ecuador.Marine Iguana
 SequencesContains bacterial
 community 454 pyrosequencing reads obtained from fecal samples of marine
 iguanas (MI) living on Isla Fernandina (F), Isla Plaza Sur (P), Isla Santa
 Fe (S), and two sites on Isla San Cristobal - La Lobería (L) and Punta
 Carola (C) in the Galápagos Islands, Ecuador.
DOI: 10.5281/zenodo.14934024
title: Epigenetic characterization of pseudogenes across human tissues

description: We provide a comprehensive table characterizing promoter activity of GENCODE v29 transcripts across tissues (Table S2), as well as functional properties of regions upstream of the TSS (Table S3). Mappings between pseudogenes and their parent protein-coding genes are provided in Table S4 and were generated using PseudoPipe (Zhang et al. 2006).
DOI: 10.5281/zenodo.14934023
title: Epigenetic characterization of pseudogenes across human tissues

description: We provide a comprehensive table characterizing promoter activity of GENCODE v29 transcripts across tissues (Table S2), as well as functional properties of regions upstream of the TSS (Table S3). Mappings between pseudogenes and their parent protein-coding genes are provided in Table S4 and were generated using PseudoPipe (Zhang et al. 2006).
DOI: 10.5061/dryad.8635cs4h
title: Data from: Development of a 44K SNP Assay focussing on the analysis of a varroa specific defense behavior in honey bees (Apis mellifera carnica)

description: Honey bees are exposed to a number of damaging pathogens and parasites.
 The most destructive among them is maybe Varroa destructor. A promising
 approach to prevent its spread is to breed for Varroa tolerant honey bees.
 A trait which has been shown to provide significant resistance against the
 Varroa mite is hygienic behavior, a behavioral response of honey bee
 workers to brood diseases in general. This study reports the development
 of a 44K SNP-assay, specifically designed for the analysis of hygienic
 behavior of individual worker bees (Apis mellifera carnica) directed
 against Varroa destructor. Initially, 70,000 SNPs published by the Honey
 Bee Genome Project were validated for their suitability in the analysis of
 Varroa tolerance. This was achieved by genotyping of pooled DNA-samples of
 trait bearers and two trait-negative controls. Roughly 36,000 of these
 validated SNPs and another 8,000 SNPs not validated in this study were
 selected for the construction of a SNP-assay. This assay will be employed
 to analyze individualized DNA-samples in order to identify quantitative
 trait loci (QTL) involved in the control of the investigated trait.
 However, this assay is not just suitable to study Varroa tolerance, it is
 as well applicable to analyze any other trait in honey bees. In addition,
 because of its high density, this assay provides access into genomic
 selection with respect to several traits considered in honey bee breeding.
 It will become publicly available via AROS Applied Biotechnology AS,
 Aarhus, Denmark before the end of the year 2011.
description: SNP_Info_HoneyBeeSNPAssay.xlsxThe columns in the file "SNP_Info_HoneyBeeSNPAssay.xlsx" are as follows: -lsid: local SNP ID referring to a file (amel_v3_asm_snps.dbsnps.gz) published by the Honey Bee Genome Project (http://www.hgsc.bcm.tmc.edu/project-species-i-Apis%20mellifera.hgsc?page Location=Apis%20mellifera), which is accessible via the URL: "http://www.hgsc.bcm.tmc.edu/ftp-archive/Amellifera/snp/"; -linkage group: Amel assembly version 3.0 linkage group 1~16; -Cooridnate: base position in linkage group containing polymorphism; -allele: polymorphism in format A/G, consensus base on left; -left flanking sequence: linkage group left flanking sequence (250 bases); -right flanking sequence: linkage group right flanking sequence (250 bases)
DOI: 10.7266/sev5za12
title: Online survey of Teachers/Instructors using OCEAN Kids
DOI: 10.5061/dryad.54nq349m
title: Data from: Concerted versus independent evolution and the search for multiple refugia: comparative phylogeography of four forest beetles

description: Phylogeographic structure and its underlying causes are not necessarily
 shared among community members, with important implications for using
 individual organisms as indicators for ecosystem evolution, such as the
 identification of forest refugia. We used mitochondrial DNA (COI),
 Bayesian coalescent ancestral state reconstruction (implemented in BEAST)
 and ecological niche models (ENMs) to construct geo-spatial histories for
 four co-distributed New Zealand forest beetles (Leiodidae, Nitidulidae,
 Staphylinidae, Zopheridae) to examine the extent to which they have
 tracked environmental changes together through time. Hindcast ENMs
 identified potential forest refugia during the Last Glacial Maximum, while
 ancestral state reconstruction identified key geographic connections for
 each species, facilitating direct comparison of dispersal patterns
 supported by the data and the time frame in which they occurred.
 Well-supported geographic state transitions for each species were mostly
 between neighboring regions, favoring a historical scenario of stepping
 stone colonization of newly-suitable habitat rather than long distance
 dispersal. No geographic state transitions were shared by all four
 species, but three shared multiple projected South Island refugia and
 recent dispersal from the southernmost refugium. In contrast, strongly
 supported dispersal patterns in the refugia-rich northern South Island
 suggest more individualistic responses to environmental change in these
 ecologically similar forest species.
description: Agyrtodes_maxentAgyrtodes labralis (Leiodidae) localities used for ecological niche modeling in Maxent. Localities are in New Zealand Map Grid (NZMG) format.Brachynopus_maxentBrachynopus scutellaris (Staphylinidae) localities used for ecological niche modeling in Maxent. Localities are in New Zealand Map Grid (NZMG) format.Epistranus_maxentEpistranus lawsoni (Zopheridae) localities used for ecological niche modeling in Maxent. Localities are in New Zealand Map Grid (NZMG) format.Hisparonia_maxentHisparonia hystrix (Nitidulidae) localities used for ecological niche modeling in Maxent. Localities are in New Zealand Map Grid (NZMG) format.GeoAgyrtodesAgyrtodes labralis (Leiodidae) BEAST profile incorporating ancestral state reconstruction with BSSVS.GeoBrachynopusBrachynopus scutellaris (Staphylinidae) BEAST profile incorporating ancestral state reconstruction with BSSVS.GeoEpistranusEpistranus lawsoni (Zopheridae) BEAST profile incorporating ancestral state reconstruction with BSSVS.GeoHisparoniaHisparonia hystrix (Nitidulidae) BEAST profile incorporating ancestral state reconstruction with BSSVS.
DOI: 10.5061/dryad.f0gg64v5
title: Data from: Genetic architecture and adaptive significance of the selfing syndrome in Capsella

description: The transition from outcrossing to predominant self-fertilization is one
 of the most common evolutionary transitions in flowering plants. This
 shift is often accompanied by a suite of changes in floral and
 reproductive characters termed the selfing syndrome. Here, we characterize
 the genetic architecture and evolutionary forces underlying evolution of
 the selfing syndrome in Capsella rubella following its recent divergence
 from the outcrossing ancestor Capsella grandiflora. We conduct genotyping
 by multiplexed shotgun sequencing and map floral and reproductive traits
 in a large (N=550) F2 population. Our results suggest that in contrast to
 previous studies of the selfing syndrome, changes at a few loci, some with
 major effects, have shaped the evolution of the selfing syndrome in
 Capsella. The directionality of QTL effects as well as population genetic
 patterns of polymorphism and divergence at 318 loci are consistent with a
 history of directional selection on the selfing syndrome. Our study
 provides an important step towards characterizing the genetic basis and
 evolutionary forces underlying the evolution of the selfing syndrome in a
 genetically accessible model system.
description: F2
 dataThis data file contains
 phenotype, genotype and linkage data for 550 F2 individuals resulting from
 an interspecific cross between C. grandiflora and C. rubella. The
 individuals were phenotyped in the greenhouse.Rqtlfile.csvCrCg_phenotypesThis file contains phenotype data for 16 samples of Capsella rubella and Capsella grandiflora. Phenotype designations are as in the README file for the F2 data file in this submission.Ancestry probabilities for scaffold 7This folder contains ancestry probabilities from MSG v0.3 for markers on scaffold 7. Each file contains ancestry probabilities for 7075 markers for each of 550 F2 individuals. File par1_sc7.tsv contains probabilities for being homozygous C. rubella, par12_sc7.tsv contains probabilities for being heterozygous and par2_sc7.tsv contains probabilities for being homozygous C. grandiflora. Individual order is as in the F2 data file, and these ancestry probabilities were used to fine-map self-compatibility.Ancestry_probs_scaffold7.zip
DOI: 10.5061/dryad.100jc764
title: Data from: Phylogeny and biogeography of the core babblers (Aves: Timaliidae)

description: The avian family Timaliidae is a species rich and morphologically diverse
 component of African and Asian tropical forests. The morphological
 diversity within the family has attracted interest from ecologists and
 evolutionary biologists, but systematists have long suspected that this
 diversity might also mislead taxonomy, and recent molecular phylogenetic
 work has supported this hypothesis. We produced and analyzed a dataset of
 six genes and almost 300 individuals to assess the evolutionary history of
 the family. Although phylogenetic analysis required extensive adjustment
 of program settings, we ultimately produced a well-resolved phylogeny for
 the family. The resulting phylogeny provided strong support for major
 subclades within the family but extensive paraphyly of genera. Only three
 genera represented by more than three species were monophyletic.
 Biogeographic reconstruction indicated a mainland Asian origin for the
 family and most major clades. Colonization of Africa, Sundaland, and the
 Philippines occurred relatively late in the family’s history and was
 mostly unidirectional. Several putative babbler genera, such as Robsonius,
 Malia, Leonardina, and Micromacronus are only distantly related to the
 Timaliidae.
description: TreeBASE
 S11986Nexus file of the final
 6-gene data set.Supplementary
 CaptionsCaptions for
 supplementary figures.Moyle et al, Supplementary
 Captions.docxSupp Fig
 1Average Standard
 Deviation of Split Frequencies plot.Moyle et al, Supp Fig
 1.epsSupp Fig
 2Consensus tree from
 Bayesian analysis of the mtDNA alone.Moyle et al, Supp Fig
 2.epsSupp Fig
 3Consensus tree from
 Bayesian analysis of the MUSK intron alone.Moyle et al, Supp Fig
 3.epsSupp Fig
 4Consensus tree from
 Bayesian analysis of the Fibrinogen 5 intron alone.Moyle et al, Supp Fig
 4.epsSupp Fig
 5Consensus tree from
 Bayesian analysis of the TGF5 intron alone.Moyle et al, Supp Fig
 5.eps
DOI: 10.5061/dryad.3mt58823
title: Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.

description: The systematics and speciation literature is rich with discussion relating
 to the potential for gene tree/species tree discordance. Numerous
 mechanisms have been proposed to generate discordance, including
 differential selection, long-branch attraction, gene duplication, genetic
 introgression, and/or incomplete lineage sorting. For speciose clades in
 which divergence has occurred recently and rapidly, recovering the true
 species tree can be particularly problematic due to incomplete lineage
 sorting. Unfortunately, the availability of multi-locus or “phylogenomic”
 data sets does not simply solve the problem, particularly when the data
 are analyzed with standard concatenation techniques. In our study, we
 conduct a phylogenetic study for a nearly complete species sample of the
 dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus,
 Microcebus) have been intensively studied over the past decade for reasons
 relating to their high level of cryptic species diversity, and although
 there has been emerging consensus regarding the evolutionary diversity
 contained within the genus, there is no agreement as to the inter-specific
 relationships within the group. We attempt to resolve cheirogaleid
 phylogeny, focusing especially on the mouse lemurs, by employing a large
 multi-locus data set. We compare the results of Bayesian concordance
 methods with those of standard gene concatenation, finding that though
 concatenation yields the strongest results as measured by statistical
 support, these results are found to be highly misleading. By employing an
 approach where individual alleles are treated as OTUs, we show that
 phylogenetic results are substantially influenced by the selection of
 alleles in the concatenation process.
description: Individual Gene
 TreesBayesian majority-rule
 consensus trees reconstructed for the 12 individual nuclear loci and the
 concatenated mitochondrial loci. Trees are presented as phylograms with
 branch lengths representing the average number of substitutions per site.
 Numbers on branches represent posterior probabilities.Individual Gene
 AlignmentsA compressed file
 containing the 12 nuclear and one mitochondrial data sets. Each gene is
 aligned as used in the original study and is presented in NEXUS
 format.Pruning
 exampleThis is the R script
 used to prune alleles from the sequence data sets and the corresponding
 tips in the posterior distribution of trees. Example files for one gene
 are included along with a "Read me" file with a few more
 snippets of information.
DOI: 10.5061/dryad.4f64ck01
title: Data from: Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

description: Phylogeographic inferences about gene flow are strengthened through
 comparison of co-distributed taxa, but also depend on adequate genomic
 sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid
 and inexpensive source of multilocus allele frequency data for making
 genomically robust inferences. Every AFLP study initially generates
 markers with a range of locus-specific genotyping error rates and applies
 criteria to select a subset for analysis. However, there has been very
 little empirical evaluation of the best tradeoff between culling all but
 the lowest-error loci to minimize overall genotyping error versus the
 potential for increasing population genetic signal by retaining more loci.
 Here, we used AFLPs to compare population structure in co-distributed
 broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris)
 oyster species. Using existing methods for almost entirely automated
 marker selection and scoring, genotyping error tradeoffs were evaluated by
 comparing results across a nested series of datasets with mean mismatch
 errors of 0, 1, 2, 3, 4 and &gt;4%. Artifactual population structure
 was diagnosed in high-error datasets and we assessed the low-error point
 at which expected population substructure signal was lost. In both species
 we identified substructure patterns deemed to be inaccurate at error rates
 {less than or equal to}2% and &gt;4%. In the species comparison, the
 optimum datasets showed higher gene flow for the brooding oyster with more
 oceanic salinity tolerances. AFLP tradeoffs may differ among studies, but
 our results suggest that important signal may be lost in the pursuit of
 'acceptable' error levels and our procedures provide a general
 method for empirically exploring these tradeoffs.
description: cv_0error_genotype_matrixThis is the AFLP genotype table of 0 error dataset in Crassostrea virginica.cv_1error_genotype_matrixThis is the AFLP genotype table of 1% error dataset in Crassostrea virginica.cv_2error_genotype_matrixThis is the AFLP genotype table of 2% error dataset in Crassostrea virginica.cv_3error_genotype_matrixThis is the AFLP genotype table of 3% error dataset in Crassostrea virginicacv_4error_genotype_matrixThis is the AFLP genotype table of 4% error dataset in Crassostrea virginicacv_matrixBThis is the AFLP genotype table of matrixB dataset in Crassostrea virginicaoe_0error_genotype_matrixThis is the AFLP genotype table of 0 error dataset in Ostrea equestris.oe_1error_genotype_matrixThis is the AFLP genotype table of 1% error dataset in Ostrea equestris.oe_2error_genotype_matrixThis is the AFLP genotype table of 2% error dataset in Ostrea equestris.oe_3error_genotype_matrixThis is the AFLP genotype table of 3% error dataset in Ostrea equestris.oe_4error_genotype_matrixThis is the AFLP genotype table of 4% error dataset in Ostrea equestris.oe_matrixBThis is the AFLP genotype table of matrixB dataset in Ostrea equestris.