cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1dm02
title: Data from: Identifying the core components of emotional intelligence: evidence from amplitude of low-frequency fluctuations during resting state

description: Emotional intelligence (EI) is a multi-faceted construct consisting of our
 ability to perceive, monitor, regulate and use emotions. Despite much
 attention being paid to the neural substrates of EI, little is known of
 the spontaneous brain activity associated with EI during resting state. We
 used resting-state fMRI to investigate the association between the
 amplitude of low-frequency fluctuations (ALFFs) and EI in a large sample
 of young, healthy adults. We found that EI was significantly associated
 with ALFFs in key nodes of two networks: the social emotional processing
 network (the fusiform gyrus, right superior orbital frontal gyrus, left
 inferior frontal gyrus and left inferior parietal lobule) and the
 cognitive control network (the bilateral pre-SMA, cerebellum and right
 precuneus). These findings suggest that the neural correlates of EI
 involve several brain regions in two crucial networks, which reflect the
 core components of EI: emotion perception and emotional control.
description: Behavioral data (EI
 scores)EI
 score.xlsxT1Raw(1-161)T1Raw.rarFunRaw(1-40)FunRaw(41-80)FunRaw(81-120)FunRaw(121-161)
DOI: 10.5061/dryad.8kq65
title: Data from: Model choice for phylogeographic inference using a large set of models

description: Model-based analyses are common in phylogeographic inference because they
 parameterize processes such as population division, gene flow and
 expansion that are of interest to biologists. Approximate Bayesian
 Computation is a model-based approach that can be customized to any
 empirical system and used to calculate the relative posterior probability
 of several models, provided that suitable models can be identified for
 comparison. The question of how to identify suitable models is explored
 using data from Plethodon idahoensis, a salamander that inhabits the North
 American inland northwest temperate rainforest. First, we conduct an ABC
 analysis using five models suggested by previous research, calculate the
 relative posterior probabilities, and find that a simple model of
 population isolation has the best fit to the data (PP = 0.70). In contrast
 to this subjective choice of models to include in the analysis, we also
 specify models in a more objective manner by simulating prior
 distributions for 143 models that included panmixia, population isolation,
 change in effective population size, migration, and range expansion. We
 then identify a smaller subset of models for comparison by generating an
 expectation of the highest posterior probability that a false model is
 likely to achieve due to chance and calculate the relative posterior
 probabilities of only those models that exceed this expected level. A
 model that parameterized divergence with population expansion and gene
 flow in one direction, offered the best fit to the P. idahoensis data (in
 contrast to an isolation only model from the first analysis). Our
 investigation demonstrates that the determination of which models to
 include in ABC model choice experiments is a vital component of
 model-based phylogeographic analysis.
description: aModelSimsUniformaModelSubsetNormalDistaruncleanbCountSStestbMakeSStestfilebRunSStestcPosteriorPredictiveSimscPPSEuclideanDistanceestats5modelfilemodelScorermsSSposteriorProbabilityPowerAnalysisSimsREADMEREADME.plREADME.pysimulationSortModelspriorabridgedAccessionNumbersAsimplecytbsimpleGAPDsimpleITS1bsimpleRAG1simple
DOI: 10.5061/dryad.rk204
title: Data from: Sequence Capture using PCR-generated Probes (SCPP): a cost-effective method of targeted high-throughput sequencing for non-model organisms

description: Recent advances in high-throughput sequencing library preparation and
 subgenomic enrichment methods have opened new avenues for population
 genetics and phylogenetics of non-model organisms. To multiplex large
 numbers of indexed samples while sequencing predominantly orthologous,
 targeted regions of the genome, we propose modifications to an existing,
 in-solution capture that utilizes PCR products as target probes to enrich
 library pools for the genomic subset of interest. The sequence capture
 using PCR-generated probes (SCPP) protocol requires no specialized
 equipment, is highly flexible, and significantly reduces experimental
 costs for projects where a modest scale of genetic data is optimal (25-100
 genomic loci). Our alterations enable application of this method across a
 wider phylogenetic range of taxa and result in higher capture efficiencies
 and coverage at each locus. Efficient and consistent capture over multiple
 SCPP experiments and at various phylogenetic distances is demonstrated,
 extending the utility of this method to both phylogeographic and
 phylogenomic studies.
description: Passerines_CleanReadsContains the cleaned reads for the Passerine samples.Passerines_Cleanreads.zipDraco_CleanReadsContains the cleaned reads for the Draco samples.Enyalius_CleanReadsContains cleaned reads for the Enyalius samples.AbyssAssembliesContains the ABySS assembly output for each library. Each file has the following naming convention: LIBRARY_KMER_KMERCOV-contigs.faFinalAssembliesContains final assemblies for each sample. These are the outputs of pooling the ABySS assemblies for each sample and performing a local clustering and long-read assembly.ReferencesContains the references recovered for each locus for each sample.Passerines_AlignmentsContains alignments for the Passerine samples.Passerine_Alignments.zipDraco_AlignmentsContains alignments for the Draco samples.Enyalius_AlignmentsContains the alignments for the Enyalius samples.HaplotypesContains 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.sq134
title: Data from: Early post-metamorphic, Carboniferous blastoid reveals the evolution and development of the digestive system in early echinoderms

description: Inferring the development of the earliest echinoderms is critical to
 uncovering the evolutionary assembly of the phylum-level body plan but has
 long proven problematic because early ontogenetic stages are rarely
 preserved as fossils. Here, we use synchrotron tomography to describe a
 new early post-metamorphic blastoid echinoderm from the Carboniferous
 (approx. 323 Ma) of China. The resulting three-dimensional reconstruction
 reveals a U-shaped tubular structure in the fossil interior, which is
 interpreted as the digestive tract. Comparisons with the developing gut of
 modern crinoids demonstrate that crinoids are an imperfect analogue for
 many extinct groups. Furthermore, consideration of our findings in a
 phylogenetic context allows us to reconstruct the evolution and
 development of the digestive system in echinoderms more broadly; there was
 a transition from a straight to a simple curved gut early in the
 phylum's evolution, but additional loops and coils of the digestive
 tract (as seen in crinoids) were not acquired until much later.
description: Data
 S2Interactive
 three-dimensional digital reconstruction of the early post-metamorphic,
 Carboniferous blastoid (NIGP 163236). The reconstruction is in VAXML
 format, compressed in a ZIP archive, and has been downsampled to reduce
 triangle count. To view: unpack the .zip file, install the SPIERS software
 suite (program and documentation available from www.spiers-software.org),
 and double-click the unpacked .vaxml file.Data_S2.zipVideo S1Video showing a three-dimensional digital reconstruction of the early post-metamorphic, Carboniferous blastoid (NIGP 163236).Video_S1.aviData S1Synchrotron tomography scan of the early post-metamorphic, Carboniferous blastoid (NIGP 163236). The slice images are in TIFF format, compressed in a ZIP archive.Data_S1.zip
DOI: 10.5061/dryad.573531d
title: Data from: Opposing patterns of intraspecific and interspecific differentiation in sex chromosomes and autosomes

description: Linking intraspecific and interspecific divergence is an important
 challenge in speciation research. X chromosomes are expected to evolve
 faster than autosomes and disproportionately contribute to reproductive
 barriers, and comparing genetic variation on X and autosomal markers
 within and between species can elucidate evolutionary processes that shape
 genome variation. We performed RADseq on a 16-population transect of two
 closely-related Australian cricket species, Teleogryllus commodus and T.
 oceanicus, covering allopatry and sympatry. This classic study system for
 sexual selection provides a rare exception to Haldane’s rule, as hybrid
 females are sterile. We found no evidence of recent introgression, despite
 the fact that the species co-exist in overlapping habitats in the wild and
 interbreed in the laboratory. Putative X-linked loci showed greater
 differentiation between species compared to autosomal loci. However,
 population differentiation within species was unexpectedly lower on
 X-linked markers than autosomal markers, and relative X-to-autosomal
 genetic diversity was inflated above neutral expectations. Populations of
 both species showed genomic signatures of recent population expansions,
 but these were not strong enough to account for the inflated X/A
 diversity. Instead, most of the excess polymorphism on the X could better
 be explained by sex-biased processes that increase the relative effective
 population size of the X, such as interspecific variation in the strength
 of sexual selection among males. Taken together, the opposing patterns of
 diversity and differentiation at X versus autosomal loci implicate a
 greater role for sex-linked genes in maintaining species boundaries in
 this system.
description: Three_assmb_X1_A1_VCF_filesVariant call format (VCF) files from the three de novo assemblies for the set of autosomal and X-linked variants identified in Teleogryllus commodus and Teleogryllus oceanicus.Three_assmb_VCF_files.replaceVariant call format (VCF) files from the three de novo assemblies for all variants identified in Teleogryllus commodus, Teleogryllus oceanicus and Teleogryllus marini.Three_assmb_VCF_files.tgzscripts to filter autosomal and X-linked SNPsPython scripts to filter autosomal and X-linked SNPs from VCF files.X_A_filtering_scripts.tgz
DOI: 10.5061/dryad.6cm1166
title: Data from: Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

description: The phylogenetic placement of the morphologically simple placozoans is
 crucial to understanding the evolution of complex animal traits. Here, we
 examine the influence of adding new genomes from placozoans to a large
 dataset designed to study the deepest splits in the animal phylogeny.
 Using site-heterogeneous substitution models, we show that it is possible
 to obtain strong support, in both amino acid and reduced-alphabet
 matrices, for either a sister-group relationship between Cnidaria and
 Placozoa, or for Cnidaria and Bilateria as seen in most published work to
 date, depending on the orthologues selected to construct the matrix. We
 demonstrate that a majority of genes show evidence of compositional
 heterogeneity, and that support for the Cnidaria+Bilateria clade can be
 assigned to this source of systematic error. In interpreting these
 results, we caution against a peremptory reading of placozoans as
 secondarily reduced forms of little relevance to broader discussions of
 early animal evolution.
description: Placozoa_cladeA_RNA_readsplacozoa_cladeA_RNA_reads.tar.gzTplx_phylobayes_full_chainsPhyloBayes chain data are available in Zenodo at 10.5281/zenodo.1197272.Tplx_phylogenyThis directory contains files associated with the eLife paper of Laumer et al 2018, "Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias",
DOI: 10.5061/dryad.p7m1v
title: Data from: A comparison of regression methods for model selection in individual-based landscape genetic analysis

description: Anthropogenic migration barriers fragment many populations and limit the
 ability of species to respond to climate-induced biome shifts.
 Conservation actions designed to conserve habitat connectivity and
 mitigate barriers are needed to unite fragmented populations into larger,
 more viable metapopulations, and to allow species to track their climate
 envelope over time. Landscape genetic analysis provides an empirical means
 to infer landscape factors influencing gene flow, and thereby inform such
 conservation actions. However, there are currently many methods available
 for model selection in landscape genetics, and considerable uncertainty as
 to which provide the greatest accuracy in identifying the true landscape
 model influencing gene flow among competing alternative hypotheses. In
 this study, we used population genetic simulations to evaluate the
 performance of seven regression-based model selection methods on a broad
 array of landscapes that varied by the number and type of variables
 contributing to resistance, the magnitude and cohesion of resistance, as
 well as the functional relationship between variables and resistance. We
 also assessed the effect of transformations designed to linearize the
 relationship between genetic and landscape distances. We found that linear
 mixed effects models had the highest accuracy in every way we evaluated
 model performance, however, other methods also performed well in many
 circumstances, particularly when landscape resistance was high and the
 correlation among competing hypotheses was limited. Our results provide
 guidance for which regression-based model selection methods provide the
 most accurate inferences in landscape genetic analysis and thereby best
 inform connectivity conservation actions.
description: Inputs and code for
 landscape genetic model selection methods comparisonSimulated landscapes,
 distance matrices, R code, and CDPOP simulation outputs are included in
 the zip file.Shirk et al 2017b
 MER.zip
DOI: 10.5061/dryad.339k00b
title: Data from: Inferring roles in defense from metabolic allocation of rice diterpenoids

description: Among their responses to microbial infection, plants deploy an arsenal of
 antibiotic natural products. While these historically have been identified
 on the basis of their antibiotic activity in vitro, this leaves open the
 question of their relevance to defense in planta. The vast majority of
 such natural products from the important crop plant rice (Oryza sativa)
 are diterpenoids whose biosynthesis proceeds via either ent- or syncopalyl
 diphosphate (CPP) intermediates, and which were isolated on the basis of
 their antibiotic activity against the fungal blast pathogen Magnaporthe
 oryzae. However, rice plants in which the gene for the syn-CPP synthase
 Os-CPS4 is knocked-out do not exhibit increased susceptibility to M.
 oryzae. Here it is further shown that knocking-out or knocking-down
 Os-CPS4 actually decreases susceptibility to the bacterial leaf blight
 pathogen Xanthomonas oryzae. On the other hand, knocking-out or
 knocking-down the gene for the ent-CPP synthase Os-CPS2 is found to
 increase susceptibility to both M. oryzae and X. oryzae, while
 over-expressing Os-CPS2 decreases susceptibility to both. Despite the
 secretion of diterpenoids dependent on Os-CPS2 or Os-CPS4 from roots
 neither knock-out exhibited significant changes in the composition of
 their rhizosphere bacterial communities. Nevertheless, rice plants
 allocate substantial metabolic resources towards syn- as well as ent-CPP
 derived diterpenoids upon infection/induction. On the basis of this
 observation further investigation was carried out, revealing that Os-CPS4
 plays a role in fungal non-host disease resistance. Thus, as exemplified
 here with rice diterpenoids, examination of metabolic allocation provides
 important clues into physiological function.
description: Raw Illumina
 data1st Illumina data out of
 6SAM1-30_S1_L001_R1_001.fastq.gzSAM1-30_S1_L001_R2_001.fastq2nd Illumina dataset out of 6SAM31-54_S2_L001_R1_001.fastq3rd Illumina dataset out of 6SAM31-54_S2_L001_R2_001.fastq4th Illumina dataset out of 6Sam1-46_S4_L001_R1_001.fastq5th Illumina dataset out of 6Sam1-46_S4_L001_R2_001.fastq6th Illumina dataset out of 6full_dataset_mapping_fileMapping file for all samplesfiltered_otu_tableOTU table was filtered to eliminate reads binning to mitochondria and chloroplasts, and samples with less than 615 reads.rep_phyloPhylogenetic tree produced in Qiime for downstream analysesotus_alignedAlignment for phylogenetic tree and downstream analyses
DOI: 10.5061/dryad.hf492bp
title: Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills

description: While many conifers produce annually variable seed crops, serotinous
 species (which hold seeds in cones for multiple years) represent unusually
 stable food resources for seed predators. Such stability is conducive to
 residency and potentially population divergence of consumers as
 exemplified by the Cassia crossbill (Loxia sinesciuris) in North America.
 We used genotyping-by-sequencing to test whether three Mediterranean
 subspecies of common crossbills (L. curvirostra) associated with the
 serotinous Aleppo pine (Pinus halepensis) were more genetically distinct
 than European crossbills associated with non-serotinous conifers. We
 assembled a Cassia crossbill draft genome as a reference for mapping GBS
 reads, and as a first step towards a more contiguous genome assembly. We
 found clear patterns of genetic divergence for each of the P.
 halepensis-associated subspecies. Geographic isolation, as promoted by
 resource stability and residency, is associated with genetic divergence of
 two of these subspecies. However, geographic isolation cannot account for
 divergence of L. c. hispana. Instead, resource stability likely
 contributed to divergence by reducing dispersal and increasing resource
 competition that may limit breeding by immigrants. In contrast, we found
 no differentiation among common crossbills associated with less stable
 resources, and only slight differentiation between common crossbills and
 parrot crossbills (L. pytyopsittacus). The substantial morphological
 divergence between common and parrot crossbills has likely originated or
 been maintained by selection despite gene flow generated by spatiotemporal
 resource fluctuation. Our results indicate that phenological as well as
 morphological characteristics of conifers have influenced crossbill
 diversification, and suggest a possible link between resource stability
 and population divergence.
description: euro_xbill_gprobsMatrix of genotype probabilities for all individuals included in the paper. File compressed with gzip.L_sinesciurus_gapcloser.faLoxia sinesciurus first draft genome assembly. Contains 64453 scaffolds and contigs. File compressed with gzip.palearctic_crossbill_fastqsDirectory containing .fastq files for all individuals analyzed in the paper. This includes 114 Loxia curvirostra (including representatives of each of 3 sedentary subspecies), 6 L. pytyopsittacus, and 3 L. leucoptera (which were used as an outgroup in phylogenetic analyses. This directory has been compressed as a tar archive. To uncompress from the command line:$ tar -zxvf palearctic_crossbill_fastqs.tgz
DOI: 10.5061/dryad.4c57d0f
title: Data from: A flicker of hope: genomic data distinguish Northern Flicker taxa despite low levels of divergence

description: Next-generation sequencing technologies are increasingly being employed to
 explore patterns of genomic variation in avian taxa previously
 characterized using morphology and/or traditional genetic markers. The
 hybridization dynamics of the Northern Flicker complex have received
 considerable attention, primarily due to the conspicuous plumage
 differences among these birds and the geographically extensive hybrid zone
 between the Red-shafted (Colaptes auratus cafer) and Yellow-shafted
 (Colaptes auratus auratus) flickers in the Great Plains region of North
 America. However, no traditional molecular techniques have been able to
 differentiate these 2 morphologically well-defined taxa from one another,
 or conclusively from the closely related Gilded Flicker (Colaptes
 chrysoides). Here, we use a next-generation sequencing approach to assess
 the genetic diversity and evolutionary history of these 3 taxa. We confirm
 the overall low levels of differentiation found using traditional
 molecular markers, but are able to distinguish between the 3 taxa for the
 first time, using a dataset of thousands of SNP loci distributed across
 the genome. Through demographic modeling and phylogenetic reconstructions,
 we find that Red-shafted and Yellow-shafted flickers are likely sister
 taxa, and that their divergence from the Gilded Flicker was comparatively
 older. The low level of divergence and lack of fixed differences in our
 dataset between Red-shafted and Yellow-shafted flickers, in particular,
 suggests whole-genome re-sequencing may be necessary to assess the
 dynamics of their hybridization and identify the genetic basis of their
 striking differences in plumage.
description: Sample
 informationSample ID with taxa
 designation and geographic locality. See Appendix Table 2 for detailed
 information on each sample.sample_info.txtDe novo STACKS output (all SNPs)STACKS output of all SNPs from the de novo assembly in VCF formatdenovo_output_allSNPs.vcfDe novo STACKS output (first SNP per STACK)STACKS output of the first SNP per STACK from the de novo assembly in VCF formatdenovo_output_firstSNP.vcfReference-based STACKS output (all SNPs)STACKS output of all SNPs from the reference-based assembly in VCF formatrefmap_output_allSNPs.vcfReference-based STACKS output (first SNP per STACK)STACKS output of the first SNP per STACK from the reference-based assembly in VCF formatrefmap_output_firstSNP.vcfIndex 2 barcodesBarcode file to demultiplex Index 2 in STACKSindex2_barcode.txtIndex 12 barcodesBarcode file to demultiplex Index 12 in STACKSindex12_barcode.txtIndex 2 sequence fileSequence data for 40 individuals of 3 flicker taxa in fastq formatindex2_CGATGT_R1.fastq.gzIndex 12 sequence fileSequence data for 40 individuals of 3 flicker taxa in fastq formatindex12_CTTGTA_R1.fastq.gz
DOI: 10.5061/dryad.sm107
title: Data from: A collection of intrinsic disorder characterizations from eukaryotic proteomes

description: Intrinsically disordered proteins and protein regions lack a stable
 three-dimensional structure under physiological conditions. Several
 proteomic investigations of intrinsic disorder have been performed to date
 and have found disorder to be prevalent in eukaryotic proteomes. Here we
 present descriptive statistics of intrinsic disorder features for ten
 model eukaryotic proteomes that have been calculated from computational
 disorder prediction algorithms. The data descriptor also provides
 consensus disorder annotations as well as additional physical parameters
 relevant to protein disorder, and further provides protein existence
 information for all proteins included in our analysis. The complete
 datasets can be downloaded freely, and it is envisaged that they will be
 updated periodically with new proteomes and protein disorder prediction
 algorithms. These datasets will be especially useful for assessing protein
 disorder, and conducting novel analyses that advance our understanding of
 intrinsic disorder and protein structure.
description: A collection of
 intrinsic disorder characterizations from eukaryotic
 proteomesThis is a sqlite3 file
 containing intrinsic disorder characterizations from ten eukaryotic
 proteomes. For detailed information regarding the content and the database
 schema, please refer to Vincent and Schnell, 2016.Vincent_and_Schnell_2016.db.zip