cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.24cb8
title: Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

description: Molluscs (snails, octopuses, clams, and relatives) have great body plan
 disparity, and among animals only arthropods surpass them in species
 number. This diversity has made Mollusca one of the best-studied groups of
 animals, yet their evolutionary relationships remain poorly resolved. Open
 questions have important implications for the origin of Mollusca and
 morphological evolution within the group. These include whether the
 shell-less vermiform aplacophoran molluscs diverged prior to the origin of
 the shelled molluscs (Conchifera), or secondarily lost their shell.
 Monoplacophora were not included in molecular studies until recently ,
 when it was proposed that they constitute a clade with chitons named
 Serialia, reflecting the serial repetition of body organs in both groups.
 Attempts to understand the early evolution of molluscs become even more
 complex when considering the large diversity of Cambrian fossils. These
 can have multiple dorsal shell plates and sclerites, or be shell-less but
 with a typical molluscan radula and serially repeated gills. In order to
 better resolve the relationships among molluscs we generated transcriptome
 data for 15 molluscs that, in combination with existing data, represent
 for the first time all major molluscan groups. We analysed multiple data
 sets containing up to 216,402 sites and 1185 gene regions using multiple
 models and methods. Our results support a clade Aculifera, containing the
 three molluscan groups with spicules but without true shells, as well as
 the monophyly of Conchifera—the shelled molluscs. Monoplacophora are not
 the sister group to other Conchifera, but constitute the sister group to
 the highly modified cephalopods. Strong support is found for a clade
 comprised of Scaphopoda (tusk shells), Gastropoda, and Bivalvia, with most
 analyses placing Scaphopoda and Gastropoda as sister groups. This
 well-resolved tree will constitute a framework for further studies in
 mollusc evolution, development and anatomy.
description: Phylogenetic matrices
 and treesContained within this
 archive are the phylogenetic matrices and trees generated for this study.
 NOTE: Please use revised_phylo.tar.gz, an updated version of the data file
 that was added on 2012-11-15.phylo.tar.gzrevised_phylo.tar.gzAssembled data generated for studyThis archive contains the transcriptome sequences generated for this study.assembled_data.tar.gz
DOI: 10.5061/dryad.7q37g6b
title: Data from: All-optical recording and stimulation of retinal neurons in vivo in retinal degeneration mice

description: Here we demonstrate the application of a method that could accelerate the
 development of novel therapies by allowing direct and repeatable
 visualization of cellular function in the living eye, to study loss of
 vision in animal models of retinal disease, as well as evaluate the time
 course of retinal function following therapeutic intervention. We use
 high-resolution adaptive optics scanning light ophthalmoscopy to image
 fluorescence from the calcium sensor GCaMP6s. In mice with photoreceptor
 degeneration (rd10), we measured restored visual responses in ganglion
 cell layer neurons expressing the red-shifted channelrhodopsin ChrimsonR
 over a six-week period following significant loss of visual responses.
 Combining a fluorescent calcium sensor, a channelrhodopsin, and adaptive
 optics enables all-optical stimulation and recording of retinal neurons in
 the living eye. Because the retina is an accessible portal to the central
 nervous system, our method also provides a novel non-invasive method of
 dissecting neuronal processing in the brain.
description: DataArchiveSee Readme
DOI: 10.15139/s3/qbgi9m
title: Data Management and Sharing Plan for: 3D human neurocircuits to determine the role of microglia in AUD and Alzheimer's neuronal pathology

description: The Data Management and Sharing Plan describes the scientific data to be generated and/or used in the research and outlines a strategy for managing and sharing project data.
description: Data Management and Sharing Plan
DOI: 10.5061/dryad.fg700
title: Data from: Out of the dark: 350 million years of conservatism and evolution in diel activity patterns in vertebrates

description: Many animals are active only during a particular time (e.g. day vs.
 night), a partitioning that may have important consequences for species
 co-existence. An open question is the extent to which this diel activity
 niche is evolutionarily conserved or labile. Here, we analyze diel
 activity data across a phylogeny of 1914 tetrapod species. We find strong
 phylogenetic signal, showing that closely related species tend to share
 similar activity patterns. Ancestral reconstructions show that
 nocturnality was the most likely ancestral diel activity pattern for
 tetrapods and many major clades within it (e.g. amphibians, mammals).
 Remarkably, nocturnal activity appears to have been maintained
 continuously in some lineages for ~350 million years. Thus, we show that
 traits involved in local-scale resource partitioning can be conserved over
 strikingly deep evolutionary time scales. We also demonstrate a
 potentially important (but often overlooked) metric of niche conservatism.
 Finally, we show that diurnal lineages appear to have faster speciation
 and diversification rates than nocturnal lineages, which may explain why
 there are presently more diurnal tetrapod species even though diurnality
 appears to have evolved more recently. Overall, our results may have
 implications for studies of community ecology, species richness, and the
 evolution of diet and communication systems.
description: Supplementary
 TablesSupplementary_File_LegendsSupp_File_Legends.docxSupp_File_1_Ericson1914Supp_File_2_Hackett1914Supp_File_3_Ericson1824Supp_File_4_Hackett1824Supp_File_5_data_and_referencesSupp_File_6_Geiger_Caper_scriptSupp_File_7_HiSSE_scriptSupp_File_8_corHMM_scriptSupp_File_9_phytools_scriptSupp_File_10_appendix1914Supp_File_11_diu1914Supp_File_12_noc1914Supp_File_13_fourstate1914Supp_Figure_LegendsFigure S1Figure S2Figure S3Figure S4Figure S5Figure S6Figure S7Figure S8Figure S9Figure S10Figure S11Figure S12Figure S13Figure S14Figure S15Figure S16Figure S17Figure S18Figure S19Figure S20Figure S21Figure S22Figure S23Figure S24
DOI: 10.5061/dryad.gs0gv
title: Data from: Moorean and Tahitian Partula tree snail survival after a mass extinction: new genomic insights using museum specimens

description: Natural history museum collections provide a biodiversity window into the
 past and are of particular importance to the study of extinction-impacted
 clades such as the Pacific Island tree snail family Partulidae. Deliberate
 introduction of the predatory rosy wolf snail Euglandina rosea in the late
 20th century led to the extinction/extirpation of 55/61 Society Island
 Partulidae species. In this study, we phylogenomically investigated the
 inter-relationships of the three surviving Society Island valley Partula
 species: P. taeniata (Moorea), P. clara and P. hyalina (Tahiti). All three
 formed a distinct clade in earlier mitochondrial phylogenies. Using Next
 Generation Sequencing (NGS) double digested Restriction Associated DNA
 sequencing (ddRADseq), we found that 46-year-old lyophilized museum
 specimens produced similar numbers of reads, sequencing depth, and loci as
 10-year old ethanol-preserved collections. Phylogenomic trees indicated
 that Tahitian P. clara and P. hyalina are the result of a single founding
 lineage from Moorea, contrasting previous mitochondrial results and
 clarifying the enigmatic taxonomic status of P. c. incrassa. Our study
 highlights the utility and viability of NGS techniques for museum
 specimens and their increased resolution of evolutionary patterns.
 Sampling will be expanded to include the remaining Society Island partulid
 taxa to further explore the evolutionary history of this radiation.
description: Haponskietal_partula_pyRADparameter_files.zip archive contains all pyRAD parameter files used to generate the 85, 90, 95% similarity threshold datasets across 4, 16, and 20 taxa as presented in Haponski et al.parameter files.zipHaponskietal_partula_MLtree_matrices.zip archive contains all ddRAD and mtDNA COI matrices used to build maximum likelihood trees in RAxML and presented in Haponski et al.MLtrees.zipHaponskietal_partula_bayestree_matrices.zip archive contains all ddRAD and mtDNA COI matrices used to generate Bayesian trees in MrBayes and presented in Haponski et al.MBtrees.zip
DOI: 10.5061/dryad.mb3gb
title: Data from: The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

description: Background: Understanding the genetic and developmental origins of
 phenotypic novelty is central to the study of biological diversity. In
 this study we identify modifications to the expression of genes at four
 developmental stages that may underlie jaw morphological differences among
 three closely related species of pupfish (genus Cyprinodon) from San
 Salvador Island, Bahamas. Pupfishes on San Salvador Island are trophically
 differentiated and include two endemic species that have evolved jaw
 morphologies unlike that of any other species in the genus Cyprinodon.
 Results: We find that gene expression differs significantly across
 recently diverged species of pupfish. Genes such as Bmp4 and calmodulin,
 previously implicated in jaw diversification in African cichlid fishes and
 Galapagos finches, were not found to be differentially expressed among
 species of pupfish. Instead we find multiple growth factors and
 cytokine/chemokine genes to be differentially expressed among these
 pupfish taxa. These include both genes and pathways known to affect
 craniofacial development, such as Wnt signaling, as well as novel genes
 and pathways not previously implicated in craniofacial development. These
 data highlight both shared and potentially unique sources of jaw diversity
 in pupfish and those identified in other evolutionary model systems such
 as Galapagos finches and African cichlids. Conclusions: We identify
 modifications to the expression of genes involved in Wnt signaling, Igf
 signaling, and the inflammation response as promising avenues for future
 research. Our project provides insight into the magnitude of gene
 expression changes contributing to the evolution of morphological
 novelties, such as jaw structure, in recently diverged pupfish species.
description: Lencer2017This file contains rpkm data, DNA sequence alignment, and a RAxML tree in nexus format
DOI: 10.5061/dryad.2529hr1
title: Data from: Worldwide phylogeny of three-spined sticklebacks

description: Stickleback fishes in the family Gasterosteidae have become model
 organisms in ecology and evolutionary biology. However, even in the case
 of the most widely studied species in this family – the three-spined
 stickleback (Gasterosteus aculeatus) – the worldwide phylogenetic
 relationships and colonization history of the different populations and
 lineages remain poorly resolved. Using a large collection of samples
 covering most parts of the species distribution range, we subjected
 thousands of single nucleotide polymorphisms to coalescent analyses in
 order to reconstruct a robust worldwide phylogeny of extant G. aculeatus
 populations, as well their ancestral geographic distributions using
 Statistical-Dispersal Vicariance and Bayesian Binary MCMC analyses. The
 results suggest that contemporary populations originated from the Pacific
 Ocean in the late Pleistocene, and the Atlantic was colonized through the
 Arctic Ocean by a lineage that diverged from Pacific sticklebacks ca 44.6
 Kya. This lineage contains two branches: one that is distributed in the
 Mediterranean area, from the Iberian Peninsula to the Black Sea (‘Southern
 European lineage’), and another that is comprised of populations from
 northern Europe and the east coast of North America (‘Trans-Atlantic
 lineage’). Hence, the results suggest that the North American East Coast
 was colonized by trans-Atlantic migration. Coalescence-based divergence
 time estimates suggest that divergence among major clades is much more
 recent than previously estimated.
description: Worldwide phylogenetic
 tree of Gasterosteus aculeatusThe time-calibrated
 worldwide phylogenetic tree of Gasterosteus aculeatus.World_3sp.treeVCF file for all samplesVCF file for all samples. It consists of 126 Gasterosteus aculeatus and 2 individuals of G. nipponicus, a sister species of G. aculeatus.128IDs_full_chrs_ref.vcfAlignments_load_to_BEASTSequence alignments used for phylogenomic analyses. The alignments include 8079 concatenated SNPs.Assembly parameters for ipyrad programAssembly parameters for the ipyrad program in the study.ipyrad_params.txtTime verification tree built from 1000 concatenated RAD lociTime verification tree built from1000 concatenated RAD loci. The tree was built for exclusively calculating divergence times given the tree topology estimated using the SNP data, and solely for the purpose of confirming divergence time estimates generated with the SNP dataset.1000_concat_loci_for_time_verification.tree
DOI: 10.5061/dryad.9r9m3
title: Data from: Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance

description: Diversifying selection on metabolic pathways can reduce intraspecific gene
 flow and promote population divergence. An opportunity to explore this
 arises from mitonuclear discordance observed in an Australian bird
 Eopsaltria australis. Across &gt;1500 km, nuclear differentiation is
 low and latitudinally structured by isolation by distance, whereas two
 highly divergent, parapatric mitochondrial lineages (&gt;6.6% in ND2)
 show a discordant longitudinal geographic pattern and experience different
 climates. Vicariance, incomplete lineage sorting and sex-biased dispersal
 were shown earlier to be unlikely drivers of the mitonuclear discordance;
 instead, natural selection on a female-linked trait was the preferred
 hypothesis. Accordingly, here we tested for signals of positive, divergent
 selection on mitochondrial genes in E. australis. We used codon models and
 physicochemical profiles of amino acid replacements to analyse complete
 mitochondrial genomes of the two mitochondrial lineages in E. australis,
 its sister species Eopsaltria griseogularis, and outgroups. We found
 evidence of positive selection on at least five amino acids, encoded by
 genes of two oxidative phosphorylation pathway complexes NADH
 dehydrogenase (ND4 and ND4L) and cytochrome bc1 (cyt-b) against a
 background of widespread purifying selection on all mitochondrial genes.
 Three of these amino acid replacements were fixed in ND4 of the
 geographically most widespread E. australis lineage. The other two
 replacements were fixed in ND4L and cyt-b of the geographically more
 restricted E. australis lineage. We discuss whether this selection may
 reflect local environmental adaptation, a by-product of other selective
 processes, or genetic incompatibilities, and propose how these hypotheses
 can be tested in future.
description: Eopsaltria australis
 mitogenomes IonTorrent readsIon Torrent reads from
 Long-Range PCR's of complete mitochondrial genomes of Eastern Yellow
 Robin (Eopsaltria australis), sister species (E. griseogularis) and
 outgroups. Morales et al. Purifying and positive selection of a widespread
 passerine with mitonuclear discordance. Molecular Ecology.Samples are
 already demultiplex and in fastq format. reference genome can be found in
 NCBI: JX901073 - http://www.ncbi.nlm.nih.gov/pubmed/23125406
 -
DOI: 10.5061/dryad.fc40s
title: Data from: Stronger neural modulation by visual motion intensity in autism spectrum disorders

description: Theories of autism spectrum disorders (ASD) have focused on altered
 perceptual integration of sensory features as a possible core deficit.
 Yet, there is little understanding of the neuronal processing of
 elementary sensory features in ASD. For typically developed individuals,
 we previously established a direct link between frequency-specific neural
 activity and the intensity of a specific sensory feature: Gamma-band
 activity in the visual cortex increased approximately linearly with the
 strength of visual motion. Using magnetoencephalography (MEG), we
 investigated whether in individuals with ASD neural activity reflect the
 coherence, and thus intensity, of visual motion in a similar fashion.
 Thirteen adult participants with ASD and 14 control participants performed
 a motion direction discrimination task with increasing levels of motion
 coherence. A polynomial regression analysis revealed that gamma-band power
 increased significantly stronger with motion coherence in ASD compared to
 controls, suggesting excessive visual activation with increasing stimulus
 intensity originating from motion-responsive visual areas V3, V6 and
 hMT/V5. Enhanced neural responses with increasing stimulus intensity
 suggest an enhanced response gain in ASD. Response gain is controlled by
 excitatory-inhibitory interactions, which also drive high-frequency
 oscillations in the gamma-band. Thus, our data suggest that a disturbed
 excitatory-inhibitory balance underlies enhanced neural responses to
 coherent motion in ASD.
description: Fig1_Behavioral_DataAccuracy data (%) related to Figure 1Fig2_Time_Frequency_Data_ControlTime-Frequency data of the control group, related to Figure 2Fig2_Time_Frequency_Data_ASDTime-Frequency data of the ASD group, related to Figure 2Fig3_Coefficients_SensorLevel_ControlCoefficients estimated with polynomial regression at sensor-level, Control group, related to Figure 3Fig3_Coefficients_SensorLevel_ASDCoefficients estimated with polynomial regression at sensor-level, ASD group, related to Figure 3Fig4_Coefficients_SourceLevel_ControlCoefficients estimated with polynomial regression at source-level, Control group, related to Figure 4Fig4_Coefficients_SourceLevel_ASDCoefficients estimated with polynomial regression at sensor-level, ASD group, related to Figure 4
DOI: 10.5061/dryad.09d0k
title: Data from: Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability

description: The kidney podocyte's function depends on finger-like projections
 (foot processes) that interdigitate with those from neighboring cells to
 form the glomerular filtration barrier. The integrity of the barrier
 depends on spatial control of dynamics of actin cytoskeleton in the foot
 processes. We determined how imbalances in regulation of actin
 cytoskeletal dynamics can result in pathological morphology. We obtained
 3-D electron microscopy images of podocytes and used quantitative features
 to build dynamical models to investigate how regulation of actin dynamics
 within foot processes controls local morphology. We find that imbalances
 in regulation of actin bundling, lead to chaotic spatial patterns that
 could impair the foot process morphology. Simulation results are
 consistent with experimental observations for cytoskeletal reconfiguration
 by dysregulated RhoA or Rac1, and they predict compensatory mechanisms for
 biochemical stability. We conclude that podocyte morphology, optimized for
 filtration, is intrinsically fragile, whereby local transient biochemical
 imbalances may lead to permanent morphological changes associated with
 pathophysiology.
description: Processed and
 Reconstructed SBEM Imaging Data for PodocytesThis data package
 contains the segmented binary images (Level 1) and the Gaussian-smoothened
 reconstructed volumes (Level 2) of individual rat kidney podocytes that
 were used to create our dynamical models. Images have 11 nm/pixel in-plane
 (XY)-resolution and 210 nm out-of-plane (Z)-resolution. Reconstructed
 volumes all use a single coordinate system. Technical details of
 segmentation and reconstruction are provided in the Supplementary
 Information file associated with the manuscript.Dryad Supp Data
 Files.zip
DOI: 10.5061/dryad.b15tr
title: Data from: Intergenerational environmental effects: functional signals in offspring transcriptomes and metabolomes after parental jasmonic acid treatment in apomictic dandelion

description: Parental environments can influence offspring traits. However, the
 magnitude of the impact of parental environments on offspring molecular
 phenotypes is poorly understood. Here, we test the direct effects and
 intergenerational effects of jasmonic acid (JA) treatment, which is
 involved in herbivory-induced defense signaling, on transcriptomes and
 metabolomes in apomictic common dandelion (Taraxacum officinale). In a
 full factorial crossed design with parental and offspring JA and control
 treatments, we performed leaf RNA-seq gene expression analysis, LC-MS
 metabolomics and total phenolics assays in offspring plants. Expression
 analysis, leveraged by a de novo assembled transcriptome, revealed an
 induced response to JA exposure that is consistent with known JA effects.
 The intergenerational effect of treatment was considerable: 307 of 858
 detected JA-responsive transcripts were affected by parental JA treatment.
 In terms of the numbers of metabolites affected, the magnitude of the
 chemical response to parental JA exposure was c. 10% of the direct JA
 treatment response. Transcriptome and metabolome analyses both identified
 the phosphatidylinositol signaling pathway as a target of
 intergenerational JA effects. Our results highlight that parental
 environments can have substantial effects in offspring generations.
 Transcriptome and metabolome assays provide a basis for zooming in on the
 potential mechanisms of inherited JA effects.
description: De novo assembled
 transcriptome of Dandelion genotype A68Transcriptome assembly
 based on RNAseq data of this study, deposited in NCBI sequence read
 archive, Bioproject number PRJNA316842. Trinity version
 trinityrnaseq-r2013-02-16.dandelion_transcriptome_assembly_A68.faLeaf chemical data of dandelion genotype A68LC-MS data of dandelion leaf tissue after direct and/or parental JA treatment: normalized peak intensity signals from nagative and positive ionisation modes. Total phenolics quantification (in tannic acid equivalents) in dandelion leaf tissue after direct and/or parental JA treatment.dandelion_leaf_chemical_data.xlsx