cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0g6k1
title: Data from: Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry

description: Hybrid zones are geographic regions where isolating barriers between
 divergent populations are challenged by admixture. Identifying factors
 that facilitate or inhibit hybridization in sympatry can illuminate the
 processes that maintain those reproductive barriers. We analyzed patterns
 of hybridization and phenotypic variation across two newly-discovered
 hybrid zones between three subspecies of barn swallow (Hirundo rustica).
 These subspecies differ in ventral coloration and wing length, traits that
 are targets of sexual and natural selection, respectively, and are
 associated with genome-wide differentiation in allopatry. We tested the
 hypothesis that the degree of divergence in these traits is associated
 with the extent of hybridization in secondary contact. We applied measures
 of population structure based on &gt; 23,000 SNPs to confirm that
 named subspecies correspond to distinct genomic clusters, and assessed
 coincidence between geographic clines for ancestry and phenotype. Although
 gene flow was ongoing across both hybrid zones and pairwise FST between
 subspecies was extremely low, we found striking differences in the extent
 of hybridization. In the more phenotypically differentiated subspecies
 pair, clines for ancestry, wing length, and ventral coloration were steep
 and coincident, suggestive of strong isolation and, potentially, selection
 associated with phenotype. In the less phenotypically differentiated pair,
 gene flow and phenotypic variation occured over a wide geographic span,
 indicative of weaker isolation. Traits associated with genome-wide
 differentiation in allopatry may thus also contribute to isolation in
 sympatry. We discuss potentially important additional roles for
 evolutionary history and ecology in shaping variation in the extent
 hybridization between closely related pairs of subspecies.
description: scordato_BARS_genotype_estimatesIndividual genotype estimates for each individual barn swallow (n=533) at each locus (n=23,251). Genotypes are continuous values derived from Bayesian estimates of genotype. They can be rounded to 0, 1, or 2 to replicated analyses that require genotype calls (see supporting information for paper)scordato_BARS_metadataMetadata for genotype estimates. File contains 533 rows corresponding to the genotype file, with individual IDs, sampling locations, GPS coordinates, and taxon classifications with corresponding color codes for plotting.
DOI: 10.5061/dryad.g5155
title: Data from: Development of visual cortical function in infant macaques: a BOLD fMRI study

description: Functional brain development is not well understood. In the visual system,
 neurophysiological studies in nonhuman primates show quite mature neuronal
 properties near birth although visual function is itself quite immature
 and continues to develop over many months or years after birth. Our goal
 was to assess the relative development of two main visual processing
 streams, dorsal and ventral, using BOLD fMRI in an attempt to understand
 the global mechanisms that support the maturation of visual behavior.
 Seven infant macaque monkeys (_Macaca mulatta_) were repeatedly scanned,
 while anesthetized, over an age range of 102 to 1431 days. Large rotating
 checkerboard stimuli induced BOLD activation in visual cortices at early
 ages. Additionally we used static and dynamic Glass pattern stimuli to
 probe BOLD responses in primary visual cortex and two extrastriate areas:
 V4 and MT-V5. The resulting activations were analyzed with standard GLM
 and multivoxel pattern analysis (MVPA) approaches. We analyzed three
 contrasts: Glass pattern present/absent, static/dynamic Glass pattern
 presentation, and structured/random Glass pattern form. For both GLM and
 MVPA approaches, robust coherent BOLD activation appeared relatively late
 in comparison to the maturation of known neuronal properties and the
 development of behavioral sensitivity to Glass patterns. Robust
 differential activity to Glass pattern present/absent and dynamic/static
 stimulus presentation appeared first in V1, followed by V4 and MT-V5 at
 older ages; there was no reliable distinction between the two extrastriate
 areas. A similar pattern of results was obtained with the two analysis
 methods, although MVPA analysis showed reliable differential responses
 emerging at later ages than GLM. Although BOLD responses to large visual
 stimuli are detectable, our results with more refined stimuli indicate
 that global BOLD activity changes as behavioral performance matures. This
 reflects an hierarchical development of the visual pathways. Since fMRI
 BOLD reflects neural activity on a population level, our results indicate
 that, although individual neurons might be adult-like, a longer maturation
 process takes place on a population level.
description: Infant fMRI
 dataInfant-fMRI-data.zip
DOI: 10.7910/dvn/qmunw7
title: Friday For Future Article Data and Analysis Code

description: This dataset was used in the article "Digital Activism and the Climate Crisis: A Visual Content Analysis of Fridays for Future Movement’s Instagram Posts" by the Authors Onur Şen, Özlem Delal Abanoz, Betül Başer, and Enes Abanoz.
description: Check the Read_Me.txt file to reach the analysis code.
DOI: 10.15468/dl.ug3m4s
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "PublishingCountry is Canada",
 "Country is Canada"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Aspidotis densa [GBIF Backbone Taxonomy])",
 "Country is one of (Canada)",
 "RecordedBy is one of (Harvie, Robert)"
 ]
 }
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000490-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3ck0v
title: Data from: The origin and genetic differentiation of the socially parasitic aphid Tamalia inquilinus

description: Social and brood parasitisms are nonconsumptive forms of parasitism
 involving the exploitation of the colonies or nests of a host. Such
 parasites are often related to their hosts and may evolve in various
 ecological contexts, causing evolutionary constraints and opportunities
 for both parasites and their hosts. In extreme cases, patterns of
 diversification between social parasites and their hosts can be coupled,
 such that diversity of one is correlated with or even shapes the diversity
 of the other. Aphids in the genus Tamalia induce galls on North American
 manzanita (Arctostaphylos) and related shrubs (Arbutoideae) and are
 parasitized by nongalling social parasites or inquilines in the same
 genus. We used RNA sequencing to identify and generate new gene sequences
 for Tamalia and performed maximum-likelihood, Bayesian and phylogeographic
 analyses to reconstruct the origins and patterns of diversity and
 host-associated differentiation in the genus. Our results indicate that
 the Tamalia inquilines are monophyletic and closely related to their
 gall-forming hosts on Arctostaphylos, supporting a previously proposed
 scenario for origins of these parasitic aphids. Unexpectedly, population
 structure and host-plant-associated differentiation were greater in the
 non-gall-inducing parasites than in their gall-inducing hosts. RNA-seq
 indicated contrasting patterns of gene expression between host aphids and
 parasites, and perhaps functional differences in host-plant relationships.
 Our results suggest a mode of speciation in which host plants drive
 within-guild diversification in insect hosts and their parasites. Shared
 host plants may be sufficient to promote the ecological diversification of
 a network of phytophagous insects and their parasites, as exemplified by
 Tamalia aphids.
description: nuclear3Three gene alignment of double-stranded RNA-specific editase, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase class I & II, and lysine-specific demethylase lidGroelAlignment of the Buchnera Groel from TamaliapepckPhosphoenolpyruvate carboxykinase intron from TamaliaRAxML_bestTree.nuclear3.reducedBest tree from the maximum likelihood analysis of the 3 gene nuclear alignmentnuclear3_bayes.nex.conConsensus tree from the Bayesian analysis of the 3 gene alignmentRAxML_bestTree.GroelBest tree from the maximum likelihood analysis of the Tamalia groelGroel_bayes.nex.conConsensus tree from the Bayesian analysis of Tamalia groelSeqFirstLocusScaffolds from the Tamalia assemblyScaffoldSummaryBLAST annotations from the Tamalia assemblyGFOLD_summaryxlsxSummary of GFOLD analysis of Tamalia differential gene expression
DOI: 10.5281/zenodo.18326713
title: Marine Biodiversity and Environmental Data: An AI-Ready, Open Dataset from the long term (1995–2023) Basque Country Monitoring Network

description: This dataset provides 28 years of environmental monitoring data (1995–2023) from 51 stations in the estuaries and coastal areas of the Basque Country in the Bay of Biscay. Covering 130 variables across water, sediments, and biota, it includes detailed records of phytoplankton, macroalgae, macroinvertebrates, and fish. Compiled in collaboration with the Basque Water Agency (URA), the dataset supports analysis of environmental responses to human pressures and management interventions, identifying patterns of environmental quality improvement within a context of natural variability. Provided in a FAIR² Data Package, the dataset is structured to ensure Findability, Accessibility, Interoperability, Reusability, and Artificial Intelligence-readiness, facilitated by structured metadata and Application Programming Interface access. This resource is intended for researchers and policymakers examining anthropogenic and natural influences on aquatic ecosystems, contributing to sustainable management, conservation practices, and alignment with European directives, including the Water Framework Directive.
DOI: 10.5281/zenodo.18326712
title: Marine Biodiversity and Environmental Data: An AI-Ready, Open Dataset from the long term (1995–2023) Basque Country Monitoring Network

description: This dataset provides 28 years of environmental monitoring data (1995–2023) from 51 stations in the estuaries and coastal areas of the Basque Country in the Bay of Biscay. Covering 130 variables across water, sediments, and biota, it includes detailed records of phytoplankton, macroalgae, macroinvertebrates, and fish. Compiled in collaboration with the Basque Water Agency (URA), the dataset supports analysis of environmental responses to human pressures and management interventions, identifying patterns of environmental quality improvement within a context of natural variability. Provided in a FAIR² Data Package, the dataset is structured to ensure Findability, Accessibility, Interoperability, Reusability, and Artificial Intelligence-readiness, facilitated by structured metadata and Application Programming Interface access. This resource is intended for researchers and policymakers examining anthropogenic and natural influences on aquatic ecosystems, contributing to sustainable management, conservation practices, and alignment with European directives, including the Water Framework Directive.
DOI: 10.5061/dryad.703h3c8
title: Data from: Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste

description: A citizen science project found that the greenhouse camel cricket
 (Diestrammena asynamora) is common in North American homes. Public
 response was to wonder “what good are they anyway?” and ecology and
 evolution guided the search for potential benefit. We predicted that camel
 crickets and similar household species would likely host bacteria with the
 ability to degrade recalcitrant carbon compounds. Lignocellulose is
 particularly relevant as it is difficult to degrade yet is an important
 feedstock for pulp and paper, chemical, and biofuel industries. We
 screened gut bacteria of greenhouse camel crickets and another household
 insect, a hide beetle (Dermestes maculatus) for the ability to grow on and
 degrade lignocellulose components as well as the lignocellulose-derived
 industrial waste product black liquor. From three greenhouse camel
 crickets and three hide beetles, 14 bacterial strains were identified
 capable of growth on lignocellulosic components, including lignin. Cedecea
 lapagei was selected for further study due to growth on most
 lignocellulose components. The C. lapagei secretome was identified using
 LC/MS/MS analysis. This work demonstrates a novel source of
 lignocellulose-degrading bacteria and introduces an effective workflow to
 identify bacterial enzymes for transforming industrial waste into
 value-added products. More generally, our research suggests the value of
 ecologically-guided discovery of novel organisms.
description: PIQM00000000Cedecea lapegi genome sequenceLC/MS/MS data C. lapageiAmino acid sequences from C. lapagei identified in secretomeC_lapgei on GCHL 6May2016.sf3Bugs in Bugs Sequencing_Data FileFasta file of 16S sequencing resultsData Collection PagesScanned pages from lab notebookLaccase Activity RSOSABTS oxidation assay using growth cultures of Cedecea lapagei
DOI: 10.5061/dryad.nh31f
title: Data from: Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes

description: Ectolecithality is a form of oogenesis unique within Metazoa but common in
 Platyhelminthes, in which nearly-yolkless oocytes and tightly associated
 yolk cells are deposited together in egg capsules. Despite profound
 impacts on the embryogenesis and morphology of its beneficiaries, the
 origins of this developmental phenomenon remain obscure. Traditionally,
 all ectolecithal flatworms were grouped in a clade called Neoophora.
 However, there are also morphological arguments for multiple origins of
 ectolecithality, and Neoophora has to date seen little support from
 molecular phylogenetic research, largely due to gaps in taxon sampling.
 Accordingly, we present a molecular phylogeny focused on resolving the
 deepest divergences among the free-living Platyhelminthes. Species were
 chosen to completely span the diversity of all major endo- and
 ectolecithal clades, including several aberrant species of uncertain
 systematic affinity, and additionally a thorough sampling of the
 “lecithoepitheliate” higher taxa Prorhynchida and Gnosonesimida,
 respectively under- and unrepresented in phylogenies to date. Our analyses
 validate the monophyly of all classical higher platyhelminth taxa, and
 also resolve a clade possessing distinct yolk-cell and oocyte generating
 organs (which we name Euneoophora new taxon). Furthermore, implied-weights
 parsimony and Bayesian mixture model analyses suggest common ancestry of
 this clade with the lecithoepitheliates, implying that these taxa may
 retain a primitive form of ectolecithality. This topology thus
 corroborates the classical hypothesis of homology between yolk cells and
 oocytes in all Neoophora, and should serve to guide future evolutionary
 research on this unique developmental innovation in Platyhelminthes.
description: BiolJLinnSoc_DryadNexus files for all alignments used in this study (by gene and concatenated, raw and sequence-masked). Newick-formatted trees with nodal resampling support values for implied-weights and unweighted parsimony analyses, maximum likelihood analyses, and representative BayesPhylogenies chains for both Matrix A and Matrix B.
DOI: 10.7910/dvn/eqzs1z
title: The Neighborhood Hangover: Housing Market Effects of Commercial Anchor Loss

description: Dataset supporting "Commercial Anchor Loss and Neighborhood Housing Markets: A Spatial Econometric Analysis of Brewery Closures." Contains 15,936 brewery closures (2020-2025) extracted through version control archaeology of the Open Brewery Database Git history, linked to USPS vacancy rates and Zillow Home Value Index (ZHVI) data via network-based walksheds computed in OSMnx. Enables difference-in-differences and event study analysis of how commercial anchor loss affects neighborhood housing markets.
DOI: 10.5061/dryad.7r7812c
title: Data from: Comparative genomics, infectivity and cytopathogenicity of Zika viruses produced by acutely and persistently Zika virus-infected human hematopoietic cell lines

description: Zika virus (ZIKV), an arthropod-borne virus, has emerged as a major human
 pathogen. Prolonged or persistent ZIKV infection of human cells and
 tissues may serve as a reservoir for the virus and present serious
 challenges to the safety of public health. Human hematopoietic cell lines
 with different developmental properties revealed differences in
 susceptibility and outcomes to ZIKV infection. In 3 separate studies
 involving the prototypic MR 766 ZIKV strain and the human monocytic
 leukemia U937 cell line, ZIKV initially developed only a low-grade
 infection at a slow rate. After continuous culture for several months,
 persistently ZIKV-infected cell lines were observed with most, if not all,
 cells testing positive for ZIKV antigen. The infected cultures produced
 ZIKV RNA (v-RNA) and infectious ZIKVs persistently ("persistent
 ZIKVs") with distinct infectivity and pathogenicity when tested using
 various kinds of host cells. When the genomes of ZIKVs from the three
 persistently infected cell lines were compared with the genome of the
 prototypic MR 766 ZIKV strain, distinct sets of mutations specific to each
 cell line were found. Significantly, all three "persistent
 ZIKVs" were capable of infecting fresh U937 cells with high
 efficiency at rapid rates, resulting in the development of a new set of
 persistently ZIKV-infected U937 cell lines. The genomes of ZIKVs from the
 new set of persistently ZIKV-infected U937 cell lines were further
 analyzed for their different mutations. The 2nd generation of persistent
 ZIKVs continued to possess most of the distinct sets of mutations specific
 to the respective 1st generation of persistent ZIKVs. We anticipate that
 the study will contribute to the understanding of the fundamental biology
 of adaptive mutations and selection during viral persistence. The
 persistently ZIKV-infected human cell lines that we developed will also be
 useful to investigate critical molecular pathways of ZIKV persistence and
 to study drugs or countermeasures against ZIKV infections and
 transmission.
description: BMA files of analyzed
 viral RNAs and the reference squenceThe compressed file
 contains BAM files of the sequencing reads mapped to the ZIKV reference
 genome NC_012532 and the reference genome in FASTA format. The file names
 of the BAM files follow the virus ID listed in the Table 3 of the
 manuscript.BMA files of analyzed viral
 RNAs and reference squence.zip
DOI: 10.5061/dryad.59rm087
title: Data from: Tuberculosis-like respiratory infection in 245-million-year-old marine reptile suggested by bone pathologies

description: An absence of archaeological and palaeontological evidence of pneumonia in
 the remote past contrasts with its recognition in the more recent
 archaeologic record. We document an apparent infection-mediated periosteal
 reaction affecting the dorsal ribs in a Middle Triassic eosauropterygian
 historically referred to as ‘Proneusticosaurus’ silesiacus.
 High-resolution X-ray microtomography (XMT) and histological studies of
 the pathologically-altered ribs revealed the presence of a continuous
 solid periosteal reaction with multiple superficial blebs (protrusions) on
 the visceral surfaces of several ribs. Increased vascularization and
 elevated lines of arrested growth document that the pathology was the
 result of a multi-seasonal disease. While visceral surface localization of
 this periosteal reaction represents the earliest identified evidence for
 pneumonia, the blebs may have an additional implication: they have only
 been previously recognized in humans with tuberculosis. Parsimonious with
 this diagnosis is the presence of focal vertebral erosions, another
 manifestation of tuberculosis in humans.
description: Supplementary Movie
 S1Three-dimensional
 visualization of extracted rib fragment showing vasculature of the
 bone.Supplementary Movie
 1.aviSupplementary Movie
 S2XMT
 sections showing microstructure of rib.Supplementary Movie
 2.aviSupplementary Movie
 S3CT
 sectioning of whole specimen MG UWr. 4438s.Supplementary Movie
 3.avi
DOI: 10.5281/zenodo.18381218
title: Association Between Wake- and Sleep-Time Masticatory Muscle Activity in Free-Living Adults
DOI: 10.5281/zenodo.18381219
title: Association Between Wake- and Sleep-Time Masticatory Muscle Activity in Free-Living Adults
DOI: 10.5061/dryad.28d2p
title: Data from: Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish

description: Crude oil spills are a worldwide ocean conservation threat. Fish are
 particularly vulnerable to the oiling of spawning habitats, and crude oil
 causes severe abnormalities in embryos and larvae. However, the underlying
 mechanisms for these developmental defects are not well understood. Here,
 we explore the transcriptional basis for four discrete crude oil injury
 phenotypes in the early life stages of the commercially important Atlantic
 haddock (Melanogrammus aeglefinus). These include defects in (1) cardiac
 form and function, (2) craniofacial development, (3) ionoregulation and
 fluid balance, and (4) cholesterol synthesis and homeostasis. Our findings
 suggest a key role for intracellular calcium cycling and
 excitation-transcription coupling in the dysregulation of heart and jaw
 morphogenesis. Moreover, the disruption of ionoregulatory pathways sheds
 new light on buoyancy control in marine fish embryos. Overall, our
 chemical-genetic approach identifies initiating events for distinct
 adverse outcome pathways and novel roles for individual genes in
 fundamental developmental processes.
description: Supporting dataset
 1Supporting dataset 1:
 Expression of all genes in control, low dose, pulse dose, high dose during
 and after embryonic exposure. Highlighted FC: Prob ≥ 0.95; Not highlighted
 FC: Prob 0.8 – 0.95; FC = 0.5: Not significant; FC = 0.75: Less than 10
 reads in both treatment and control. SP, swissprot; GB, genebank; E1, 3
 dpf; E2, 6 dpf; E3, 10 dpf; E4, 11 dpf; E5, 0 dph; E6, 3 dph; C, control;
 L, low dose; P, pulse dose; H, high dose; FC; fold change; prob;
 probability BioNoiseq.Dataset_1.xlsSupporting dataset 2Expression of all genes in control, low dose, pulse dose, high dose during larval exposure. Highlighted FC: Prob ≥ 0.95; Not highlighted FC: Prob 0.8 – 0.95; FC = 0.5: Not significant; FC = 0.75: Less than 10 reads in both treatment and control. SP, swissprot; GB, genebank; L1, 1 dph; L2, 3 dph; L3, 9 dph; L4, 14 dph; L5, 18 dph; C, control; L, low dose; P, pulse dose; H, high dose; FC; fold change; prob; probability BioNoiseq.Dataset_2.xls