cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bm21
title: Data from: Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

description: The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of
 conservation biology. Isolated in a 50 m2 pool (Devils Hole), DHP is one
 of the rarest vertebrate species known and an evolutionary anomaly, having
 survived in complete isolation for thousands of years. However, recent
 findings suggest DHP might be younger than commonly thought, potentially
 introduced to Devils Hole by humans in the past thousand years. As a
 result, the significance of DHP from an evolutionary and conservation
 perspective has been questioned. Here we present a high-resolution genomic
 analysis of DHP and two closely related species, with the goal of
 thoroughly examining the temporal divergence of DHP. To this end, we
 inferred the evolutionary history of DHP from multiple random genomic
 subsets and evaluated four historical scenarios using the multispecies
 coalescent. Our results provide substantial information regarding the
 evolutionary history of DHP. Genomic patterns of secondary contact present
 strong evidence that DHP were isolated in Devils Hole prior to 20–10 ka
 and the model best supported by geological history and known mutation
 rates predicts DHP diverged around 60 ka, approximately the same time
 Devils Hole opened to the surface. We make the novel prediction that DHP
 colonized and have survived in Devils Hole since the cavern opened, and
 the two events (colonization and collapse of the cavern's roof) were
 caused by a common geologic event. Our results emphasize the power of
 evolutionary theory as a predictive framework and reaffirm DHP as an
 important evolutionary novelty, worthy of continued conservation and
 exploration.
description: Phylogenetic_data_setsfasta formatted sequence files for 200 random RAD lociBEAST_xml_filesXML files used in *BEAST analysisPupfish_contigs.fade-novo partial reference genome for Cyprinodon diabolis containing 793,068 RAD contigs ranging between 300 - 796 bp.cramfilesIndividual alignment files in CRAM format.
DOI: 10.5061/dryad.p4q04
title: Data from: Increased dopamine release after working-memory updating training: neurochemical correlates of transfer

description: Previous work demonstrates that working-memory (WM) updating training
 results in improved performance on a letter-memory criterion task,
 transfers to an untrained n-back task, and increases striatal dopamine
 (DA) activity during the criterion task. Here, we sought to replicate and
 extend these findings by also examining neurochemical correlates of
 transfer. Four positron emission tomography (PET) scans using the
 radioligand raclopride were performed. Two of these assessed DAD2 binding
 (letter memory; n-back) before 5 weeks of updating training, and the same
 two scans were performed post training. Key findings were (a) pronounced
 training-related behavioral gains in the letter-memory criterion task, (b)
 altered striatal DAD2 binding potential after training during
 letter-memory performance, suggesting training-induced increases in DA
 release, and (c) increased striatal DA activity also during the n-back
 transfer task after the intervention, but no concomitant behavioral
 transfer. The fact that the training-related DA alterations during the
 transfer task were not accompanied by behavioral transfer suggests that
 increased DA release may be a necessary, but not sufficient, condition for
 behavioral transfer to occur.
description: Behavioral
 dataMEMTRAIN2_BehavioralData.xlsxPET Motion dataCSV-Motion.zipPET DICOM Data part1PET data in DICOM format. Note! All packages must be downloaded and combined before unzipping.MEMTRAIN_FINAL_DICOM.zip.001PET DICOM data part 2Download all packages and combine before unzipping.MEMTRAIN_FINAL_DICOM.zip.002PET DICOM data part 3Please combine all parts before unzipping.MEMTRAIN_FINAL_DICOM.zip.003PET DICOM data part 4MEMTRAIN_FINAL_DICOM.zip.004PET DICOM part 5MEMTRAIN_FINAL_DICOM.zip.005PET DICOM part 6MEMTRAIN_FINAL_DICOM.zip.006PET DICOM part 7MEMTRAIN_FINAL_DICOM.zip.007PET DICOM part 8MEMTRAIN_FINAL_DICOM.zip.008PET DICOM part 9MEMTRAIN_FINAL_DICOM.zip.009PET DICOM part 10MEMTRAIN_FINAL_DICOM.zip.010PET DICOM part 11MEMTRAIN_FINAL_DICOM.zip.011PET DICOM part 12MEMTRAIN_FINAL_DICOM.zip.012PET DICOM part 13MEMTRAIN_FINAL_DICOM.zip.013PET DICOM part 14MEMTRAIN_FINAL_DICOM.zip.014PET DICOM part 15MEMTRAIN_FINAL_DICOM.zip.015PET DICOM part 16MEMTRAIN_FINAL_DICOM.zip.016NIFTI-MRI-defaced-MEMTRAIN
DOI: 10.5061/dryad.3c190
title: Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia

description: Although the gut microbiome influences numerous aspects of organismal
 fitness, its role in animal evolution and the origin of new species is
 largely unknown. Here we present evidence that beneficial bacterial
 communities in the guts of closely related species of the genus Nasonia
 form species-specific phylosymbiotic assemblages that cause lethality in
 interspecific hybrids. Bacterial constituents and abundance are irregular
 in hybrids relative to parental controls, and antibiotic curing of the gut
 bacteria significantly rescues hybrid survival. Moreover, feeding bacteria
 to germ-free hybrids reinstates lethality and recapitulates the expression
 of innate immune genes observed in conventionally reared hybrids. We
 conclude that in this animal complex, the gut microbiome and host genome
 represent a coadapted “hologenome” that breaks down during hybridization,
 promoting hybrid lethality and assisting speciation.
description: seqs_rep_set_tax_assignmentsThe representative sequences for all samples: hybrids, non-hybrid species, and S. bullata fly host. Only larval microbes represented for the conventional rearing condition. Barcode identifiers found in the supplemental section online.1/15 RNAseq filesee readme fileRNAseq_fileaa2/15 RNAseq fileRNAseq_fileab3/15 RNAseq fileRNAseq_fileac4/15 RNAseq fileRNAseq_filead5/15 RNAseq fileRNAseq_fileae6/15 RNAseq fileRNAseq_fileaf7/15 RNAseq fileRNAseq_fileag8/15 RNAseq fileRNAseq_fileah9/15 RNAseq fileRNAseq_fileai10/15 RNAseq fileRNAseq_fileaj11/15 RNAseq fileRNAseq_fileak12/15 RNAseq fileRNAseq_fileal13/15 RNAseq fileRNAseq_fileam14/15 RNAseq fileRNAseq_filean15/15 RNAseq fileRNAseq_fileao
DOI: 10.5061/dryad.2d8b5
title: Data from: Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association

description: A key component to understanding the evolutionary response to a changing
 climate is linking underlying genetic variation to phenotypic variation in
 stress response. Here we use a genome-wide association approach (GWAS) to
 understand the genetic architecture of calcification rates under simulated
 climate stress. We take advantage of the genomic gradient across the blue
 mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of
 Maine (GOM) to link genetic variation with variance in calcification rates
 in response to simulated climate change. Falling calcium carbonate
 saturation states are predicted to negatively impact many marine organisms
 that build calcium carbonate shells - like blue mussels. We sampled wild
 mussels and measured net calcification phenotypes after exposing mussels
 to a “climate change” common garden, where we raised temperature 3°C,
 decreased pH by 0.2 units, and limited food supply by filtering out
 planktonic particles &gt; 5 μm, compared to ambient GOM conditions in
 the summer. This climate change exposure greatly increased phenotypic
 variation in net calcification rates compared to ambient conditions. We
 then used regression models to link the phenotypic variation with over
 170,000 single nucleotide polymorphism loci (SNPs) generated by genotype
 by sequencing to identify genomic locations associated with calcification
 phenotype, and estimate heritability and architecture of the trait. We
 identified at least one of potentially 2-10 genomic regions responsible
 for 30% of the phenotypic variation in calcification rates that are
 potential targets of natural selection by climate change. Our simulations
 suggest a power of 13.7% with our study's average effective sample
 size of 118 individuals and rare alleles, but a power of &gt; 90% when
 effective sample size is 900.
description: Stress calcification
 phenotypes and sampling populationsText file containing
 standardized change in buoyant weight (calcification rate) as well as
 sampling population origin for each mussel. Mussels that did not survive
 to final buoyant weight measurement are not included.Mytilus_phenotypes_metadata_final.txtGenotype file (vcf)Variant call format genotypes file for SNP loci (322 mussels from the climate stress group).Mytilus_Kingstonetal2017.vcfCompressed directory containing sequence readsCompressed directory containing demultiplexed sequence reads (fastq format) for the 322 mussels genotyped.Mytilus_fastq.tar.gz
DOI: 10.5061/dryad.65d97
title: Data from: Genome divergence and diversification within a geographic mosaic of coevolution

description: Despite substantial interest in coevolution's role in
 diversification, examples of coevolution contributing to speciation have
 been elusive. Here, we build upon past studies that have shown both
 coevolution between South Hills crossbills and lodgepole pine (Pinus
 contorta), and high levels of reproductive isolation between South Hills
 crossbills and other ecotypes in the North American red crossbill (Loxia
 curvirostra) complex. We used genotyping by sequencing to generate
 population genomic data and applied phylogenetic and population genetic
 analyses to characterize the genetic structure within and among nine of
 the ecotypes. Although genome-wide divergence was slight between ecotypes
 (FST = 0.011–0.035), we found evidence of relative genetic differentiation
 (as measured by FST) between and genetic cohesiveness within many of them.
 As expected for nomadic and opportunistic breeders, we detected no
 evidence of isolation by distance. The one sedentary ecotype, the South
 Hills crossbill, was genetically most distinct because of elevated
 divergence at a small number of loci rather than pronounced overall
 genome-wide divergence. These findings suggest that mechanisms related to
 recent local coevolution between South Hills crossbills and lodgepole pine
 (e.g. strong resource-based density dependence limiting gene flow) have
 been associated with genome divergence in the face of gene flow. Our
 results further characterize a striking example of coevolution driving
 speciation within perhaps as little as 6000 years.
description: rfseq_protocol
 (GBS)An updated protocol for
 the Genotyping By Sequencing approach we employedrfseq_protocol.pdfloxia_gprobs_widsbam_filestgz directory containing .bam assembly files.bams.tgz
DOI: 10.5061/dryad.96p8p
title: Data from: Adhesion forces and mechanics in mannose-mediated acanthamoeba interactions

description: The human pathogenic amoeba Acanthamoeba castellanii (A. castellanii)
 causes severe diseases, including acanthamoeba keratitis and encephalitis.
 Pathogenicity arises from the killing of target-cells by an extracellular
 killing mechanism, where the crucial first step is the formation of a
 close contact between A. castellanii and the target-cell. This process is
 mediated by the glycocalix of the target-cell and mannose has been
 identified as key mediator. The aim of the present study was to carry out
 a detailed biophysical investigation of mannose-mediated adhesion of A.
 castellanii using force spectroscopy on single trophozoites. In detail, we
 studied the interaction of a mannose-coated cantilever with an A.
 castellanii trophozoite, as mannose is the decisive part of the cellular
 glycocalix in mediating pathogenicity. We observed a clear increase of the
 force to initiate cantilever detachment from the trophozoite with
 increasing contact time. This increase is also associated with an increase
 in the work of detachment. Furthermore, we also analyzed single rupture
 events during the detachment process and found that single rupture
 processes are associated with membrane tether formation, suggesting that
 the cytoskeleton is not involved in mannose binding events during the
 first few seconds of contact. Our study provides an experimental and
 conceptual basis for measuring interactions between pathogens and
 target-cells at different levels of complexity and as a function of
 interaction time, thus leading to new insights into the biophysical
 mechanisms of parasite pathogenicity.
description: Mannose 10
 secondsForce-distance curves at
 10 sec contact time between an Acanthamoeba castellanii trophozoite and a
 mannose-coated cantilever.Mannose_10s_c.h.zipMannose 0.5 secondsForce-distance curves at 0.5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever.Mannose0.5s_c.h.zipMannose 5 seconds mannoseblockForce-distance curves at 5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever in a mannose containing medium.Mannose5s_c.f_mannoseblock.zipMannose 5 secondsForce-distance curves at 5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever.Mannose5s_c.h.zip
DOI: 10.5281/zenodo.18385994
title: LINF_320010100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.b971k
title: Data from: Rab6 is required for multiple apical transport pathways but not the basolateral transport pathway in Drosophila photoreceptors

description: Polarized membrane trafficking is essential for the construction and
 maintenance of multiple plasma membrane domains of cells. Highly polarized
 Drosophila photoreceptors are an excellent model for studying polarized
 transport. A single cross-section of Drosophila retina contains many
 photoreceptors with 3 clearly differentiated plasma membrane domains: a
 rhabdomere, stalk, and basolateral membrane. Genome-wide high-throughput
 ethyl methanesulfonate screening followed by precise immunohistochemical
 analysis identified a mutant with a rare phenotype characterized by a loss
 of 2 apical transport pathways with normal basolateral transport. Rapid
 gene identification using whole-genome resequencing and single nucleotide
 polymorphism mapping identified a nonsense mutation of Rab6 responsible
 for the apical-specific transport deficiency. Detailed analysis of the
 trafficking of a major rhabdomere protein Rh1 using blue light-induced
 chromophore supply identified Rab6 as essential for Rh1 to exit the Golgi
 units. Rab6 is mostly distributed from the trans-Golgi network to a
 Golgi-associated Rab11-positive compartment that likely recycles endosomes
 or transport vesicles going to recycling endosomes. Furthermore, the Rab6
 effector, Rich, is required for Rab6 recruitment in the trans-Golgi
 network. Moreover, a Rich null mutation phenocopies the Rab6 null mutant,
 indicating that Rich functions as a guanine nucleotide exchange factor for
 Rab6. The results collectively indicate that Rab6 and Rich are essential
 for the trans-Golgi network–recycling endosome transport of cargoes
 destined for 2 apical domains. However, basolateral cargos are sorted and
 exported from the trans-Golgi network in a Rab6-independent manner.
description: Reference genome
 modified with SNVs in starterDrosophila melenogaster
 reference genome release 5 modified based on the SNVs detected in
 isogenized 2nd and 3rd chromosomes FRT40A and FRT80B, used as starters in
 the EMS screening. Fasta format.40A80B2013_8.faMapped NGS reads of starter FRT40AMapped NGS reads obtained form isogenized starter chromosome carrying FRT40A, used in the EMS screening. This BAM file includes only reads on chromosome 2L.40A_2013_2L.bamMapped NGS reads of 546P mutantMapped NGS reads obtained form homozygous embryos of 546P mutant. This BAM file includes only reads on chromosome 2L.546Pn_2L.bamVariants found in 546P mutantAnnotated VCF file containing variants in 2L chromosome of 546P, called against reference genome 40A80B2013_8.546Pn_2L_variants_eff.vcfVariants unique in 546P mutantsVariants in 546P but not overlapped with the variants in starter FRT40A chromosome.546Pn_2L_unique_variants.vcf
DOI: 10.5281/zenodo.18385993
title: LINF_320010100

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.5061/dryad.c57c1s0
title: Data from: Chimeric antigen receptors that trigger phagocytosis

description: Chimeric antigen receptors (CARs) are synthetic receptors that reprogram T
 cells to kill cancer. The success of CAR-T cell therapies highlights the
 promise of programmed immunity and suggests that applying CAR strategies
 to other immune cell lineages may be beneficial. Here, we engineered a
 family of Chimeric Antigen Receptors for Phagocytosis (CAR-Ps) that direct
 macrophages to engulf specific targets, including cancer cells. CAR-Ps
 consist of an extracellular antibody fragment, which can be modified to
 direct CAR-P activity towards specific antigens. By screening a panel of
 engulfment receptor intracellular domains, we found that the cytosolic
 domains from Megf10 and FcRɣ robustly triggered engulfment independently
 of their native extracellular domain. We show that CAR-Ps drive specific
 engulfment of antigen-coated synthetic particles and whole human cancer
 cells. Addition of a tandem PI3K recruitment domain increased cancer cell
 engulfment. Finally, we show that CAR-P expressing murine macrophages
 reduce cancer cell number in co-culture by over 40%.
description: Run1_A2_A3.omeImage stack fileRun1_D2_D3.omeImage Stack FileRun2_B4_B3.omeImage Stack FileRun3_F4_F3.omeImage Stack File
DOI: 10.5061/dryad.62d6b1h
title: Data from: The neuroscience of Romeo and Juliet: an fMRI study of acting

description: The current study represents a first attempt at examining the neural basis
 of dramatic acting. While all people play multiple roles in daily life –
 for example “spouse” or “employee” – these roles are all facets of the
 “self” and thus the first-person (1P) perspective. Compared to such
 everyday role-playing, actors are required to portray other people and to
 adopt their gestures, emotions, and behaviors. Consequently, actors must
 think and behave not as themselves but as the characters they are
 pretending to be. In other words, they have to assume a “fictional
 first-person” (Fic1P) perspective. In this functional MRI study, we sought
 to identify brain regions preferentially activated when actors adopt a
 Fic1P perspective during dramatic role playing. In the scanner,
 university-trained actors responded to a series of hypothetical questions
 from either their own 1P perspective or from that of Romeo (male
 participants) or Juliet (female participants) from Shakespeare’s drama.
 Compared to responding as oneself, responding in character produced global
 reductions in brain activity and, particularly, deactivations in the
 cortical midline network of the frontal lobe, including the dorsomedial
 and ventromedial prefrontal cortices. Thus, portraying a character through
 acting seems to be a negative process, perhaps representing a “loss of
 self”.
description: Acting_raw_anon_partaaPart 1. Please see readme file.Acting_anon_skullstrip_nifti_partaaActing_raw_anon_partabPart 2. Please see readme.Acting_anon_skullstrip_nifti_partab
DOI: 10.5061/dryad.57n3b70
title: Data from: Development of epithelial tissues: how are cleavage planes chosen?

description: The cross-section of a cell in a monolayer epithelial tissue can be
 modeled mathematically as a k-sided polygon. Empirically studied
 distributions of the proportions of k-sided cells in epithelia show
 remarkable similarities in a wide range of evolutionarily distant
 organisms. A variety of mathematical models have been proposed for
 explaining this phenomenon. The highly parsimonious simulation model of
 (Patel et al., PLoS Comput. Biol., 2009) that takes into account only the
 number of sides of a given cell and cell division already achieves a
 remarkably good fit with empirical distributions from Drosophila, Hydra,
 Xenopus, Cucumber, and Anagallis. Within the same modeling framework as in
 that paper, we introduce additional options for the choice of the
 endpoints of the cleavage plane that appear to be biologically more
 realistic. By taking the same data sets as our benchmarks, we found that
 combinations of some of our new options consistently gave better fits with
 each of these data sets than previously studied ones. Both our algorithm
 and simulation data are made available as research tools for future
 investigations.
description: Data_RandomData_Strict
DOI: 10.15468/djuw73
title: The Australian issid planthopper genus Orinda Kirkaldy, 1907: New subgenera, new species, host plant and identification key (Hemiptera: Fulgoromorpha: Issidae)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Constant, Jérôme, Semeraro, Linda (2023): The Australian issid planthopper genus Orinda Kirkaldy, 1907: New subgenera, new species, host plant and identification key (Hemiptera: Fulgoromorpha: Issidae). European Journal of Taxonomy 891: 128-150, DOI: 10.5852/ejt.2023.891.2277, URL: https://europeanjournaloftaxonomy.eu/index.php/ejt/article/download/2277/9811Abstract. A new subgenus of Orinda Kirkaldy, 1907, Montorinda subgen. nov., is described to accommodate two new species from southeastern Queensland, O. (Montorinda) eungellana sp. nov. from Eungella National Park and O. (Montorinda) montana sp. nov. from Mount Walsh National Park. The new species are compared to the other species of the genus and a new subgenus Scapulorinda subgen. nov. is described to accommodate Orinda (Scapulorinda) scapularis (Jacobi, 1928), leaving a single species in the subgenus Orinda: O. (Orinda) lucindae (Kirkaldy, 1906). Illustrations of the male holotype, a female paratype and male genitalia are provided for both new species as well as habitus and wing of O. (Scapulorinda) scapularis (Jacobi, 1928), the most closely related species, for comparison. The type series of the O. (Montorinda) montana sp. nov. was collected on Grevillea whiteana Mc Gill. (Proteaceae). The genus Orinda is only recorded from Queensland and now contains four species.