cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ck1qs
title: Data from: Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

description: Host-associated microbiomes perform many beneficial functions including
 resisting pathogens and training the immune system. Here, we show that
 amphibians developing in captivity lose substantial skin bacterial
 diversity, primarily due to reduced ongoing input from environmental
 sources. We combined studies of wild and captive amphibians with a
 database of over 1 000 strains that allows us to examine antifungal
 function of the skin microbiome. We tracked skin bacterial communities of
 62 endangered boreal toads, Anaxyrus boreas, across 18 time points, four
 probiotic treatments, and two exposures to the lethal fungal pathogen
 Batrachochytrium dendrobatidis (Bd) in captivity, and compared these to 33
 samples collected from wild populations at the same life stage. As the
 amphibians in captivity lost the Bd-inhibitory bacteria through time, the
 proportion of individuals exposed to Bd that became infected rose from 33%
 to 100% in subsequent exposures. Inoculations of the Bd-inhibitory
 probiotic Janthinobacterium lividum resulted in a 40% increase in survival
 during the second Bd challenge, indicating that the effect of microbiome
 depletion was reversible by restoring Bd-inhibitory bacteria. Taken
 together, this study highlights the functional role of ongoing
 environmental inputs of skin-associated bacteria in mitigating a
 devastating amphibian pathogen, and that long-term captivity decreases
 this defensive function.
description: Captive Wild Environment
 ComparisonCaptive_wild_enviroment_comparison_Dryad.csvMapping FileMapping_MCE_7_MCE_8_Time_Treat_exp.txtOTU Tableotu_table_RSPB20161553_Dryad.biomPlate_1_6_Frog_Undetermined_S0_L001_I1_001Plate_1-6_Frog_Undetermined_S0_L001_R1_001Plate_1-6_Frog_Undetermined_S0_L001_R2_001Plate_1_6_Frog_Undetermined_S0_L001_R2_001.fastq.gzPlates_7_12_Frog_Undetermined_S0_L001_I1_001Plates_7_12_Undetermined_S0_L001_R1_001Plates_7_12_Undetermined_S0_L001_R2_001
DOI: 10.35079/hbm947.zmdx.755
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.v8k18m8
title: Data from: Lineage space and the propensity of bacterial cells to undergo growth transitions

description: The molecular makeup of the offspring of a dividing cell gradually becomes
 phenotypically decorrelated from the parent cell by noise and regulatory
 mechanisms that amplify phenotypic heterogeneity. Such regulatory
 mechanisms form networks that contain thresholds between phenotypes.
 Populations of cells can be poised near the threshold so that a subset of
 the population probabilistically undergoes the phenotypic transition. We
 sought to characterize the diversity of bacterial populations around a
 growth-modulating threshold via analysis of the effect of non-genetic
 inheritance, similar to conditions that create antibiotic-tolerant
 persister cells and other examples of bet hedging. Using simulations and
 experimental lineage data in Escherichia coli, we present evidence that
 regulation of growth amplifies the dependence of growth arrest on cellular
 lineage, causing clusters of related cells undergo growth arrest in
 certain conditions. Our simulations predict that lineage correlations and
 the sensitivity of growth to changes in toxin levels coincide in a
 critical regime. Below the critical regime, the sizes of related growth
 arrested clusters are distributed exponentially, while in the critical
 regime clusters sizes are more likely to become large. Furthermore,
 phenotypic diversity can be nearly as high as possible near the critical
 regime, but for most parameter values it falls far below the theoretical
 limit. We conclude that lineage information is indispensable for
 understanding regulation of cellular growth.
description: Toxin production
 scansContains data for
 Figures 4, 6, S4a, and S4d.toxicity_scan.tar.gzBursting scanData from toxin and antitoxin bursting simulations used in Figure S4.bursting_scan.zipAntitoxin degradation scanData from antitoxin degradation scan simulations used in Figure S4.atoxin_degradation_scan.zip
DOI: 10.35079/hbm624.nllb.278
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.p5cf4
title: Data from: Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove

description: Background: Understanding how past climatic oscillations have affected
 organismic evolution will help predict the impact that current climate
 change has on living organisms. The European turtle dove, Streptopelia
 turtur, is a warm-temperature adapted species and a long distance migrant
 that uses multiple flyways to move between Europe and Africa. Despite
 being abundant, it is categorized as vulnerable because of a long-term
 demographic decline. We studied the demographic history and population
 genetic structure of the European turtle dove using genomic data and
 mitochondrial DNA sequences from individuals sampled across Europe, and
 performing paleoclimatic niche modelling simulations. Results: Overall our
 data suggest that this species is panmictic across Europe, and is not
 genetically structured across flyways. We found the genetic signatures of
 demographic fluctuations, inferring an effective population size (Ne)
 expansion that occurred between the late Pleistocene and early Holocene,
 followed by a decrease in the Ne that started between the mid Holocene and
 the present. Our niche modelling analyses suggest that the variations in
 the Ne are coincident with recent changes in the availability of suitable
 habitat. Conclusions: We argue that the European turtle dove is prone to
 undergo demographic fluctuations, a trait that makes it sensitive to
 anthropogenic impacts, especially when its numbers are decreasing. Also,
 considering the lack of genetic structure, we suggest all populations
 across Europe are equally relevant for conservation.
description: Turtle Dove sequencing
 dataSingle end Illumina
 reads for the 104 Turlte dove samples used in this study (one sample per
 file). All reads are 115 bp in length after trimming and removing barcodes
 as described in the manuscript. Reads with a single base under Phred 10 or
 more than 5% under Phred 20 were discarded.Sturtur_Calderon2016.tar.gz
DOI: 10.35079/hbm735.nbmp.282
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.b9482
title: Data from: Introgression and selection shaped the evolutionary history of sympatric sister-species of coral reef fishes (genus: Haemulon)

description: Closely related marine species with large sympatric ranges provide
 opportunities to study the mechanisms of speciation, particularly when
 there is evidence of gene flow between the lineages. Here we focus on a
 case of hybridization between the sympatric sister-species Haemulon
 maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial
 and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs)
 obtained via Restriction-site Associated DNA Sequencing (RADSeq).
 Mitochondrial markers revealed a shared haplotype for COI and low
 divergence for CytB and CR between the sister species. On the other hand,
 complete lineage sorting was observed at the nuclear loci and most of the
 SNPs. Under neutral expectations, the smaller effective population size of
 mtDNA should lead to fixation of mutations faster than nDNA. Thus, these
 results suggest that hybridization in the recent past (0.174 to 0.263 Ma)
 led to introgression of the mtDNA, with little effect on the nuclear
 genome. Analyses of the SNP data revealed 28 loci potentially under
 divergent selection between the two species. The combination of mtDNA
 introgression and limited nuclear DNA introgression provides a mechanism
 for the evolution of independent lineages despite recurrent hybridization
 events. This study adds to the growing body of research that exemplifies
 how genetic divergence can be maintained in the presence of gene flow
 between closely related species.
description: Sanger
 sequencesAlignments for the
 Sanger sequences of mitochondrial markers COI, CytB and CR, and nuclear
 markers TMO and RAG2. The names of the individuals include the respective
 collection sites. The abbreviation Hmacu corresponds to Haemulon
 maculicauda, and Hflav to Haemulon flaviguttatum.Grunts-sanger-sequences.zipGenotype data in STRUCTURE formatThe analyses corresponding to the SNP dataset (obtained via RADSeq) are based on this genotype dataset in STRUCTURE format. The first column represents the sample name, second column corresponds to the "population" of origin (2 species and 2 locations), and the rest of the columns represent the genotypes for the specific loci. The names of the individuals contain the location site and the abbreviation Hmac corresponds to Haemulon maculicauda, and Hflav corresponds to Haemulon flaviguttatum.Grunts-structure.txtInput file for Migrate-nThis text file contains the sequences that were used for the analysis of migration presented in the manuscript, which were performed with Migrate-n. Sequences of both species were separated, but there was no distinction made by collection site.HMA-HFL-migrateCOICytB-2016.txtRaw readsGrunts-RADSeq.zip
DOI: 10.5061/dryad.vk3fg
title: Data from: Three-dimensional reconstruction on cell level: case study elucidates the ultrastructure of the spinning apparatus of Embia sp. (Insecta: Embioptera)

description: Spinning is a phenomenon not only present in spiders, but also in many
 other arthropods. The functional morphology and complexity of spinning
 organs is often poorly understood. Their elements are minute and studying
 them poses substantial methodological difficulties. This study presents a
 three-dimensional reconstruction of a silk gland of Embia sp. on cellular
 level, based on serial sections acquired with serial block-face scanning
 electron microscopy (SBFSEM) to showcase the power of this method.
 Previous studies achieved either high resolution to elucidate the
 ultrastructure or satisfying three-dimensional representations. The
 high-resolution achieved by SBFSEM can be easily used to reconstruct the
 three-dimensional ultrastructural organization of cellular structures. The
 herein investigated spinning apparatus of Embioptera can be taken as an
 example demonstrating the potential of this method. It was possible to
 reconstruct a multinucleated silk gland containing 63 nuclei. We focused
 on the applicability of this method in the field of morphological research
 and provide a step-by-step guide to the methodology. This will help in
 applying the method to other arthropod taxa and will help significantly in
 adapting the method to other animals, animal parts and tissues.
description: S1 - SBFSEM
 ProtocolStep-by-step Protocol
 for using serial block-face scanning electron microscopy (SBFSEM). The
 precise concentrations and compositions of each chemical used can be found
 within the ‘Material & Methods’ section of "3D-Reconstruction on
 cell level – case study elucidates the three dimensional ultrastructure of
 the spinning apparatus of Embioptera (Insecta)" Büsse et
 al.S2 - raw
 dataUsed raw-data as mp4
 videoS3 -
 Embia_Tarsus-TiffUsed raw-data as
 Tiff-stackS3-Embia_Tarsus-Tiff.zipS4 - Embia_Tarsus-AmiraUsed raw-data as Amira file (use Amira® - www.vsg3d.com)S4-Embia_Tarsus-Amira.zip
DOI: 10.15468/dl.yrhzjs
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Brown Marmorated Stink Bug (Halyomorpha halys) in Portugal"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000436-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.35079/hbm588.gljr.289
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.35079/hbm369.zgtr.825
title: Visium (no probes) data from the uterus of a 19-year-old white female
DOI: 10.5061/dryad.j897m
title: Data from: Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform

description: Genetic information is a valuable component of biosystematics, especially
 specimen identification through the use of species-specific DNA barcodes.
 Although many genomics applications have shifted to High-Throughput
 Sequencing (HTS) or Next-Generation Sequencing (NGS) technologies, sample
 identification (e.g., via DNA barcoding) is still most often done with
 Sanger sequencing. Here, we present a scalable double dual-indexing
 approach using an Illumina Miseq platform to sequence DNA barcode markers.
 We achieved 97.3% success by using half of an Illumina Miseq flowcell to
 obtain 658 base pairs of the cytochrome c oxidase I DNA barcode in 1,010
 specimens from eleven orders of arthropods. Our approach recovers a
 greater proportion of DNA barcode sequences from individuals than does
 conventional Sanger sequencing, while at the same time reducing both per
 specimen costs and labor time by nearly 80%. In addition, the use of HTS
 allows the recovery of multiple sequences per specimen, for deeper
 analysis of genetic variation in target gene regions.
description: Plate01-malaise-BR_S13_L001_R1_001.fastqPlate01-malaise-BR_S13_L001_R2_001.fastqPlate01-malaise-FC_S1_L001_R1_001.fastqPlate01-malaise-FC_S1_L001_R2_001.fastqPlate02-malaise-BR_S14_L001_R1_001.fastqPlate02-malaise-BR_S14_L001_R2_001.fastqPlate02-malaise-FC_S2_L001_R1_001.fastqPlate02-malaise-FC_S2_L001_R2_001.fastqPlate03-malaise-BR_S15_L001_R1_001.fastqPlate03-malaise-BR_S15_L001_R2_001.fastqPlate03-malaise-FC_S3_L001_R1_001.fastqPlate03-malaise-FC_S3_L001_R2_001.fastqPlate04-malaise-BR_S16_L001_R1_001.fastqPlate04-malaise-BR_S16_L001_R2_001.fastqPlate04-malaise-FC_S4_L001_R1_001.fastqPlate04-malaise-FC_S4_L001_R2_001.fastqPlate05-malaise-BR_S17_L001_R1_001.fastqPlate05-malaise-BR_S17_L001_R2_001.fastqPlate05-malaise-FC_S5_L001_R1_001.fastqPlate05-malaise-FC_S5_L001_R2_001.fastqPlate06-malaise-BR_S18_L001_R1_001.fastqPlate06-malaise-BR_S18_L001_R2_001.fastqPlate06-malaise-FC_S6_L001_R1_001.fastqPlate06-malaise-FC_S6_L001_R2_001.fastqPlate07-malaise-BR_S19_L001_R1_001.fastqPlate07-malaise-BR_S19_L001_R2_001.fastqPlate07-malaise-FC_S7_L001_R1_001.fastqPlate07-malaise-FC_S7_L001_R2_001.fastqPlate08-malaise-BR_S20_L001_R1_001.fastqPlate08-malaise-BR_S20_L001_R2_001.fastqPlate08-malaise-FC_S8_L001_R1_001.fastqPlate09-malaise-BR_S21_L001_R1_001.fastqPlate08-malaise-FC_S8_L001_R2_001.fastqPlate09-malaise-BR_S21_L001_R2_001.fastqPlate09-malaise-FC_S9_L001_R1_001.fastqPlate09-malaise-FC_S9_L001_R2_001.fastqPlate10-malaise-BR_S22_L001_R1_001.fastqPlate10-malaise-BR_S22_L001_R2_001.fastqPlate10-malaise-FC_S10_L001_R1_001.fastqPlate10-malaise-FC_S10_L001_R2_001.fastq
DOI: 10.5061/dryad.k3v8j
title: Data from: Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider

description: Mediterranean mountain ranges harbour highly endemic biota in islandlike
 habitats. Their topographic diversity offered the opportunity for mountain
 species to persist in refugial areas during episodes of major climatic
 change. We investigate the role of Quaternary climatic oscillations in
 shaping the demographic history and distribution ranges in the spider
 Harpactocrates ravastellus, endemic to the Pyrenees. Gene trees and
 multispecies coalescent analyses on mitochondrial and nuclear DNA
 sequences unveiled two distinct lineages with a hybrid zone around the
 northwestern area of the Catalan Pyrenees. The lineages were further
 supported by morphological differences. Climatic niche-based species
 distribution models (SDMs) identified two lowland refugia at the western
 and eastern extremes of the mountain range, which would suggest secondary
 contact following postglacial expansion of populations from both refugia.
 Neutrality test and approximate Bayesian computation (ABC) analyses
 indicated that several local populations underwent severe bottlenecks
 followed by population expansions, which in combination with the deep
 population differentiation provided evidence for population survival
 during glacial periods in microrefugia across the mountain range, in
 addition to the main Atlantic and Mediterranean (western and eastern)
 refugia. This study sheds light on the complexities of Quaternary climatic
 oscillations in building up genetic diversity and local endemicity in the
 southern Europe mountain ranges.
description: Original sequence
 alignmentsSequences alignments
 including all individuals, mitochondrial haplotypes, uphased and phased
 sequences of the srp54 nuclear intron and phased, and gene partition
 specifications.Original_sequence_alignments.zipMaxEnt input filesMaxEnt input files used to used to calibrate a set of SDMsMaxEnt_input_files.zipMorphological identificationIncident light photography digital images of a subset of specimens analyzedMorpho_identification_photos.zip
DOI: 10.5061/dryad.0pc151n
title: Data from: Acherontiscus caledoniae, the earliest heterodont and durophagous tetrapod

description: The enigmatic tetrapod Acherontiscus caledoniae from the Pendleian stage
 of the Early Carboniferous shows heterodontous and durophagous teeth,
 representing the earliest known examples of significant adaptations in
 tetrapod dental morphology. Tetrapods of the Late Devonian and Early
 Carboniferous (Mississippian), now known in some depth, are generally
 conservative in their dentition and body morphologies. Their teeth are
 simple and uniform, being cone-like and sometimes recurved at the tip.
 Modifications such as keels occur for the first time in Early
 Carboniferous Tournaisian tetrapods. Acherontiscus, dated as from the
 Pendleian stage, is notable for being very small with skull length of
 about 15 mm, having an elongate vertebral column, and being limbless.
 Cladistic analysis places it close to the Early Carboniferous
 adelospondyls, aïstopods, and colosteids, and supports the hypothesis of
 ‘lepospondyl’ polyphyly. Heterodonty is associated with a varied diet in
 tetrapods, while durophagy suggests a diet that includes hard tissue such
 as chitin or shells. The mid-Carboniferous saw a significant increase in
 morphological innovation among tetrapods, with an expanded diversity of
 body forms, skull shapes, and dentitions appearing for the first time.
description: Acherontiscus scan data
 and 3D filesThe CT scan images and
 metadata for 'Acherontiscus' along with the 3D files used to
 create images for the paper. This data consists of over 2000
 images.Acherontiscus CT Scan
 NHM.zipAcherontiscus
 moviesAcherontiscus left lower
 jaw removed.mov, Acherontiscus left lower jaw.mov, Acherontiscus skull
 roof.movAcherontiscus_movies.zipElectronic Supplementary MaterialElectronic supplementary material for RSOS-182087.R1
DOI: 10.5061/dryad.8b414
title: Data from: One QTL for intra- and interspecific variation in a sex pheromone

description: Even though premating isolation is hypothesized to be a major driving
 force in speciation, its genetic basis is poorly known. In the noctuid
 moth Heliothis subflexa, one group of sex pheromone components, the
 acetates, emitted by the female, plays a crucial isolating role in
 preventing interspecific matings to males of the closely related Heliothis
 virescens, in which females do not produce acetates and males are repelled
 by them. We previously found intraspecific variation in acetates in H.
 subflexa: females in eastern North America contain significantly more
 acetates than females in Western Mexico. Here we describe the persistence
 of this intraspecific variation in laboratory-reared strains and the
 identification of one major quantitative trait locus (QTL), explaining 40%
 of the variance in acetate amounts. We homologized this intraspecific QTL
 to our previously identified interspecific QTL using
 restriction-associated DNA (RAD) tags. We found that a major intraspecific
 QTL overlaps with one of the two major interspecific QTL. To identify
 candidate genes underlying the acetate variation, we investigated a number
 of gene families with known or suspected acetyl- or acyltransferase
 activity. The most likely candidate genes did not map to our QTL, so that
 we currently hypothesize that a transcription factor underlies this QTL.
 Finding a single, large QTL that impacts variation in pheromone blends
 between and within species is, to our knowledge, the first such example
 for traits that have been demonstrated to affect premating isolation.
description: Fig5A-DataqPCR data for Figure 5AFig5B-DataqPCR data for Figure 5Bped_parentals_f1_bc1Phenotype data (amount of acetates) for all parental, F1 and backcross females that were phenotypedAFLP data mapAFLP map of the HsNC-HsMXW backcross family (called 7cap) showing all AFLP markers per chromosome for all backcross individuals110506_SN365_A_s_8_1_seq_GKW-36.txt.gz.001110506_SN365_A_s_8_1_seq_GKW-36.txt.gz.002110506_SN365_A_s_8_1_seq_GKW-36.txt.gz.003110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.001110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.002110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.003110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.004
DOI: 10.5061/dryad.6kg29
title: Data from: Automated single particle detection and tracking for large microscopy datasets

description: Recent advances in optical microscopy have enabled the acquisition of very
 large datasets from living cells with unprecedented spatial and temporal
 resolutions. Our ability to process these datasets now plays an essential
 role in order to understand many biological processes. In this paper, we
 present an automated particle detection algorithm capable of operating in
 low signal-to-noise fluorescence microscopy environments and handling
 large datasets. When combined with our particle linking framework, it can
 provide hitherto intractable quantitative measurements describing the
 dynamics of large cohorts of cellular components from organelles to single
 molecules. We begin with validating the performance of our method on
 synthetic image data, and then extend the validation to include experiment
 images with ground truth. Finally, we apply the algorithm to two
 single-particle-tracking photo-activated localization microscopy
 biological datasets, acquired from living primary cells with very high
 temporal rates. Our analysis of the dynamics of very large cohorts of
 10 000 s of membrane-associated protein molecules show that they behave as
 if caged in nanodomains. We show that the robustness and efficiency of our
 method provides a tool for the examination of single-molecule behaviour
 with unprecedented spatial detail and high acquisition rates.
description: Figure 2
 DataFigure 3 Data (Supp Fig
 1 and 2)Figure 4
 DataFigure 5
 DataTracking
 SoftwareFigure 6 Data Part
 1Image Data for Figure 6
 Part 1Figure 6
 Data.7z.001Figure 6 Data Part
 2Image data for Figure 6
 Part 2Figure 6
 Data.7z.002Figure 6 Data Part
 3Image Data for Figure 6
 Part 3Figure 6
 Data.7z.003Figure 6 Data Part
 4Image Data for Figure 6
 Part 4Figure 6
 Data.7z.004Figure 6 Data Part
 5Image Data for Figure 6
 Part 5Figure 6
 Data.7z.005Figure 6 Data Part
 6Image Data for Figure 6
 Part 6Figure 6
 Data.7z.006
DOI: 10.6084/m9.figshare.31151509
title: 2026_HuangAnand

description: Experiment RH281 contains wildtype neural tube organoid data (after 2 days of BMP4 treatment). Experiment RH282 and RH294 contain neural tube organoid data (After 4 days of BMP4 treatment) after perturbation with scramble guides or guides targeting neural transcription factors.
DOI: 10.6084/m9.figshare.31151509.v1
title: 2026_HuangAnand

description: Experiment RH281 contains wildtype neural tube organoid data (after 2 days of BMP4 treatment). Experiment RH282 and RH294 contain neural tube organoid data (After 4 days of BMP4 treatment) after perturbation with scramble guides or guides targeting neural transcription factors.