cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m42d17g
title: Data from: Serial-section atlas of the Tritonia pedal ganglion

description: The pedal ganglion of the nudibranch gastropod Tritonia diomedea has been
 the focus of neurophysiological studies for more than 50 years. These
 investigations have examined the neural basis of behaviors as diverse as
 swimming, crawling, reflex withdrawals, orientation to water flow,
 orientation to the earth’s magnetic field, and learning. In spite of this
 sustained research focus, most studies have confined themselves to the
 layer of neurons that are visible on the ganglion’s surface, leaving many
 neurons, which reside in deeper layers, largely unknown and thus
 unstudied. To facilitate work on such neurons, the present study used
 serial section light microscopy to generate a detailed pictorial atlas of
 the pedal ganglion. One pedal ganglion was sectioned horizontally at 2 µm,
 and another vertically at 5 µm intervals. The resulting images were
 examined separately or combined into stacks to generate movie tours
 through the ganglion. These were also used to generate 3D reconstructions
 of individual neurons, and rotating movies of digitally desheathed whole
 ganglia to reveal all surface neurons. A complete neuron count of the
 horizontally sectioned ganglion yielded 1885 neurons. Real and virtual
 sections from the image stacks were used to reveal the morphology of
 individual neurons, as well as the major axon bundles traveling within the
 ganglion to and between its several nerves and connectives. Extensive
 supplemental data are provided, as well as a link to the Dryad Data
 Repository site where the complete sets of high resolution serial section
 images can be downloaded.
description: Ped Horiz High res
 croppedHorizontal serial
 section series of the Tritonia left pedal ganglion, taken at 2 µm
 intervals. 266 aligned and background-cropped 1200 x 1600 pixel tiff
 images. To generate 3D ganglion views in NIH Fiji, load as an image
 sequence and use voxel depth 3.474 in Image Properties to obtain the
 correct 3D aspect ratio.Ped Vert High res
 croppedVertical serial section
 series of the Tritonia left pedal ganglion, taken at 5 µm intervals. 121
 aligned and background-cropped 2560 x 1920 pixel tiff images. To generate
 3D ganglion views in NIH Fiji, load as an image sequence and use voxel
 depth 15.658 in Image Properties to obtain the correct 3D aspect
 ratio.Pedal_2um_horizontalPowerpoint file of the horizontal series, with scale grid and orientation information. Not background-cropped.Pedal_5um_verticalPowerpoint file of the vertical series, with scale grid and orientation information. Not background-cropped.
DOI: 10.5061/dryad.368n7d9
title: Data from: Female mate preferences on high dimensional shape variation for male species recognition traits

description: Females in many animal species must discriminate between conspecific and
 heterospecific males when choosing mates. Such mating preferences that
 discriminate against heterospecifics may inadvertently also affect the
 mating success of conspecific males, particularly those with more extreme
 phenotypes. From this expectation, we hypothesized that female mate choice
 should cause Enallagma females (Odonata: Coenagrionidae) to discriminate
 against conspecific males with more extreme phenotypes of the claspers
 males use to grasp females while mating – the main feature of species mate
 recognition in these species. To test this, we compared cerci sizes and
 shapes between males that were captured while mating with females to males
 that were captured at the same time but not mating in three Enallagma
 species. In contrast to our hypothesis, we found only one of forty
 comparisons of shape variation that was consistent with females
 discriminating against males with more extreme cerci shapes. Instead,
 differences in cerci shape between mating and single males suggested that
 females displayed directional preferences on 1-4 aspects of cerci shape in
 two of the species in our samples. These results suggest that while some
 directional biases in mating based on cerci shape occur, the intraspecific
 phenotypic variation in male cerci size and shape is likely not large
 enough for females to express any significant incidental discrimination
 among conspecifics with more extreme shapes.
description: Cerci SPHARM models of
 male Enallagma DamselfliesThis zip file contains
 raw and spherical harmonics representations of morphological structures
 used by Enallagma damselfly males to grasp females during mating, and
 principal components scores extracted from these
 models.Siepielski_etal_2018_JEB.zip
DOI: 10.5061/dryad.s3h97
title: Data from: Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus)

description: General parameters of selection, such as the frequency and strength of
 positive selection in natural populations or the role of introgression are
 still insufficiently understood. The house mouse (Mus musculus) is a
 particularly well-suited model system to approach such questions, since it
 has a defined history of splits into subspecies and populations and
 extensive genome information is available. We have used high-density
 single nucleotide polymorphism (SNP) typing arrays to assess genomic
 patterns of positive selection and introgression of alleles in two natural
 populations of each of the subspecies M. m. domesticus and M. m. musculus.
 Applying different statistical procedures, we find a large number of
 regions subject to apparent selective sweeps, indicating frequent positive
 selection on rare alleles or novel mutations. Genes in the regions include
 well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes
 involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases
 (e.g. Huntingtin and Parkin). Haplotype matching between the two
 subspecies reveals a large number of haplotypes that show patterns of
 introgression from specific populations of the respective other
 subspecies, with at least 10% of the genome being affected by partial or
 full introgression. Using neutral simulations for comparison, we find that
 the size and the fraction of introgressed haplotypes are not compatible
 with a pure migration or incomplete lineage sorting model. Hence, it
 appears that introgressed haplotypes can rise in frequency due to positive
 selection and thus contribute to the adaptive genomic landscape of natural
 populations. Our data support the notion that natural genomes are subject
 to complex adaptive processes, including the introgression of haplotypes
 from other differentiated populations or species at a larger scale than
 previously assumed for animals. This implies that some of the admixture
 found in inbred strains of mice may also have a natural origin.
description: Staubach2012dataSNP calls from Affymetrix Mouse Diversity Genotyping Arrays; applied to individuals from two populations each of Mus musculus domesticus and Mus musculus musculus, as well as single individuals from Mus outgroups
DOI: 10.5061/dryad.rc073
title: Data from: Long-term test–retest reliability of striatal and extrastriatal dopamine D2/3 receptor binding: study with [11C]raclopride and high-resolution PET

description: We measured the long-term test–retest reliability of [11C]raclopride
 binding in striatal subregions, the thalamus and the cortex using the
 bolus-plus-infusion method and a high-resolution positron emission
 scanner. Seven healthy male volunteers underwent two positron emission
 tomography (PET) [11C]raclopride assessments, with a 5-week retest
 interval. D2/3 receptor availability was quantified as binding potential
 using the simplified reference tissue model. Absolute variability (VAR)
 and intraclass correlation coefficient (ICC) values indicated very good
 reproducibility for the striatum and were 4.5%/0.82, 3.9%/0.83, and
 3.9%/0.82, for the caudate nucleus, putamen, and ventral striatum,
 respectively. Thalamic reliability was also very good, with VAR of 3.7%
 and ICC of 0.92. Test-retest data for cortical areas showed good to
 moderate reproducibility (6.1% to 13.1%). Our results are in line with
 previous test–retest studies of [11C]raclopride binding in the striatum. A
 novel finding is the relatively low variability of [11C]raclopride
 binding, providing suggestive evidence that extrastriatal D2/3 binding can
 be studied in vivo with [11C]raclopride PET to be verified in future
 studies.
description: DICOM data part
 1Combine xaa (part 1) and
 xab (part 2) to obtain a zip-file of size 1.67 GB. The zip-file contains
 anonymized DICOM PET and MRI data from 7 subjects in their respective
 folders named C01-C07.xaaDICOM data part 2Combine xaa (part 1) and xab (part 2) to obtain a zip-file of size 1.67 GB. The zip-file contains anonymized DICOM PET and MRI data from 7 subjects in their respective folders named C01-C07.xab
DOI: 10.5061/dryad.63h8fd4
title: Data from: An integrated genotyping-by-sequencing polymorphism map for over 10,000 sorghum genotypes

description: [No abstract entered]
description: SNPs_imp.recode.vcfImputed SNP dataset for over 10,000 sorghum accessions.Original_chr1.recode.vcf.gzOriginal SNP which not merged, not imputed on chromosome 1.original_chr1.recode.vcf.gzOriginal_chr2.recode.vcfOriginal SNP which not merged, not imputed on chromosome 2original_chr2.recode.vcf.gzOriginal_chr3.recode.vcfOriginal SNP which not merged, not imputed on chromosome 3.original_chr3.recode.vcf.gzoriginal_chr4.recode.vcfOriginal SNP which not merged, not imputed on chromosome 4.Original_chr5.recode.vcfOriginal SNP which not merged, not imputed on chromosome 5.original_chr5.recode.vcf.gzOriginal_chr6.recode.vcfOriginal SNP which not merged, not imputed on chromosome 6.original_chr6.recode.vcf.gzOriginal_chr7.recode.vcfOriginal SNP which not merged, not imputed on chromosome 7.original_chr7.recode.vcf.gzOriginal_chr8.recode.vcfOriginal SNP which not merged, not imputed on chromosome 8.original_chr8.recode.vcf.gzOriginal_chr9.recode.vcfOriginal SNP which not merged, not imputed on chromosome 9.original_chr9.recode.vcf.gzOriginal_chr10.recode.vcfOriginal SNP which not merged, not imputed on chromosome 10.original_chr10.recode.vcf.gzFlowering_time_phenotype_NAMFlowering time data for NAM population was used in GWAS. The data collected in 2015 was fresh data in the present study.Flowering_time_phenotype.csvPlant_height_phenotype_NAMPlant height data for the NAM population used in GWAS. The data collected in 2015 was fresh data in the present study.Plant_height_phenotype.csv
DOI: 10.5061/dryad.261v1
title: Data from: How well can we detect lineage-specific diversification-rate shifts? A simulation study of sequential AIC methods

description: Evolutionary biologists have long been fascinated by the extreme
 differences in species numbers across branches of the Tree of Life. This
 has motivated the development of statistical methods for detecting shifts
 in the rate of lineage diversification across the branches of phylogenic
 trees. One of the most frequently used methods, MEDUSA, explores a set of
 diversification-rate models, where each model assigns branches of the
 phylogeny to a set of diversification-rate categories. Each model is first
 fit to the data, and the Akaike information criterion (AIC) is then used
 to identify the optimal diversification model. Surprisingly, the
 statistical behavior of this popular method is uncharacterized, which is a
 concern in light of: (1) the poor performance of the AIC as a means of
 choosing among models in other phylogenetic contexts; (2) the ad hoc
 algorithm used to visit diversification models, and; (3) errors that we
 reveal in the likelihood function used to fit diversification models to
 the phylogenetic data. Here, we perform an extensive simulation study
 demonstrating that MEDUSA (1) has a high false-discovery rate (on average,
 spurious diversification-rate shifts are identified ≈30% of the time), and
 (2) provides biased estimates of diversification-rate parameters.
 Understanding the statistical behavior of MEDUSA is critical both to
 empirical researchers—in order to clarify whether these methods can make
 reliable inferences from empirical datasets—and to theoretical
 biologists—in order to clarify the specific problems that need to be
 solved in order to develop more reliable approaches for detecting shifts
 in the rate of lineage diversification.
description: Data from: How Well Can
 We Detect Shifts in Rates of Lineage Diversification? A Simulation Study
 of Sequential AIC MethodsThe supplemental data
 archives include trees and stem ages simulated under constant-rate
 birth-death processes for four different simulation experiments
 (simulation_1, simulation_2, simulation_3 and simulation_4), as well as a
 src folder which contains scripts for simulation and conducting the
 analyses.medusa_simulation.zipSupplemental MaterialSupplemental material, including descriptions and results from supplemental simulation studies.supp_mat.pdf
DOI: 10.5061/dryad.251h1
title: Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways

description: Background: Functional magnetic resonance imaging (fMRI) is an advanced
 and frequently used technique for studying brain functions in humans and
 increasingly so in animals. A key element of analyzing fMRI data is group
 analysis, for which valid spatial normalization is a prerequisite. In the
 current study we applied normalization and group analysis to a dataset
 from an auditory functional MRI experiment in anesthetized beagles. The
 stimulation paradigm used in the experiment was composed of simple
 Gaussian noise and regular interval sounds (RIS), which included a
 periodicity pitch as an additional sound feature. The results from the
 performed group analysis were compared with those from single animal
 analysis. In addition to this, the data were examined for brain regions
 showing an increased activation associated with the perception of pitch.
 Results: With the group analysis, significant activations matching the
 position of the right superior olivary nucleus, lateral lemniscus and
 internal capsule were identified, which could not be detected in the
 single animal analysis. In addition, a large cluster of activated voxels
 in the auditory cortex was found. The contrast of the RIS condition
 (including pitch) with Gaussian noise (no pitch) showed a significant
 effect in a region matching the location of the left medial geniculate
 nucleus. Conclusion: By using group analysis additional activated areas
 along the canine auditory pathways could be identified in comparison to
 single animal analysis. It was possible to demonstrate a pitch-specific
 effect, indicating that group analysis is a suitable method for improving
 the results of auditory fMRI studies in dogs and extending our knowledge
 of canine neuroanatomy.
description: auditory_fmri_dog.zip.001This is the first part of the zip file containing all data necessary for the functional analysis as presented in the manuscript. For further information see the attached ReadMe file.auditory_fmri_dog.zip.002This is the second part of the zip file containing all data necessary for the functional analysis as presented in the manuscript.auditory_fmri_dog.zip.003This is the third part of the zip file containing all data necessary for the functional analysis as presented in the manuscript.
DOI: 10.5281/zenodo.18385448
title: NOVAC_BRAND6_3.3F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 3.3F SC sample 4 Novac - EDLC Single - Brand6Part of the Constant Temperature DataBase
DOI: 10.5281/zenodo.18385447
title: NOVAC_BRAND6_3.3F_4_23C_0k_EDLC_single

description: MetSuperCap Project Dataset 3.3F SC sample 4 Novac - EDLC Single - Brand6Part of the Constant Temperature DataBase
DOI: 10.5061/dryad.9v8f5v5
title: Data from: Recent chapters of Neotropical history overlooked in phylogeography: shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins

description: Establishing links between phenotypic and genotypic variation is a central
 goal of evolutionary biology, as they might provide important insights
 into evolutionary processes shaping genetic and species diversity in
 nature. One of the more intriguing possibilities is when no genetic
 divergence is found to be associated with conspicuous phenotypic
 divergence. In that case, speciation theory predicts that phenotypic
 divergence may still occur in the presence of significant gene
 flow—thereby resulting in little genomic divergence—when genetic loci
 underpinning phenotypes are under strong divergent selection. However, a
 finding of phenotypic distinctiveness with weak or no population genetic
 structure may simply result from low statistical power to detect shallow
 genetic divergences when small datasets are used. Here, we used a
 subgenomic dataset of 2386 ultraconserved elements to explore genome-wide
 divergence between two species of Antilophia manakins, which are
 phenotypically distinct yet evidently lack strong genetic differentiation
 according to previous studies based on a limited number of loci. Our
 results revealed clear population structure that matches the two
 phenotypes, supporting the idea that smaller datasets lacked the power to
 detect this recent divergence event (likely &lt; 100 k ya). Indeed, we
 found little or no introgression between the species, as well as evidence
 of genome-wide divergence. One implication of our study is that the
 Araripe plateau may be a hotspot of cryptic-diverging forest Cerrado
 populations. Besides their use in biogeography, subgenomic datasets may
 help redefine local conservation programs by revealing cryptic population
 structure that may be key to population management.
description: Raw Illumina
 filesraw_files.tar.gzReduced set of SNPs (Antilophia_1736_SNPs.vcf)Antilophia_1736_SNPs.vcfComplete set of SNPs (Antilophia_7070_SNPs.vcf)Antilophia_7070_SNPs.vcfDadi input, obtained from a single snp per loci. (Antilophia.dadi)Antilophia.dadiJoint SFS between the Helmeted manakin and Araripe manakin used as input on Fastsimcoal (Antilophia_jointMAFpop1_0.obs)Antilophia_jointMAFpop1_0.obsAntilophia_GPhoCSG-PhoCS control file (Antilophia_GPhocs.ctl)Antilophia_GPhoCS.ctlG-PhoCS sequence file (Antilophia_GPhoCS_Sequences.txt)Antilophia_GPhoCS_Sequences.txtBayescan input file (Antilophia_bialelic_bayescan.txt)Antilophia_bialelic_bayescan.txt
DOI: 10.5061/dryad.23d30
title: Data from: Phenotype classification of zebrafish embryos by supervised learning

description: Zebrafish is increasingly used to assess biological properties of chemical
 substances and thus is becoming a specific tool for toxicological and
 pharmacological studies. The effects of chemical substances on embryo
 survival and development are generally evaluated manually through
 microscopic observation by an expert and documented by several typical
 photographs. Here, we present a methodology to automatically classify
 brightfield images of wildtype zebrafish embryos according to their
 defects by using an image analysis approach based on supervised machine
 learning. We show that, compared to manual classification, automatic
 classification results in 90 to 100% agreement with consensus voting of
 biological experts in nine out of eleven considered defects in 3 days old
 zebrafish larvae. Automation of the analysis and classification of
 zebrafish embryo pictures reduces the workload and time required for the
 biological expert and increases the reproducibility and objectivity of
 this classification.
description: JeanrayEtAl-Data-PlosOneImages used in PLOS ONE article "Phenotype Classification of Zebrafish Embryos by Supervised Learning" in TIFF format (orginal images without any preprocessing). A readme file is added to describe all the subdirectories.
DOI: 10.5061/dryad.qg1p0
title: Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone

description: Hybrid zones provide unique opportunities to examine reproductive
 isolation and introgression in nature. We utilized 45,384 Single
 Nucleotide Polymorphism (SNP) loci to perform association mapping of 14
 floral, vegetative, and ecological traits that differ between Iris
 hexagona and Iris fulva, and to investigate, using a Bayesian Genomic
 Cline (BGC) framework, patterns of genomic introgression in a large and
 phenotypically diverse hybrid zone in southern Louisiana. Many loci of
 small effect-size were consistently found to be associated with phenotypic
 variation across all traits, and several individual loci were revealed to
 influence phenotypic variation across multiple traits. Patterns of genomic
 introgression were quite heterogeneous throughout the Louisiana Iris
 genome, with I. hexagona alleles tending to be favored over those of I.
 fulva. Loci that were found to have exceptional patterns of introgression
 were also found to be significantly associated with phenotypic variation
 in a small number of morphological traits. However, this was the exception
 rather than the rule, as most loci that were associated with morphological
 trait variation were not significantly associated with excess ancestry.
 These findings provide insights into the complexity of the genomic
 architecture of phenotypic differences and are a first step towards
 identifying loci that are associated with both trait variation and
 reproductive isolation in nature.
description: Morphological_DataMorphological data for putative Iris hybrids from Lake Martin, LA. 346 individuals x 14 traits.irisLakeMartin_reads.tarThe file contains all of the parsed reads for the Lake Martin Iris hybrid zone project. Please note: the uncompressed file size is ~55GB.