cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p56p6
title: Data from: Evolutionary shifts in the melanin-based color system of birds

description: Melanin pigments contained in organelles (melanosomes) impart earthy
 colors to feathers. Such melanin-based colors are distributed across birds
 and thought to be the ancestral color-producing mechanism in birds.
 However, we have had limited data on melanin-based color and melanosome
 diversity in Palaeognathae, which includes the flighted tinamous and
 large-bodied, flightless ratites and is the sister taxon to all other
 extant birds. Here, we use scanning electron microscopy and
 spectrophotometry to assess melanosome morphology and quantify reflected
 color for 19 species within this clade. We find that brown colors in
 ratites are uniquely associated with elongated melanosomes nearly
 identical in shape to those associated with black colors. Melanosome and
 color diversity in large-bodied ratites is limited relative to other birds
 (including flightless penguins) and smaller-bodied basal maniraptoran
 dinosaur outgroups of Aves, whereas tinamous show a wider range of
 melanosome forms similar to neognaths. The repeated occurrence of novel
 melanosome forms in the non-monophyletic ratites suggests that
 melanin-based color tracks changes in body size, physiology or other life
 history traits associated with flight loss, but not feather morphology. We
 further anticipate these findings will be useful for future color
 reconstructions in extinct species, as variation in melanosome shape may
 potentially be linked to a more nuanced palette of melanin-based colors.
description: Feather SEM
 imagesCollection of SEM images
 used for measuring melanosome shape in Palaeognathae. See separate
 metadata.csv file for species names.Eliasonetal_Palaeognathae_feather_SEM_images.zipFeather SEM metadataImage ID, species names, and museum metadata associated with SEM imagesmetadata.csvMelanosome shape and color measurementsMean values for melanosome and color traits measured for different palaeognath feather samplesMelanosome and color variables - species means.csv
DOI: 10.5061/dryad.j20f0
title: Data from: Genetic mapping of MAPK-mediated complex traits across S. cerevisiae

description: Signaling pathways enable cells to sense and respond to their environment.
 Many cellular signaling strategies are conserved from fungi to humans, yet
 their activity and phenotypic consequences can vary extensively among
 individuals within a species. A systematic assessment of the impact of
 naturally occurring genetic variation on signaling pathways remains to be
 conducted. In S. cerevisiae, both response and resistance to stressors
 that activate signaling pathways differ between diverse isolates. Here, we
 present a quantitative trait locus (QTL) mapping approach that enables us
 to identify genetic variants underlying such phenotypic differences across
 the genetic and phenotypic diversity of S. cerevisiae. Using a Round-robin
 cross between twelve diverse strains, we identified QTL that influence
 phenotypes critically dependent on MAPK signaling cascades. Genetic
 variants under these QTL fall within MAPK signaling networks themselves as
 well as other interconnected signaling pathways. Finally, we demonstrate
 how the mapping results from multiple strain background can be leveraged
 to narrow the search space of causal genetic variants.
description: Treusch et al.
 DataThe data archive
 contains VCF files derived from the sequenced X-QTL samples, allele
 frequency measurements based on the VCF files and the R scripts used to
 process the allele frequency measurements to map and plot
 QTL.
DOI: 10.15468/dl.jw68ef
title: Occurrence Download

description: A dataset containing 80 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus americanus machetes"
 ]
}

 The dataset includes 80 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000385-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.p0h3t
title: Data from: Microstructure and cerebral blood flow within white matter of the human brain: a TBSS analysis

description: Background: White matter (WM) fibers connect different brain regions and
 are critical for proper brain function. However, little is known about the
 cerebral blood flow in WM and its relation to WM microstructure. Recent
 improvements in measuring cerebral blood flow (CBF) by means of arterial
 spin labeling (ASL) suggest that the signal in white matter may be
 detected. Its implications for physiology needs to be extensively
 explored. For this purpose, CBF and its relation to anisotropic diffusion
 was analyzed across subjects on a voxel-wise basis with tract-based
 spatial statistics (TBSS) and also across white matter tracts within
 subjects. Methods: Diffusion tensor imaging and ASL were acquired in 43
 healthy subjects (mean age = 26.3 years). Results: CBF in WM was observed
 to correlate positively with fractional anisotropy across subjects in
 parts of the splenium of corpus callosum, the right posterior thalamic
 radiation (including the optic radiation), the forceps major, the right
 inferior fronto-occipital fasciculus, the right inferior longitudinal
 fasciculus and the right superior longitudinal fasciculus. Furthermore,
 radial diffusivity correlated negatively with CBF across subjects in
 similar regions. Moreover, CBF and FA correlated positively across white
 matter tracts within subjects. Conclusion: The currently observed findings
 on a macroscopic level might reflect the metabolic demand of white matter
 on a microscopic level involving myelination processes or axonal function.
 However, the exact underlying physiological mechanism of this relationship
 needs further evaluation.
description: TBSS_FA_CBF_N43dataN=43 files for TBSS analysis of FA and CBF data
DOI: 10.5061/dryad.6796b9j
title: Data from: Fat in the leg: function of the expanded hind leg in gasteruptiid wasps (Hymenoptera: Gasteruptiidae)

description: Among some of the most unusual traits of the gasteruptiid wasps is their
 unique hovering flight and the expansion of their hind tibiae. Tibial
 expansions in female parasitoid hymenopterans often involve an enlarged
 sensory structure for vibration detection, the subgenual organ, thus
 enabling refined substrate-borne detection of concealed hosts. In the
 present paper, we utilize a combination of microscopy, chemical analysis,
 gene expression, and behavior to explore the function of the expanded hind
 tibia of gasteruptiid wasps. We find that the expanded hind tibia of
 gasteruptiids is filled largely with fat body, a cell cluster thought not
 typically to occur in insect legs. Based on its position relative to
 flexible tibial structures and the subgenual organ, the gasteruptiid
 tibial fat body may function to amplify vibrational signals. We show the
 tibial fat body to be filled with both trophocytes and, depending on
 gasteruptiid lineage, oenocytes. Transcriptomics reveals enrichment for
 fat-related genes more than expected in an insect leg and raises several
 additional possibilities for functions of fat in the leg including
 detoxification. Finally, our flight observations support the hypothesis
 that this structure may also function in balance and maneuvering in the
 unusual leg-dangling flight behavior of this wasp.
description: Supplementary Figures
 Tables and DocumentsSupplementary files figures and
 tables.zipTranscriptome_Analysis_additional_filesSupplementary videos 1-7
DOI: 10.5061/dryad.n7v41
title: Data from: A descending neuron correlated with the rapid steering maneuvers of flying Drosophila

description: To navigate through the world, animals must stabilize their path against
 disturbances and change direction to avoid obstacles and to search for
 resources. Locomotion is thus guided by sensory cues but also depends on
 intrinsic processes, such as motivation and physiological state. Flies,
 for example, turn with the direction of large-field rotatory motion, an
 optomotor reflex that is thought to help them fly straight. Occasionally,
 however, they execute fast turns, called body saccades, either
 spontaneously or in response to patterns of visual motion such as
 expansion. These turns can be measured in tethered flying Drosophila,
 which facilitates the study of underlying neural mechanisms. Whereas there
 is evidence for an efference copy input to visual interneurons during
 saccades, the circuits that control spontaneous and visually elicited
 saccades are not well known. Using two-photon calcium imaging and
 electrophysiological recordings in tethered flying Drosophila, we have
 identified a descending neuron whose activity is correlated with both
 spontaneous and visually elicited turns during tethered flight. The cell’s
 activity in open- and closed-loop experiments suggests that it does not
 underlie slower compensatory responses to horizontal motion but rather
 controls rapid changes in flight path. The activity of this neuron can
 explain some of the behavioral variability observed in response to visual
 motion and appears sufficient for eliciting turns when artificially
 activated. This work provides an entry point into studying the circuits
 underlying the control of rapid steering maneuvers in the fly brain.
description: Schnell_et_al_2017_dataSchnell_et_al_2017_data contains specific information about and all data described in the manuscript. See the README file for details.
DOI: 10.5061/dryad.bj0b2
title: Data from: Transition from one- to two-dimensional development facilitates maintenance of multicellularity

description: Filamentous organisms represent an example where incomplete separation
 after cell division underlies the development of multicellular formations.
 With a view to understanding the evolution of more complex multicellular
 structures, we explore the transition of multicellular growth from one to
 two dimensions. We develop a computational model to simulate multicellular
 development in populations where cells exhibit density-dependent division
 and death rates. In both the one- and two-dimensional contexts,
 multicellular formations go through a developmental cycle of growth and
 subsequent decay. However, the model shows that a transition to a higher
 dimension increases the size of multicellular formations and facilitates
 the maintenance of large cell clusters for significantly longer periods of
 time. We further show that the turnover rate for cell division and death
 scales with the number of iterations required to reach the stationary
 multicellular size at equilibrium. Although size and life cycles of
 multicellular organisms are affected by other environmental and genetic
 factors, the model presented here evaluates the extent to which the
 transition of multicellular growth from one to two dimensions contributes
 to the maintenance of multicellular structures during development.
description: Dataset
 folderThe Dataset folder
 contains all the individual raw data used to plot the figures presented in
 the study. The folder contains a README.pdf file describing the meaning of
 each column in the files.Dataset.zip
DOI: 10.5061/dryad.bt848
title: Data from: Use of a natural hybrid zone for genome-wide association mapping of craniofacial traits in the house mouse

description: The identification of the genes involved in morphological variation in
 nature is still a major challenge. Here we explore a new approach: we
 combine 178 samples from a natural hybrid zone between two subspecies of
 the house mouse (Mus musculus domesticus and Mus musculus musculus), and
 high coverage of the genome (~145K SNPs) to identify loci underlying
 craniofacial shape variation. Due to the long history of recombination in
 the hybrid zone, high mapping resolution is anticipated. The combination
 of genomes from subspecies allows the mapping of both, variation within
 subspecies and intersubspecific differences, thereby increasing the
 overall amount of causal genetic variation than can be detected. Skull and
 mandible shape were measured using 3D landmarks and geometric
 morphometrics. Using principle component axes as phenotypes, and a linear
 mixed model accounting for genetic relatedness in the mapping populations,
 we identified 9 genomic regions associated with skull and 10 with mandible
 shape. High mapping resolution (median size of significant regions = 148
 kb) enabled identification of single or few candidate genes in most cases.
 Some of the genes act as regulators or modifiers of signaling pathways
 relevant for morphological development and bone formation, including
 several with known craniofacial phenotypes in mice and humans. The
 significant associations combined explain 13% and 7% of the skull and
 mandible shape variation. In addition, a positive correlation was found
 between chromosomal length and proportion of variation explained. Our
 results suggest a complex genetic architecture for shape traits, and
 support a polygenic model.
description: Phenotype_CraniofacialShapeThe file contains the skull and mandible shape and size data. Centroid size (CS) and principal components (PC) were standardized to have mean=0 and standard deviation =1. Data was obtained after analyzing raw landmark coordinates in MorphoJ.KinshipMatrixCentered kinship matrix generated in GEMMA using all LD-pruned SNPssample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_allMarkers.cXX.txtSNPdata.bedBed file generated in PLINK using the LD-pruned SNPs.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.bedSNPdata.bimBim file generated in PLINK using all LD-pruned SNPssample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.bimSNPdata.famFam file generated in PLINK using all the LD-pruned SNPssample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned.famOriginalSNPdata.map.map file with the original set of SNPs previous to LD-pruningsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted_plk.mapOriginalSNPdata.ped.ped file with the original set of SNPs previous to LD-pruningsample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted_plk.ped
DOI: 10.5281/zenodo.18380645
title: Alternatives for the extraction of bioactives and biopolymers from Evernia prunastri for the formulation of antimicrobial bio-based films
DOI: 10.5281/zenodo.18380646
title: Alternatives for the extraction of bioactives and biopolymers from Evernia prunastri for the formulation of antimicrobial bio-based films
DOI: 10.5061/dryad.642jt90
title: Data from: Cell size, photosynthesis and the package effect: an artificial selection approach

description: Cell size correlates with most traits among phytoplankton species. Theory
 predicts that larger cells should show poorer photosynthetic performance,
 perhaps due to reduced intracellular self‐shading (i.e. package effect).
 Yet current theory relies heavily on interspecific correlational
 approaches and causal relationships between size and photosynthetic
 machinery have remained untested. As a more direct test, we applied 250
 generations of artificial selection (c. 20 months) to evolve the green
 microalga Dunaliella teriolecta (Chlorophyta) toward different mean cell
 sizes, while monitoring all major photosynthetic parameters. Evolving
 larger sizes (&gt; 1500% difference in volume) resulted in reduced
 oxygen production per chlorophyll molecule – as predicted by the package
 effect. However, large‐evolved cells showed substantially higher rates of
 oxygen production – a finding unanticipated by current theory. In
 addition, volume‐specific photosynthetic pigments increased with size
 (Chla+b), while photo‐protectant pigments decreased (β‐carotene). Finally,
 larger cells displayed higher growth performances and Fv/Fm, steeper
 slopes of rapid light curves (α) and smaller light‐harvesting antennae
 (σPSII) with higher connectivity (ρ). Overall, evolving a common ancestor
 into different sizes showed that the photosynthetic characteristics of a
 species coevolves with cell volume. Moreover, our experiment revealed a
 trade‐off between chlorophyll‐specific (decreasing with size) and
 volume‐specific (increasing with size) oxygen production in a cell.
description: The data include physiological measurements of
 photosynthetic characteristics of cells of Dunaliella tertiolecta as we
 were evolving their cell volumes toward smaller or larger sizes, using
 artificial selection. Also in the data, scanning electron microscopy
 photos and optical microscopy photos of the size-evolved cells. Please
 refer to the "READ ME_Instructions" file hosted on Zenodo for
 more information on the data files and R scripts included.
DOI: 10.5061/dryad.rg6k9
title: Data from: Using the Mus musculus hybrid zone to assess covariation and genetic architecture of limb bone lengths

description: Two subspecies of the house mouse, Mus musculus domesticus and Mus
 musculus musculus, meet in a narrow contact zone across Europe. Mice in
 the hybrid zone are highly admixed, representing the full range of mixed
 ancestry from the two subspecies. Given the distinct morphologies of these
 subspecies, these natural hybrids can be used for genome-wide association
 mapping at sufficiently high resolution to directly infer candidate genes.
 We focus here on limb bone length differences, which is of special
 interest for understanding the evolution of developmentally correlated
 traits. We used 172 first-generation descendants of wild-caught mice from
 the hybrid zone to measure the length of stylopod (humerus / femur),
 zeugopod (ulna / tibia) and autopod (metacarpal / metatarsal) elements in
 skeletal CT scans. We find phenotypic covariation between limb elements in
 the hybrids similar to patterns previously described in M. m. domesticus
 inbred strains, suggesting that the hybrid genotypes do not influence the
 covariation pattern in a major way. Mapping was performed using 143,592
 SNPs and identified several genomic regions associated with length
 differences in each bone. Each candidate region explains only a small
 proportion of phenotypic variance, suggesting that bone length is highly
 polygenic. None of the candidate regions includes the canonical genes
 known to control embryonic limb development. Instead, we are able to
 identify candidate genes with known roles in osteoblast differentiation
 and bone structure determination, as well as recently evolved genes of, as
 yet, unknown function.
description: Phenotype_Limb_Bone_Length_rawPhenotype data for the length of each limb bone from the raw measurements.Phenotype_Residuals_AgePhenotype data for the length of each limb bone after linear regression on age (residual values).Kinship_MatrixCentered kinship matrix generated in GEMMA using LD-pruned SNPs from autosomes.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_MM10_noX.cXX.txtBED_fileBed file generated in PLINK using the LD-pruned SNPs.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_MM10.bedBIM_fileBim file generated in PLINK using the LD-pruned SNPs.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_MM10.bimFAM_fileFam file generated in PLINK using the LD-pruned SNPs.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted.pruned_MM10.famMAP_fileMap file with the original set of SNPs prior to LD-pruning.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted_MM10.mapPED_filePed file with the original set of SNPs prior to LD-pruning. Containing genotype data for 185 individuals.sample.data_noVinonoNA1_FstALL_5MAF.txtHYBS.sorted_MM10.ped
DOI: 10.5061/dryad.8sc5p
title: Data from: Proprioceptive interaction between the two arms in a single-arm pointing task

description: Proprioceptive signals coming from both arms are used to determine the
 perceived position of one arm in a two-arm matching task. Here, we
 examined whether the perceived position of one arm is affected by
 proprioceptive signals from the other arm in a one-arm pointing task in
 which participants specified the perceived position of an unseen reference
 arm with an indicator paddle. Both arms were hidden from the participant’s
 view throughout the study. In Experiment 1, with both arms placed in front
 of the body, the participants received 70–80 Hz vibration to the elbow
 flexors of the reference arm (= right arm) to induce the illusion of elbow
 extension. This extension illusion was compared with that when the left
 arm elbow flexors were vibrated or not. The degree of the
 vibration-induced extension illusion of the right arm was reduced in the
 presence of left arm vibration. In Experiment 2, we found that this
 kinesthetic interaction between the two arms did not occur when the left
 arm was vibrated in an abducted position. In Experiment 3, the
 vibration-induced extension illusion of one arm was fully developed when
 this arm was placed at an abducted position, indicating that the brain
 receives increased proprioceptive input from a vibrated arm even if the
 arm was abducted. Our results suggest that proprioceptive interaction
 between the two arms occurs in a one-arm pointing task when the two arms
 are aligned with one another. The position sense of one arm measured using
 a pointer appears to include the influences of incoming information from
 the other arm when both arms were placed in front of the body and parallel
 to one another.
description: S1-1S2-1-1S2-1-2S2-1-3S3-1S4-1-1S4-1-2S4-1-3S5-1S6-1S7-1S8-1S9-1S10-1-1S10-1-2S10-1-3S1-2S2-2S3-2S4-2S5-2S9-2S10-2S11-2S12-2S13-2S1-3S2-3S4-3S5-3S8-3S9-3S11-3S13-3S14-3S15-3
DOI: 10.5061/dryad.f9n8t
title: Data from: Lack of experience-based stratification in homing pigeon leadership hierarchies

description: In societies that make collective decisions through leadership, a
 fundamental question concerns the individual attributes that allow certain
 group members to assume leadership roles over others. Homing pigeons form
 transitive leadership hierarchies during flock flights, where flock
 members are ranked according to the average time differences with which
 they lead or follow others' movement. Here, we test systematically
 whether leadership ranks in navigational hierarchies are correlated with
 prior experience of a homing task. We constructed experimental flocks of
 pigeons with mixed navigational experience: half of the birds within each
 flock had been familiarized with a specific release site through multiple
 previous releases, while the other half had never been released from the
 same site. We measured the birds' hierarchical leadership ranks, then
 switched the same birds' roles at a second site to test whether the
 relative hierarchical positions of the birds in the two subsets would
 reverse in response to the reversal in levels of experience. We found that
 while across all releases the top hierarchical positions were occupied by
 experienced birds significantly more often than by inexperienced ones, the
 remaining experienced birds were not consistently clustered in the top
 half—in other words, the network did not become stratified. We discuss our
 results in light of the adaptive value of structuring leadership
 hierarchies according to ‘merit’ (here, navigational experience).
description: GPS tracking data of
 homing pigeon flights from a release siteEach csv file contains
 the data recoded from a GPS device from one pigeon. Initially birds were
 released in flocks of five from either site HC or BE, eight times. This is
 the first half of the data. The release site is followed by the name of
 the individual and then the release number (release
 site_individual_release number). Then groups were combined into two groups
 of ten labelled AB or CD. The second half of the data release site and
 then group, individual and release (Release site Group _ individual_
 release number). The columns are labeled. It is 5 Hz
 data.Data
 Dryad.zip