cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wm37pvmn8
title: Data from: Phenotypic plasticity in floral scent in response to nutrient, but not water, availability in the perennial plant Arabis alpina (Brassicaceae)

description: Floral scent is an important mediator of plant-pollinator interactions.
 Multiple recent studies report ample intraspecific scent variation among
 populations and individuals. Yet, few studies have estimated effects of
 phenotypic plasticity on floral scent in response to differing
 environmental factors. In this study, we investigated effects of nutrient
 and water availability on floral scent in self-compatible and
 self-incompatible populations of the perennial herb Arabis alpina. We
 subjected greenhouse grown plants to different nutrient and water
 treatments in a crossed design, examined the effects on floral scent
 emission rate and composition, compared the level of plasticity to that of
 other plant traits, and tested for a potential cost of scent production.
 For both self-compatible and self-incompatible populations, the per-flower
 scent emission rate was 1.2-4 times higher when nutrients were abundant,
 but this effect explained little variation in scent emission rate and was
 limited compared to plasticity in flower number. There was no effect of
 water treatment on scent emission. Additionally, neither treatment had an
 effect on the composition of the floral scent, and there was no detectable
 trade-off between scent and seed production that would imply a cost of
 floral scent production. Overall, while per-flower floral scent emission
 displayed limited phenotypic plasticity in response to nutrient
 conditions, the total amount of scent emitted by plants may increase more
 strongly at higher nutrient availabilities due to an increase in flower
 production. Hence, our results suggest that fitness benefits due to
 increased scent emission rates under favorable nutrient conditions might
 depend on the extent to which floral scent serves as a long or short
 distance pollinator attractant for the focal plant species.
description: Data are found in "Luizzi_etal_Data.csv". All
 associated information is in "Luizzi_etal_README.txt".
DOI: 10.5061/dryad.fj6q573v8
title: Ecological variation drives morphological differentiation in a highly social vertebrate

description: 1. Animals may respond to ecological heterogeneity by genetic
 differentiation or phenotypic plasticity. Responses of organisms to their
 ecology can include adaptation at various levels of organization,
 including morphology, behaviour and social structure. Adaptations at one
 level might con-strain or enhance adaptations on other levels, which
 highlights the importance of understanding their interactions. 2. In
 highly social animals, understanding the influence of ecology on the
 evolution and maintenance of complex social organization poses an
 intriguing challenge. Predation risk and habitat characteristics determine
 social structure in the cooperatively breeding cichlid Neolamprologus
 pulcher. Here we examine how varying combinations of these ecological
 factors across eight distinct populations influence morphological
 differentiation. 3. We investigated the relationship between body shape
 and ecological parameters for 137 wild-caught individuals from eight
 distinct populations. Furthermore, we examined the genetic structure and
 differentiation among these populations using microsatellites. Finally, to
 disentangle heritable from plastic responses we raised two successive
 generations from six populations in the laboratory under common garden
 conditions and screened 188 individuals for morphological differentiation.
 4. We found that body shape of N. pulcher strongly correlates with the
 measured ecological parameters. Low predation risk, low habitat structure
 and small shelter size favoured shallow bodies, whereas at the opposite
 end of these environmental gradients deep body shapes prevail. These
 consistent morphological differences persisted over two laboratory-reared
 generations, revealing a heritable basis. In contrast to the significant
 effect of local ecology on morphological differentiation between
 populations, both geographic and genetic distance had little explanatory
 power, suggesting that morphological differentiation between populations
 is not a simple by-product of genetic isolation. Remarkably, the largest
 difference in body depth emerged between the two populations located
 closest to each other, but differing most strongly in their ecological
 niche. 5. These results highlight that morphological variation is a key
 component of local adaptation in neighbouring populations of a highly
 social species. Such morphological differentiation has the potential to
 influence individual cooperative behaviour, which will eventually feedback
 on group structure and mediate the evolution and maintenance of complex
 social systems.
description: See Methods section of publication
description: Morphological data: tps file, landmarks on x-ray images
 Genetic data: excel file, microsatellites
 Ecological data: excel file, ecological parameters
 Population code: excel file, which population code (data)
 corresponds to which population number (paper)
DOI: 10.5061/dryad.2rbnzs7nn
title: Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings

description: Saprotrophic fungi play an important role in ecosystem functioning and
 plant performance, but their abundance in intensively managed arable soils
 is low. Saprotrophic fungal biomass in arable soils can be enhanced with
 amendments of cellulose-rich materials. Here we examined if
 sawdust-stimulated saprotrophic fungi extend their activity to the
 rhizosphere of crop seedlings and influence the composition and activity
 of other rhizosphere and root inhabitants. After growing carrot seedlings
 in sawdust-amended arable soil, we determined fungal and bacterial biomass
 and community structure in roots, rhizosphere and soil. Utilization of
 root exudates was assessed by stable isotope probing (SIP)
 following 13CO2-pulse-labeling of seedlings. This was combined
 with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids
 (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the
 seedling's rhizosphere and roots and actively consumed root exudates.
 This did not reduce the abundance and activity of bacteria, yet higher
 proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and
 activity of mycorrhizal fungi increased with sawdust amendments, whereas
 exudate consumption and root colonization by functional groups containing
 plant pathogens did not change. Sawdust amendment of arable soil enhanced
 abundance and exudate-consuming activity of saprotrophic fungi in the
 rhizosphere of crop seedlings and promoted potential beneficial microbial
 groups in root-associated microbiomes.
description: See the published article
DOI: 10.5061/dryad.1zcrjdfs9
title: eDNA metabarcoding in lakes to quantify influences of landscape features and human activity on aquatic invasive species prevalence and fish community diversity

description: Aim: Our goal was to use eDNA metabarcoding to characterize fish community
 diversity, detect aquatic invasive species (AIS), and assess how measures
 of community (or AIS) diversity are influenced by lake physical and
 environmental covariates, measures of hydrological connectivity, and human
 accessibility. Location: Michigan, USA. Methods: eDNA samples collected
 from 22 lakes were sequenced using two mitochondrial gene regions (12S and
 16S rRNA). Metabarcoding data were compared to traditional fisheries
 survey data for a subset of lakes, and data from all 22 lakes were
 combined with environmental information to identify significant
 associations with community diversity and AIS relative abundance. Results:
 Occupancy modeling indicated that detection probabilities were generally
 higher with eDNA than traditional fisheries gear. Measures of connectivity
 with upstream aquatic habitats were positively associated with both AIS
 relative abundance and fish species diversity. We also demonstrate the use
 of spatial interpolation methods to map distributions of species diversity
 and AIS relative abundance within lakes. Conclusions: eDNA metabarcoding
 methods provided information on the composition and diversity of fish
 assemblages and the presence of AIS in freshwater lakes that varied
 greatly in drainage connectivity and anthropogenic development. Our case
 study identified associations between environmental covariates and fish
 diversity or AIS relative abundance across lakes. This information is of
 particular importance given increasing anthropogenic disturbance, invasive
 species spread, and associated declines in aquatic biodiversity.
 Incorporating eDNA metabarcoding as a supplement to traditional fisheries
 surveys will permit managers to identify greater numbers of taxa,
 including early detection of AIS, with less field effort and fish
 mortality. Further, eDNA methods may more accurately identify physical and
 biological features that correlate with diversity and abundance, and allow
 agencies to more effectively direct AIS management activities.
DOI: 10.5061/dryad.rbnzs7hbq
title: Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence

description: Aim: The need to forecast range shifts under future climate change has
 motivated an increasing interest in better understanding the role of
 biotic interactions in driving diversity patterns. The contribution of
 biotic interactions to shaping broad-scale species distributions is
 however, still debated, partly due to the difficulty of detecting their
 effects. We aim to test whether spatial exclusion between potentially
 competing species can be detected at the species range scale, and whether
 this pattern relates to fine-scale mechanisms of coexistence. Location:
 Western Palearctic Time period: Anthropocene Taxa: bats (Chiroptera)
 Methods: We develop and evaluate a measure of geographic avoidance that
 uses outputs of species distribution models to quantify geographic
 exclusion patterns expected if interspecific competition affects
 broad-scale distributions. We apply the measure to 10 Palearctic bat
 species belonging to four morphologically similar cryptic groups in which
 competition is likely to occur. We compare outputs to null models based on
 pairs of virtual species and to expectations based on ecological
 similarity and fine-scale coexistence mechanisms. We project changes in
 range suitability under climate change taking into account effects of
 geographic avoidance. Results: Values of geographic avoidance were above
 null expectations for two cryptic species pairs, suggesting that
 interspecific competition could have contributed to shaping their
 broad-scale distributions. These two pairs showed highest levels of
 ecological similarity and no trophic or habitat partitioning. Considering
 the role of competition modified predictions of future range suitability.
 Conclusions: Our results support the role of interspecific competition in
 limiting the geographic ranges of morphologically similar species in the
 absence of fine-scale mechanisms of coexistence. This study highlights the
 importance of incorporating biotic interactions into predictive models of
 range shifts under climate change, and the need for further integration of
 community ecology with species distribution models to understand the role
 of competition in ecology and biogeography.
DOI: 10.5061/dryad.qrfj6q5g0
title: A novel and accurate full-length HTT mouse model for Huntington’s disease

description: Here we report the generation and characterization of a novel Huntington’s
 disease (HD) mouse model BAC226Q by using a bacterial artificial
 chromosome (BAC) system, expressing full-length human HTT with ~226
 CAG-CAA repeats and containing endogenous human HTT promoter and
 regulatory elements. BAC226Q recapitulated a full-spectrum of
 age-dependent and progressive HD-like phenotypes without unwanted and
 erroneous phenotypes. BAC226Q mice developed normally, and gradually
 exhibited HD-like mood and cognitive phenotypes at 2 months. From 3-4
 months, BAC226Q mice showed robust progressive motor deficits. At 11
 months, BAC226Q mice showed significant reduced life span, gradual weight
 loss and exhibit neuropathology including significant brain atrophy
 specific to striatum and cortex, striatal neuronal death, widespread
 huntingtin inclusions and reactive pathology. Therefore, the novel BAC226Q
 mouse accurately recapitulating robust, age-dependent, progressive HD-like
 phenotypes will be a valuable tool for studying disease mechanisms,
 identifying biomarkers and testing gene-targeting therapeutic approaches
 for HD.
DOI: 10.5061/dryad.m63xsj427
title: Data Supplements - N-of-1 trials in neurological disorders: Personalizing treatment

description: Supplemental data including: Study details of each included N-of-1 trial
 that reported individual responses (on a pre-defined primary outcome
 measure) and post-trial treatment decisions (eTable 1); PubMed and Medline
 primary search strategy for N-of-1 trials in neurological disorders
 (eAppendix 1); More specified inclusion and exclusion criteria (eAppendix
 2); eReferences (eReferences).
DOI: 10.5061/dryad.95x69p8kw
title: Brood success of northern bobwhite is biased by incomplete detectability during flush-counts

description: Flush-count surveys of game bird broods are a common method of deriving
 estimates of brood survival, but detection of chicks during surveys is
 &lt; 1 due to factors such as vegetation obscurity, adult brooding
 behavior and variation by observer. Radio-telemetry is an alternative
 method for estimating survival that circumvents such factors and allow for
 higher detection. However, this practice is costly and labor-intensive and
 therefore not readily adopted. We sought to estimate detection probability
 of chicks during flush-counts as a function of vegetation height and adult
 brooding behavior. Secondly, we evaluated compromises in detection by
 comparing estimates of brood survival derived from flush-counts and
 radiotelemetry. Lastly, we compared counts between two observers to
 discern whether an additional observer could increase accuracy of counts.
 We radiomarked 247 northern bobwhite Colinus virginianus chicks at 10–12
 days of age and conducted 46 flush-counts at 21 days of age. Vegetation
 height substantially decreased detection (β = −1.18; 95 CrI: −1.68 to
 −0.73); mean detection probability was 0.30 (95 CrI: 0.22–0.40). Observers
 failed to detect radio-marked chicks when adults exhibited running
 behavior (n = 16 chicks, n = 6 surveys), orphaning occurred (n = 11
 chicks, n = 5 surveys) or brooding adults died or had transmitter failures
 (n = 4 chicks, n = 3 surveys). An additional observer did not affect
 counts with a mean difference of −0.6 chicks (95 CrI: −4.0 to 2.7) counted
 between observers. Chicks were not detected during 47% of surveys when ≥ 1
 radio-marked individuals were known to be alive. Brood survival was 0.83
 (95 CrI: 0.70–0.92) and 0.48 (95 CrI: 0.34– 0.62) for radiotelemetry and
 naïve flush-counts, respectively. Because of low detectability of chicks
 during flush-counts, alternative methods should be considered by future
 researchers.
description: Comments made using notes tool in Excel and comments column.
DOI: 10.5061/dryad.wm37pvmn9
title: Physiological and environmental data from: Are you ready for the heat? Plasticity vs adaptation of heat tolerance in three-spined stickleback

description: Heat waves constitute a challenge for aquatic ectotherms. However, the
 thermal tolerance of animals and their individual phenotypic plasticity to
 respond to heat waves may be influenced by thermal history. We tested
 these hypotheses by comparing the upper thermal tolerance and the
 individual capacities of three-spined sticklebacks from populations with
 different thermal histories to respond to heat waves. Two populations
 originated from thermally polluted nuclear power plant (NPP) habitats,
 while four locations represented geographically adjacent control areas. To
 disentangle the genetic adaptation from the phenotypic plastic response,
 we measured the individual upper thermal tolerance and the responses at
 molecular level in common garden conditions before and after a
 laboratory-mimicked heat wave. We found that the sticklebacks exhibit
 considerable phenotypic plasticity in thermal tolerance since the heat
 wave increased fish upper thermal tolerance significantly. The individual
 plasticity to respond to the heat wave was also negatively correlated to
 initial thermal tolerance. On the other hand, neither the thermal
 tolerance nor the plastic responses differed between NPP and control sites
 despite detection of significant but low genome-wide divergence in 10 out
 of 15 pairwise comparisons. Our results suggest that five decades of
 nuclear power plant activity with warmer water has not resulted in a
 detectable evolutionary change in either the upper thermal tolerance or
 its plasticity in three-spined sticklebacks potentially rendering them
 sensitive to frequent heat waves.
DOI: 10.5061/dryad.9zw3r22f8
title: Guidelines for conducting ethical AI research in neurology: Supplementary materials

description: Pre-emptive recognition of  the ethical implications of study
 design and algorithm choices in artificial intelligence (AI) research is
 an important but challenging process. AI applications have begun to
 transition from a promising future to clinical reality in neurology. As
 the clinical management of neurology is often concerned with discrete,
 often unpredictable, and highly consequential events linked to multimodal
 data streams over long timescales, forthcoming advances in AI have great
 potential to transform care for patients. However, critical ethical
 questions have been raised with implementation of the first AI
 applications in clinical practice. Clearly, AI will have far-reaching
 potential to promote, but also to endanger, ethical clinical practice.
 This article employs an anticipatory ethics approach to scrutinize how
 researchers in neurology can methodically identify ethical ramifications
 of design choices early in the research and development process, with a
 goal of pre-empting unintended consequences that may violate principles of
 ethical clinical care. First, we discuss the use of a systematic framework
 for researchers to identify ethical ramifications of various study design
 and algorithm choices. Second, using epilepsy as a paradigmatic example,
 anticipatory clinical scenarios that illustrate unintended ethical
 consequences are discussed, and failure points in each scenario evaluated.
 Third, we provide practical recommendations for understanding and
 addressing ethical ramifications early in methods development stages.
 Awareness of the ethical implications of study design and algorithm
 choices that may unintentionally enter AI is crucial to ensuring that
 incorporation of AI into neurology care leads to patient benefit rather
 than harm.
DOI: 10.5061/dryad.3tx95x6gk
title: Demographic history shapes genomic ancestry in hybrid zones

description: Demographic factors such as migration rate and population size can impede
 or facilitate speciation. In hybrid zones, reproductive boundaries between
 species are tested and demography mediates the opportunity for admixture
 between lineages that are partially isolated. Genomic ancestry is a
 powerful tool for revealing the history of admixed populations, but models
 and methods based on local ancestry are rarely applied to structured
 hybrid zones. To understand the effects of demography on ancestry in
 hybrids zones, we performed individual-based simulations under a
 stepping-stone model, treating migration rate, deme size, and hybrid zone
 age as parameters. We find that the number of ancestry junctions (the
 transition points between genomic regions with different ancestries), as
 well as heterogenicity (the genomic proportion heterozygous for ancestry),
 are often closely connected to demographic history. Reducing deme size
 reduces junction number and heterogenicity. Elevating migration increases
 heterogenicity, but migration affects junction number in more complex
 ways. We highlight the junction frequency spectrum as a novel and
 informative summary of ancestry that responds to demographic history. A
 substantial proportion of junctions are expected to fix when migration is
 limited or deme size is small, changing the shape of the spectrum. Our
 findings suggest that genomic patterns of ancestry could be used to infer
 demographic history in hybrid zones.
description: This dataset includes simulated genomic ancestry
 information.
description: See README.txt for explanation of folders and files.
DOI: 10.5061/dryad.76hdr7sww
title: Rapid mechanical stimulation of inner-ear hair cells by photonic pressure

description: Hair cells, the receptors of the inner ear, detect sounds by transducing
 mechanical vibrations into electrical signals. From the top surface of
 each hair cell protrudes a mechanical antenna, the hair bundle, which the
 cell uses to detect and amplify auditory stimuli, thus sharpening
 frequency selectivity and providing a broad dynamic range. Current methods
 for mechanically stimulating hair bundles are too slow to encompass the
 frequency range of mammalian hearing and are plagued by inconsistencies.
 To overcome these challenges, we have developed a method to move
 individual hair bundles with photonic force. This technique uses an
 optical fiber whose tip is tapered to a diameter of a few micrometers and
 endowed with a ball lens to minimize divergence of the light beam. Here we
 describe the fabrication, characterization, and application of this
 optical system and demonstrate the rapid application of photonic force to
 vestibular and cochlear hair cells.
description: Data were collected as described in the manuscript.
description: Each dataset corresponds to a different figure. The data are
 saved in .txt files where the columns are <em>time</em>,
 <em>laser redout</em> and <em>photodiode
 measurements</em>. The traces reported in the manuscript are
 averages over 25 repetitions and the uploaded files contain every trace.
 The .log files contain all other relevant information: stimuls type,
 duration, delay, intensity of the laser, outputs, range of frequencies,
 <em>et cetera</em>. The file
 "Data_Fig5_Histogram.txt" includes the Time, <em>X
 position</em>, <em>Y position</em> and <em>Vector
 X+Y</em> of the hair bundle oscillations before and after laser
 irradiation used to compose the histogram in Figure 5.