cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7wm37pvs8
title: Widespread Ranavirus and Perkinsea infections in Cuban Treefrogs (Osteopilus septentrionalis) invading New Orleans, USA

description: Invasive species can negatively impact ecosystems in numerous ways,
 including vectoring pathogenic organisms. In amphibians, a
 lineage globally threatened by multiple pathogens, this spread of disease
 via invasive species could contribute to declines in native populations.
 The Cuban Treefrog (Osteopilus septentrionalis) is invasive in the
 southeastern USA. To assess whether O. septentrionalis is a potential
 reservoir host for the pathogens Batrachochytrium dendrobatidis (Bd),
 Ranavirus (Rv), and Perkinsea (Pr), we sampled 82 individuals from a
 recently invaded site in New Orleans, Louisiana, USA. We used quantitative
 PCR to assess prevalence and intensity of Bd, Rv and Pr in mouthparts and
 tail clips from 22 larvae and in toe clips from 60 metamorphosed frogs. We
 compared infection prevalence and intensity across host characteristics,
 including Fulton’s body condition (K), sex, and life stage. None of the
 individuals were infected with Bd, 72% were infected with Rv, and 44% were
 infected with Pr. Twenty-three individuals (28%) were co-infected with Rv
 and Pr, but co-infection did not significantly predict the prevalence or
 intensity of either Rv or Pr. Although we did not observe any disease
 signs, Pr infections were significantly associated with lower body
 condition, suggesting sub-lethal fitness costs. Our study establishes that
 invasive O. septentrionalis in New Orleans are infected with two pathogens
 of global concern for amphibians. Understanding host-pathogen dynamics in
 O. septentrionalis in Louisiana is a critical step towards understanding
 how this invasive species could threaten amphibian biodiversity in the
 region by transmitting infectious pathogens.
description: We collected Cuban Treefrogs (Osteopilus septentrionalis) from
 Audobon Zoo and Riverview Park in New Orleans, Louisiana, USA, during
 visual surveys and we then subsampled 15 individuals per sampling occasion
 for disease analysis. We collected toe clips (adults and juveniles) and
 tail clips/mouth parts (tadpoles only) from these individuals and
 extracted the DNA from these tissues using a Qiagen Dneasy kit based on
 the manufacturers protocols. We then used established qPCR protocols for
 three major amphibian pathogens in the southeastern United States,
 Perkinsea (Pr), Ranavirus (Rv) and Batrachochytrium dendrobatidis (Bd), to
 determine the presence and infection intensity (in genomic equivalents)
 for each pathogen for each individual that we subsampled. We then compared
 the infection presence and infection intensity against a number of
 demographic categories collected on each individual including: location,
 month (this excluded tadpoles/larvae as they were only collected during a
 single month), age class, sex, K (a fitness coefficient), Co-infection
 status, and the overall prevalence for each pathogen.
description: Please see uploaded ReadMe file.
DOI: 10.5061/dryad.qrfj6q5dw
title: Data from: Nanotransfection-based vasculogenic cell reprogramming drives functional recovery in a mouse model of ischemic stroke

description: Ischemic stroke causes vascular and neuronal tissue deficiencies that
 could lead to significant functional impairment and/or death. Although
 progenitor-based vasculogenic cell therapies have shown promise as a
 potential rescue strategy following ischemic stroke, current approaches
 face major hurdles. Here we used fibroblasts nanotransfected with Etv2,
 Foxc2, and Fli1 (EFF), to drive reprogramming-based vasculogenesis,
 intracranially, as a potential therapy for ischemic stroke. Perfusion
 analyses suggest that intracranial delivery of EFF-nanotransfected
 fibroblasts led to a dose-dependent increase in perfusion 14 days
 post-injection. MRI and behavioral tests revealed ~70% infarct resolution
 and up to ~90% motor recovery for mice treated with EFF-nanotransfected
 fibroblasts. Immunohistological analysis confirmed increases in
 vascularity and neuronal cellularity, as well as reduced glial scar
 formation in response to treatment with EFF-nanotransfected fibroblasts.
 Altogether, our results suggest that vasculogenic cell therapies based on
 nanotransfection-driven (i.e., non-viral) cellular reprogramming represent
 a promising strategy for the treatment of ischemic stroke.
DOI: 10.5061/dryad.t76hdr808
title: Data from: A sensory bias overrides learned preferences of bumblebees for honest signals in Mimulus guttatus

description: Insect pollinators readily learn olfactory cues, and this is expected to
 select for “honest signals” that provide reliable information about floral
 rewards. However, plants might alternatively produce signals that exploit
 pollinators’ sensory biases, thereby relaxing selection for signal
 honesty. We examined the innate and learned preferences of Bombus
 impatiens for Mimulus guttatus floral scent phenotypes corresponding to
 different levels of pollen rewards in the presence and absence of the
 innately attractive floral volatile compound β-trans-bergamotene. Bees
 learned to prefer honest signals after foraging on live M. guttatus
 flowers, but only exhibited this preference when presented floral scent
 phenotypes that did not include β-trans-bergamotene. Our results suggest
 that a sensory bias for β-trans-bergamotene overrides the ability of B.
 impatiens to use honest signals when foraging on M. guttatus. This may
 represent a deceptive pollination strategy that allows plants to minimize
 investment in costly rewards without incurring reduced rates of pollinator
 visitation.
DOI: 10.5061/dryad.866t1g1px
title: Rwenzori colobus core unit SNA data - association scans between units, simple association index per dyad, male dispersal events, rainfall and food availability

description: 1. Multi-level societies are complex, nested social systems where basic
 social groups (i.e., core units) associate in a hierarchical manner,
 allowing animals to adjust their group sizes in response to variables such
 as food availability, predation, or conspecific threat. These pressures
 fluctuate over time and examining the extent to which this variation
 affects the clustering of core units into different tiers may be
 instrumental in understanding the evolution of multi-level societies. 2.
 The goal of our study was to determine the degree of temporal variability
 in inter-unit associations in a multi-level society of Rwenzori Angolan
 colobus monkey (Colobus angolensis ruwenzorii), and to determine the
 social and ecological factors that underlie association patterns. The C.
 a. ruwenzorii multi-level society consists of at least three tiers, with
 core units clustering into clans that share a home range in a band tier.
 3. We performed social network analyses on 21 months of association data
 from 13 core units (totaling 139 identifiable individuals) at Lake
 Nabugabo, Uganda. We described the patterns of variation in core-unit
 associations over time and investigated how changes in rainfall, food
 availability, and inter-unit dispersals were correlated with these
 associations over the short-term (month to month) and long-term (year to
 year). 4. Although clans were relatively stable, larger-scale changes in
 association patterns included the formation of an all-male unit and the
 transfer of one core unit between clans (within the band tier).
 Seasonally, core units associated significantly more when fruit, their
 preferred food source, was abundant (i.e., social networks were denser and
 more clustered) and there was no direct effect of rainfall seasonality or
 young leaf availability. Male dispersals also occurred more during periods
 of high fruit availability, suggesting that greater band cohesion allowed
 males to prospect and transfer between core units. Once males transferred,
 their previous and new units associated significantly more with one
 another than with other core units for 1-2 months post-dispersal. The
 dispersal of five males from one core unit to another in a different clan
 co-occurred with this core unit switching its clan affiliation. 5. By
 examining temporal shifts in social network structure among core units,
 this study shows the inter-connected roles that food availability and
 dispersal have in shaping the C. a. ruwenzorii multi-level social system.
 Our findings highlight how ecological conditions can drive association
 patterns, impact interunit relationships, and influence social
 organization.
DOI: 10.6084/m9.figshare.30976894.v1
title: Malus×robusta

description: Genome assembly and annotation of Malus×robusta. The dataset includes the chromosome-level genome sequence and its structural gene annotation.
DOI: 10.5061/dryad.41ns1rncp
title: Pupil and gaze during binocular rivalry

description: The pupil provides a rich, non-invasive measure of the neural bases of
 perception and cognition, and has been of particular value in uncovering
 the role of arousal-linked neuromodulation, which alters cortical
 processing as well as pupil size. But pupil size is subject to a multitude
 of influences, which complicates unique interpretation. We measured pupils
 of observers experiencing perceptual multistability -- an ever-changing
 subjective percept in the face of unchanging but inconclusive sensory
 input. In separate conditions the endogenously generated perceptual
 changes were either task-relevant or not, allowing a separation between
 perception-related and task-related pupil signals. Perceptual changes were
 marked by a complex pupil response that could be decomposed into two
 components: a dilation tied to task execution and plausibly indicative of
 an arousal-linked noradrenaline surge, and an overlapping constriction
 tied to the perceptual transient and plausibly a marker of altered visual
 cortical representation. Constriction, but not dilation, amplitude
 systematically depended on the time interval between perceptual changes,
 possibly providing an overt index of neural adaptation. These results show
 that the pupil provides a simultaneous reading on interacting but
 dissociable neural processes during perceptual multistability, and suggest
 that arousal-linked neuromodulation shapes action but not perception in
 these circumstances.
description: Details about the collection of these data can be found in the
 published article.
DOI: 10.15468/dl.7vkfyp
title: Occurrence Download

description: A dataset containing 52902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Uruguay",
 "OccurrenceStatus is Present",
 "TaxonKey is Pitangus"
 ]
}

 The dataset includes 52902 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002734-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7hv
title: Telemetry validated nitrogen stable isotope clocks identify ocean-to-estuarine habitat shifts in mobile organisms

description: 1. Throughout their life history, many animals transition among
 heterogenous environments to facilitate behaviors such as reproduction,
 foraging, and predator avoidance. The dynamic environmental and biological
 conditions experienced by mobile species are integrated in the chemical
 composition of their tissues, providing retrospective insight into
 movement. 2. Here, we present a unique nitrogen stable isotope clocks
 (‘isotopic clocks’), which integrate tissue turnover rates, consumer
 stable isotope ratios, and habitat-specific isotope baselines and can be
 used to predict time-since-immigration and the timing of habitat shifts in
 migratory animals. Isotope values of blood plasma to derive
 time-since-immigration estimates and timing of seasonal habitat shifts for
 juvenile sand tiger sharks (Carcharias taurus); a species known to perform
 seasonal movements between ocean and estuarine environments. 3. Isotopic
 clocks estimated for 65 individuals sampled across six years illustrated
 that juvenile sand tiger sharks predominantly arrived at estuarine
 habitats between June and July, with some individuals arriving as early as
 mid-May. Our modeling approach was validated by comparing isotope-derived
 estuarine arrival times with those from acoustically tracked individuals.
 The median day of entry for each sampling population were within the range
 of entry times estimated from acoustic telemetry. 4. Sensitivity analyses
 indicated isotopically inferred time-since-immigration and estuarine
 arrival estimates were robust to variation in isotopic turnover rate and
 diet tissue discrimination factors under multiple modelling scenarios.
 This suggests that parameterization of the isotopic clock provides
 reliable estimates of time-since-immigration and day of arrival into new
 habitats if isotopic variation is existing between origin and new
 locations. 5. Our study presents a unique application of
 telemetry-validated isotope clocks to derive retrospective estimates of
 time-since-immigration and timing of habitat shifts for animals that
 seasonally traverse heterogeneous environments. This approach can be
 readily applied across many temporal and spatial scales, and to other
 species and ecosystems to facilitate rapid assessment of changes in animal
 habitat use and broader ecosystem structure.   
description: Bulk stable isotope data. Oven dried for 72 hours with no
 chemical pretreatment prior to isotopic analysis. 
description: Corresponding d13C data is also available, but is not provided
 with this upload. Please contact authors directly.
DOI: 10.5061/dryad.5dv41ns5d
title: Data from: Multispecies for multifunctions: combining four complementary species enhances multifunctionality of sown grassland

description: Assessing the overall performance of ecosystems requires a quantitative
 evaluation of multifunctionality. We investigated plant species diversity
 effects on individual functions and overall multifunctionality in a
 grassland experiment with sown monocultures and mixtures comprising four
 key grass and legume species. Nitrogen fertilisation rates were 50, 150,
 and 450 kg N ha-1 yr-1 (N50, N150, N450). Ten functions were measured
 representing forage production, N cycling, and forage quality, all being
 related to either productivity or environmental footprint.
 Multifunctionality was analysed by a novel approach using the mean log
 response ratio across functions. Over three experimental years, mixture
 effects benefited all forage production and N cycling functions, while
 sustaining high forage quality. Thus, mixture effects did not provoke any
 trade-off among the analysed functions. High N fertilisation rates
 generally diminished mixture benefits. Multifunctionality of four-species
 mixtures was considerably enhanced, and mixture overall performance was up
 to 1.9 (N50), 1.8 (N150), and 1.6 times (N450) higher than in averaged
 monocultures. Multifunctionality of four-species mixtures at N50 was at
 least as high as in grass monocultures at N450. Sown grass–legume mixtures
 combining few complementary species at low to moderate N fertilisation
 sustain high multifunctionality and are a ‘ready-to-use’ option for the
 sustainable intensification of agriculture.
description: <strong>Suter et al. 2021 Functional responses of ten
 functions from 78 plant communities</strong> Data
 contains the functional responses of monocultures and of two- and
 four-species mixtures for ten functions at three nitrogen fertilisation
 levels, averaged across the three experimental years and scaled to range
 between 0 and 1 .<br> The functions "stability",
 "weed biomass", and "NO3 in soil solution" were first
 natural log transformed and then scaled to 0-1.
DOI: 10.5061/dryad.8sf7m0cm8
title: Phosphatidylserine exposure promotes increased adhesion in Dictyostelium Copine A mutants

description: The phospholipid phosphatidylserine (PS) is a key signaling molecule and
 binding partner for many intracellular proteins. PS is normally found on
 the inner surface of the cell membrane, but PS can be flipped to the outer
 surface in a process called PS exposure. PS exposure is important in many
 cell functions yet the mechanisms that control PS exposure have not been
 extensively studied. Copines (Cpn), found in most eukaryotic organisms,
 make up a family of calcium-dependent phospholipid binding proteins. In
 Dictyostelium, which has six copine genes, CpnA strongly binds to PS and
 translocates from the cytosol to the plasma membrane in response to a rise
 in calcium.  Cells lacking the cpnA gene (cpnA- ) have defects in
 adhesion, chemotaxis, membrane trafficking and cytokinesis. In this study
 we used both flow cytometry and fluorescent microscopy to show that cpnA-
 cells have increased adhesion to beads and bacteria and that the increased
 adhesion was not due to changes in the actin cytoskeleton or cell surface
 proteins. We found that cpnA- cells bound higher amounts of Annexin V, a
 PS binding protein, than parental cells and showed that unlabeled Annexin
 V reduced the increased cell adhesion property of cpnA- cells. We also
 found that cpnA- cells were more sensitive to Polybia-MP1, which binds to
 external PS and induces cell lysis. Overall, this suggests that cpnA-
 cells have increased PS exposure and this property contributes to the
 increased cell adhesion of cpnA- cells. We conclude that CpnA has a role
 in the regulation of plasma membrane lipid composition and may act as a
 negative regulator of PS exposure.
DOI: 10.5061/dryad.4qrfj6q8v
title: Contrasting patterns of phylogenetic diversity and alpine specialization across the alpine flora of the American mountain range system

description: Although mountainous habitats contribute substantially to global
 biodiversity, comparatively little is known about biogeographic patterns
 of distributions of alpine species across multiple mountain ranges. Here,
 we present a detailed analysis of the distributions and phylogenetic
 affinities of alpine seed plant lineages across North, Central, and South
 American mountain systems. Using a comprehensive dataset that
 characterized the elevational niches of American seed plants in a
 continuously valued way, we were able to quantitatively investigate how
 the proportion of alpine habitat occupied by plants related to their
 biogeographic distributions at a regional scale and place these results in
 a phylogenetic context. We found alpine species diversity to be greatest
 in the central Andes and western North America, and that sites with lower
 phylogenetic diversity contained species with a greater degree of alpine
 specialization. In particular, near Arctic/ boreal alpine communities were
 characterized by low phylogenetic diversity and higher degrees of alpine
 specialization, whereas the opposite was observed for southern Patagonian
 communities. These results suggest that abiotic filtering alone in these
 climatically similar regions is unlikely to explain alpine community
 assembly. Nevertheless, the overall relative rarity of alpine specialists,
 and the tendency for such specialists to be most closely related to
 montane lineages, suggested that filtering was still an important factor
 in shaping alpine community structure. This work corroborates the
 importance of a nuanced and scale-dependent perspective on the
 ‘history-filtering’ debate axis, as both factors have likely contributed
 to modern biodiversity patterns observed in alpine plant communities
 across the Americas.
description: File Descriptions: 
 "alpine_taxonomy_v9.csv" This CSV
 file lists all 2397 alpine species in our dataset.
 "strategy" column indicates if this species was
 classified as Alpine Specialist (AS), or Alpine Generalist (AG), with
 subcategories of primarily montane (MN) or primarily lowland (LW) for
 generalists based on the majority of their non-alpine range.
 "specialization" column indicates whether that genus
 contains only specialists, generalists, or both. 
 "SUPPLEMENTAL FIGURES AND TABLES"
 Contains a copy of the supplemental figures and
 tables referred to in the main text. 
 "mountain_composition" This
 folder contains alpine species lists for each mountain or mountain range
 in the Americas, as defined by the Global Mountain Biodiversity Assessment
 (GMBA).
DOI: 10.5061/dryad.j6q573ncs
title: Supporting Data To: Shark tooth collagen stable isotopes (δ15N and δ13C) as ecological proxies

description: The isotopic composition of tooth-bound collagen has long been used to
 reconstruct dietary patterns of animals in extant and paleoecological
 systems. For sharks that replace teeth rapidly in a conveyor-like system,
 stable isotopes of tooth collagen (δ13Ctooth & δ15Ntooth)
 are poorly understood and lacking in ecological context relative to other
 non-lethally sampled tissues. This tissue holds promise, because shark
 jaws may preserve isotopic chronologies from which to infer
 individual-level ecological patterns across a range of temporal
 resolutions.   Carbon and nitrogen stable isotope values
 were measured and compared between extracted tooth collagen and four
 other, non-lethally sampled tissues of varying isotopic turnover rates:
 blood plasma, red blood cells, fin, and muscle, from eight species of
 sharks. Individual-level isotopic variability of shark tooth collagen was
 evaluated by profiling teeth of different ages across whole jaws for the
 shortfin mako shark Isurus oxyrinchus and sandbar
 shark Carcharhinus plumbeus. Measurements of
 δ13Ctooth and δ15Ntooth were positively correlated with
 isotopic values from the four other tissues. Collagen δ13C was
 consistently 13C-enriched relative to all other tissues. Patterns
 for δ15N were slightly less uniform; tooth collagen was
 generally 15N-enriched relative to muscle and red blood cells,
 but congruent with fin and blood plasma (values clustered around a 1:1
 relationship).  Significant within-individual isotopic
 variability was observed across whole shortfin mako shark (δ13C
 range = 3.5‰, δ15N range = 3.8‰) and sandbar shark (δ13C
 range = 2.4‰ -5.4‰, δ15N range = 2.4‰ – 5.8‰)
 jaws, which trended with tooth age.  We conclude that tissue
 amino acid composition and associated patterns of isotopic fractionation
 result in predictable isotopic offsets between tissues. Future
 measurements will refine the use of this tissue as an ecological and
 paleoecological proxy. Within-individual variability of tooth stable
 isotope values suggests teeth of different ages may serve as ecological
 chronologies, which could be applied to studies on migration and
 individual-level diet variation across diverse time scales. Improvements
 in understanding tooth replacement rates, isotopic turnover, and
 associated fractionation of tooth collagen will enhance inferences that
 can be made from the isotopic composition of shark tooth, outlining clear
 goals for future scientific inquiry.  
description: See published article for information on sample collection,
 processing, and stable isotope measurements.