cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wm37pvmpp
title: Data and code from: A spectral three-dimensional color space model of tree crown health

description: Protecting the future of forests in the United States and other countries
 depends in part on our ability to monitor and map forest health conditions
 in a timely fashion to facilitate management of emerging threats and
 disturbances over a multitude of spatial scales. Remote sensing data and
 technologies have contributed to our ability to meet these needs, but
 existing methods relying on supervised classification are often limited to
 specific areas by the availability of imagery or training data, as well as
 model transferability. Scaling up and operationalizing these methods for
 general broadscale monitoring and mapping may be promoted by using simple
 models that are easily trained and projected across space and time with
 widely available imagery. Here, we describe a new model that classifies
 high resolution (~1 m2) 3-band red, green, blue (RGB) imagery from a
 single point in time into one of four color classes corresponding to tree
 crown condition or health: green healthy crowns, red damaged or dying
 crowns, gray damaged or dead crowns, and shadowed crowns where the
 condition status is unknown. These Tree Crown Health (TCH) models trained
 on data from the United States (US) Department of Agriculture, National
 Agriculture Imagery Program (NAIP), for all 48 States in the contiguous US
 and spanning years 2012 to 2019, exhibited high measures of model
 performance and transferability when evaluated using randomly withheld
 testing data (n = 122 NAIP state x year combinations; median
 overall accuracy 0.89-0.90; median Kappa 0.85-0.86). We present examples
 of how TCH models can detect and map individual tree mortality resulting
 from a variety of nationally significant native and invasive forest
 insects and diseases in the US. We conclude with discussion of
 opportunities and challenges for extending and implementing TCH models in
 support of broadscale monitoring and mapping of forest health.
description: Please read and review the journal publication for important
 methodological details associated with this record.
description: Please read and review the associated README files for important
 usage notes and metadata concerning all files (data, scripts, etc.)
 associated with this record.
DOI: 10.15468/dl.rkjreu
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is General Herbarium – Cryptogamy & Phanerogamy (CJBG-G) of Conservatoire et Jardin botaniques de Genève",
 "RecordedBy is Sandoz, F. & M. Wells"
 ]
}

 The dataset includes 39 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003026-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.v6wwpzgxk
title: Data from: Synergism, bifunctionality, and the evolution of a gradual sensory trade-off in hummingbird taste receptors

description: Sensory receptor evolution can imply trade-offs between ligands, but the
 extent to which such trade-offs occur and the underlying processes shaping
 their evolution is not well understood. For example, hummingbirds have
 re-purposed their ancestral savory receptor (T1R1-T1R3) to detect sugars,
 but the impact of this sensory shift on amino acid perception is unclear.
 Here, we use functional and behavioral approaches to show that the
 hummingbird T1R1-T1R3 acts as a bifunctional receptor responsive to both
 sugars and amino acids. Our comparative analyses reveal substantial
 functional diversity across the hummingbird radiation and suggest an
 evolutionary timeline for T1R1-T1R3 re-tuning. Finally, we identify a
 novel form of synergism between sugars and amino acids in vertebrate taste
 receptors. This work uncovers an unexplored axis of sensory diversity,
 suggesting new ways in which nectar chemistry and pollinator preferences
 can coevolve.
DOI: 10.5061/dryad.4qrfj6qbs
title: Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice

description: To understand the genetic basis of main culm panicle node number, maximum
 node production rate, and degree-days to heading in rice (Oryza sativa),
 we conducted genome-wide association studies using a diversity panel of
 220 rice accessions and 854,832 SNP markers generated using
 genotyping-by-sequencing (GBS), with 1X coverage. The raw genotype data
 was filtered, selecting single nucleotide polymorphisms (SNPs) having less
 than 50% missing data and minimum allele frequency (MAF) &gt;5%. After
 initial filtering, imputation was conducted using BEAGLE V4.0 in 1,075,302
 SNP markers. After imputation, the dataset was filtered a second time by
 removing SNPs with less than 5% MAF and more than 5% missing data. A total
 of 854,832 SNPs were used in the genome-wide association analyses. The
 dataset representing the genotype data of 854,832 SNP markers by 220 rice
 accessions is presented here.
description: The SNP markers were
 generated using genotyping-by-sequencing (GBS), with 1X coverage. The raw
 genotype data was filtered, selecting single nucleotide polymorphisms
 (SNPs) having less than 50% missing data and minimum allele frequency
 (MAF) &gt;5%. After initial filtering, imputation was conducted using
 BEAGLE V4.0 in 1,075,302 SNP markers. After imputation, the dataset was
 filtered a second time by removing SNPs with less than 5% MAF and more
 than 5% missing data. A total of 854,832 SNPs were used in the genome-wide
 association analyses.
DOI: 10.5061/dryad.zw3r22892
title: Data from: Not just females: the socio-ecology of social interactions between spider monkey males

description: Male-male relationships are mostly characterized by competition. However,
 males also cooperate with one another if socio-ecological conditions are
 suitable. Due to their male philopatry, need for cooperation in home range
 defence and high degree of fission-fusion dynamics, spider monkeys provide
 an opportunity to investigate how male-male interactions are associated
 with socio-ecological factors, such as the presence of potentially
 receptive females, the degree of food availability and the likelihood of
 home range defence. We tested predictions about changes in social
 interactions between wild spider monkey males in relation to these
 factors. First, males did not change their interaction patterns when
 potentially receptive females were in the subgroup compared to when they
 were absent. Second, males tended to be less tolerant of one another when
 feeding, but spent more time grooming, in contact and proximity with one
 another when food availability was lower than when it was higher. Third,
 males exchanged fewer embraces, spent less time grooming, in proximity and
 in contact with one another, and spent more time vigilant at the home
 range boundary area than at other locations. Our findings contribute to
 the understanding of social flexibility and the importance of considering
 males in socio-ecological models of any group-living species.
DOI: 10.5061/dryad.msbcc2g0f
title: Hemodynamic data from the Inspired Therapeutics NeoMate Mechanical Circulatory Support System for neonates and infants as tested in static mock circulatory loops, dynamic mock circulatory loops, and acute animal studies

description: Inspired Therapeutics (Merritt Island, FL) is developing a mechanical
 circulatory support (MCS) system designed as a single driver with
 interchangeable, extracorporeal, magnetically levitated pumps. The NeoMate
 system design features an integrated centrifugal rotary pump, motor, and
 controller that will be housed in a single compact unit. 
 Conceptually, the primary innovation of this technology will be the
 combination of disposable, low-cost pumps for use with a single,
 multi-functional, universal controller to support multiple pediatric
 cardiopulmonary indications.  In response to the paucity of
 clinically available pediatric devices, Inspired Therapeutics is
 specifically targeting the underserved neonate and infant heart failure
 (HF) patient population first.  In this article, we present the
 development of the prototype Inspired Therapeutics NeoMate System for
 pediatric left ventricular assist device (LVAD) support, and feasibility
 testing in static mock flow loops (H-Q curves), dynamic mock flow loops
 (hemodynamics), and in an acute healthy ovine model (hemodynamics and
 clinical applicability).  The resultant hydrodynamic and
 hemodynamic data demonstrated the ability of this prototype pediatric LVAD
 and universal controller to function over a range of rotary pump speeds
 (500-6000 RPM), to provide pump flow rates of up to 2.6 L/min, and to
 volume unload the left ventricle in acute animals.  Key
 engineering challenges observed and proposed solutions for the next design
 iteration are also presented.
DOI: 10.5061/dryad.4xgxd25bk
title: Reservoir water quality data

description: Potable source-water reservoirs are the main water supplies in many
 urbanizing regions, yet their long-term responses to cultural
 eutrophication are poorly documented in comparison to natural lakes,
 creating major management uncertainties. Here, long-term discrete data
 (June 2006–June 2018) for classical eutrophication water quality
 indicators, continuous depth-profile data for dissolved oxygen (DO), and
 an enhanced hybrid statistical trend analysis model were used to evaluate
 the eutrophication status of a potable source-water reservoir. Based on
 classical indicators (nitrogen - N and phosphorus - P concentrations and
 ratios; phytoplankton biomass as chlorophyll a, chla; and trophic state
 indices), the reservoir was eutrophic to hypereutrophic and
 stoichiometrically imbalanced. Anoxia/hypoxia occurred for 7-8 months
 annually system-wide, even throughout the water column for days to weeks
 in some years; and elevated total ammonia (up to ~900 µg tNH3 
 L-1) in surface waters from late summer/fall through late winter/early
 spring suggested substantial internal legacy nutrient loading. These
 surprising DO and tNH3 phenomena may characterize many reservoirs in
 urbanizing areas, and the associated cascade of negative impacts may
 increasingly affect them under global warming. Total organic carbon (TOC),
 seasonally influenced by phytoplankton biomass, commonly exceeded 6 mg L-1
 which is problematic for potable water treatment, and significantly
 trended up over time. Wet-year inflow dilution influenced an apparent
 decreasing trend in nutrients within the hypereutrophic upper reservoir,
 which receives most tributary inputs. Nevertheless, significant
 reservoir-wide trends (increasing TP, phytoplankton chla, TOC) and mid-
 and/or lower region trends (increasing TN, tNH3, decreasing TN:TP ratios)
 suggest that water quality degradation from eutrophication has worsened
 over time. These findings support broadly applicable recommendations to
 strengthen protection of potable source-water reservoirs in urbanizing
 watersheds: (i) Protective numeric water quality criteria are needed for
 TOC as well as TN, TP, and chla; (ii) Continuous diel data capture more
 realistic DO conditions than traditional sampling, and can provide
 important insights for water treatment managers; and (iii) Assessment of
 reservoir eutrophication status to track management progress over time
 should emphasize classic indicators equally as statistical trends, which
 are highly sensitive to short-term meteorological forcing.
DOI: 10.5061/dryad.pg4f4qrrc
title: Data from: Landscape complementation is a driver of bumble bee (Bombus sp.) abundance in the Canadian Rocky Mountains

description: Context: Land use change is a major factor influencing biodiversity, but
 the mechanisms that drive species losses require further examination.
 Habitat loss often reduces biodiversity, but habitat fragmentation can
 increase biodiversity when examined independently. Processes driving this
 pattern remain largely unclear. Objectives: We aimed to determine the
 effects of habitat fragmentation on bumble bee populations after
 controlling for habitat amount, and to examine possible mechanisms behind
 observed effects. Methods: We sampled 22 species of bumble bees (Bombus
 sp.) across 50 unique sites located throughout the Canadian Rockies using
 a sampling design that minimized correlations between amount and spatial
 arrangement of land covers that may represent important habitat for bees.
 We modeled bumble bee abundance, species richness and diversity as a
 function of land cover metrics. Results: Effects of land cover
 fragmentation were dependent on both the measure of fragmentation used,
 and landscape scale. Bumble bee abundance was higher where nesting habitat
 (forest) and foraging habitat (grassland) were found adjacent to each
 other within 300 m, suggesting a landscape complementation effect where
 bees benefit from having access to both land cover types in proximity to
 one another. Having available habitat split into a greater number of
 patches was detrimental when considering the immediate area (0-300 m), but
 beneficial when quantified in more distant areas (300-600 m). Conclusions:
 Landscape complementation may be an important component behind positive
 fragmentation effects. Estimates of multiple measures of fragmentation are
 important when testing the impacts of land cover and landscape changes on
 species abundance and biodiversity.
description: Bumble bee abundance data collected in 2017 and 2019 using blue
 vane traps.
description: See README file for additional information.
DOI: 10.7941/d17w62
title: Burn hot or tolerate trees: flammability decreases with shade tolerance in grasses

description: In ecosystems where trees and grasses coexist, some grass species are
 found only in open habitats and others persist under trees. The
 persistence of shade intolerant grasses in ecosystems such as open
 woodlands and savannas depends on recurrent fires to open the tree canopy.
 Therefore, grasses that depend on open sites might benefit from high
 flammability. We tested if shade intolerant grasses are more flammable
 than shade tolerant grasses and if flammability differences affected
 post-fire grass growth. We examined the relationship between shade
 tolerance and flammability by determining individual-level flammability
 and species shade tolerance of 17 grass species. We also measured grass
 traits to determine trait effects on flammability and the post-fire
 response. Grass species varied in flammability, mainly in the amount of
 heat produced during burning. Shade tolerant species produced less heat at
 50 cm above the ground. Biomass and live fuel moisture had the greatest
 effects on heat release. However, the negative effect of live fuel
 moisture on heat release at the soil surface was weakened in plants with
 high specific leaf area. In addition, grass bulk density negatively
 influenced heat release at 50 cm height. Heat release at the soil surface
 negatively influenced post-fire growth. However, the influences of soil
 heating and species-specific traits on individual survival were more
 complex with 2- and 3-way interactions. Shade tolerance was negatively
 correlated with a major axis of flammability variation: shade tolerant
 grasses produced less heat where that heat could damage tree boles. Such
 heterogeneity in grass flammability may help maintain the tree-grass
 mixture in natural plant communities. If shade tolerant grasses near trees
 cause less fire damage to woody plants, especially tree saplings, this may
 weaken positive grass-fire feedbacks and thus aid the long-term
 coexistence of trees and grasses.
DOI: 10.5061/dryad.x3ffbg7md
title: Data and analysis code for: Global protected areas seem insufficient to safeguard half of the world's mammals from human-induced extinction

description: Protected areas (PAs) are a cornerstone of global conservation and central
 to international plans to minimize global extinctions. During the coming
 century, global ecosystem destruction and fragmentation associated with
 increased human population and economic activity could make the long-term
 survival of most terrestrial vertebrates even more dependent on PAs.
 However, the capacity of the current global PA network to sustain species
 for the long term is unknown. Here, we explore this question for all
 nonvolant terrestrial
 mammals for which we found sufficient data, ∼4,000 species. We first estimate the potential population size of each such mammal species in each PA and then use three different criteria to estimate if solely the current global network of PAs might be sufficient for their long-term survival. Our analyses suggest that current PAs may fail to provide robust protection for about half the species analyzed, including most species currently listed as threatened with extinction and a third of species not currently listed as threatened. Hundreds of mammal species appear to have no viable protected populations. Underprotected species were found across all body sizes, taxonomic groups, and geographic regions. Large-bodied mammals, endemic species, and those in high-biodiversity tropical regions were particularly poorly protected by existing PAs. As new international biodiversity targets are formulated, our results suggest that the global network of PAs must be greatly expanded and most importantly that PAs must be located in diverse regions that encompass species not currently protected and must be large enough to ensure that protected species can persist for the long term.
description: Data on available habitat from Rondinini et al (2011) has been
 overlaid with the World Database on Protected Areas (https://www.protectedplanet.net/) and the population size of each species in each protected area estimated and compared to three population viability criteria. Full details in the methods of the paper.
description: Scripts should be run using R either on a computer or on a
 cluster. There are five scripts that should be run in order. The directory
 is assumed to be set up with the following subdirectories:
 Data GeneratedData
 Scripts Note, please contact
 Carlo Rondinini for access to maps of available habitat for each mammal
 species.
DOI: 10.5061/dryad.47d7wm3fq
title: Influence of beaver mimicry restoration on habitat availability for fishes, including Arctic grayling (Thymallus arcticus)

description: Beaver-dam-mimicry is an emergent conservation practice. We evaluated the
 influence of constructed riffles, a unique type of beaver mimicry aimed to
 store water and allow fish passage, on habitat for fishes in one control
 reach and one manipulated reach with mimicry structures added. The beaver
 mimicry reach had deeper pool habitats and deeper and wider riffle
 habitats compared to an unmanipulated control reach. Dissolved oxygen was
 similar among reaches, averaging 8.7 ± 0.2 and 8.9 mg/L in the beaver
 mimicry and control reaches, respectively. Sediment size was also similar
 among reaches, with a D50 of 8.1 and 10.6 mm in the beaver mimicry and
 control reaches, respectively. The beaver mimicry reach had little to no
 overhanging bank vegetation or riparian vegetation shade cover, while the
 control had 38% of its bank covered by canopy and 56% overhung by
 vegetation. These riparian characteristics result from a legacy of
 livestock grazing and lack of consistent vegetation planting during
 restoration. Longnose dace (Rhinichthys cataractae) and white sucker
 (Catostomus commersonii) dominated in the beaver mimicry reach, together
 comprising 70% of the fish assemblage post-structure installation. Arctic
 grayling (Thymallus arcticus) were not found in the beaver mimicry reach
 but were present in the control, albeit in small numbers of only 3% of the
 assemblage post-structure installation. These results highlight the need
 to consider both in-stream and riparian habitat features for fishes, as
 well as timescales of both hydrological and ecological outcomes in
 restoration design.
DOI: 10.6071/m3wm3g
title: SnowClim v1.0: High-resolution snow model and data for the western United States

description: Seasonal snowpack dynamics shape the biophysical and societal
 characteristics of many global regions. However, snowpack accumulation and
 duration have generally declined in recent decades largely due to
 anthropogenic climate change. Mechanistic understanding of snowpack
 spatiotemporal heterogeneity and climate change impacts will benefit from
 snow data products that are based on physical principles, that are
 simulated at high spatial resolution, and that cover large geographic
 domains. Most existing datasets do not meet these requirements, hindering
 our ability to understand both contemporary and changing snow regimes and
 to develop adaptation strategies in regions where snowpack patterns and
 processes are important components of Earth systems. We developed a
 computationally efficient process-based snow model, SnowClim, that can be
 run in the cloud. The model was evaluated and calibrated at Snowpack
 Telemetry sites across the western United States (US), achieving a
 site-median root mean square error for daily snow water equivalent of 64
 mm, bias in peak snow water equivalent of -2.6 mm, and bias in snow
 duration of -4.5 days when run hourly. Positive biases were found at sites
 with mean winter temperature above freezing where the estimation of
 precipitation phase is prone to errors. The model was applied to the
 western US (a domain covering 3.1 million km2) using newly developed
 forcing data created by statistically downscaling pre-industrial,
 historical, and pseudo-global warming climate data from the Weather
 Research and Forecasting (WRF) model. The resulting product is the
 SnowClim dataset, a suite of summary climate and snow metrics, including
 monthly snow water equivalent (SWE) and snow depth, as well as annual
 maximum SWE and snow cover duration, for the western US at 210 m spatial
 resolution (Lute et al., 2021). The physical basis, large extent,
 and high spatial resolution of this dataset enable novel analyses of
 changing hydroclimate and its implications for natural and human systems.
DOI: 10.5061/dryad.5tb2rbp5k
title: A new bohaiornithid-like bird from the Lower Cretaceous of China fills a gap in enantiornithine disparity

description: A new enantiornithine – Musivavis amabilis n. gen. n. sp. – is reported
 from the Lower Cretaceous Jehol Biota in western Liaoning, China. The new
 taxon is similar to the bohaiornithids in the robust subconical teeth,
 bluntly expanded omal ends of the furcula, caudolaterally oriented lateral
 trabeculae with triangular distal ends of the sternum, and a robust second
 pedal digit, yet it differs from members of Bohaiornithidae in several
 features recalling other enantiornithine lineages, such as the acuminate
 rostral ramus of maxilla, the shape of the coracoid lateral margin, the
 presence of craniolateral processes on the sternum, the proportions of the
 manual phalanges, and the unspecialized third pedal ungual phalanx. A
 comprehensive phylogenetic analysis of Mesozoic birds shows that homoplasy
 significantly impacts the reconstruction of enantiornithine relationships.
 When all phylogenetic characters are considered of equal weight, Musivavis
 is reconstructed in a lineage related to a radiation of large-bodied
 enantiornithines including Bohaiornithidae and Pengornithidae. Alternative
 scenarios based on progressive downweighting of the homoplastic characters
 support more basal placements of the pengornithids among Enantiornithes,
 but do not alter the affinity of Musivavis as a member of the
 “bohaiornithid-grade” group.