cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.eg4mjf
title: Occurrence Download

description: A dataset containing 492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bowringia callicarpa",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 492 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002454-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7gb
title: Foraging and spatial ecology of a polydomous carpenter ant (Camponotus leydigi) in tropical cerrado savanna: A natural history account

description: Carpenter ants (genus Camponotus) are considered to be predominantly
 omnivorous, mixing several feeding habits that include predation,
 scavenging of animal matter, and plant-derived resources. Nitrogen
 acquisition is crucial for the nutritional ecology of ant colonies since
 growing larvae require sustainable protein provisioning. Here, we
 investigate the foraging ecology and the spatial nesting structure of the
 carpenter ant Camponotus leydigi in Brazilian cerrado savanna. By marking
 workers from different nests with distinct colors, we revealed that C.
 leydigi occupies physically separated but socially connected nests (up to
 30 m apart), a phenomenon known as polydomy. Observational data on
 aboveground internest movements in C. leydigi corroborate cooperative
 exchanges between nest units and confirm several types of social
 connections, including internest transfer of liquid and solid food,
 transport of colony members (brood, workers), movement of solitary
 workers, and internest recruitment. Polydomous C. leydigi allocate
 foragers throughout 1,700 m2, feeding mostly on termites and plant-derived
 exudates. Influx of exudates is threefold higher compared to solid food.
 Uric acid pellets excreted by lizards comprise 20% of the solid diet in C.
 leydigi, a rare quantitative assessment of this peculiar type of nitrogen
 complementation in ants. Based on video recordings, we hypothesize that
 nest decentralization in C. leydigi may reduce foraging constraints caused
 by overt interference by the aggressive ant Ectatomma brunneum, which
 regularly blocks nest entrances. Our field study enhances the importance
 of natural history data to clarify selective pressures underlying the
 evolution of particular behavioral patterns (nutritional and nesting
 habits) in ants.
DOI: 10.5061/dryad.2rbnzs7kk
title: Data from: Machine learning to predict delayed cerebral ischemia and outcomes in subarachnoid hemorrhage

description: Objective: To determine whether machine learning (ML) algorithms can
 improve the prediction of delayed cerebral ischemia (DCI) and
 functional-outcomes after subarachnoid hemorrhage (SAH). Methods: ML
 models and standard models (SM) were trained to predict DCI and
 functional-outcomes with data collected within 3 days of admission.
 Functional-outcomes at discharge and at 3-months were quantified using the
 modified Rankin scale (mRS) for neurological disability (dichotomized as
 ‘good’ (mRS≤3) vs ‘bad’ (mRS≥4) outcomes). Concurrently, clinicians
 prospectively prognosticated 3-month outcomes of patients.  The
 performance of ML, SM and clinicians are retrospectively compared.
 Results: DCI status, discharge, and 3-month outcomes were available for
 399, 393 and 240 subjects respectively. Prospective clinician (an
 attending, a fellow and a nurse) prognostication of 3-month outcomes was
 available for 90 subjects. ML models yielded predictions with the
 following AUC (area under the receiver operating curve) scores: 0.75 ±
 0.07 (95% CI: 0.64 to 0.84) for DCI, 0.85 ± 0.05 (95% CI: 0.75 to 0.92)
 for discharge outcome, and 0.89 ± 0.03 (95% CI: 0.81 to 0.94) for 3-month
 outcome. ML outperformed SMs, improving AUC by 0.20 (95% CI: -0.02–0.4)
 for DCI, by 0·07 ± 0.03 (95% CI: -0.0018–0.14) for discharge outcomes, by
 0.14 (95% CI: 0.03 –0.24) for 3-month outcomes and matched physician’s
 performance in predicting 3-month outcomes. Conclusion: ML models
 significantly outperform SMs in predicting DCI and functional-outcomes and
 has the potential to improve SAH management.
DOI: 10.5061/dryad.2jm63xsmc
title: Data from: Chromosome-level genome assembly of the coastal horseshoe crab (Tachypleus gigas)

description: Horseshoe crabs, represented by only four extant species, have existed for
 around 500 million years. However, their existence is now under threat
 because of anthropogenic activities. The availability of genomic resources
 for these species will be valuable in planning appropriate conservation
 measures. Whole-genome sequences are currently available for three
 species. In this study, we have generated a chromosome‐level genome
 assembly of the fourth species, the Asian coastal horseshoe crab
 Tachypleus gigas (genome size 2.0 Gb). The genome
 assembly has a scaffold N50 value of 140 Mb with approximately 97% of the
 assembly mapped to 14 scaffolds representing 14 chromosomes of T. gigas.
 In addition, we have generated the complete mitochondrial genome sequence
 and deep-coverage transcriptome assemblies for four tissues. A total of
 26,159 protein-coding genes were predicted in the genome. The T. gigas
 genome contains five Hox clusters similar to the mangrove horseshoe crab
 Carcinoscorpius rotundicauda, suggesting that the common ancestor of
 horseshoe crabs already possessed five Hox clusters. Phylogenomic and
 divergence time analysis suggested that the American and Asian horseshoe
 crab lineages shared a common ancestor around the Silurian period (~436
 Ma). Comparison of the T. gigas genome with those of other horseshoe crab
 species with chromosome-level assemblies provided insights into the
 chromosomal rearrangement events that occurred during the emergence of
 these species. The genomic resources of T. gigas will be useful for
 understanding their genetic diversity and population structure and would
 help in designing strategies for managing and conserving their stocks
 across Asia.
DOI: 10.5061/dryad.cvdncjt22
title: Data from: The costs of ignoring species detectability on functional diversity estimation

description: Functional diversity (FD) approaches have been increasingly used to
 understand ecosystem functioning in bird communities. These typically rely
 on the assumption that species are perfectly detected in the field,
 despite the fact that imperfect detection represents a ubiquitous source
 of bias in biodiversity studies. This may be notably important in FD
 studies, because detection may depend on the functional traits used to
 compute FD metrics. However, little effort has been devoted to account for
 imperfect detection in FD studies, and therefore the degree to which
 species traits and detectability affects FD remains poorly understood. We
 predict that observed FD metrics may either under- or overestimate
 detection-corrected FD, because FD has multiple independent dimensions
 with different data properties. We assessed whether detection was related
 to bird traits (body mass, diet, and foraging stratum), accounting for
 habitat type, season, and phylogeny. We then used a multi-species
 occupancy model to obtain detection-corrected FD metrics (functional
 richness FRic, functional evenness FEve, and functional divergence FDiv),
 and compared observed and detection-corrected FD estimates in bird
 communities from east-central Argentina. Some functional types of birds
 (raptors and insectivores) were more easily overlooked, whereas others
 (seed and leave eaters) were more easily detected. Some observed FD
 metrics underestimated detection-corrected FD (FRic and FDiv), whereas
 some others (FEve) overestimated detection-corrected FD. Both observed and
 detection-corrected FRic revealed differences between seasons, but not
 between habitat types. However, detection-corrected FEve and FDiv showed
 differences between seasons, contrary to observed estimates. Our results
 indicate that failure to account for unequal ease of detecting species can
 lead to erroneous estimates of FD because some functional types of birds
 are more easily overlooked. We outline some guidelines to help
 ornithologists identifying under which circumstances detection may be a
 concern and warn against the indiscriminate use of FD metrics without
 accounting for species detection.
description: Datasets used to estimate detection-corrected
 occurrence probabilites (Bayesian multi-species multi-season occupancy
 model) and compute bird functional diversity metrics.
description: <strong>Multi-species multi-season occupancy
 model</strong> This dataset serves as input for
 the Script S1. R code to fit the multi-species
 multi-season occupancy model. To compute functional diversity metrics,
 this data frame should be transposed. See README file for a
 description of the content of all
 datafiles. multispecies_occupancy_model.csv
 <strong>Bird functional trait data</strong>
 See README file for a description of the content of all
 datafiles. bird_functional_traits.csv
DOI: 10.5061/dryad.dncjsxkx2
title: Species diversity and biological trait function: Effectiveness of ant–plant mutualism decreases as ant species diversity increases

description: One of the major concerns of ecological and evolutionary research is the
 prediction of community function in relation to the degree of
 biodiversity. To clarify the relationship between biodiversity and the
 expression of plant defence traits, we investigated ant–plant defensive
 mutualism in the pioneer plant Mallotus japonicus at several sites across
 Japan. The plant bears ant-attracting extrafloral nectaries (EFNs) and
 food bodies (FBs) as indirect defence traits. To reveal variations in
 ant–plant interactions in the field, we measured species richness of
 nectar-feeding ants and interaction strength between each ant species and
 the plant (visiting frequency of each ant species to the plant). We also
 investigated the expression of EFNs and FBs in natural plant populations
 at the study sites. To assess the defensive quality of each ant species,
 we then experimentally estimated the aggressiveness of the dominant ant
 species. To examine the link between ant species richness and the
 defensive function of ants, we conducted an ant-exclusion experiment and a
 common garden experiment to clarify whether the defence efficacy of ants
 varied in relation to ant species richness. Ant species richness differed
 among the study sites. We found negative relationships between ant species
 richness and the mean interaction strength of ant species, the interaction
 strength of aggressive ant species, and the number of EFNs per leaf. The
 effectiveness of indirect defence by ants was poor at sites where ant
 species richness was high. When cultivated in the same environment, plants
 from sites with low ant species richness developed a larger number of EFNs
 per leaf than those from sites with high ant species richness. Our results
 suggest that facultative ant–plant defensive mutualism is weakened at
 sites where ant species richness is high, resulting in a decrease in the
 number of EFNs per leaf. Such a link between species richness and an
 indirect trait function may help us to understand the evolutionary
 patterns of various species traits in complex biological communities.
DOI: 10.5061/dryad.6wwpzgmwc
title: Data from: Tradeoffs in moving citizen-based anuran call surveys online during the SARS-CoV-2 pandemic: lessons from rural Appalachia, USA

description: Citizen science approaches provide adaptable methodologies for enhancing
 the natural history knowledge of understudied taxa and engaging
 underserved populations with biodiversity. However, transitions to remote,
 virtual training and participant recruitment in response to public health
 crises like the SARS-CoV-2 pandemic have the potential to disrupt citizen
 science projects. We present a comparison of outputs from a citizen
 science initiative built around call surveys for the Mountain Chorus Frog
 (Pseudacris brachyphona), an understudied anuran, in Appalachian Virginia,
 USA prior to and during the SARS-CoV-2 pandemic. A transition to virtual
 training in this initiative did not lead to a decrease in scientific
 output and led to unexpected natural history insight about our focal
 taxon; however, a reliance on virtual instruction did decrease overall
 participation by local residents, particularly for rural K-12 students. We
 discuss the tradeoffs exhibited by the adaptation of our initiative to a
 virtual format and provide recommendations for other citizen science
 initiatives facing similar restrictions in the face of current and future
 public health crises.
description: This dataset represents verified citizen science submissions for
 Mountain Chorus Frogs (<em>Pseudacris brachyphona</em>) across
 southwest Virginia, USA in 2019 and 2020. Project participants recorded
 observations of calling Mountain Chorus Frogs from private and public
 lands following training by the project investigators, recording audio
 and/or video evidence of calling frogs with their smartphone device. Only
 those observations that could be verified by accompanying audio/video or
 photographic evidence are included. We have processed the data presented
 here in two important ways: (i) removing the names of observers to align
 with institutional protocols involving the use of human subjects,
 replacing names with generalized observer categories (Student Trainees and
 Non-Student/Amateur Naturalist Participants), and (ii) obscuring
 geographic coordinates to two decimal places. The latter step was taken to
 avoid presenting precise locality data for our focal taxon, which is of
 high conservation concern, at the recommendation of our state's
 wildlife agency, as well as to avoid publishing the precise locality data
 for private citizens' places of residence, where several observations
 were made.
description: Please see the Methods description accompanying this dataset for
 information on the dataset's geographic coordinates. The
 "Habitat Type" and "Landownership Type"
 columns reflect the location of each observation relative to aquatic
 habitat features and public versus private lands, as determined via field
 visits and remote sensing data. "Submission Format" refers to
 the type of data (audio/video recording, photograph) used by citizen
 scientists to communicate observations with the investigators.
DOI: 10.5061/dryad.p8cz8w9n3
title: Data from: Cyanophage propagation in the freshwater cyanobacterium Phormidium is constrained by phosphorus limitation and enhanced by elevated pCO2

description: Intensification of human activities has led to changes in the
 availabilities of CO2 and nutrients in freshwater ecosystems,
 which may greatly alter the physiological status
 of phytoplankton. Viruses require hosts for their reproduction
 and shifts in phytoplankton host physiology through global
 environmental change may thus affect viral infections as well.
 Various studies have investigated the impacts of single environmental
 factors on phytoplankton virus propagation, yet little is known
 about the impacts of multiple factors, particularly in freshwater
 systems. We therefore tested the combined effects of phosphorus
 limitation and elevated pCO2 on the propagation of a
 cyanophage infecting a freshwater cyanobacterium. To this end, we
 cultured Phormidium in P-limited chemostats under ambient (400
 µatm) and elevated (800 µatm) pCO2 at growth rates of 0.6, 0.3,
 and 0.05 d-1. Host C:P ratios generally increased with
 strengthened P-limitation and with elevated pCO2. Upon host
 steady state conditions, virus growth characteristics were
 obtained in separate infection assays where hosts were infected
 by the double-stranded DNA cyanophage PP. Severe P-limitation
 (host growth 0.05 d-1) led to a 85% decrease in cyanophage
 production rate and a 73% decrease in burst size compared to the
 0.6 d-1 grown P-limited cultures. Elevated pCO2 induced a
 96% increase in cyanophage production rate and a 57% increase in
 burst size, as well as an 85% shorter latent period as compared to ambient
 pCO2 at the different host growth rates. In addition, elevated
 pCO2 caused a decrease in the plaquing efficiency and an increase
 in the abortion percentage for the 0.05 d-1 P-limited treatment,
 while the plaquing efficiency increased for the 0.6 d-1 P-limited
 cultures. Together, our results demonstrate interactive effects
 of elevated pCO2 and P-limitation on cyanophage propagation, and
 show that viral propagation is generally constrained by
 P-limitation but enhanced with elevated pCO2. Our findings
 indicate that global change will likely have a severe impact on
 virus growth characteristics and thereby on the control
 of cyanobacterial hosts in freshwater ecosystems.
description: This dataset was collected based on laboratory experiments. The
 cyanobacterial host (<em>Phormidium</em> sp.) was grown in
 chemostats at three different dilution rates, each at an ambient and
 elevated pCO<sub>2</sub> treatment. Once in steady state,
 cells were plated and a number of plaque assays were performed to test
 several infection characteristics.
description: The host data was not replicated, and the means were taking over
 time in steady state. All virus data was obtained through replicated
 plaque assays.
DOI: 10.5061/dryad.h70rxwdgg
title: Variance in lifetime reproductive success of male polar bears

description: Despite the important role that population density plays in ecological and
 evolutionary processes, studies of solitary species that occur at low
 densities remain scarce. In the context of mating systems, density is
 expected to influence the ability of males to find and monopolize mates,
 in turn influencing variance in lifetime mating/reproductive success and
 the opportunity for selection. Herein we investigate variance in male
 lifetime mating success, lifetime reproductive success, and the mating
 system of a sexually dimorphic carnivore that occurs at low densities, the
 polar bear (Ursus maritimus). Across 17 cohorts, born from 1975 to 1991,
 male lifetime mating success ranged from 0 to10 mates and lifetime
 reproductive success from 0 to 14 cubs; 40% of known-age males were not
 known to have reproduced. The opportunity for sexual selection (Is = 1.66,
 range = 0.60-4.99) and selection (I = 1.76, range: 0.65-4.89) were low
 compared to species with similar levels of sexual size dimorphism. Skew in
 male lifetime reproductive success was also low but significant for most
 cohorts indicating non-random reproductive success. Age-specific
 reproductive success was biased toward males from 11-17 years of age, with
 variation in fecundity (54%) but not longevity (10%) playing an important
 role in male reproduction. Our results support a growing body of evidence
 that suggests that male-biased size dimorphism and polygynous mating
 systems need not be associated with high variance in male mating and/or
 reproductive success.
description: All methods are descriped in the publication.
description: <strong>Fitness measurements of adult male polar
 bears</strong> Fitness measurements and year of
 birth are provided for all male bears in the study. Details on data
 collection and abbreviations can be found in the publication. (see data
 file Richardson et al. cohort data.xlsx)
 <strong>Age frequency data</strong>
 Age frequency data for paternal assignments (see Malenfant et al.
 2016) and capture sample from the western Hudson Bay polar bear program.
 Data file (Richardson et al. age frequency data.xlsx) contains two work
 books. 'Paternity age frequency' contains the frequency of
 paternal assignments for each age class and 'Capture age
 frequency' contains the age frequency of male bears from
 1980-2010.
DOI: 10.5061/dryad.p2ngf1vnn
title: Data from: Evidence for a thoracic crop in the workers of some Neotropical Pheidole species (Formicidae: Myrmicinae)

description: The ability of ant colonies to transport, store, and distribute food
 resources through trophallaxis is a key advantage of social
 life.  Nonetheless, how the structure of the digestive system has
 adapted across the ant phylogeny to facilitate these abilities is still
 not well understood.  The crop and proventriculus, structures in
 the ant foregut (stomodeum), have received most attention for their roles
 in trophallaxis. However, potential roles of the esophagus have not been
 as well studied. Here, we report for the first time the presence of an
 auxiliary thoracic crop in Pheidole aberrans and Pheidole deima using
 X-ray micro-computed tomography and 3D segmentation. Additionally, we
 describe morphological modifications involving the endo and exoskeleton
 that are associated with the presence of the thoracic crop. Our results
 indicate that the presence of a thoracic crop in major workers suggests
 their potential role as repletes or live food reservoirs, expanding the
 possibilities of tasks assumed by these individuals in the colony. Our
 contribution emphasizes the utility of combining data from external and
 internal morphology to better understand functional and behavioral
 mechanisms.
DOI: 10.5061/dryad.gb5mkkwmx
title: Disease management in two sympatric Apterostigma fungus-growing ants for control the parasitic fungus Escovopsis

description: Antagonistic interactions between host and parasites are often embedded in
 networks of interacting species, in which hosts may be attacked by
 competing parasites species, and parasites may infect more than one host
 species. To better understand the evolution of host defenses and parasite
 counter defenses in the context of a multihost, multiparasite system, we
 studied two sympatric species, of congeneric fungus-growing ants (Attini)
 species and their symbiotic fungal cultivars, which are attacked by
 multiple morphotypes of parasitic fungi in the genus, Escovopsis. To
 assess whether closely-related ant species and their cultured fungi are
 evolving defenses against the same or different parasitic strains, we
 characterized Escovopsis that were isolated from colonies of sympatric
 Apterostigma dentigerum and A. pilosum. We assessed in vitro and in vivo
 interactions of these parasites with their hosts. While the ant cultivars
 are parasitized by similar Escovopsis spp., the frequency of infection by
 these pathogens differs between the two ant species. The ability of the
 host fungi to suppress Escovopsis growth, as well as ant defensive
 responses towards the parasites, differ depending on the parasite strain
 and on the host ant species.
description: Nest collection Fungal isolation and dna
 extraction Infection experiments