cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21554466
title: Population genomics of emerging <i>Elizabethkingia anophelis</i> pathogens reveals potential outbreak and rapid global dissemination

description: <i>Elizabethkingia anophelis</i> is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the <i>E. anophelis</i> geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of <i>E. anophelis</i> pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original <i>E. anophelis</i> shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair <i>mutY</i> gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI <i>E. anophelis</i> was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of <i>E. anophelis</i> causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of <i>E. anophelis</i> populations will generate further knowledge for optimizing future prevent global outbreak infections.
DOI: 10.6084/m9.figshare.21554466.v2
title: Population genomics of emerging <i>Elizabethkingia anophelis</i> pathogens reveals potential outbreak and rapid global dissemination

description: <i>Elizabethkingia anophelis</i> is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the <i>E. anophelis</i> geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of <i>E. anophelis</i> pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original <i>E. anophelis</i> shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair <i>mutY</i> gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI <i>E. anophelis</i> was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of <i>E. anophelis</i> causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of <i>E. anophelis</i> populations will generate further knowledge for optimizing future prevent global outbreak infections.
DOI: 10.6084/m9.figshare.19298659.v2
title: Molecular epidemiology of carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> in China

description: The epidemiological features of the newly emerged carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-HvKP) and its potential threat to human health are currently unknown. In this study, a total of 784 <i>bla</i><sub>KPC-2</sub>-bearing CRKP strains collected from three hospitals located at different geographical locales in China during 2014–2017 were subjected to molecular typing, screening of virulence plasmid, string test and WGS (367/784 strains). The proportion of CRKP among all clinical <i>K. pneumoniae</i> strains increased sharply in China during 2014–2017. A large proportion (58%) of these CRKP strains were found to harbour a virulence-encoding plasmid, while only 13% of such strains exhibited a hypervirulent phenotype by string test and neutrophil assay. The lack of hypervirulent phenotype in virulent plasmid-bearing CRKP strains was found to be due to the mutation’s presence on <i>rmpA</i> and <i>rmpA2</i> genes, which rendered them non-functional, while some strains carrying wild type <i>rmpA</i> did not exhibit hypervirulent phenotype either suggesting that other factors might also contribute to the hypervirulence of CRKP. Phylogenetic and SNP analysis indicated that the transmission of these CRKP strains in China likely involved several major clones of ST11. Carriage of IncFII pSWU01-like, <i>bla</i><sub>KPC-2</sub>-bearing plasmid was found to be the major mechanism of carbapenem resistance in these CRKP strains. In conclusion, our data indicated that the prevalence of CRKP strains carrying the virulence plasmid has rapidly increased in China, while genetic markers were not correlated well with the hypervirulent phenotypes, which call for a better definition and screening for these truly hypervirulent CR-HvKP strains in clinical settings.
DOI: 10.6084/m9.figshare.21554466.v1
title: Population genomics of emerging <i>Elizabethkingia anophelis</i> pathogens reveals potential outbreak and rapid global dissemination

description: <i>Elizabethkingia anophelis</i> is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the <i>E. anophelis</i> geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of <i>E. anophelis</i> pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original <i>E. anophelis</i> shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair <i>mutY</i> gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI <i>E. anophelis</i> was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of <i>E. anophelis</i> causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of <i>E. anophelis</i> populations will generate further knowledge for optimizing future prevent global outbreak infections.
DOI: 10.5061/dryad.1366f
title: Data from: Workforce effects and the evolution of complex sociality in wild Damaraland mole rats

description: Explaining the evolution of eusocial and cooperatively breeding societies
 demands that we understand the effects of workforce size on the
 reproductive success of breeders. This challenge has yet to be addressed
 in the family that arguably exhibits the most extreme outcomes of
 vertebrate social evolution, the African mole rats (Bathyergidae), leaving
 the ultimate causes of their many unusual adaptations open to debate. Here
 we report—using a 14-year field study of wild Damaraland mole rats,
 Fukomys damarensis—that workers appear to have strong but unusual effects
 on offspring. Groups with larger workforces exhibited substantially higher
 rates of offspring recruitment while maintaining high juvenile survival
 rates, relationships that may have favored the evolution of the delayed
 dispersal, cooperation, morphological specialization, and unusual patterns
 of longevity that characterize such societies. Offspring reared by larger
 workforces also showed slower growth, however. That reduced offspring
 growth in larger groups has also been documented under ad lib. food
 conditions in the laboratory raises the possibility that this reflects
 socially induced growth restraint rather than simple constraints on
 resource availability. Our findings shed new light on the evolution of
 complex sociality in this enigmatic clade and highlight further departures
 from the norms reported for other cooperative vertebrates.
description: DATA for WORKFORCE
 EFFECTS IN MOLE-RAT SOCIETIESThe data file contains
 three data sheets, corresponding to each of the three major analyses in
 the paper. The column headings describe the contents of each field and
 should be self-explanatory.
DOI: 10.6084/m9.figshare.20387119
title: Induction of amphotericin B resistance in susceptible <i>Candida auris</i> by extracellular vesicles

description: Drug resistance derived from extracellular vesicles (EVs) is an increasingly important research area but has seldom been described regarding fungal pathogens. Here, we characterized EVs derived from a triazole-resistant but amphotericin B-susceptible strain of <i>Candida auris</i>. Nano- to microgram concentrations of <i>C. auris</i> EVs prepared from both broth and solid agar cultures could robustly increase the yeast’s survival against both pure and clinical amphotericin B formulations in a dose-dependent manner, resulting in up to 16-fold changes of minimum inhibitory concentration. Meanwhile, this effect was not observed upon addition of these EVs to <i>C. albicans</i>, nor upon addition of <i>C. albicans</i> EVs to <i>C. auris</i>. No change in susceptibilities was observed upon EV treatment for fluconazole, voriconazole, micafungin, and flucytosine. Mass spectrometry indicated the presence of immunogenic-/drug resistance-implicated proteins in <i>C. auris</i> EVs, including alcohol dehydrogenase 1 as well as <i>C. albicans</i> Mp65-like and Xog1-like proteins in high quantities. Based on these observations, we propose a potential species-specific role for EVs in amphotericin B resistance in <i>C. auris</i>. These observations may provide critical insights into treatment of multidrug-resistant <i>C. auris</i>.
DOI: 10.6084/m9.figshare.20387119.v2
title: Induction of amphotericin B resistance in susceptible <i>Candida auris</i> by extracellular vesicles

description: Drug resistance derived from extracellular vesicles (EVs) is an increasingly important research area but has seldom been described regarding fungal pathogens. Here, we characterized EVs derived from a triazole-resistant but amphotericin B-susceptible strain of <i>Candida auris</i>. Nano- to microgram concentrations of <i>C. auris</i> EVs prepared from both broth and solid agar cultures could robustly increase the yeast’s survival against both pure and clinical amphotericin B formulations in a dose-dependent manner, resulting in up to 16-fold changes of minimum inhibitory concentration. Meanwhile, this effect was not observed upon addition of these EVs to <i>C. albicans</i>, nor upon addition of <i>C. albicans</i> EVs to <i>C. auris</i>. No change in susceptibilities was observed upon EV treatment for fluconazole, voriconazole, micafungin, and flucytosine. Mass spectrometry indicated the presence of immunogenic-/drug resistance-implicated proteins in <i>C. auris</i> EVs, including alcohol dehydrogenase 1 as well as <i>C. albicans</i> Mp65-like and Xog1-like proteins in high quantities. Based on these observations, we propose a potential species-specific role for EVs in amphotericin B resistance in <i>C. auris</i>. These observations may provide critical insights into treatment of multidrug-resistant <i>C. auris</i>.
DOI: 10.6084/m9.figshare.20387119.v1
title: Induction of amphotericin B resistance in susceptible <i>Candida auris</i> by extracellular vesicles

description: Drug resistance derived from extracellular vesicles (EVs) is an increasingly important research area but has seldom been described regarding fungal pathogens. Here, we characterized EVs derived from a triazole-resistant but amphotericin B-susceptible strain of <i>Candida auris</i>. Nano- to microgram concentrations of <i>C. auris</i> EVs prepared from both broth and solid agar cultures could robustly increase the yeast’s survival against both pure and clinical amphotericin B formulations in a dose-dependent manner, resulting in up to 16-fold changes of minimum inhibitory concentration. Meanwhile, this effect was not observed upon addition of these EVs to <i>C. albicans</i>, nor upon addition of <i>C. albicans</i> EVs to <i>C. auris</i>. No change in susceptibilities was observed upon EV treatment for fluconazole, voriconazole, micafungin, and flucytosine. Mass spectrometry indicated the presence of immunogenic-/drug resistance-implicated proteins in <i>C. auris</i> EVs, including alcohol dehydrogenase 1 as well as <i>C. albicans</i> Mp65-like and Xog1-like proteins in high quantities. Based on these observations, we propose a potential species-specific role for EVs in amphotericin B resistance in <i>C. auris</i>. These observations may provide critical insights into treatment of multidrug-resistant <i>C. auris</i>.
DOI: 10.5061/dryad.k231g
title: Data from: Determinants of individual foraging specialisation in large marine vertebrates, the Antarctic and Subantarctic fur seals

description: 1. The degree of individual specialization in resource use differs widely
 among wild populations where individuals range from fully generalized to
 highly specialized. This interindividual variation has profound
 implications in many ecological and evolutionary processes. A recent
 review proposed four main ecological causes of individual specialization:
 interspecific and intraspecific competition, ecological opportunity and
 predation. 2. Using the isotopic signature of subsampled whiskers, we
 investigated to what degree three of these factors (interspecific and
 intraspecific competition and ecological opportunity) affect the
 population niche width and the level of individual foraging specialization
 in two fur seal species, the Antarctic and subantarctic fur seals
 (Arctocephalus gazella and Arctocephalus tropicalis), over several years.
 3. Population niche width was greater when the two seal species bred in
 allopatry (low interspecific competition) than in sympatry or when seals
 bred in high-density stabilized colonies (high intraspecific competition).
 In agreement with the niche variation hypothesis (NVH), higher population
 niche width was associated with higher interindividual niche variation.
 However, in contrast to the NVH, all Antarctic females increased their
 niche width during the interbreeding period when they had potential access
 to a wider diversity of foraging grounds and associated prey (high
 ecological opportunities), suggesting they all dispersed to a similar
 productive area. 4. The degree of individual specialization varied among
 populations and within the annual cycle. Highest levels of interindividual
 variation were found in a context of lower interspecific or higher
 intraspecific competition. Contrasted results were found concerning the
 effect of ecological opportunity. Depending on seal species, females
 exhibited either a greater or lower degree of individual specialization
 during the interbreeding period, reflecting species-specific biological
 constraints during that period. 5. These results suggest a significant
 impact of ecological interactions on the population niche width and degree
 of individual specialization. Such variation at the individual level may
 be an important factor in the species plasticity with significant
 consequences on how it may respond to environmental variability.
description: Kernaleguen_et_al_JAE_dataCarbon and nitrogen isotopic values of whiskers of Antarctic and subantarctic fur seal females during the pup-rearing and inter-breeding periods.
DOI: 10.5061/dryad.b233b
title: Data from: Sunbird hovering behavior is determined by both the forager and resource plant

description: The long-standing paradigm that pollination systems adapted to hovering
 birds evolved only in the New World was recently challenged by the
 discovery of hovering pollination by Old World specialized passerine
 pollinators. This raises the possibility that hovering pollination may
 evolve more easily than previously believed, given sufficient selective
 pressure on plant traits, on nectarivory, or both. We observed foraging
 behavior by the sunbird Cyanomitra oritis at flowers of the native Old
 World plant Impatiens sakeriana. We measured the length of pedicels and
 peduncles (PedPed length), which can make the flowers difficult to reach
 while the bird perches on the stem, and determined if it influenced
 sunbird hovering or perching at a flower. Detailed analyses of video
 recordings showed that sunbirds only hovered at flowers with a long
 PedPed, whereas they employed both foraging modes when an adequate perch
 was available. A hovering sunbird could deplete nectar in a shorter time
 than a perching one. The frequency of visits was not greater at flowers
 with longer PedPed or with more open I. sakeriana flowers in the vicinity.
 Our study provides evidence that sunbird behavior does not follow simple
 energetic models, and that some sunbird pollination systems in the Old
 World resemble highly specialized hummingbird systems in the New World
 much more than expected, especially the overall adaptation of the system
 to bird hovering.
description: Sunbird behaviour at
 flowersSunbird behaviour manner
 while feeding at flowers according to the plant traits.Data.xlsx
DOI: 10.5061/dryad.g23f6
title: Data from: Rapid increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests

description: The current unprecedented outbreak of mountain pine beetle (Dendroctonus
 ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada
 has resulted in a landscape consisting of a mosaic of forest stands at
 different stages of mortality. Within forest stands, understory
 communities are the reservoir of the majority of plant species diversity
 and influence the composition of future forests in response to
 disturbance. Although changes to stand composition following beetle
 outbreaks are well documented, information on immediate responses of
 forest understory plant communities is limited. The objective of this
 study was to examine the effects of D. ponderosae-induced tree mortality
 on initial changes in diversity and productivity of understory plant
 communities. We established a total of 110 1-m2 plots across eleven mature
 lodgepole pine forests to measure changes in understory diversity and
 productivity as a function of tree mortality and below ground resource
 availability across multiple years. Overall, understory community
 diversity and productivity increased across the gradient of increased tree
 mortality. Richness of herbaceous perennials increased with tree mortality
 as well as soil moisture and nutrient levels. In contrast, the diversity
 of woody perennials did not change across the gradient of tree mortality.
 Understory vegetation, namely herbaceous perennials, showed an immediate
 response to improved growing conditions caused by increases in tree
 mortality. How this increased pulse in understory richness and
 productivity affects future forest trajectories in a novel system is
 unknown.
description: pec_et_al_understory_diversity_environment
DOI: 10.5061/dryad.09h8p8d
title: Data from: Effects of increased N and P availability on biomass allocation and root carbohydrate reserves differ between N‐fixing and non‐N‐fixing savanna tree seedlings

description: In mixed tree‐grass ecosystems, tree recruitment is limited by demographic
 bottlenecks to seedling establishment arising from inter‐ and
 intra‐life‐form competition, and disturbances such as fire. Enhanced
 nutrient availability resulting from anthropogenic nitrogen (N) and
 phosphorus (P) deposition can alter the nature of these bottlenecks by
 changing seedling growth and biomass allocation patterns, and lead to
 longer‐term shifts in tree community composition if different plant
 functional groups respond differently to increased nutrient availability.
 However, the extent to which tree functional types characteristic of
 savannas differ in their responses to increased N and P availability
 remains unclear. We quantified differences in above‐ and belowground
 biomass, and root carbohydrate contents in seedlings of multiple N‐fixing
 and non‐N‐fixing tree species characteristic of Indian savanna and dry
 forest ecosystems in response to experimental N and P additions. These
 parameters are known to influence the ability of plants to compete, as
 well as survive and recover from fires. N‐fixers in our study were
 co‐limited by N and P availability, while non‐N‐fixers were N limited.
 Although both functional groups increased biomass production following
 fertilization, non‐N‐fixers were more responsive and showed greater
 relative increases in biomass with fertilization than N‐fixers. N‐fixers
 had greater baseline investment in belowground resources and root
 carbohydrate stocks, and while fertilization reduced root:shoot ratios in
 both functional groups, root carbohydrate content only reduced with
 fertilization in non‐N‐fixers. Our results indicate that, even within a
 given system, plants belonging to different functional groups can be
 limited by, and respond differentially to, different nutrients, suggesting
 that long‐term consequences of nutrient deposition are likely to vary
 across savannas contingent on the relative amounts of N and P being
 deposited in sites.
description: Savanna tree seedling
 responses to fertilisation - biomass, root carbohydrate and
 nodulationThis dataset is from an
 experiment which assessed the effect of nitrogen and phosphorus
 fertilisation on seedlings of multiple N-fixing and non-N-fixing savanna
 tree species. The zip folder contains three csv files with data on
 seedling biomass, root storage carbohydrate and root nodule mass responses
 to nutrient addition.Varma_et_al_savanna_seedlings_nutrients_data.zip