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Lipid profile and differential lipids in serum related to severity of community-acquired pneumonia--a pilot study
<p>This study aimed to characterize the lipidomic responses to community-acquired pneumonia (CAP) and provide new insight into the underlying mechanisms of pathogenesis and potential avenues for diagnostic and therapeutic treatments. Lipidomic profiles were generated using ultra high-performance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) platform. Spearman’s rank correlation test and multiple linear regression analysis were applied to explore the lipids correlation with clinical parameters. Kaplan–Meier methods were used to build 30-day survival curves. From UHPLC-MS/MS a total of 509 and 195 lipid species were detected in the positive and negative ionisation mode respectively. Positive ionisation covered six lipid classes (glycerol-phospholipids, glycerolipids, sphingolipids, sterol-lipids, prenol-lipids, and fatty acid), whilst negative ionisation covered three (glycerol-phospholipids, sphingolipids, fatty acid). Four lipids were selected as target: PC (16:0_18:1), PC (18:2_20:4), PC (36:4), and PC (38:6). Areas under the curve for all four lipids were superior to pneumonia severity index and CURB-65 (confusion, urea, respiratory rate, blood pressure, and age ≥65 years old) for discriminating severe CAP from CAP. PC (18:2_20:4), PC (38:6), and PC (36:4) were negatively related to fraction of inspiration O<sub>2</sub>; PC (16:0_18:1) and PC (18:2_20:4) had significantly linear relationship with the procalcitonin. Patients with an elevated level of PC (16:0_18:1) had significantly increased hospital stays. As the relative abundance of PC (18:2_20:4), PC (36:4), and PC (38:6) decreased, the length of hospitalization days and 30-day mortality rate increased significantly (all log-rank <em>p</em><0.05). Therefore, the UHPLC-MS/MS platform’s serum lipidomics approach can help reveal lipid changes during CAP and establish lipid profiles related to disease severity.</p>
Data from: Host species composition influences infection severity among amphibians in the absence of spillover transmission
Wildlife epidemiological outcomes can depend strongly on the composition of an ecological community, particularly when multiple host species are affected by the same pathogen. However, the relationship between host species richness and disease risk can vary with community context and with the degree of spillover transmission that occurs among co-occurring host species. We examined the degree to which host species composition influences infection by Batrachochytrium dendrobatidis (Bd), a widespread fungal pathogen associated with amphibian population declines around the world, and whether transmission occurs from one highly susceptible host species to other co-occurring host species. By manipulating larval assemblages of three sympatric amphibian species in the laboratory, we characterized the relationship between host species richness and infection severity, whether infection mediates growth and survivorship differently across various combinations of host species, and whether Bd is transmitted from experimentally inoculated tadpoles to uninfected tadpoles. We found evidence of a dilution effect where Bd infection severity was dramatically reduced in the most susceptible of the three host species (Anaxyrus boreas). Infection also mediated survival and growth of all three host species such that the presence of multiple host species had both positive (e.g., infection reduction) and negative (e.g., mortality) effects on focal species. However, we found no evidence that Bd infection is transmitted by this species. While these results demonstrate that host species richness as well as species identity underpin infection dynamics in this system, dilution is not the product of reduced transmission via fewer infectious individuals of a susceptible host species. We discuss various mechanisms, including encounter reduction and antagonistic interactions such as competition and opportunistic cannibalism that may act in concert to mediate patterns of infection severity, growth, and mortality observed in multihost communities.
Data from: Disassembly of an epibenthic assemblage in a sustained severely hypoxic event in a northeast Pacific basin
As global ocean deoxygenation proceeds and the frequency of extreme low-oxygen (hypoxic) events increases, seafloor ecosystems will inevitably be affected. Our study examines how benthic community responses scale with the severity and spatial extent of hypoxia. Saanich Inlet is a natural model system for testing the effects of hypoxic conditions that determine the benthic megafaunal community structure during annual deoxygenation and reoxygenation. In 2016, an anomalously severe and widespread hypoxic event occurred in the fjord after a decade of oxygen decline at a rate of 0.07 mL L−1 y−1 as measured by a cabled seafloor observatory. We use a living ecological time-series generated from remotely operated vehicle surveys to assess how the benthic megafaunal community disassembled in response to this extreme hypoxic event. Three benthic surveys at similar times in 2013 and 2016 reveal large increases in the area of seafloor bathed in anoxic and hypoxic waters in the latter year. Both bottom oxygen and species depth distributions shoaled from 2013 to 2016, accompanied by a 56% overall decline in megafauna. The abundant habitat-forming pennatulacean octocoral, Halipteris willemoesi, decreased in abundance by 92.3% from fall 2013 to fall 2016, and pandalid shrimp disappeared from the community. Hypoxia-tolerant species experienced milder losses, and two new species occurred in 2016 – one a predator on the coral. Co-occurrence analyses revealed loss of significant community segregation from 2013 to 2016, and a re-mix of pairwise species co-occurrences in the latter year. The loss of oxygenated habitat compressed species into narrower depth ranges and led to disassembly probably through niche space constriction, while decimation of some populations eliminated key community associations. Community fragmentation and disruption of interactions is a possible outcome for many marine benthic ecosystems as marine hypoxia intensifies.
Data from: Association between severity of MERS-CoV infection and incubation period
We analyzed data for 170 patients in South Korea who had laboratory-confirmed infection with Middle East respiratory syndrome coronavirus. A longer incubation period was associated with a reduction in the risk for death (adjusted odds ratio/1-day increase in incubation period 0.83, 95% credibility interval 0.68–1.03).
Data from: Maintenance of genetic diversity in an introduced island population of Guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation
Fifteen Guanacos were introduced to Staats Island in Falklands/Malvinas archipelago from Patagonia in the 1930s. After introduction, the Guanaco population increased to almost 400 animals that retained a footprint of the founding effect and bottleneck reflected in the genetic status of this isolated population. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulation, and (ii) assess the likely source population of the introduced Guanacos. Genetic variation estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci were compared among 154 Guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variation on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island Guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the 'all at once' taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing 'chirosurveillance' and conservation strategies.
Assessing the Ecological Impacts of Biomass Harvesting along a Disturbance Severity Gradient
<p>Disturbance is a central driver of forest development and ecosystem processes with variable effects within and across ecosystems. Despite the high levels of variation in disturbance severity often observed in forests following natural and anthropogenic disturbance, studies quantifying disturbance impacts often rely on categorical classifications, thus limiting opportunities to examine potential gradients in ecosystem response to a given disturbance or management regime. Given the potential increases in disturbance severity associated with global change, as well as shifts in management regimes related to procurement of biofuel feedstocks, there is an increasing need to quantitatively describe disturbance severity and associated responses of forest development, soil processes, and structural conditions. This study took advantage of two replicated large-scale studies of forest biomass harvesting in <i>Populus tremuloides</i> and <i>Pinus bansksiana </i>forests, respectively, to develop and test the utility of a continuous, quantitative disturbance severity index (DSI) for describing post-harvest response of plant communities and nutrient pools to different levels of biomass removal and legacy retention (i.e., live trees and coarse woody material). There was a high-degree of variability in DSI within categorical treatments associated with different levels of legacy retention and regression models using DSI as a predictor explained a portion of the variation (>50%) for many of the ecosystem- and community-level responses to biomass harvesting examined. Nutrient losses associated with biomass harvesting were positively related to disturbance severity, particularly in <i>P. tremuloides</i> forests, with post-harvest nutrient availability generally declining along the gradient of impacts. Consistent with expectations from ecological theory, species richness and diversity of woody plant communities were greatest at intermediate disturbance severities and regeneration densities of dominant trees species were most abundant at highest levels of disturbance. Although categorical benchmarks will continue to be the primary way through which management guidelines are conveyed to practitioners, evaluation of their effectiveness at sustaining ecosystem functioning should be through continuous analyses, such as the DSI approach used in this study, to allow for the more precise identification of thresholds that ensure a range of desirable outcomes exist across managed landscapes.</p>
Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)
AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. RESULTS: Between five and eight genetically distinct lineages were identified that appear comparable to species with minimal or no hybridization. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (c. seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations.
Data from: Neurofunctional abnormalities during sustained attention in severe childhood abuse
Childhood maltreatment is associated with adverse affective and cognitive consequences including impaired emotion processing, inhibition and attention. However, the majority of functional magnetic resonance imaging (fMRI) studies in childhood maltreatment have examined emotion processing, while very few studies have tested the neurofunctional substrates of cognitive functions and none of attention. This study investigated the association between severe childhood abuse and fMRI brain activation during a parametric sustained attention task with a progressively increasing load of sustained attention in 21 medication-naïve, drug-free young people with a history of childhood abuse controlling for psychiatric comorbidities by including 19 psychiatric controls matched for psychiatric diagnoses, and 27 healthy controls. Behaviorally, the participants exposed to childhood abuse showed increased omission errors in the task which correlated positively trend-wise with the duration of their abuse. Neurofunctionally, the participants with a history of childhood abuse, but not the psychiatric controls, displayed significantly reduced activation relative to the healthy controls during the most challenging attention condition only in typical attention regions including left inferior and dorsolateral prefrontal cortex, insula and temporal areas. We therefore show for the first time that severe childhood abuse is associated with neurofunctional abnormalities in key ventral frontal-temporal sustained attention regions. The findings represent a first step towards the delineation of abuse-related neurofunctional abnormalities in sustained attention, which may help in the development of effective treatments for victims of childhood abuse.
Data from: Soil types select for plants with matching nutrient‐acquisition and ‐use traits in hyperdiverse and severely nutrient‐impoverished campos rupestres and cerrado in Central Brazil
1. Understanding the mechanisms that underlie the generation of beta-diversity remains a challenge in ecology. Underground plant adaptations to environmental gradients have received relatively little attention. 2. We studied plant nutrient-acquisition strategies and nutrient-use efficiency at three stages of pedogenesis in infertile soils from campos rupestres and on less infertile soil from cerrado sensu stricto in Brazil. All soils support very high plant diversity with high species turnover between soil types at small spatial scales (meters). We expected that differences in nutrient–acquisition and –use strategies would be associated with this high species turnover. With severely decreasing phosphorus (P) availability, we expected the effectiveness of arbuscular mycorrhizal (AM) symbioses for plant P acquisition to decrease, and reliance on non-mycorrhizal strategies (NM) to increase, while maintaining efficient nutrient-use. 3. Concentrations of total soil P and nitrogen (N) were greater in soils in cerrado than in those from campos rupestres, and the more weathered soils from campos rupestres were severely P– and N–impoverished. The proportion of the root length colonised by AM fungi was 71% in the soils from the cerrado and campos rupestres. Conversely, the proportion of species with non-mycorrhizal P-acquisition strategies such as rhizosheaths was greater in the most P-impoverished soils. Leaf [P] and [N] were very low and decreased with decreasing soil [P] and [N]. Leaf N: P ratios suggest P-limitation of plant productivity in the campos rupestres but N-P co-limitation in the cerrado. Photosynthetic rates decreased with increasing P-impoverishment, but photosynthetic P-use efficiency was very high and photosynthetic N-use efficiency moderately high on all soils. Most species had very high P-remobilisation efficiency during leaf senescence (>70%), but only moderate N-remobilisation efficiency (~50%). 4. Synthesis. We observed very high P-use efficiency and moderately high N-use efficiency in campos rupestres and cerrado species, consistent with plant productivity being more strongly limited by P than by N. Our findings demonstrate that different soil characteristics (nutrient availability and soil texture) select for species differing in nutrient-acquisition and -use strategies (especially belowground traits) which is likely key for the very high species turnover at a very small scale between soil types (i.e. beta-diversity) in campos rupestres and cerrado.
Serum levels of tau protein increase according to the severity of the injury in DAI rat model
<p><span><span><span><span><span><span><span><span><span><span><span>Traumatic brain injury (TBI) in the form of diffuse axonal injury (DAI) is difficult to diagnose in the early phase of the injury. Early diagnosis of DAI may provide opportunity for developing treatment and management strategies. Tau protein has been demonstrated to increase in the early phase of TBI with high diagnostic accuracy in patients with DAI. We tested the biological plausibility of tau protein using a rat DAI model by evaluating the association between serum tau levels and the severity of brain injury. DAI was induced in animals using the Marmarou model. After a survival of 60 minutes, rats were anesthetized and sacrificed after obtaining blood samples (5ml) from the heart. Eighteen rats were employed in the present study and were randomly subjected to sham-operated control (n=4), mild DAI (n=7), and severe DAI (n=7). Of seven severe DAI rats, two rats that had focal injury caused by skull fracture were excluded in the measurement of tau protein level. The serum levels of tau protein in the rat DAI model were found to increase significantly and consistently according to the severity of the injury. Rats with DAI showed significantly higher serum levels of tau protein compared to sham rats; the severe DAI rats had higher levels of tau than moderate DAI and sham rats (sham vs. mild, <i>P</i>=0.02; mild vs. severe, <i>P</i>=0.02). In conclusion, serum tau protein levels may be useful as a biomarker for diagnosing and estimating the severity of DAI in the early phase.</span></span></span></span></span></span></span></span></span></span></span></p> <div> </div>
Modelling the impact of antibody-dependent enhancement on disease severity of ZIKV and DENV sequential and co-infection
<p>Human infections with viruses of the genus <em>Flavivirus</em>, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Due to antibody dependent enhancement, secondary infection with one <em>Flavivirus</em> following primary infection with another {\it Flavivirus} can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV, little progress has been made regarding secondary infection of DENV after a primary infection of ZIKV, or DENV-ZIKV co-infection. Here, we address this critical gap by developing compartmental models of virus dynamics. We first fitted the models to published data on dengue viral loads of the primary and secondary infections with the observation that the primary infection reaches its peak much more gradually than the secondary infection. We then quantitatively show that antibody dependent enhancement (ADE) is the key factor determining a sharp increase/decrease of viral load near the peak time in the secondary infection. In comparison, our simulations of DENV and ZIKV co-infection (simultaneous rather than sequential) show that ADE has very limited influence on the peak DENV viral load. This indicates pre-existing immunity to ZIKV is the determinant of a high level of ADE effect. Our numerical simulations show that 1) in the absence of ADE effect, a subsequent co-infection is beneficial to the second virus; 2) if ADE is feasible, then a subsequent co-infection can induce greater damage to the host with a higher peak viral load and a much earlier peak time for the second virus, and for the second peak for the first virus.</p>
Data from: The journey from traffic offender to severe road trauma victim: destiny or preventive opportunity?
Background: Road trauma is a leading cause of death and injury in young people. Traffic offences are common, but their importance as a risk indicator for subsequent road trauma is unknown. This cohort study assessed whether severe road trauma could be predicted by a history of prior traffic offences. Methodology and Principal Findings: Clinical data of all adult road trauma patients admitted to the Western Australia (WA) State Trauma Centre between 1998 and 2013 were linked to traffic offences records at the WA Department of Transport. The primary outcomes were alcohol exposure prior to road trauma, severe trauma (defined by Injury Severity Score >15), and intensive care admission (ICU) or death, analyzed by logistic regression. Traffic offences directly leading to the road trauma admissions were excluded. Of the 10,330 patients included (median age 34 years-old, 78% male), 1955 (18.9%) had alcohol-exposure before road trauma, 2415 (23.4%) had severe trauma, 1360 (13.2%) required ICU admission, and 267 (2.6%) died. Prior traffic offences were recorded in 6269 (60.7%) patients. The number of prior traffic offences was significantly associated with alcohol-related road trauma (odds ratio [OR] per offence 1.03, 95% confidence interval [CI] 1.02–1.05), severe trauma (OR 1.13, 95%CI 1.14–1.15), and ICU admission or death (OR 1.10, 95%CI 1.08–1.11). Drink-drinking, seat-belt, and use of handheld electronic device offences were specific offences strongly associated with road trauma leading to ICU admission or death—all in a 'dose-related' fashion. For those who recovered from road trauma after an ICU admission, there was a significant reduction in subsequent traffic offences (mean difference 1.8, 95%CI 1.5 to 2.0) and demerit points (mean difference 7.0, 95%CI 6.5 to 7.6) compared to before the trauma event. Significance: Previous traffic offences were a significant risk factor for alcohol-related road trauma and severe road trauma leading to ICU admission or death.
Data from: Genetic and morphometric evidence for the recognition of several recently synonymized species of trans-Andean Rhamdia (Pisces: Siluriformes: Heptapteridae)
A recent taxonomic revision of the Neotropical catfish genus Rhamdia (Pisces: Siluriformes: Heptapteridae) reduced a number of described species to synonymy, especially under a broadly circumscribed R. quelen. Evidence is presented here from DNA sequence data, external morphology, and morphometrics that argues for the recognition of R. guatemalensis in Central and northern South America and R. saijaensis and R. cinerascens in the Pacific drainages of Colombia and Ecuador, respectively. The DNA data indicate that all trans-Andean samples form a monophyletic group, within which there are separate clades corresponding to R. laticauda and the synonymized R. guatemalensis, R. saijaensis, and R. cinerascens. The morphometric data substantiate the phylogenetic groupings, and in external morphology, each putative species has diagnostic characters. Rhamdia guatemalensis is characterized by insertion of the adipose fin closer to the dorsal fin than to the caudal fin and presence of a conspicuous lateral longitudinal dark band; R. saijaensis is characterized by a small head with head length 20.8–23.4% of standard length and by lacking a lateral longitudinal band; and R. cinerascens is characterized by a large head with head length 25.8–30.1% of standard length, base of the adipose fin 30.3–33.3% of standard length, outer mental barbels extending to the base of the pectoral rays, and presence of a faint lateral longitudinal band. The external morphological differences and phylogenetic relationships indicate that these groups are both recognizable and represent independent lineages, which argue for their recognition as species.
Data from: Prevalence and severity of asthmatic symptoms in Grenadian school children: the Grenada National Asthma Survey
Objective: The goal of this study was to determine the prevalence of asthma in school children in the tri-island Caribbean nation of Grenada. Setting, participants and outcomes: This was a self-report study provided to the guardians of all primary school children between ages 6 and 7 throughout Grenada, Carriacou and Petite Martinique in 2013. Of the 2362 surveys provided, 1374 were returned, resulting in a response rate of 58.2%. Only responders listing birthdays between 1 January 2006 and 31 December 2007 were included in the analysis, resulting in 1165 qualifying responders. Asthma diagnosis was based on previous physician diagnosed asthma and/or self-reported presence of wheeze in the past 12 months (current wheeze). Severity of asthma, medication usage, environmental exposures, physician and emergency department visits were compared among respondents. Results: The prevalence of wheezing in the past year was 30.5±1.8%, and of these 68.4% were previously diagnosed with asthma. Of the current wheeze participants, 39.9±9.2% reported moderate to severe asthma symptoms and increased exposure to cigarette smoke, excessive dust, burning brush and landfills. Carriacou and Petite Martinique, the two smaller islands, had a lower incidence of current wheeze (14.1±7.7%) and exposure rates to cigarette smoke and burning brush as compared to the larger, denser island of Grenada. Although 65.7% of respondents diagnosed with asthma reported taking medication, the number of annual doctor and emergency department visits were high (2.82 and 0.86, respectively). Respondents with the most severe asthma symptoms reported the most emergency department visits with an average of 1.05 visits annually, whereas respondents with moderate asthma symptoms had the most doctor visits with an average of 3.33 visits annually. Conclusions: This study indicates that the prevalence of childhood asthma in Grenada is very high and warrants policy consideration in public health and education to decrease its morbidity.
Data from: Flying between raindrops: strong seasonal turnover of several Lepidoptera groups in lowland rainforests of Mount Cameroon
1. Although seasonality in the tropics is often less pronounced than in temperate areas, tropical ecosystems show seasonal dynamics as well. Nevertheless, individual tropical insects' phenological patterns are still poorly understood, especially in the Afrotropics. To fill this gap, we investigated biodiversity patterns of Lepidoptera communities at three rainforest localities in the foothills of Mount Cameroon, West Africa, one of the wettest places in the world. 2. Our multi-taxa approach covered six lepidopteran groups (fruit-feeding butterflies and moths, the families Sphingidae, Saturniidae, and Eupterotidae, and the subfamily Arctiinae of Erebidae) with diverse life strategies. We sampled adults of the focal groups in three distinct seasons. Our sampling included standardised bait-trapping (80 traps exposed for ten days per locality and season) and attraction by light (six full nights per locality and season). 3. Altogether, our dataset comprised 20,576 specimens belonging to 559 (morpho)species of the focal groups. The biodiversity of Lepidoptera generally increased in the high-dry season, and either increased (fruit-feeding moths, Arctiinae, Saturniidae) or decreased (butterflies, Sphingidae) in the transition to the wet season in particular groups. Simultaneously, we revealed a strong species turnover of fruit-feeding Lepidoptera and Arctiinae among the seasons, indicating relatively high specialisation of these communities for particular seasons. 4. Such temporal specialisation can make the local communities of butterflies and moths especially sensitive to the expected seasonal perturbations caused by the global change. Because of the key role of Lepidoptera across trophic levels, such changes in their communities could strengthen this impact on entire tropical ecosystems.
Data from: A phylogeny of the genus Amaranthus (Amaranthaceae), based on several low-copy nuclear loci and chloroplast regions
The genus Amaranthus (pigweeds) is a group of ∼74 monoecious or dioecious annual species native to every continent but Antarctica, frequently associated with natural and human disturbance, with several economically important domesticated and weedy species. We set out to reconstruct the phylogeny of Amaranthus, with broad geographic sampling, in order to answer questions about biogeographic relationships in the genus and the monophyly of the subgenera. Fifty-eight species were included inmaximum parsimony and Bayesian phylogenetic analyses based on ITS and three low-copy nuclear genes (A36, G3PDH, and Waxy), as well as two chloroplast regions (trnL5′-trnL3′ and matK/trnK). Topology tests were also employed to test taxonomic hypotheses about incongruence between trees and the monophyly of clades containing Galápagos species. Our analyses support the origin of the genus in the Americas, with a single long-distance dispersal event to the Old World, and both nuclear and chloroplast trees recover three to fourmajor clades, roughly corresponding to three subgenera recognized based on morphology. However, there are species in all of these clades that were not predicted based on morphology, and we discover previously unsuspected relationships between Galápagos species and species from the North American Southwest, which comprise small monophyletic groups outside of the three recognized subgenera. Additionally, an important herbicide resistant weed species (A. palmeri) and its sister species are placed into different large clades based on nuclear or chloroplast data, suggesting a chloroplast capture event. These results will provide a basis for further exploration of the evolution of weedy ecological strategies in the group.
Data from: The shift from plant–plant facilitation to competition under severe water deficit is spatially explicit
The stress-gradient hypothesis predicts a higher frequency of facilitative interactions as resource limitation increases. Under severe resource limitation, it has been suggested that facilitation may revert to competition, and identifying the presence as well as determining the magnitude of this shift is important for predicting the effect of climate change on biodiversity and plant community dynamics. In this study, we perform a meta-analysis to compare temporal differences of species diversity and productivity under a nurse plant (Retama sphaerocarpa) with varying annual rainfall quantity to test the effect of water limitation on facilitation. Furthermore, we assess spatial differences in the herbaceous community under nurse plants in situ during a year with below-average rainfall. We found evidence that severe rainfall deficit reduced species diversity and plant productivity under nurse plants relative to open areas. Our results indicate that the switch from facilitation to competition in response to rainfall quantity is nonlinear. The magnitude of this switch depended on the aspect around the nurse plant. Hotter south aspects under nurse plants resulted in negative effects on beneficiary species, while the north aspect still showed facilitation. Combined, these results emphasize the importance of spatial heterogeneity under nurse plants for mediating species loss under reduced precipitation, as predicted by future climate change scenarios. However, the decreased water availability expected under climate change will likely reduce overall facilitation and limit the role of nurse plants as refugia, amplifying biodiversity loss.
Within-host priority effects and epidemic timing determine outbreak severity in coinfected populations
Coinfections of hosts by multiple pathogen species are ubiquitous, but predicting their impact on disease remains challenging. Interactions between coinfecting pathogens within hosts can alter pathogen transmission, with the impact on transmission typically dependent on the relative arrival order of pathogens within hosts (within-host priority effects). However, it is unclear how these within-host priority effects influence multi-pathogen epidemics, particularly when the arrival order of pathogens at the host population scale varies. Here we combined models and experiments with zooplankton and their naturally co-occurring fungal and bacterial pathogens to examine how within-host priority effects influence multi-pathogen epidemics. Epidemiological models parameterized with within-host priority effects measured at the single host scale predicted that advancing the start date of bacterial epidemics relative to fungal epidemics would decrease mean bacterial prevalence in a multi-pathogen setting, while models without within-host priority effects predicted the opposite effect. We tested these predictions with experimental multi-pathogen epidemics. Empirical dynamics matched predictions from the model including within-host priority effects, providing evidence that within-host priority effects influenced epidemic dynamics. Overall, within-host priority effects may be a key element of predicting multi-pathogen epidemic dynamics in the future, particularly as shifting disease phenology alters the order of infection within hosts.
Data from: Home loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing
Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove since the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mtDNA across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation result from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.