Airborne DNA reveals predictable spatial and seasonal dynamics of fungi.

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores3. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms4,5.

Geographical migration and fitness dynamics of Streptococcus pneumoniae.

Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. Many different serotypes co-circulate endemically in any one location1,2. The extent and mechanisms of spread and vaccine-driven changes in fitness and antimicrobial resistance remain largely unquantified. Here using geolocated genome sequences from South Africa (n = 6,910, collected from 2000 to 2014), we developed models to reconstruct spread, pairing detailed human mobility data and genomic data. Separately, we estimated the population-level changes in fitness of strains that are included (vaccine type (VT)) and not included (non-vaccine type (NVT)) in pneumococcal conjugate vaccines, first implemented in South Africa in 2009. Differences in strain fitness between those that are and are not resistant to penicillin were also evaluated. We found that pneumococci only become homogenously mixed across South Africa after 50 years of transmission, with the slow spread driven by the focal nature of human mobility. Furthermore, in the years following vaccine implementation, the relative fitness of NVT compared with VT strains increased (relative risk of 1.68; 95% confidence interval of 1.59-1.77), with an increasing proportion of these NVT strains becoming resistant to penicillin. Our findings point to highly entrenched, slow transmission and indicate that initial vaccine-linked decreases in antimicrobial resistance may be transient.

Groundwater-dependent ecosystem map exposes global dryland protection needs.

Groundwater is the most ubiquitous source of liquid freshwater globally, yet its role in supporting diverse ecosystems is rarely acknowledged1,2. However, the location and extent of groundwater-dependent ecosystems (GDEs) are unknown in many geographies, and protection measures are lacking1,3. Here, we map GDEs at high-resolution (roughly 30 m) and find them present on more than one-third of global drylands analysed, including important global biodiversity hotspots4. GDEs are more extensive and contiguous in landscapes dominated by pastoralism with lower rates of groundwater depletion, suggesting that many GDEs are likely to have already been lost due to water and land use practices. Nevertheless, 53% of GDEs exist within regions showing declining groundwater trends, which highlights the urgent need to protect GDEs from the threat of groundwater depletion. However, we found that only 21% of GDEs exist on protected lands or in jurisdictions with sustainable groundwater management policies, invoking a call to action to protect these vital ecosystems. Furthermore, we examine the linkage of GDEs with cultural and socio-economic factors in the Greater Sahel region, where GDEs play an essential role in supporting biodiversity and rural livelihoods, to explore other means for protection of GDEs in politically unstable regions. Our GDE map provides critical information for prioritizing and developing policies and protection mechanisms across various local, regional or international scales to safeguard these important ecosystems and the societies dependent on them.

Development of a multimodal geomarker pipeline to assess the impact of social, economic, and environmental factors on pediatric health outcomes.

OBJECTIVES: We sought to create a computational pipeline for attaching geomarkers, contextual or geographic measures that influence or predict health, to electronic health records at scale, including developing a tool for matching addresses to parcels to assess the impact of housing characteristics on pediatric health. MATERIALS AND METHODS: We created a geomarker pipeline to link residential addresses from hospital admissions at Cincinnati Children's Hospital Medical Center (CCHMC) between July 2016 and June 2022 to place-based data. Linkage methods included by date of admission, geocoding to census tract, street range geocoding, and probabilistic address matching. We assessed 4 methods for probabilistic address matching. RESULTS: We characterized 124 244 hospitalizations experienced by 69 842 children admitted to CCHMC. Of the 55 684 hospitalizations with residential addresses in Hamilton County, Ohio, all were matched to 7 temporal geomarkers, 97% were matched to 79 census tract-level geomarkers and 13 point-level geomarkers, and 75% were matched to 16 parcel-level geomarkers. Parcel-level geomarkers were linked using our exact address matching tool developed using the best-performing linkage method. DISCUSSION: Our multimodal geomarker pipeline provides a reproducible framework for attaching place-based data to health data while maintaining data privacy. This framework can be applied to other populations and in other regions. We also created a tool for address matching that democratizes parcel-level data to advance precision population health efforts. CONCLUSION: We created an open framework for multimodal geomarker assessment by harmonizing and linking a set of over 100 geomarkers to hospitalization data, enabling assessment of links between geomarkers and hospital admissions.

Global quantification of emerging and legacy per- and polyfluoroalkyl substances in indoor dust: Levels, profiles and human exposure.

This study investigated the occurrence and distribution of per- and polyfluoroalkyl substances (PFASs) in house dust samples from six regions across four continents. PFASs were detected in all indoor dust samples, with total median concentrations ranging from 17.3 to 197 ng/g. Among the thirty-one PFAS analytes, eight compounds, including emerging PFASs, exhibited high detection frequencies in house dust from all six locations. The levels of PFASs varied by region, with higher concentrations found in Adelaide (Australia), Tianjin (China), and Carbondale (United States, U.S.). Moreover, PFAS composition profiles also differed among regions. Dust from Australia and the U.S. contained high levels of 6:2 fluorotelomer phosphate ester (6:2 diPAP), while perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) were predominant in other regions. Furthermore, our results indicate that socioeconomic factors impact PFAS levels. The assessment of human exposure through dust ingestion and dermal contact indicates that toddlers may experience higher exposure levels than adults. However, the hazard quotients of PFASs for both toddlers and adults were below one, indicating significant health risks are unlikely. Our study highlights the widespread occurrence of PFASs in global indoor dust and the need for continued monitoring and regulation of these chemicals.

Climate velocities and species tracking in global mountain regions.

Mountain ranges contain high concentrations of endemic species and are indispensable refugia for lowland species that are facing anthropogenic climate change1,2. Forecasting biodiversity redistribution hinges on assessing whether species can track shifting isotherms as the climate warms3,4. However, a global analysis of the velocities of isotherm shifts along elevation gradients is hindered by the scarcity of weather stations in mountainous regions5. Here we address this issue by mapping the lapse rate of temperature (LRT) across mountain regions globally, both by using satellite data (SLRT) and by using the laws of thermodynamics to account for water vapour6 (that is, the moist adiabatic lapse rate (MALRT)). By dividing the rate of surface warming from 1971 to 2020 by either the SLRT or the MALRT, we provide maps of vertical isotherm shift velocities. We identify 17 mountain regions with exceptionally high vertical isotherm shift velocities (greater than 11.67 m per year for the SLRT; greater than 8.25 m per year for the MALRT), predominantly in dry areas but also in wet regions with shallow lapse rates; for example, northern Sumatra, the Brazilian highlands and southern Africa. By linking these velocities to the velocities of species range shifts, we report instances of close tracking in mountains with lower climate velocities. However, many species lag behind, suggesting that range shift dynamics would persist even if we managed to curb climate-change trajectories. Our findings are key for devising global conservation strategies, particularly in the 17 high-velocity mountain regions that we have identified.

Creating an interactive map visualising the geographic variations of the burden of diabetes to inform policymaking: An example from a cohort study in Tasmania, Australia.

OBJECTIVES: To visualise the geographic variations of diabetes burden and identify areas where targeted interventions are needed. METHODS: Using diagnostic criteria supported by hospital codes, 51,324 people with diabetes were identified from a population-based dataset during 2004-2017 in Tasmania, Australia. An interactive map visualising geographic distribution of diabetes prevalence, mortality rates, and healthcare costs in people with diabetes was generated. The cluster and outlier analysis was performed based on statistical area level 2 (SA2) to identify areas with high (hot spot) and low (cold spot) diabetes burden. RESULTS: There were geographic variations in diabetes burden across Tasmania, with highest age-adjusted prevalence (6.1%), excess cost ($2627), and annual costs per person ($5982) in the West and Northwest. Among 98 SA2 areas, 16 hot spots and 25 cold spots for annual costs, and 10 hot spots and 10 cold spots for diabetes prevalence were identified (p<0.05). 15/16 (94%) and 6/10 (60%) hot spots identified were in the West and Northwest. CONCLUSIONS: We have developed a method to graphically display important diabetes outcomes for different geographical areas. IMPLICATIONS FOR PUBLIC HEALTH: The method presented in our study could be applied to any other diseases, regions, and countries where appropriate data are available to identify areas where interventions are needed to improve diabetes outcomes.

Evaluating Methods for Mapping Historical Redlining to Census Tracts for Health Equity Research.

Neighborhood characteristics including housing status can profoundly influence health. Recently, increasing attention has been paid to present-day impacts of "redlining," or historic area classifications that indicated less desirable (redlined) areas subject to decreased investment. Scholarship of redlining and health is emerging; limited guidance exists regarding optimal approaches to measuring historic redlining in studies of present-day health outcomes. We evaluated how different redlining approaches (map alignment methods) influence associations between redlining and health outcomes. We first identified 11 existing redlining map alignment methods and their 37 logical extensions, then merged these 48 map alignment methods with census tract life expectancy data to construct 9696 linear models of each method and life expectancy for all 202 redlined cities. We evaluated each model's statistical significance and R2 values and compared changes between historical and contemporary geographies and populations using Root Mean Squared Error (RMSE). RMSE peaked with a normal distribution at 0.175, indicating persistent difference between historical and contemporary geographies and populations. Continuous methods with low thresholds provided higher neighborhood coverage. Weighting methods had more significant associations, while high threshold methods had higher R2 values. In light of these findings, we recommend continuous methods that consider contemporary population distributions and mapping overlap for studies of redlining and health. We developed an R application {holcmapr} to enable map alignment method comparison and easier method selection.

Latitudinal patterns in stabilizing density dependence of forest communities.

Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10-12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.

Mutualisms weaken the latitudinal diversity gradient among oceanic islands.

The latitudinal diversity gradient (LDG) dominates global patterns of diversity1,2, but the factors that underlie the LDG remain elusive. Here we use a unique global dataset3 to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography4-namely area and isolation-contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth.

Examining rehabilitation access disparities: an integrated analysis of electronic health record data and population characteristics through bivariate choropleth mapping.

BACKGROUND: Despite efforts to view electronic health records (EHR) data through an equity lens, crucial contextual information regarding patients' social environments remains limited. Integrating EHR data and Geographic Information Systems (GIS) technology can give deeper insights into the relationships between patients' social environments, health outcomes, and geographic factors. This study aims to identify regions with the fastest and slowest access to outpatient physical therapy services using bivariate choropleth maps to provide contextual insights that may contribute to health disparity in access. METHODS: This was a retrospective cohort study of patients' access timelines for the first visit to outpatient physical therapy services (n = 10,363). The three timelines evaluated were (1) referral-to-scheduled appointment time, (2) scheduled appointment to first visit time, and (3) referral to first visit time. Hot and coldspot analyses (CI 95%) determined the fastest and slowest access times with patient-level characteristics and bivariate choropleth maps that were developed to visualize associations between access patterns and disadvantaged areas using Area Deprivation Index scores. Data were collected between January 1, 2016 and January 1, 2020. EHR data were geocoded via GIS technology to calculate geospatial statistics (Gi∗ statistic from ArcGIS Pro) in an urban area. RESULTS: Statistically significant differences were found for all three access timelines between coldspot (i.e., fast access group) and hotspot (i.e., slow access group) comparisons (p < .05). The hotspot regions had higher deprivation scores; higher proportions of residents who were older, privately insured, female, lived further from clinics; and a higher proportion of Black patients with orthopaedic diagnoses compared to the coldspot regions. CONCLUSIONS: Our study identified and described local areas with higher densities of patients that experienced longer access times to outpatient physical therapy services. Integration of EHR and GIS data is a more robust method to identify health disparities in access to care. With this approach, we can better understand the intricate interplay between social, economic, and environmental factors contributing to health disparities in access to care.

Satellite mapping reveals extensive industrial activity at sea.

The world's population increasingly relies on the ocean for food, energy production and global trade1-3, yet human activities at sea are not well quantified4,5. We combine satellite imagery, vessel GPS data and deep-learning models to map industrial vessel activities and offshore energy infrastructure across the world's coastal waters from 2017 to 2021. We find that 72-76% of the world's industrial fishing vessels are not publicly tracked, with much of that fishing taking place around South Asia, Southeast Asia and Africa. We also find that 21-30% of transport and energy vessel activity is missing from public tracking systems. Globally, fishing decreased by 12 ± 1% at the onset of the COVID-19 pandemic in 2020 and had not recovered to pre-pandemic levels by 2021. By contrast, transport and energy vessel activities were relatively unaffected during the same period. Offshore wind is growing rapidly, with most wind turbines confined to small areas of the ocean but surpassing the number of oil structures in 2021. Our map of ocean industrialization reveals changes in some of the most extensive and economically important human activities at sea.

Temporal analysis and spatial distribution of acquired syphilis in the state of Mato Grosso, Brazil, 2010-2021: an ecological study.

OBJECTIVE: To analyze the temporal trend and the spatial distribution of acquired syphilis in Mato Grosso, Brazil, between 2010 and 2021. METHODS: This was an ecological study using notifications of acquired syphilis held on the Notifiable Health Conditions Information System. Detection rates were calculated by health macro-region and three-year periods (2010-2012, 2013-2015, 2016-2018, 2019-2021). The jointpoint method was used to calculate annual percentage change (APC). Thematic maps of Bayesian rates were built and distribution was analyzed using Local Moran. RESULTS: The detection rate increased from 16.2 per 100,000 inhabitants in the first three-year period (2010-2012) to 70.0 in the last three-year period (2019-2021). The Central-North macro-region had the highest rate in the last three years (94.3/100,000 inhab.), while the highest upward trend occurred in the Central-Northwest macro-region, from 2013 to 2018 (APC = 50.2; 95%CI 26.3;78.6). There was an increase in Bayesian rates in most municipalities. CONCLUSION: There was a trend towards an increase in acquired syphilis, especially in the last two three-year periods.

A unified explanation for the morphology of raised peatlands.

Raised peatlands, or bogs, are gently mounded landforms that are composed entirely of organic matter1-4 and store the most carbon per area of any terrestrial ecosystem5. The shapes of bogs are critically important because their domed morphology4,6,7 accounts for much of the carbon that bogs store and determines how they will respond to interventions8,9 to stop greenhouse gas emissions and fires after anthropogenic drainage10-13. However, a general theory to infer the morphology of bogs is still lacking4,6,7. Here we show that an equation based on the processes universal to bogs explains their morphology across biomes, from Alaska, through the tropics, to New Zealand. In contrast to earlier models of bog morphology that attempted to describe only long-term equilibrium shapes4,6,7 and were, therefore, inapplicable to most bogs14-16, our approach makes no such assumption and makes it possible to infer full shapes of bogs from a sample of elevations, such as a single elevation transect. Our findings provide a foundation for quantitative inference about the morphology, hydrology and carbon storage of bogs through Earth's history, as well as a basis for planning natural climate solutions by rewetting damaged bogs around the world.

The genetic legacy of the expansion of Bantu-speaking peoples in Africa.

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1-7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000-4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.

Revising the global biogeography of annual and perennial plants.

There are two main life cycles in plants-annual and perennial1,2. These life cycles are associated with different traits that determine ecosystem function3,4. Although life cycles are textbook examples of plant adaptation to different environments, we lack comprehensive knowledge regarding their global distributional patterns. Here we assembled an extensive database of plant life cycle assignments of 235,000 plant species coupled with millions of georeferenced datapoints to map the worldwide biogeography of these plant species. We found that annual plants are half as common as initially thought5-8, accounting for only 6% of plant species. Our analyses indicate that annuals are favoured in hot and dry regions. However, a more accurate model shows that the prevalence of annual species is driven by temperature and precipitation in the driest quarter (rather than yearly means), explaining, for example, why some Mediterranean systems have more annuals than desert systems. Furthermore, this pattern remains consistent among different families, indicating convergent evolution. Finally, we demonstrate that increasing climate variability and anthropogenic disturbance increase annual favourability. Considering future climate change, we predict an increase in annual prevalence for 69% of the world's ecoregions by 2060. Overall, our analyses raise concerns for ecosystem services provided by perennial plants, as ongoing changes are leading to a higher proportion of annual plants globally.

Geocoding processes in cohort studies: methods applied in the EpiFloripa Aging.

OBJECTIVE: To describe the process and epidemiological implications of georeferencing in EpiFloripa Aging samples (2009-2019). METHOD: The EpiFloripa Aging Cohort Study sought to investigate and monitor the living and health conditions of the older adult population (≥ 60) of Florianópolis in three study waves (2009/2010, 2013/2014, 2017/2019). With an automatic geocoding tool, the residential addresses were spatialized, allowing to investigate the effect of the georeferencing sample losses regarding 19 variables, evaluated in the three waves. The influence of different neighborhood definitions (census tracts, Euclidean buffers, and buffers across the street network) was examined in the results of seven variables: area, income, residential density, mixed land use, connectivity, health unit count, and public open space count. Pearson's correlation coefficients were calculated to evaluate the differences between neighborhood definitions according to three variables: contextual income, residential density, and land use diversity. RESULT: The losses imposed by geocoding (6%, n = 240) caused no statistically significant difference between the total sample and the geocoded sample. The analysis of the study variables suggests that the geocoding process may have included a higher proportion of participants with better income, education, and living conditions. The correlation coefficients showed little correspondence between measures calculated by the three neighborhood definitions (r = 0.37-0.54). The statistical difference between the variables calculated by buffers and census tracts highlights limitations in their use in the description of geospatial attributes. CONCLUSION: Despite the challenges related to geocoding, such as inconsistencies in addresses, adequate correction and verification mechanisms provided a high rate of assignment of geographic coordinates, the findings suggest that adopting buffers, favored by geocoding, represents a potential for spatial epidemiological analyses by improving the representation of environmental attributes and the understanding of health outcomes.

High-resolution maps show that rubber causes substantial deforestation.

Understanding the effects of cash crop expansion on natural forest is of fundamental importance. However, for most crops there are no remotely sensed global maps1, and global deforestation impacts are estimated using models and extrapolations. Natural rubber is an example of a principal commodity for which deforestation impacts have been highly uncertain, with estimates differing more than fivefold1-4. Here we harnessed Earth observation satellite data and cloud computing5 to produce high-resolution maps of rubber (10 m pixel size) and associated deforestation (30 m pixel size) for Southeast Asia. Our maps indicate that rubber-related forest loss has been substantially underestimated in policy, by the public and in recent reports6-8. Our direct remotely sensed observations show that deforestation for rubber is at least twofold to threefold higher than suggested by figures now widely used for setting policy4. With more than 4 million hectares of forest loss for rubber since 1993 (at least 2 million hectares since 2000) and more than 1 million hectares of rubber plantations established in Key Biodiversity Areas, the effects of rubber on biodiversity and ecosystem services in Southeast Asia could be extensive. Thus, rubber deserves more attention in domestic policy, within trade agreements and in incoming due-diligence legislation.