The bii4africa dataset of faunal and floral population intactness estimates across Africa’s major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/ taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Does defoliation frequency and severity influence plant productivity? The role of grazing management and soil nutrients

Rangeland management approaches, including rotational grazing, rely on assumptions about plant growth responses to the intensity, or severity (sward height) plus frequency, of defoliation. We tested these assumptions at the farm, patch and plant scale using data from a grazing management trial in an Eastern Cape mesic grassland of South Africa along with field plot and glasshouse pot experiments. The grazing trial tested season-long grazing (SLG), four-camp grazing (FCG) and holistic planned grazing (HPG) at equivalent stocking rates over three years. We found that grass growth responses in both potted plants and field plots were reduced under more frequent and severe defoliation but that this was mitigated under elevated soil nutrients, in line with the Compensatory Continuum Hypothesis which predicts that compensatory growth will increase across an increasing fertility gradient. In the farm trial, SLG, which theoretically causes high frequency, low severity defoliation, reduced bare ground cover and increased vegetation greenness with increasing defoliation intensity on nutrient-rich soils. This effect was not present under FCG or HPG and disappeared under very high defoliation intensities and on relatively water- and nutrient-poor soils. Managers are advised to only increase grazing frequency on relatively high nutrient soils, while maximizing recovery on poorer nutrient soilspublishedVersio

Linking green infrastructure to urban heat and human health risk mitigation in Oslo, Norway

The predicted extreme temperatures of globalwarming aremagnified in cities due to the urban heat island effect. Even if the target for average temperature increase in the Paris Climate Agreement is met, temperatures during the hottest month in a northern city like Oslo are predicted to rise by over 5 °C by 2050. We hypothesised that heat-related diagnoses for heat-sensitive citizens (75+) in Oslo are correlated to monthly air temperatures, and that green infrastructure such as tree canopy cover reduces extreme land surface temperatures and thus reduces health risk from heat exposure. Monthly air temperatures were significantly correlated to the number of skin-related diagnoses at the city level, but were unrelated to diagnoses under circulatory, nervous system, or general categories. Satellite-derived spatially-explicit measures revealed that on one of the hottest days during the summer of 2018, landscape units composed of paved, midrise or lowrise buildings gave off the most heat (39 °C), whereas units composed of complete tree canopy cover, ormixed (i.e. tree and grass) vegetation maintained temperatures of between 29 and 32 °C. Land surface temperatureswere negatively correlated to tree canopy cover (R2=0.45) and vegetation greenness (R2=0.41). In a scenario inwhich each city treewas replaced by the most common non-tree cover in its neighbourhood, the area of Oslo exceeding a 30 °C health risk threshold during the summerwould increase from23 to 29%. Combiningmodelling resultswith population at risk at census tract level, we estimated that each tree in the city currently mitigates additional heat exposure of one heatsensitive person by one day. Our results indicate that maintaining and restoring tree cover provides an ecosystem service of urban heat reduction. Our findings have particular relevance for health benefit estimation in urban ecosystem accounting and municipal policy decisions regarding ecosystem-based climate adaptation.publishedVersio

COVID-19 lockdowns cause global air pollution declines

The lockdown response to coronavirus disease 2019 (COVID-19) has caused an unprecedented reduction in global economic and transport activity. We test the hypothesis that this has reduced tropospheric and ground-level air pollution concentrations, using satellite data and a network of >10,000 air quality stations. After accounting for the effects of meteorological variability, we find declines in the population-weighted concentration of ground-level nitrogen dioxide (NO2: 60% with 95% CI 48 to 72%), and fine particulate matter (PM2.5: 31%; 95% CI: 17 to 45%), with marginal increases in ozone (O3: 4%; 95% CI: −2 to 10%) in 34 countries during lockdown dates up until 15 May. Except for ozone, satellite measurements of the troposphere indicate much smaller reductions, highlighting the spatial variability of pollutant anomalies attributable to complex NOx chemistry and long-distance transport of fine particulate matter with a diameter less than 2.5 μm (PM2.5). By leveraging Google and Apple mobility data, we find empirical evidence for a link between global vehicle transportation declines and the reduction of ambient NO2 exposure. While the state of global lockdown is not sustainable, these findings allude to the potential for mitigating public health risk by reducing “business as usual” air pollutant emissions from economic activities. Explore trends here: https:// nina.earthengine.app/view/lockdown-pollution. air quality | COVID-19 confinement | emissions | nitrogen dioxide |particulate matteracceptedVersio

Application of Landsat-derived vegetation trends over South Africa: Potential for monitoring land degradation and restoration

Monitoring vegetation change is important because the nature, extent and rate of change in key measures, such as plant biomass, cover and species composition, provides critical insight into broader environmental and land use drivers and leads to the development of appropriate policy. We used Landsat data between 1984 and 2018 to produce a map of Enhanced Vegetation Index (EVI) change over South Africa at 30 m resolution and an interactive web application to make the analysis both globally applicable and locally meaningful. We found an increase in EVI of 0.37 ± 0.59% yr−1 (mean ± standard deviation), confirming global vegetation greening trends observed with lower-resolution satellites. Mesic, productive biomes including the Albany Thicket and Savanna, exhibited the largest greening trends while browning trends were dominant in more arid biomes, such as the Succulent Karoo and Desert. Although overall EVI trends correspond to vegetation index trends derived from the Advanced Very-High-Resolution Radiometer (8 km resolution), the relative scarcity of Landsat data availability during the 1980 s is a potential source of error. Using repeat very-high-resolution satellite (ca. 3 m resolution) imagery and ground-based photography as reference, we found good correspondence with EVI trends, revealing patterns of degradation (e.g. woody plant encroachment, desertification), and restoration (e.g. increased rangeland productivity, alien clearing) over selected landscapes. The utility of the EVI trend layer to government and industry for monitoring ecosystem changes will be enhanced by the ability to distinguish climatic from anthropogenic drivers of change. This may be partially achieved though interactive exploration of the EVI trends using the application found here: http://evitrend.zsv.co.zaacceptedVersio

Urban nature in a time of crisis: recreational use of green space increases during the COVID-19 outbreak in Oslo, Norway

The global response to the COVID-19 pandemic has brought with it significant changes to human mobility patterns and working environments. We aimed to explore how social distancing measures affected recreational use of urban green space during the partial lockdown in Oslo, Norway. Mobile tracking data from thousands of recreationists were used to analyze high resolution spatio-temporal changes in activity. We estimated that outdoor recreational activity increased by 291% during lockdown relative to a 3 yr average for the same days. This increase was significantly greater than expected after adjusting for the prevailing weather and time of year and equates to approx. 86 000 extra activities per day over the municipality (population of 690 000). Both pedestrians (walking, running, hiking) and cyclists appeared to intensify activity on trails with higher greenviews and tree canopy cover, but with differences in response modulated by trail accessibility and social distancing preferences. The magnitude of increase was positively associated with trail remoteness, suggesting that green spaces facilitated social distancing and indirectly mitigated the spread of COVID-19. Finally, pedestrian activity increased in city parks, peri-urban forest, as well as protected areas, highlighting the importance of access to green open spaces that are interwoven within the built-up matrix. These findings shed new light on the value of urban nature as resilience infrastructure during a time of crisis. The current pandemic also reveals some important dilemmas we might face regarding green justice on the path towards urban planning for future sustainable cities.publishedVersio

Green Apartheid: Urban green infrastructure remains unequally distributed across income and race geographies in South Africa

Urban green infrastructure provides ecosystem services that are essential to human wellbeing. A dearth of national-scale assessments in the Global South has precluded the ability to explore how political regimes, such as the forced racial segregation in South Africa during and after Apartheid, have influenced the extent of and Access to green infrastructure over time. We investigate whether there are disparities in green infrastructure distributions across race and income geographies in urban South Africa. Using open-source satellite imagery and geographic information, along with national census statistics, we find that public and private green infrastructure is more abundant, accessible, greener and more treed in high-income relative to low-income areas, and in areas where previously advantaged racial groups (i.e. White citizens) reside. Areas with White residents report 6-fold higher income, have 11.7% greater tree cover, 8.9% higher vegetation greenness and live 700 m closer to a public park than areas with predominantly Black African, Indian, and Coloured residents. The inequity in neighborhood greenness levels has been maintained (for Indian and Coloured areas) and further entrenched (for Black African areas) since the end of Apartheid in 1994 across the country. We also find that these spatial inequities are mirrored in both private (gardens) and public (street verges, parks, green belts) spaces, hinting at the failure of governance structures to plan for and implement urban greening initiatives. By leveraging openaccess satellite data and methods presented here, there is scope for civil society to monitor urban green infrastructure over time and thereby hold governments accountable to addressing environmental justice imperatives in the future. Interact with the data here: green-apartheid.zsv.co.za.publishedVersio

Hyperlocal mapping of urban air temperature using remote sensing and crowdsourced weather data

The impacts of climate change such as extreme heat waves are exacerbated in cities where most of the world's population live. Quantifying urbanization impacts on ambient air temperatures (Tair) has relevance for human health risk, building energy use efficiency, vector-borne disease control and urban biodiversity. Remote sensing of urban climate has been focused on land surface temperature (LST) due to a scarcity of data on Tair which is usually interpolated at 1 km resolution. We assessed the efficacy of mapping hyperlocal Tair (spatial resolutions of 10–30 m) over Oslo, Norway, by integrating Sentinel, Landsat and LiDAR data with crowd-sourced Tair measurements from 1310 private weather stations during 2018. Using Random Forest regression modelling, we found that annual mean, daily maximum and minimum Tair can be mapped with an average RMSE of 0.52 °C (R2 = 0.5), 1.85 °C (R2 = 0.05) and 1.46 °C (R2 = 0.33), respectively. Mapping accuracy decreased sharply with<250 weather stations (approx. 1 station km−2) and remote sensing data averaged within a 100-500 m buffer zone around each station maximized accuracy. Further, models performed best outside of summer months when the spatial variation in temperatures were low and wind velocities were high. Finally, accuracies were not evenly distributed over space and we found the lowest mapping errors in the local climate zone characterized by compact lowrise buildings which are most relevant to city residents. We conclude that this method is transferable to other cities given there was little difference (0.02 °C RMSE) between models trained on open- (satellite and terrain) vs closed-source (LiDAR) remote sensing data. These maps can provide a complement to and validation of traditional urban canopy models and may assist in identifying hyperlocal hotspots and coldspots of relevance to urban planners