Diversification of refugia types needed to secure the future of coral reefs subject to climate change.

Identifying locations of refugia from the thermal stresses of climate change for coral reefs and better managing them is one of the key recommendations for climate change adaptation. We review and summarize approximately 30 years of applied research focused on identifying climate refugia to prioritize the conservation actions for coral reefs under rapid climate change. We found that currently proposed climate refugia and the locations predicted to avoid future coral losses are highly reliant on  excess heat metrics, such as degree heating weeks. However, many existing alternative environmental, ecological, and life-history variables could be used to identify other types of refugia that lead to the desired diversified portfolio for coral reef conservation. To improve conservation priorities for coral reefs, there is a need to evaluate and validate the predictions of climate refugia with long-term field data on coral abundance, diversity, and functioning. There is also the need to identify and safeguard locations displaying resistance toprolonged exposure to heat waves and the ability to recover quickly after thermal exposure. We recommend using more metrics to identify a portfolio of potential refugia sites for coral reefs that can avoid, resist, and recover from exposure to high ocean temperatures and the consequences of climate change, thereby shifting past efforts focused on avoidance to a diversified risk-spreading portfolio that can be used to improve strategic coral reef conservation in a rapidly warming climate.

Diversificación de los tipos de refugio necesarios para asegurar el futuro de los arrecifes de coral sujetos al cambio climático Resumen Una de las principales recomendaciones para la adaptación al cambio climático es identificar los refugios de los arrecifes de coral frente al estrés térmico del cambio climático y mejorar su gestión. Revisamos y resumimos ∼30 años de investigación aplicada centrada en la identificación de refugios climáticos para priorizar las acciones de conservación de los arrecifes de coral bajo un rápido cambio climático. Descubrimos que los refugios climáticos propuestos actualmente y las ubicaciones que pueden evitarlos dependen en gran medida de métricas de exceso de calor, como las semanas de calentamiento en grados (SCG). Sin embargo, existen muchas variables alternativas de historia vital, ambientales y ecológicas que podrían utilizarse para identificar otros tipos de refugios que resulten en el acervo diversificado que se desea para la conservación de los arrecifes de coral. Para mejorar las prioridades de conservación de los arrecifes de coral, es necesario evaluar y validar las predicciones sobre refugios climáticos con datos de campo a largo plazo sobre abundancia, diversidad y funcionamiento de los corales. También es necesario identificar y salvaguardar lugares que muestren resistencia a la exposición climática prolongada a olas de calor y la capacidad de recuperarse rápidamente tras la exposición térmica. Recomendamos utilizar más métricas para identificar un acervo de posibles lugares de refugio para los arrecifes de coral que puedan evitar, resistir y recuperarse de la exposición a las altas temperaturas oceánicas y las consecuencias del cambio climático, para así desplazar los esfuerzos pasados centrados en la evitación hacia un acervo diversificado de riesgos que pueda utilizarse para mejorar la conservación estratégica de los arrecifes de coral en un clima que se calienta rápidamente.

Nature-based climate solutions require a mix of socioeconomic and governance attributes.

Nature-based climate solutions (NCS) can play a crucial role in reducing climate change. There is, however, a lack of understanding of the biophysical, social, and political contexts surrounding NCS, which hampers its practical implementation. Here, we used estimates of carbon sink potential to identify socioeconomic and ecological factors that may stimulate NCS implementation in developing economies. We considered carbon sink potential for eight NCS, including reforestation, peatland restoration, natural forest management, improved rice cultivation, optimal grazing intensity, grazing (legumes), avoided peatland impacts, and avoided coastal impacts. Food insecurity hotspots, which currently receive the most development aid, have the lowest likelihood of realizing NCS' potential. Poor governance structures and food insecurity impede the implementation of NCS projects at the country level. By carefully assessing complementary food security, sustainable financing, and soil quality safeguards, NCS as a nationally determined contribution to climate mitigation can be made more effective.

Land-use and climate risk assessment for Earth's remaining wilderness.

Earth's wilderness areas are reservoirs of genetic information and carbon storage systems, and are vital to reducing extinction risks. Retaining the conservation value of these areas is fundamental to achieving global biodiversity conservation goals; however, climate and land-use risk can undermine their ability to provide these functions. The extent to which wilderness areas are likely to be impacted by these drivers has not previously been quantified. Using climate and land-use change during baseline (1971-2005) and future (2016-2050) periods, we estimate that these stressors within wilderness areas will increase by ca. 60% and 39%, respectively, under a scenario of high emission and land-use change (SSP5-RCP8.5). Nearly half (49%) of all wilderness areas could experience substantial climate change by 2050 under this scenario, potentially limiting their capacity to shelter biodiversity. Notable climate (>5 km year-1) and land-use (>0.25 km year-1) changes are expected to occur more rapidly in the unprotected wilderness, including the edges of the Amazonian wilderness, Northern Russia, and Central Africa, which support unique assemblages of species and are critical for the preservation of biodiversity. However, an alternative scenario of sustainable development (SSP1-RCP2.6) would attenuate the projected climate velocity and land-use instability by 54% and 6%, respectively. Mitigating greenhouse gas emissions and preserving the remaining intact natural ecosystems can help fortify these bastions of biodiversity.

Protecting connectivity promotes successful biodiversity and fisheries conservation.

The global decline of coral reefs has led to calls for strategies that reconcile biodiversity conservation and fisheries benefits. Still, considerable gaps in our understanding of the spatial ecology of ecosystem services remain. We combined spatial information on larval dispersal networks and estimates of human pressure to test the importance of connectivity for ecosystem service provision. We found that reefs receiving larvae from highly connected dispersal corridors were associated with high fish species richness. Generally, larval "sinks" contained twice as much fish biomass as "sources" and exhibited greater resilience to human pressure when protected. Despite their potential to support biodiversity persistence and sustainable fisheries, up to 70% of important dispersal corridors, sinks, and source reefs remain unprotected, emphasizing the need for increased protection of networks of well-connected reefs.

Land use planning to support climate change adaptation in threatened plant communities.

Among the many causes of habitat loss, urbanization coupled with climate change has produced some of the greatest local extinction rates and has led to the loss of many native species. Managing native vegetation in a rapidly expanding urban setting requires land management strategies that are cognizant of these impacts and how species and communities may adapt to a future climate. Here, we demonstrate how identifying climate refugia for threatened vegetation communities in an urban matrix can be used to support management decisions by local government authorities under the dual pressures of urban expansion and climate change. This research was focused on a local government area in New South Wales, Australia, that is undergoing significant residential, commercial and agricultural expansion resulting in the transition of native forest to other more intensive land-uses. Our results indicate that the key drivers of change from native vegetation to urban and agriculture classes were population density and the proximity to urban areas. We found two of the most cleared vegetation community types are physically restricted to land owned or managed by council, suggesting their long-term ecological viability is uncertain under a warming climate. We propose that land use planning decisions must recognize the compounding spatial and temporal pressures of urban development, land clearing and climate change, and how current policy responses, such as biodiversity offsetting, can respond positively to habitat shifts in order to secure the longevity of important ecological communities.

The socio-economic impacts of Covid-19 restrictions: Data from the coastal city of Mombasa, Kenya.

The novel corona virus disease (Covid-19) outbreak has caused great uncertainty in all spheres of human life. The experience has been incredibly humbling given that no country or section of society, regardless of its wealth or status, has been spared. The pandemic is not only a health crisis, but is also having serious damaging effects on societies, economies and vulnerable groups. Timely response is necessary in order to alleviate human suffering and to prevent irreversible destruction of livelihoods. This paper provides preliminary data on the socio-economic impacts of Covid-19 in the coastal city of Mombasa, Kenya, at the time of government-imposed curfews and cessation of movement. We conducted online surveys for two weeks during the restrictions period. The data was collected using online questionnaires directed at the city residents. The data highlights the mobile gender gap resulting from gender inequalities, residents' reliance on the government for Covid-19 information but lack of trust for government interventions, inadequate provisions of essential services, and the residents' lack of preparedness to tackle similar challenges in the future.

Meeting fisheries, ecosystem function, and biodiversity goals in a human-dominated world.

The worldwide decline of coral reefs necessitates targeting management solutions that can sustain reefs and the livelihoods of the people who depend on them. However, little is known about the context in which different reef management tools can help to achieve multiple social and ecological goals. Because of nonlinearities in the likelihood of achieving combined fisheries, ecological function, and biodiversity goals along a gradient of human pressure, relatively small changes in the context in which management is implemented could have substantial impacts on whether these goals are likely to be met. Critically, management can provide substantial conservation benefits to most reefs for fisheries and ecological function, but not biodiversity goals, given their degraded state and the levels of human pressure they face.

A reproducible picture of open access health facility data in Africa and R tools to support improvement.

Background: Open data on the locations and services provided by health facilities have, in some countries, allowed the development of software tools contributing to COVID-19 response. The UN and WHO encourage countries to make health facility location data open, to encourage use and improvement. We provide a summary of open access health facility location data in Africa using re-useable R code. We aim to support data analysts developing software tools to address COVID-19 response in individual countries. In Africa there are currently three main sources of such open data; 1) direct from national ministries of health, 2) a database for sub-Saharan Africa collated and published by a team from KEMRI-Wellcome Trust Research Programme and now hosted by WHO, and 3) The Global Healthsites Mapping Project in collaboration with OpenStreetMap.      Methods: We searched for and documented official national facility location data that were openly available. We developed re-useable open-source R code to summarise and visualise facility location data by country from the three sources. This re-useable code is used to provide a web user interface allowing data exploration through maps and plots of facility type. Results: Out of 52 African countries, seven currently provide an official open facility list that can be downloaded and analysed reproducibly. Considering all three sources, there are over 185,000 health facility locations available for Africa. However, there are differences and overlaps between sources and a lack of data on capacities and service provision. Conclusions: These summaries and software tools can be used to encourage greater use of existing health facility location data, incentivise further improvements in the provision of those data by national suppliers, and encourage collaboration within wider data communities. The tools are a part of the afrimapr project, actively developing R building blocks to facilitate the use of health data in Africa.

Climate-driven shift in coral morphological structure predicts decline of juvenile reef fishes.

Rapid intensification of environmental disturbances has sparked widespread decline and compositional shifts in foundation species in ecosystems worldwide. Now, an emergent challenge is to understand the consequences of shifts and losses in such habitat-forming species for associated communities and ecosystem processes. Recently, consecutive coral bleaching events shifted the morphological makeup of habitat-forming coral assemblages on the Great Barrier Reef (GBR). Considering the disparity of coral morphological growth forms in shelter provision for reef fishes, we investigated how shifts in the morphological structure of coral assemblages affect the abundance of juvenile and adult reef fishes. We used a temporal dataset from shallow reefs in the northern GBR to estimate coral convexity (a fine-scale quantitative morphological trait) and two widely used coral habitat descriptors (coral cover and reef rugosity) for disentangling the effects of coral morphology on reef fish assemblages. Changes in coral convexity, rather than live coral cover or reef rugosity, disproportionately affected juvenile reef fishes when compared to adults, and explained more than 20% of juvenile decline. The magnitude of this effect varied by fish body size with juveniles of small-bodied species showing higher vulnerability to changes in coral morphology. Our findings suggest that continued large-scale shifts in the relative abundance of morphological groups within coral assemblages are likely to affect population replenishment and dynamics of future reef fish communities. The different responses of juvenile and adult fishes according to habitat descriptors indicate that focusing on coarse-scale metrics alone may mask fine-scale ecological responses that are key to understand ecosystem functioning and resilience. Nonetheless, quantifying coral morphological traits may contribute to forecasting the structure of reef fish communities on novel reef ecosystems shaped by climate change.

Endemicity of Yaws and Seroprevalence of Treponema pallidum Antibodies in Nonhuman Primates, Kenya.

Human yaws has historically been endemic to Kenya, but current epidemiologic data are lacking. We report seroprevalence for Treponema pallidum antibodies in olive baboons (Papio anubis) and vervet monkeys (Chlorocebus pygerythrus) in Laikipia County, Kenya. Our results suggest endemicity of the yaws bacterium in monkeys, posing a possible zoonotic threat to humans.

Social-environmental drivers inform strategic management of coral reefs in the Anthropocene.

Without drastic efforts to reduce carbon emissions and mitigate globalized stressors, tropical coral reefs are in jeopardy. Strategic conservation and management requires identification of the environmental and socioeconomic factors driving the persistence of scleractinian coral assemblages-the foundation species of coral reef ecosystems. Here, we compiled coral abundance data from 2,584 Indo-Pacific reefs to evaluate the influence of 21 climate, social and environmental drivers on the ecology of reef coral assemblages. Higher abundances of framework-building corals were typically associated with: weaker thermal disturbances and longer intervals for potential recovery; slower human population growth; reduced access by human settlements and markets; and less nearby agriculture. We therefore propose a framework of three management strategies (protect, recover or transform) by considering: (1) if reefs were above or below a proposed threshold of >10% cover of the coral taxa important for structural complexity and carbonate production; and (2) reef exposure to severe thermal stress during the 2014-2017 global coral bleaching event. Our findings can guide urgent management efforts for coral reefs, by identifying key threats across multiple scales and strategic policy priorities that might sustain a network of functioning reefs in the Indo-Pacific to avoid ecosystem collapse.

A spatial database of health facilities managed by the public health sector in sub Saharan Africa.

Health facilities form a central component of health systems, providing curative and preventative services and structured to allow referral through a pyramid of increasingly complex service provision. Access to health care is a complex and multidimensional concept, however, in its most narrow sense, it refers to geographic availability. Linking health facilities to populations has been a traditional per capita index of heath care coverage, however, with locations of health facilities and higher resolution population data, Geographic Information Systems allow for a more refined metric of health access, define geographic inequalities in service provision and inform planning. Maximizing the value of spatial heath access requires a complete census of providers and their locations. To-date there has not been a single, geo-referenced and comprehensive public health facility database for sub-Saharan Africa. We have assembled national master health facility lists from a variety of government and non-government sources from 50 countries and islands in sub Saharan Africa and used multiple geocoding methods to provide a comprehensive spatial inventory of 98,745 public health facilities.

National and sub-national variation in patterns of febrile case management in sub-Saharan Africa.

Given national healthcare coverage gaps, understanding treatment-seeking behaviour for fever is crucial for the management of childhood illness and to reduce deaths. Here, we conduct a modelling study triangulating household survey data for fever in children under the age of five years with georeferenced public health facility databases (n = 86,442 facilities) in 29 countries across sub-Saharan Africa, to estimate the probability of seeking treatment for fever at public facilities. A Bayesian item response theory framework is used to estimate this probability based on reported fever episodes, treatment choice, residence, and estimated travel-time to the nearest public-sector health facility. Findings show inter- and intra-country variation, with the likelihood of seeking treatment for fever less than 50% in 16 countries. Results highlight the need to invest in public healthcare and related databases. The variation in public sector use illustrates the need to include such modelling in future infectious disease burden estimation.

Cross-border movement, economic development and malaria elimination in the Kingdom of Saudi Arabia.

Malaria at international borders presents particular challenges with regards to elimination. International borders share common malaria ecologies, yet neighboring countries are often at different stages of the control-to-elimination pathway. Herein, we present a case study on malaria, and its control, at the border between Saudi Arabia and Yemen. Malaria program activity reports, case data, and ancillary information have been assembled from national health information systems, archives, and other related sources. Information was analyzed as a semi-quantitative time series, between 2000 and 2017, to provide a plausibility framework to understand the possible contributions of factors related to control activities, conflict, economic development, migration, and climate. The malaria recession in the Yemeni border regions of Saudi Arabia is a likely consequence of multiple, coincidental factors, including scaled elimination activities, cross-border vector control, periods of low rainfall, and economic development. The temporal alignment of many of these factors suggests that economic development may have changed the receptivity to the extent that it mitigated against surges in vulnerability posed by imported malaria from its endemic neighbor Yemen. In many border areas of the world, malaria is likely to be sustained through a complex congruence of factors, including poverty, conflict, and migration.

Access to emergency hospital care provided by the public sector in sub-Saharan Africa in 2015: a geocoded inventory and spatial analysis.

BACKGROUND: Timely access to emergency care can substantially reduce mortality. International benchmarks for access to emergency hospital care have been established to guide ambitions for universal health care by 2030. However, no Pan-African database of where hospitals are located exists; therefore, we aimed to complete a geocoded inventory of hospital services in Africa in relation to how populations might access these services in 2015, with focus on women of child bearing age. METHODS: We assembled a geocoded inventory of public hospitals across 48 countries and islands of sub-Saharan Africa, including Zanzibar, using data from various sources. We only included public hospitals with emergency services that were managed by governments at national or local levels and faith-based or non-governmental organisations. For hospital listings without geographical coordinates, we geocoded each facility using Microsoft Encarta (version 2009), Google Earth (version 7.3), Geonames, Fallingrain, OpenStreetMap, and other national digital gazetteers. We obtained estimates for total population and women of child bearing age (15-49 years) at a 1 km2 spatial resolution from the WorldPop database for 2015. Additionally, we assembled road network data from Google Map Maker Project and OpenStreetMap using ArcMap (version 10.5). We then combined the road network and the population locations to form a travel impedance surface. Subsequently, we formulated a cost distance algorithm based on the location of public hospitals and the travel impedance surface in AccessMod (version 5) to compute the proportion of populations living within a combined walking and motorised travel time of 2 h to emergency hospital services. FINDINGS: We consulted 100 databases from 48 sub-Saharan countries and islands, including Zanzibar, and identified 4908 public hospitals. 2701 hospitals had either full or partial information about their geographical coordinates. We estimated that 287 282 013 (29·0%) people and 64 495 526 (28·2%) women of child bearing age are located more than 2-h travel time from the nearest hospital. Marked differences were observed within and between countries, ranging from less than 25% of the population within 2-h travel time of a public hospital in South Sudan to more than 90% in Nigeria, Kenya, Cape Verde, Swaziland, South Africa, Burundi, Comoros, São Tomé and Príncipe, and Zanzibar. Only 16 countries reached the international benchmark of more than 80% of their populations living within a 2-h travel time of the nearest hospital. INTERPRETATION: Physical access to emergency hospital care provided by the public sector in Africa remains poor and varies substantially within and between countries. Innovative targeting of emergency care services is necessary to reduce these inequities. This study provides the first spatial census of public hospital services in Africa. FUNDING: Wellcome Trust and the UK Department for International Development.

Coverage of routine reporting on malaria parasitological testing in Kenya, 2015-2016.

BACKGROUND: Following the launch of District Health Information System 2 across facilities in Kenya, more health facilities are now capable of carrying out malaria parasitological testing and reporting data as part of routine health information systems, improving the potential value of routine data for accurate and timely tracking of rapidly changing disease epidemiology at fine spatial resolutions. OBJECTIVES: This study evaluates the current coverage and completeness of reported malaria parasitological testing data in DHIS2 specifically looking at patterns in geographic coverage of public health facilities in Kenya. METHODS: Monthly facility level data on malaria parasitological testing were extracted from Kenya DHIS2 between November 2015 and October 2016. DHIS2 public facilities were matched to a geo-coded master facility list to obtain coordinates. Coverage was defined as the geographic distribution of facilities reporting any data by region. Completeness of reporting was defined as the percentage of facilities reporting any data for the whole 12-month period or for 3, 6 and 9 months. RESULTS: Public health facilities were 5,933 (59%) of 10,090 extracted. Fifty-nine per Cent of the public facilities did not report any data while 36, 29 and 22% facilities had data reported at least 3, 6 and 9 months, respectively. Only 8% of public facilities had data reported for every month. There were proportionately more hospitals (86%) than health centres (76%) and dispensaries/clinics (30%) reporting. There were significant geographic variations in reporting rates. Counties along the malaria endemic coast had the lowest reporting rate with only 1% of facilities reporting consistently for 12 months. CONCLUSION: Current coverage and completeness of reporting of malaria parasitological diagnosis across Kenya's public health system remains poor. The usefulness of routine data to improve our understanding of sub-national heterogeneity across Kenya would require significant improvements to the consistency and coverage of data captured by DHIS2.

The prevalence of Plasmodium falciparum in sub-Saharan Africa since 1900.

Malaria transmission is influenced by climate, land use and deliberate interventions. Recent declines have been observed in malaria transmission. Here we show that the African continent has witnessed a long-term decline in the prevalence of Plasmodium falciparum from 40% prevalence in the period 1900-1929 to 24% prevalence in the period 2010-2015, a trend that has been interrupted by periods of rapidly increasing or decreasing transmission. The cycles and trend over the past 115 years are inconsistent with explanations in terms of climate or deliberate intervention alone. Previous global initiatives have had minor impacts on malaria transmission, and a historically unprecedented decline has been observed since 2000. However, there has been little change in the high transmission belt that covers large parts of West and Central Africa. Previous efforts to model the changing patterns of P. falciparum transmission intensity in Africa have been limited to the past 15 years or have used maps drawn from historical expert opinions. We provide quantitative data, from 50,424 surveys at 36,966 geocoded locations, that covers 115 years of malaria history in sub-Saharan Africa; inferring from these data to future trends, we would expect continued reductions in malaria transmission, punctuated with resurgences.

Tracing the influence of land-use change on water quality and coral reefs using a Bayesian model.

Coastal ecosystems can be degraded by poor water quality. Tracing the causes of poor water quality back to land-use change is necessary to target catchment management for coastal zone management. However, existing models for tracing the sources of pollution require extensive data-sets which are not available for many of the world's coral reef regions that may have severe water quality issues. Here we develop a hierarchical Bayesian model that uses freely available satellite data to infer the connection between land-uses in catchments and water clarity in coastal oceans. We apply the model to estimate the influence of land-use change on water clarity in Fiji. We tested the model's predictions against underwater surveys, finding that predictions of poor water quality are consistent with observations of high siltation and low coverage of sediment-sensitive coral genera. The model thus provides a means to link land-use change to declines in coastal water quality.

Correction: To Fish or Not to Fish: Factors at Multiple Scales Affecting Artisanal Fishers' Readiness to Exit a Declining Fishery.

[This corrects the article DOI: 10.1371/journal.pone.0031460.].

Correction: Modeling Reef Fish Biomass, Recovery Potential, and Management Priorities in the Western Indian Ocean.

[This corrects the article DOI: 10.1371/journal.pone.0154585.].