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1.  Global Conservation Significance of Ecuador's Yasuní National Park 
PLoS ONE  2010;5(1):e8767.
Background
The threats facing Ecuador's Yasuní National Park are emblematic of those confronting the greater western Amazon, one of the world's last high-biodiversity wilderness areas. Notably, the country's second largest untapped oil reserves—called “ITT”—lie beneath an intact, remote section of the park. The conservation significance of Yasuní may weigh heavily in upcoming state-level and international decisions, including whether to develop the oil or invest in alternatives.
Methodology/Principal Findings
We conducted the first comprehensive synthesis of biodiversity data for Yasuní. Mapping amphibian, bird, mammal, and plant distributions, we found eastern Ecuador and northern Peru to be the only regions in South America where species richness centers for all four taxonomic groups overlap. This quadruple richness center has only one viable strict protected area (IUCN levels I–IV): Yasuní. The park covers just 14% of the quadruple richness center's area, whereas active or proposed oil concessions cover 79%. Using field inventory data, we compared Yasuní's local (alpha) and landscape (gamma) diversity to other sites, in the western Amazon and globally. These analyses further suggest that Yasuní is among the most biodiverse places on Earth, with apparent world richness records for amphibians, reptiles, bats, and trees. Yasuní also protects a considerable number of threatened species and regional endemics.
Conclusions/Significance
Yasuní has outstanding global conservation significance due to its extraordinary biodiversity and potential to sustain this biodiversity in the long term because of its 1) large size and wilderness character, 2) intact large-vertebrate assemblage, 3) IUCN level-II protection status in a region lacking other strict protected areas, and 4) likelihood of maintaining wet, rainforest conditions while anticipated climate change-induced drought intensifies in the eastern Amazon. However, further oil development in Yasuní jeopardizes its conservation values. These findings form the scientific basis for policy recommendations, including stopping any new oil activities and road construction in Yasuní and creating areas off-limits to large-scale development in adjacent northern Peru.
doi:10.1371/journal.pone.0008767
PMCID: PMC2808245  PMID: 20098736
2.  Elevational Distribution and Conservation Biogeography of Phanaeine Dung Beetles (Coleoptera: Scarabaeinae) in Bolivia 
PLoS ONE  2013;8(5):e64963.
Insect macroecology and conservation biogeography studies are disproportionately scarce, especially in the Neotropics. Dung beetles are an ideal focal taxon for biodiversity research and conservation. Using distribution and body size data on the ecologically important Phanaeini, the best-known Neotropical dung beetle tribe, we determined elevational patterns of species richness, endemism, body size, and elevational range in Bolivia, specifically testing Bergmann’s and Rapoport’s rule. Richness of all 39 species and of 15 ecoregional endemics showed a hump-shaped pattern peaking at 400 m, but overall declined strongly with elevation up to 4000 m. The relationship between endemic and total species richness appeared to be curvilinear, providing only partial support for the null hypothesis that species-rich areas are more likely to be centers of endemism by chance alone. An elevational increase in the proportion of ecoregional endemics suggests that deterministic factors also appear to influence endemism in the Andes. When controlling for the effect of area using different species-area relationships, the statistically significant richness peak became more pronounced and shifted upslope to 750 m. Larger species did not have higher elevational mid-points, and mean body size decreased significantly with elevation, contradicting Bergmann’s rule. Rapoport’s rule was supported: species with higher elevational mid-points had broader elevational ranges, and mean elevational range increased significantly with elevation. The elevational decrease of phanaeine richness is in accordance with studies that demonstrated the combined influence of temperature and water availability on species diversity, but also is consistent with niche conservatism. For invertebrates, confirmation of Rapoport’s and refutation of Bergmann’s rule appear to be scale-invariant general patterns. Analyses of biogeographic patterns across elevational gradients can provide important insights for identifying conservation priorities. Phanaeines with narrow elevational ranges on isolated low-elevation mountains in eastern Bolivia are at greatest climate-change related extinction risk from range-shift gaps and mountaintop extinctions.
doi:10.1371/journal.pone.0064963
PMCID: PMC3661563  PMID: 23717678
3.  A Long Neglected World Malaria Map: Plasmodium vivax Endemicity in 2010 
Background
Current understanding of the spatial epidemiology and geographical distribution of Plasmodium vivax is far less developed than that for P. falciparum, representing a barrier to rational strategies for control and elimination. Here we present the first systematic effort to map the global endemicity of this hitherto neglected parasite.
Methodology and Findings
We first updated to the year 2010 our earlier estimate of the geographical limits of P. vivax transmission. Within areas of stable transmission, an assembly of 9,970 geopositioned P. vivax parasite rate (PvPR) surveys collected from 1985 to 2010 were used with a spatiotemporal Bayesian model-based geostatistical approach to estimate endemicity age-standardised to the 1–99 year age range (PvPR1–99) within every 5×5 km resolution grid square. The model incorporated data on Duffy negative phenotype frequency to suppress endemicity predictions, particularly in Africa. Endemicity was predicted within a relatively narrow range throughout the endemic world, with the point estimate rarely exceeding 7% PvPR1–99. The Americas contributed 22% of the global area at risk of P. vivax transmission, but high endemic areas were generally sparsely populated and the region contributed only 6% of the 2.5 billion people at risk (PAR) globally. In Africa, Duffy negativity meant stable transmission was constrained to Madagascar and parts of the Horn, contributing 3.5% of global PAR. Central Asia was home to 82% of global PAR with important high endemic areas coinciding with dense populations particularly in India and Myanmar. South East Asia contained areas of the highest endemicity in Indonesia and Papua New Guinea and contributed 9% of global PAR.
Conclusions and Significance
This detailed depiction of spatially varying endemicity is intended to contribute to a much-needed paradigm shift towards geographically stratified and evidence-based planning for P. vivax control and elimination.
Author Summary
Plasmodium vivax is one of five parasites causing malaria in humans. Whilst it is found across a larger swathe of the globe and potentially affects a larger number of people than its more notorious cousin, Plasmodium falciparum, it receives a tiny fraction of the research attention and financing: around 3%. This neglect, coupled with the inherently more complex nature of vivax biology, means important knowledge gaps remain that limit our current ability to control the disease effectively. This patchy knowledge is becoming recognised as a cause for concern, in particular as the global community embraces the challenge of malaria elimination which, by definition, includes P. vivax and the other less common Plasmodium species as well as P. falciparum. Particularly conspicuous is the absence of an evidence-based map describing the intensity of P. vivax endemicity in different parts of the world. Such maps have proved important for other infectious diseases in supporting international policy formulation and regional disease control planning, implementation, and monitoring. In this study we present the first systematic effort to map the global endemicity of P. vivax. We assembled nearly 10,000 surveys worldwide in which communities had been tested for the prevalence of P. vivax infections. Using a spatial statistical model and additional data on environmental characteristics and Duffy negativity, a blood disorder that protects against P. vivax, we estimated the level of infection prevalence in every 5×5 km grid square across areas at risk. The resulting maps provide new insight into the geographical patterns of the disease, highlighting areas of the highest endemicity in South East Asia and small pockets of Amazonia, with very low endemic setting predominating in Africa. This new level of detailed mapping can contribute to a wider shift in our understanding of the spatial epidemiology of this important parasite.
doi:10.1371/journal.pntd.0001814
PMCID: PMC3435256  PMID: 22970336
4.  The conservation status of the herpetofauna of Honduras 
The conservation status of the members of the Honduran herpetofauna is discussed. Based on current and projected future human population growth, it is posited that the entire herpetofauna is endangered. The known herpetofauna of Honduras currently consists of 334 species, including 117 amphibians and 217 reptiles (including six marine reptiles, which are not discussed in this paper). The greatest number of species occur at low and moderate elevations in lowland and/or mesic forest formations, in the Northern and Southern Cordilleras of the Serranía, and the ecophysiographic areas of the Caribbean coastal plain and foothills. Slightly more than one-third of the herpetofauna consists of endemic species or those otherwise restricted to Nuclear Middle America. Honduras is an area severely affected by amphibian population decline, with close to one-half of the amphibian fauna threatened, endangered, or extinct. The principal threats to the survival of members of the herpetofauna are uncontrolled human population growth and its corollaries, habitat alteration and destruction, pollution, pest and predator control, overhunting, and overexploitation. No Honduran amphibians or reptiles are entirely free of human impact. A gauge is used to estimate environmental vulnerability of amphibian species, using measures of extent of geographic range, extent of ecological distribution, and degree of specialization of reproductive mode. A similar gauge is developed for reptiles, using the first two measures for amphibian vulnerability, and a third scale for the degree of human persecution. Based on these gauges, amphibians and reptiles show an actual range of Environmental Vulnerability Scores (EVS) almost as broad as the theoretical range. Based on the actual EVS, both amphibian and reptilian species are divided into three categories of low, medium, and high vulnerability. There are 24 low vulnerability amphibians and 47 reptiles, 43 medium vulnerability amphibians and 111 reptiles, and 50 high vulnerability amphibians and 53 reptiles. Theoretical EVS values are assessed against available information on current population status of endemic and Nuclear Middle American taxa. Almost half (48.8%) of the endemic species of Honduran amphibians are already extinct or have populations that are in decline. Populations of 40.0% of the Nuclear Middle American amphibian species are extirpated or in decline. A little less than a third (27.0%) of the endemic reptiles are thought to have declining populations. Almost six of every ten (54.5%) of the Nuclear Middle American reptilian species are thought to have declining populations. EVS values provide a useful indicator of potential for endangerment, illustrating that the species whose populations are currently in decline or are extinct or extirpated have relatively high EVS. All high EVS species need to be monitored closely for changes in population status. A set of recommendations are offered, assuming that biotic reserves in Honduras can be safeguarded, that it is hoped will lead to a system of robust, healthy, and economically self-sustaining protected areas for the country's herpetofauna. These recommendations will have to be enacted swiftly, however, due to unremitting pressure from human population growth and the resulting deforestation.
doi:10.1514/journal.arc.0000012
PMCID: PMC289144  PMID: 15029252
Conservation status; amphibians; reptiles; herpetofauna; Honduras; distribution
5.  The Effects of Governmental Protected Areas and Social Initiatives for Land Protection on the Conservation of Mexican Amphibians 
PLoS ONE  2009;4(9):e6878.
Traditionally, biodiversity conservation gap analyses have been focused on governmental protected areas (PAs). However, an increasing number of social initiatives in conservation (SICs) are promoting a new perspective for analysis. SICs include all of the efforts that society implements to conserve biodiversity, such as land protection, from private reserves to community zoning plans some of which have generated community-protected areas. This is the first attempt to analyze the status of conservation in Latin America when some of these social initiatives are included. The analyses were focused on amphibians because they are one of the most threatened groups worldwide. Mexico is not an exception, where more than 60% of its amphibians are endemic. We used a niche model approach to map the potential and real geographical distribution (extracting the transformed areas) of the endemic amphibians. Based on remnant distribution, all the species have suffered some degree of loss, but 36 species have lost more than 50% of their potential distribution. For 50 micro-endemic species we could not model their potential distribution range due to the small number of records per species, therefore the analyses were performed using these records directly. We then evaluated the efficiency of the existing set of governmental protected areas and established the contribution of social initiatives (private and community) for land protection for amphibian conservation. We found that most of the species have some proportion of their potential ecological niche distribution protected, but 20% are not protected at all within governmental PAs. 73% of endemic and 26% of micro-endemic amphibians are represented within SICs. However, 30 micro-endemic species are not represented within either governmental PAs or SICs. This study shows how the role of land conservation through social initiatives is therefore becoming a crucial element for an important number of species not protected by governmental PAs.
doi:10.1371/journal.pone.0006878
PMCID: PMC2731544  PMID: 19721719
6.  Rare Species Support Vulnerable Functions in High-Diversity Ecosystems 
PLoS Biology  2013;11(5):e1001569.
The most unusual, and thus irreplaceable, functions performed by species in three different species-rich ecosystems are fulfilled by only the rare species in these ecosystems.
Around the world, the human-induced collapses of populations and species have triggered a sixth mass extinction crisis, with rare species often being the first to disappear. Although the role of species diversity in the maintenance of ecosystem processes has been widely investigated, the role of rare species remains controversial. A critical issue is whether common species insure against the loss of functions supported by rare species. This issue is even more critical in species-rich ecosystems where high functional redundancy among species is likely and where it is thus often assumed that ecosystem functioning is buffered against species loss. Here, using extensive datasets of species occurrences and functional traits from three highly diverse ecosystems (846 coral reef fishes, 2,979 alpine plants, and 662 tropical trees), we demonstrate that the most distinct combinations of traits are supported predominantly by rare species both in terms of local abundance and regional occupancy. Moreover, species that have low functional redundancy and are likely to support the most vulnerable functions, with no other species carrying similar combinations of traits, are rarer than expected by chance in all three ecosystems. For instance, 63% and 98% of fish species that are likely to support highly vulnerable functions in coral reef ecosystems are locally and regionally rare, respectively. For alpine plants, 32% and 89% of such species are locally and regionally rare, respectively. Remarkably, 47% of fish species and 55% of tropical tree species that are likely to support highly vulnerable functions have only one individual per sample on average. Our results emphasize the importance of rare species conservation, even in highly diverse ecosystems, which are thought to exhibit high functional redundancy. Rare species offer more than aesthetic, cultural, or taxonomic diversity value; they disproportionately increase the potential breadth of functions provided by ecosystems across spatial scales. As such, they are likely to insure against future uncertainty arising from climate change and the ever-increasing anthropogenic pressures on ecosystems. Our results call for a more detailed understanding of the role of rarity and functional vulnerability in ecosystem functioning.
Author Summary
In ecological systems most species are rare—that is, represented by only a few individuals or restricted to particular habitats—and are vulnerable to being lost. Yet the ecological consequences of such biodiversity loss are often overlooked and remain controversial. In the best-case scenario, the functions that these rare species provide to their ecosystems might be insured by more common species, which share combinations of functional traits with the rare species, thereby helping to maintain ecosystem functioning despite rare species loss. In the worst-case scenario, rare species would have functional traits that are distinct from those of common species; thus, the functions they support would also be vulnerable to extinction. We examined three highly diverse ecosystems (coral reefs, alpine meadows, and tropical forests) and addressed whether common species would insure against the loss of functions carried by rare species. We demonstrate that highly distinct combinations of traits are supported predominantly by rare species. It is thus not only the quantity but also the quality of biodiversity that matters. Thus, our findings highlight that we need to change how we think about biodiversity in general, and about conservation strategies in particular, by moving beyond the protection of biodiversity per se and beyond focusing on iconic, charismatic, or phylogenetically distinct species, to protecting species that support irreplaceable functional roles and associated services.
doi:10.1371/journal.pbio.1001569
PMCID: PMC3665844  PMID: 23723735
7.  Endemicity and evolutionary value: a study of Chilean endemic vascular plant genera 
Ecology and Evolution  2014;4(6):806-816.
This study uses phylogeny-based measures of evolutionary potential (phylogenetic diversity and community structure) to evaluate the evolutionary value of vascular plant genera endemic to Chile. Endemicity is regarded as a very important consideration for conservation purposes. Taxa that are endemic to a single country are valuable conservation targets, as their protection depends upon a single government policy. This is especially relevant in developing countries in which conservation is not always a high resource allocation priority. Phylogeny-based measures of evolutionary potential such as phylogenetic diversity (PD) have been regarded as meaningful measures of the “value” of taxa and ecosystems, as they are able to account for the attributes that could allow taxa to recover from environmental changes. Chile is an area of remarkable endemism, harboring a flora that shows the highest number of endemic genera in South America. We studied PD and community structure of this flora using a previously available supertree at the genus level, to which we added DNA sequences of 53 genera endemic to Chile. Using discrepancy values and a null model approach, we decoupled PD from taxon richness, in order to compare their geographic distribution over a one-degree grid. An interesting pattern was observed in which areas to the southwest appear to harbor more PD than expected by their generic richness than those areas to the north of the country. In addition, some southern areas showed more PD than expected by chance, as calculated with the null model approach. Geological history as documented by the study of ancient floras as well as glacial refuges in the coastal range of southern Chile during the quaternary seem to be consistent with the observed pattern, highlighting the importance of this area for conservation purposes.
doi:10.1002/ece3.960
PMCID: PMC3967905  PMID: 24683462
Community structure; endemicity; phylogenetic diversity; vascular plants
8.  Use of Arthropod Rarity for Area Prioritisation: Insights from the Azorean Islands 
PLoS ONE  2012;7(3):e33995.
We investigated the conservation concern of Azorean forest fragments and the entire Terceira Island surface using arthropod species vulnerability as defined by the Kattan index, which is based on species rarity. Species rarity was evaluated according to geographical distribution (endemic vs. non endemic species), habitat specialization (distribution across biotopes) and population size (individuals collected in standardized samples). Geographical rarity was considered at ‘global’ scale (species endemic to the Azorean islands) and ‘regional’ scale (single island endemics).
Measures of species vulnerability were combined into two indices of conservation concern for each forest fragment: (1) the Biodiversity Conservation Concern index, BCC, which reflects the average rarity score of the species present in a site, and (2) one proposed here and termed Biodiversity Conservation Weight, BCW, which reflects the sum of rarity scores of the same species assemblage. BCW was preferable to prioritise the areas with highest number of vulnerable species, whereas BCC helped the identification of areas with few, but highly threatened species due to a combination of different types of rarity.
A novel approach is introduced in which BCC and BCW indices were also adapted to deal with probabilities of occurrence instead of presence/absence data. The new probabilistic indices, termed pBCC and pBCW, were applied to Terceira Island for which we modelled species distributions to reconstruct species occurrence with different degree of probability also in areas from which data were not available. The application of the probabilistic indices revealed that some island sectors occupied by secondary vegetation, and hence not included in the current set of protected areas, may in fact host some rare species. This result suggests that protecting marginal non-natural areas which are however reservoirs of vulnerable species may also be important, especially when areas with well preserved primary habitats are scarce.
doi:10.1371/journal.pone.0033995
PMCID: PMC3316514  PMID: 22479498
9.  Global Diversity Hotspots and Conservation Priorities for Sharks 
PLoS ONE  2011;6(5):e19356.
Sharks are one of the most threatened groups of marine animals, as high exploitation rates coupled with low resilience to fishing pressure have resulted in population declines worldwide. Designing conservation strategies for this group depends on basic knowledge of the geographic distribution and diversity of known species. So far, this information has been fragmented and incomplete. Here, we have synthesized the first global shark diversity pattern from a new database of published sources, including all 507 species described at present, and have identified hotspots of shark species richness, functional diversity and endemicity from these data. We have evaluated the congruence of these diversity measures and demonstrate their potential use in setting priority areas for shark conservation. Our results show that shark diversity across all species peaks on the continental shelves and at mid-latitudes (30–40 degrees N and S). Global hotspots of species richness, functional diversity and endemicity were found off Japan, Taiwan, the East and West coasts of Australia, Southeast Africa, Southeast Brazil and Southeast USA. Moreover, some areas with low to moderate species richness such as Southern Australia, Angola, North Chile and Western Continental Europe stood out as places of high functional diversity. Finally, species affected by shark finning showed different patterns of diversity, with peaks closer to the Equator and a more oceanic distribution overall. Our results show that the global pattern of shark diversity is uniquely different from land, and other well-studied marine taxa, and may provide guidance for spatial approaches to shark conservation. However, similar to terrestrial ecosystems, protected areas based on hotspots of diversity and endemism alone would provide insufficient means for safeguarding the diverse functional roles that sharks play in marine ecosystems.
doi:10.1371/journal.pone.0019356
PMCID: PMC3088674  PMID: 21573162
10.  Controlling Endemic Cholera with Oral Vaccines 
PLoS Medicine  2007;4(11):e336.
Background
Although advances in rehydration therapy have made cholera a treatable disease with low case-fatality in settings with appropriate medical care, cholera continues to impose considerable mortality in the world's most impoverished populations. Internationally licensed, killed whole-cell based oral cholera vaccines (OCVs) have been available for over a decade, but have not been used for the control of cholera. Recently, these vaccines were shown to confer significant levels of herd protection, suggesting that the protective potential of these vaccines has been underestimated and that these vaccines may be highly effective in cholera control when deployed in mass immunization programs. We used a large-scale stochastic simulation model to investigate the possibility of controlling endemic cholera with OCVs.
Methods and Findings
We construct a large-scale, stochastic cholera transmission model of Matlab, Bangladesh. We find that cholera transmission could be controlled in endemic areas with 50% coverage with OCVs. At this level of coverage, the model predicts that there would be an 89% (95% confidence interval [CI] 72%–98%) reduction in cholera cases among the unvaccinated, and a 93% (95% CI 82%–99%) reduction overall in the entire population. Even a more modest coverage of 30% would result in a 76% (95% CI 44%–95%) reduction in cholera incidence for the population area covered. For populations that have less natural immunity than the population of Matlab, 70% coverage would probably be necessary for cholera control, i.e., an annual incidence rate of ≤ 1 case per 1,000 people in the population.
Conclusions
Endemic cholera could be reduced to an annual incidence rate of ≤ 1 case per 1,000 people in endemic areas with biennial vaccination with OCVs if coverage could reach 50%–70% depending on the level of prior immunity in the population. These vaccination efforts could be targeted with careful use of ecological data.
Using data from Bangladesh, Ira Longini and colleagues develop a mathematical model predicting that oral vaccination of 50%-70% of the population could control cholera transmission in an endemic region.
Editors' Summary
Background.
Throughout history, there have been devastating outbreaks of cholera—a gut infection characterized by diarrhea and severe dehydration—around the world. These days, cholera is mainly confined to developing countries where it disrupts social structures, impedes economic development, and probably causes about 100,000 deaths a year. People get cholera, which is caused by a bacterium called Vibrio cholerae, by eating food or drinking water contaminated with feces (stools) from an infected person. Most infected people have no or mild symptoms but shed the bug in their feces for up to two weeks. Other people develop severe diarrhea, producing stools that look like water with flecks of rice in it. If untreated, patients with severe cholera can die from dehydration within hours of developing symptoms. The standard treatment for cholera is replacement of the fluids and salts lost through diarrhea by drinking an oral rehydration solution or, in the worst cases, by fluid replacement directly into a vein. Without this treatment, which is not always available in the developing countries where cholera is endemic (always present), one in every two people with severe symptoms die.
Why Was This Study Done?
The best way to control cholera is to ensure that everyone has access to safe water and good sanitation, but this is not possible in some poor countries, in refugee camps, or after natural disasters such as floods. Oral cholera vaccines (preparations given by mouth that stimulate the immune system to attack V. cholerae) are available but they are not 100% effective and the protection they provide wanes over time. Consequently, vaccination has not been adopted as a control measure for endemic cholera. Recently, however, researchers have suggested that oral cholera vaccines induce “herd immunity.” With a disease that passes between people, when most of the population is immune to it, it is unlikely that an infected person will come into contact with a susceptible person and pass the disease on. In effect, both vaccinated and unvaccinated people are protected from the disease. If cholera vaccines do induce herd immunity, then mass immunization might help to control endemic cholera. In this study, the researchers have used a mathematical model to investigate this possibility.
What Did the Researchers Do and Find?
The researchers built a large-scale model of cholera transmission using information about the population of Matlab, Bangladesh (a region where cholera is endemic), together with data on the biology of cholera and data from a large oral vaccine trial done in Matlab in the 1980s. They used this model to predict whether cholera would be controlled after vaccination of different proportions of the population. They found that cholera transmission would be controlled if half the population in the region was vaccinated. This level of vaccine coverage reduced the number of cholera cases among unvaccinated people by 89% and among the entire population by 93%. With only one-third of the population vaccinated, the number of cases of cholera still fell by three-fourths. The model also predicted that in areas where there is less natural immunity to cholera (the people in Matlab are constantly exposed to V. cholerae, so they have some immunity to the bug even without vaccination), 70% of the population would probably need to be vaccinated to control cholera.
What Do These Findings Mean?
These findings suggest that, because of herd immunity, vaccinating only half the population could control cholera transmission in endemic regions where there is a high level of natural immunity. Where there is less natural immunity, more of the population would need to be immunized. Although mass immunization of even 70% of a population should be achievable, for maximal protection against V. cholerae, two doses of the oral cholera vaccine need to be given a week apart followed by a booster every two years. In developing countries this regimen might not always be logistically feasible or affordable. Furthermore, because the accuracy of the model's predictions depends on the assumptions made to construct it and on the data incorporated into it, these findings need to be checked in field trials in other endemic areas. Nevertheless, these findings suggest that public-health officials should consider including mass vaccination in their efforts to control endemic cholera.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0040336.
The MedlinePlus encyclopedia contains a page on cholera (in English and Spanish)
Information is available from the World Health Organization on cholera, including a fact sheet on the disease (in English, Spanish, French, Russian, Arabic, and Chinese)
The US Centers for Disease Control and Prevention provide information on cholera (in English, Spanish and Portuguese).
The UK National Health service provides simple information on vaccines and immunization, which includes an animation that explains herd immunity
doi:10.1371/journal.pmed.0040336
PMCID: PMC2082648  PMID: 18044983
11.  Restricted-Range Fishes and the Conservation of Brazilian Freshwaters 
PLoS ONE  2010;5(6):e11390.
Background
Freshwaters are the most threatened ecosystems on earth. Although recent assessments provide data on global priority regions for freshwater conservation, local scale priorities remain unknown. Refining the scale of global biodiversity assessments (both at terrestrial and freshwater realms) and translating these into conservation priorities on the ground remains a major challenge to biodiversity science, and depends directly on species occurrence data of high taxonomic and geographic resolution. Brazil harbors the richest freshwater ichthyofauna in the world, but knowledge on endemic areas and conservation in Brazilian rivers is still scarce.
Methodology/Principal Findings
Using data on environmental threats and revised species distribution data we detect and delineate 540 small watershed areas harboring 819 restricted-range fishes in Brazil. Many of these areas are already highly threatened, as 159 (29%) watersheds have lost more than 70% of their original vegetation cover, and only 141 (26%) show significant overlap with formally protected areas or indigenous lands. We detected 220 (40%) critical watersheds overlapping hydroelectric dams or showing both poor formal protection and widespread habitat loss; these sites harbor 344 endemic fish species that may face extinction if no conservation action is in place in the near future.
Conclusions/Significance
We provide the first analysis of site-scale conservation priorities in the richest freshwater ecosystems of the globe. Our results corroborate the hypothesis that freshwater biodiversity has been neglected in former conservation assessments. The study provides a simple and straightforward method for detecting freshwater priority areas based on endemism and threat, and represents a starting point for integrating freshwater and terrestrial conservation in representative and biogeographically consistent site-scale conservation strategies, that may be scaled-up following naturally linked drainage systems. Proper management (e. g. forestry code enforcement, landscape planning) and conservation (e. g. formal protection) of the 540 watersheds detected herein will be decisive in avoiding species extinction in the richest aquatic ecosystems on the planet.
doi:10.1371/journal.pone.0011390
PMCID: PMC2894945  PMID: 20613986
12.  Assessing Conservation Values: Biodiversity and Endemicity in Tropical Land Use Systems 
PLoS ONE  2011;6(1):e16238.
Despite an increasing amount of data on the effects of tropical land use on continental forest fauna and flora, it is debatable whether the choice of the indicator variables allows for a proper evaluation of the role of modified habitats in mitigating the global biodiversity crisis. While many single-taxon studies have highlighted that species with narrow geographic ranges especially suffer from habitat modification, there is no multi-taxa study available which consistently focuses on geographic range composition of the studied indicator groups. We compiled geographic range data for 180 bird, 119 butterfly, 204 tree and 219 understorey plant species sampled along a gradient of habitat modification ranging from near-primary forest through young secondary forest and agroforestry systems to annual crops in the southwestern lowlands of Cameroon. We found very similar patterns of declining species richness with increasing habitat modification between taxon-specific groups of similar geographic range categories. At the 8 km2 spatial level, estimated richness of endemic species declined in all groups by 21% (birds) to 91% (trees) from forests to annual crops, while estimated richness of widespread species increased by +101% (trees) to +275% (understorey plants), or remained stable (- 2%, butterflies). Even traditional agroforestry systems lost estimated endemic species richness by - 18% (birds) to - 90% (understorey plants). Endemic species richness of one taxon explained between 37% and 57% of others (positive correlations) and taxon-specific richness in widespread species explained up to 76% of variation in richness of endemic species (negative correlations). The key implication of this study is that the range size aspect is fundamental in assessments of conservation value via species inventory data from modified habitats. The study also suggests that even ecologically friendly agricultural matrices may be of much lower value for tropical conservation than indicated by mere biodiversity value.
doi:10.1371/journal.pone.0016238
PMCID: PMC3029302  PMID: 21298054
13.  The West Indies as a laboratory of biogeography and evolution 
Islands have long provided material and inspiration for the study of evolution and ecology. The West Indies are complex historically and geographically, providing a rich backdrop for the analysis of colonization, diversification and extinction of species. They are sufficiently isolated to sustain endemic forms and close enough to sources of colonists to develop a dynamic interaction with surrounding continental regions. The Greater Antilles comprise old fragments of continental crust, some very large; the Lesser Antilles are a more recent volcanic island arc, and the low-lying Bahama Islands are scattered on a shallow oceanic platform. Dating of island lineages using molecular methods indicates over-water dispersal of most inhabitants of the West Indies, although direct connections with what is now southern Mexico in the Early Tertiary, and subsequent land bridges or stepping stone islands linking to Central and South America might also have facilitated colonization. Species–area relationships within the West Indies suggest a strong role for endemic radiations and extinction in shaping patterns of diversity. Diversification is promoted by opportunities for allopatric divergence between islands, or within the large islands of the Greater Antilles, with a classic example provided by the Anolis lizards. The timing of colonization events using molecular clocks permits analysis of colonization–extinction dynamics by means of species accumulation curves. These indicate low rates of colonization and extinction for reptiles and amphibians in the Greater Antilles, with estimated average persistence times of lineages in the West Indies exceeding 30 Myr. Even though individual island populations of birds might persist an average of 2 Myr on larger islands in the Lesser Antilles, recolonization from within the archipelago appears to maintain avian lineages within the island chain indefinitely. Birds of the Lesser Antilles also provide evidence of a mass extinction event within the past million years, emphasizing the time-heterogeneity of historical processes. Geographical dynamics are matched by ecological changes in the distribution of species within islands over time resulting from adaptive radiation and shifts in habitat, often following repeatable patterns. Although extinction is relatively infrequent under natural conditions, changes in island environments as a result of human activities have exterminated many populations and others—especially old, endemic species—remain vulnerable. Conservation efforts are strengthened by recognition of aesthetic, cultural and scientific values of the unique flora and fauna of the West Indies.
doi:10.1098/rstb.2007.2068
PMCID: PMC2606802  PMID: 17446164
island biogeography; colonization; extinction; speciation; adaptive radiation; diversification
14.  Extinction processes in hot spots of avian biodiversity and the targeting of pre-emptive conservation action. 
Hot spots of endemism are regarded as important global sites for conservation as they are rich in threatened endemic species and currently experiencing extensive habitat loss. Targeting pre-emptive conservation action to sites that are currently relatively intact but which would be vulnerable to particular human activities if they occurred in the future is, however, also valuable but has received less attention. Here, we address this issue by using data on Endemic Bird Areas (EBAs). First, we identify the ecological factors that affect extinction risk in the face of particular human activities, and then use these insights to identify EBAs that should be priorities for pre-emptive conservation action. Threatened endemic species in EBAs are significantly more likely to be habitat specialists or relatively large-bodied than non-threatened species, when compared across avian families. Increasing habitat loss causes a significant increase in extinction risk among habitat specialists, but we found no evidence to suggest that the presence of alien species/human exploitation causes a significant increase in extinction risk among large-bodied species. This suggests that these particular human activities are contributing to high extinction risk among habitat specialists, but not among large-bodied species. Based on these analyses, we identify 39 EBAs containing 570 species (24% of the total in EBAs) that are not currently threatened with severe habitat loss, but would be ecologically vulnerable to future habitat loss should it occur. We show that these sites tend to be poorly represented in existing priority setting exercises involving hot spots, suggesting that vulnerability must be explicitly included within these exercises if such sites are to be adequately protected.
PMCID: PMC1691574  PMID: 15058387
15.  Little ecological divergence associated with speciation in two African rain forest tree genera 
Background
The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa.
Results
A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods.
Conclusions
Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.
Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae
doi:10.1186/1471-2148-11-296
PMCID: PMC3203876  PMID: 21985574
16.  Complementarity as a biodiversity indicator strategy. 
Richness, rarity, endemism and complementarity of indicator taxon species are often used to select conservation areas, which are then assumed to represent most regional biodiversity. Assessments of the degree to which these indicator conservation areas coincide across different taxa have been conducted on a variety of vertebrate, invertebrate and plant groups at a national scale in Britain, Canada, USA and South Africa and at a regional scale in Cameroon, Uganda and the USA. A low degree of spatial overlap among and within these selected indicator conservation areas has been demonstrated. These results tend to suggest that indicator conservation areas display little congruence across different taxa. However, some of these studies demonstrate that many conservation areas for indicator taxa capture a high proportion of non-target species. Thus it appears that indicator conservation areas might sample overall biodiversity efficiently. These indicator conservation areas may, however, exclude species essential for effective conservation, e.g. rare, endemic or endangered species. The present study investigated the value of indicator taxa as biodiversity surrogates using spatial congruence and representativeness of different indicator priority conservation areas. The conservation status of species excluded by the indicator approaches is also assessed. Indicator priority conservation areas demonstrate high land area requirements in order to fully represent non-target species. These results suggest that efficient priority area selection techniques must reach a compromise between maximizing non-target species gains and minimizing land-use requirements. Reserve selection procedures using indicator-based complementarity appear to be approaches which best satisfy this trade-off.
PMCID: PMC1690558  PMID: 10737409
17.  Ecoregion Prioritization Suggests an Armoury Not a Silver Bullet for Conservation Planning 
PLoS ONE  2010;5(1):e8923.
In the face of accelerating species extinctions, map-based prioritization systems are increasingly useful to decide where to pursue conservation action most effectively. However, a number of seemingly inconsistent schemes have emerged, mostly focussing on endemism. Here we use global vertebrate distributions in terrestrial ecoregions to evaluate how continuous and categorical ranking schemes target and accumulate endangered taxa within the IUCN Red List, Alliance for Zero Extinction (AZE), and EDGE of Existence programme. We employed total, endemic and threatened species richness and an estimator for richness-adjusted endemism as metrics in continuous prioritization, and WWF's Global200 and Conservation International's (CI) Hotspots in categorical prioritization. Our results demonstrate that all metrics target endangerment more efficiently than by chance, but each selects unique sets of top-ranking ecoregions, which overlap only partially, and include different sets of threatened species. Using the top 100 ecoregions as defined by continuous prioritization metrics, we develop an inclusive map for global vertebrate conservation that incorporates important areas for endemism, richness, and threat. Finally, we assess human footprint and protection levels within these areas to reveal that endemism sites are more impacted but have more protection, in contrast to high richness and threat ones. Given such contrasts, major efforts to protect global biodiversity must involve complementary conservation approaches in areas of unique species as well as those with highest diversity and threat.
doi:10.1371/journal.pone.0008923
PMCID: PMC2811746  PMID: 20111722
18.  Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages 
PLoS Biology  2009;7(3):e1000056.
The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.
Author Summary
The Neotropics, which includes South and Central America, contains half of remaining rainforests and the largest reservoir of amphibian diversity. Why there are so many species in certain areas and how such diversity arose before the Quaternary (i.e., more that 1.8 million years ago [MYA]) are largely unstudied. One hypothesis is that the Amazon Basin was the key source of diversity, and species dispersed from there to other areas. Here, we reconstruct a time-calibrated phylogeny and track, in space and time, the distribution of the endemic and species-rich clade of poison frogs (Dendrobatidae) during the Cenozoic (more than 65 MYA) across the continental Neotropics. Our results indicate a far more complex pattern of lineage dispersals and radiations during the past 10 MY. Rather than the Amazon Basin being the center of origin, our results show that the diversity stemmed from repeated dispersals from adjacent areas, especially from the Andes. We also found a recurrent pattern of colonization of Central America from the Chocó at 4–5 MY earlier than the formation of the Panamanian Land Bridge at 1.5 MYA. Thus, the major patterns of dispersals and radiations in the Neotropics were already set by ∼5–6 MYA (the Miocene–Pliocene boundary), but the ongoing process of Neotropical radiation is still happening now, especially in the Chocó–Central America region and Amazonian rainforest.
Phylogenetic analysis and ancestral range modeling of the poison-frog clade (Dendrobatidae) indicates that Amazonian species richness derives from repeated dispersals from adjacent regions, especially the Andes.
doi:10.1371/journal.pbio.1000056
PMCID: PMC2653552  PMID: 19278298
19.  Intermittent Preventive Treatment for Malaria in Papua New Guinean Infants Exposed to Plasmodium falciparum and P. vivax: A Randomized Controlled Trial 
PLoS Medicine  2012;9(3):e1001195.
A three-arm randomized trial conducted among infants in Papua New Guinea estimates the preventive effect against malaria episodes of intermittent preventive treatment, in an area where children are exposed to both falciparum and vivax malaria.
Background
Intermittent preventive treatment in infants (IPTi) has been shown in randomized trials to reduce malaria-related morbidity in African infants living in areas of high Plasmodium falciparum (Pf) transmission. It remains unclear whether IPTi is an appropriate prevention strategy in non-African settings or those co-endemic for P. vivax (Pv).
Methods and Findings
In this study, 1,121 Papua New Guinean infants were enrolled into a three-arm placebo-controlled randomized trial and assigned to sulfadoxine-pyrimethamine (SP) (25 mg/kg and 1.25 mg/kg) plus amodiaquine (AQ) (10 mg/kg, 3 d, n = 374), SP plus artesunate (AS) (4 mg/kg, 3 d, n = 374), or placebo (n = 373), given at 3, 6, 9 and 12 mo. Both participants and study teams were blinded to treatment allocation. The primary end point was protective efficacy (PE) against all episodes of clinical malaria from 3 to 15 mo of age. Analysis was by modified intention to treat. The PE (compared to placebo) against clinical malaria episodes (caused by all species) was 29% (95% CI, 10–43, p≤0.001) in children receiving SP-AQ and 12% (95% CI, −11 to 30, p = 0.12) in those receiving SP-AS. Efficacy was higher against Pf than Pv. In the SP-AQ group, Pf incidence was 35% (95% CI, 9–54, p = 0.012) and Pv incidence was 23% (95% CI, 0–41, p = 0.048) lower than in the placebo group. IPTi with SP-AS protected only against Pf episodes (PE = 31%, 95% CI, 4–51, p = 0.027), not against Pv episodes (PE = 6%, 95% CI, −24 to 26, p = 0.759). Number of observed adverse events/serious adverse events did not differ between treatment arms (p>0.55). None of the serious adverse events were thought to be treatment-related, and the vomiting rate was low in both treatment groups (1.4%–2.0%). No rebound in malaria morbidity was observed for 6 mo following the intervention.
Conclusions
IPTi using a long half-life drug combination is efficacious for the prevention of malaria and anemia in infants living in a region highly endemic for both Pf and Pv.
Trial registration
ClinicalTrials.gov NCT00285662
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Malaria is a major global public health problem. Half the world's population is at risk of this parasitic disease, which kills about one million people (mainly young children in sub-Saharan Africa) every year. Most of these deaths are caused by Plasmodium falciparum but P. vivax, the commonest and most widely distributed malaria parasite, is a major cause of malaria-related morbidity (illness and death) in many of the tropical and subtropical regions of the world where malaria is endemic (always present). Malaria is transmitted to people through the bites of night-flying mosquitoes. It can be prevented by controlling the mosquitoes that spread the parasite and by sleeping under insecticide-treated nets to avoid mosquito bites. Prompt treatment of malaria with antimalarial drugs can also reduce malaria transmission. In addition, intermittent preventative treatment (IPT)—the treatment of symptom-free individuals with full therapeutic courses of antimalarial drugs at fixed intervals regardless of their infection status—has been shown to reduce malaria-related morbidity among pregnant women in malaria-endemic areas and among African infants living in areas of high P. falciparum transmission.
Why Was This Study Done?
The World Health Organization recently recommended that, in Africa, IPT should be given during infancy (called IPTi) at the same time as routine immunizations. Because the studies on which this recommendation is based were all carried out in sub-Saharan Africa, in populations where P. falciparum is the predominant parasite and P. vivax is uncommon, it is not known whether IPTi would be an appropriate prevention strategy in non-African settings or in regions where both P. falciparum and P. vivax are endemic. In this randomized placebo-controlled trial, the researchers investigate the efficacy of IPTi in infants living in an area of Papua New Guinea where P. falciparum and P. vivax are both highly endemic. In a randomized placebo-controlled trial, the effects of an intervention and of a placebo (dummy) intervention are compared in groups of individuals chosen through the play of chance.
What Did the Researchers Do and Find?
The researchers assigned more than 1,000 infants to receive sulfadoxine/pyrimethamine (SP) plus amodiaquine (AQ) (SP and AQ are long-lasting antimalarial drugs), SP plus artesunate (AS) (AS is a short-lasting antimalarial), or placebo at 3, 6, 9, and 12 months old. They recorded the number of malaria episodes that occurred among the children between the ages of 3 and 15 months. Then, by comparing the number of episodes occurring among the children receiving SP-AS or SP-AQ with the number occurring among the children receiving placebo, the researchers calculated the protective efficacy of the two drug combinations over the study period. The protective efficacy of IPTi against all clinical malaria episodes (P. falciparum and P. vivax combined) was 29% for SP-AQ, but SP-AS was not associated with a statistically significant reduction in all malaria episodes as compared to placebo. For the two species of malaria separately, the incidence of P. falciparum malaria was 35% lower among the children receiving SP-AQ than among the children receiving placebo, whereas the incidence of P. vivax was reduced by 23%; IPTi with SP-AS provided protection only against P. falciparum malaria (protective efficacy 31%). Importantly, the number of adverse events (possible drug side effects) was similar in all the treatment arms, none of the severe adverse events were treatment-related, and there was no rebound in malaria-related morbidity for six months following the end of the intervention.
What Do These Findings Mean?
These findings show that IPTi using a combination of long-lasting antimalarial drugs (SP-AQ) can effectively and safely prevent malaria in a non-African population living in a region where P. falciparum and P. vivax are both highly endemic. Importantly, they also show that IPTi with SP-AQ can prevent both P. falciparum and P. vivax malaria. For Papua New Guinea, these findings suggest that SP-AQ is an appropriate drug choice for IPTi, particularly since the replacement of SP-AQ by artemether-lumefantrine as the national first line treatment for malaria will reduce the selection pressure for resistance against SP and AQ. However, although these finding provide proof-of-principle evidence for the efficacy and safety of IPTi, further studies are needed to identify the most effective combinations of long-lasting antimalarial drugs for use in IPTi in other malaria-endemic regions.
Additional Information
Please access these web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001195.
Information is available from the World Health Organization on malaria (in several languages); the 2011 World Malaria Report provides details of the current global malaria situation; and the WHO policy recommendation on IPTi for P. falciparum malaria control in Africa is available
The US Centers for Disease Control and Prevention provide information on malaria (in English and Spanish), including a selection of personal stories about malaria
Information is available from the Roll Back Malaria Partnership on the global control of malaria, including a fact sheet about malaria in children and information on malaria in Papua New Guinea
The IPTi Consortium was established to evaluate IPTi and inform public health policy making
The Malaria Vaccine Initiative has a fact sheet on P. vivax malaria
Vivaxmalaria.com provides information about P. vivax
MedlinePlus provides links to additional information on malaria (in English and Spanish)
doi:10.1371/journal.pmed.1001195
PMCID: PMC3313928  PMID: 22479155
20.  G6PD Deficiency Prevalence and Estimates of Affected Populations in Malaria Endemic Countries: A Geostatistical Model-Based Map 
PLoS Medicine  2012;9(11):e1001339.
Rosalind Howes and colleagues present a map of glucose-6-phosphate dehydrogenase deficiency prevalence and severity. Individuals with the deficiency are at risk of mild to severe hemolysis when taking the antimalarial primaquine.
Background
Primaquine is a key drug for malaria elimination. In addition to being the only drug active against the dormant relapsing forms of Plasmodium vivax, primaquine is the sole effective treatment of infectious P. falciparum gametocytes, and may interrupt transmission and help contain the spread of artemisinin resistance. However, primaquine can trigger haemolysis in patients with a deficiency in glucose-6-phosphate dehydrogenase (G6PDd). Poor information is available about the distribution of individuals at risk of primaquine-induced haemolysis. We present a continuous evidence-based prevalence map of G6PDd and estimates of affected populations, together with a national index of relative haemolytic risk.
Methods and Findings
Representative community surveys of phenotypic G6PDd prevalence were identified for 1,734 spatially unique sites. These surveys formed the evidence-base for a Bayesian geostatistical model adapted to the gene's X-linked inheritance, which predicted a G6PDd allele frequency map across malaria endemic countries (MECs) and generated population-weighted estimates of affected populations. Highest median prevalence (peaking at 32.5%) was predicted across sub-Saharan Africa and the Arabian Peninsula. Although G6PDd prevalence was generally lower across central and southeast Asia, rarely exceeding 20%, the majority of G6PDd individuals (67.5% median estimate) were from Asian countries. We estimated a G6PDd allele frequency of 8.0% (interquartile range: 7.4–8.8) across MECs, and 5.3% (4.4–6.7) within malaria-eliminating countries. The reliability of the map is contingent on the underlying data informing the model; population heterogeneity can only be represented by the available surveys, and important weaknesses exist in the map across data-sparse regions. Uncertainty metrics are used to quantify some aspects of these limitations in the map. Finally, we assembled a database of G6PDd variant occurrences to inform a national-level index of relative G6PDd haemolytic risk. Asian countries, where variants were most severe, had the highest relative risks from G6PDd.
Conclusions
G6PDd is widespread and spatially heterogeneous across most MECs where primaquine would be valuable for malaria control and elimination. The maps and population estimates presented here reflect potential risk of primaquine-associated harm. In the absence of non-toxic alternatives to primaquine, these results represent additional evidence to help inform safe use of this valuable, yet dangerous, component of the malaria-elimination toolkit.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Malaria is a parasitic infection that is transmitted to people through the bites of infected mosquitoes. Of the four parasites that cause malaria, Plasmodium falciparum is the most deadly and P. vivax is the commonest and most widely distributed. Malaria parasites have a complex life cycle. Infected mosquitoes inject “sporozoites” into people, a form of the parasite that replicates inside human liver cells. After a few days, the liver cells release “merozoites,” which invade red blood cells where they replicate rapidly before bursting out and infecting other red blood cells. This increase in the parasitic burden causes malaria's characteristic fever and can cause organ damage and death. Infected red blood cells also release “gametocytes,” which infect mosquitoes when they take a blood meal. In the mosquito, gametocytes multiply and develop into sporozoites, thus completing the parasite's life cycle. Malaria can be prevented by controlling the mosquitoes that spread the parasite and by avoiding mosquito bites by sleeping under insecticide-treated bed nets. Treatment with effective antimalarial drugs also decreases malaria transmission.
Why Was This Study Done?
The Global Malaria Action Plan aims to reduce malaria deaths to zero by 2015 and to eradicate malaria in the long-term through its progressive elimination in malaria-endemic countries (countries where malaria is always present). Primaquine is a key drug for malaria elimination. It is the only treatment effective against the gametocytes that transmit malaria between people and mosquitoes and against P. vivax “hypnozoites,” which hibernate in the liver and cause malaria relapses. Unfortunately, primaquine induces mild to severe destruction of red blood cells (hemolysis) in people who have a deficiency in the enzyme glucose-6-phosphate dehydrogenase (G6PD). G6PD deficiency (G6PDd) is common in some ethnic groups but the global distribution of individuals at risk of primaquine-induced hemolysis is unknown and there is no practical field test for G6PDd. Consequently, it is hard to design and implement primaquine treatment practices that balance the benefits of malaria transmission reduction and relapse prevention against the risk of hemolysis. Here, the researchers use a geostatistical model to map the prevalence (frequency in a population) of G6PDd in malaria-endemic countries and to estimate how many people are affected in these countries. They also develop a national index of relative hemolytic risk.
What Did the Researchers Do and Find?
The researchers fed data from community surveys of the prevalence of phenotypic G6PDd (reduced enzyme activity) for 1,734 sites (including 1,289 sites in malaria-endemic countries) into a geostatistical model originally developed to map global malaria endemicity. The model predicted that G6PDd is widespread across malaria-endemic regions, with the lowest prevalences in the Americas and the highest in tropical Africa and the Arabian Peninsula, but that most G6PDd individuals live in Asian countries. The predicted prevalence of G6PDd varied considerably over relatively short distances in many areas but, averaged across malaria-endemic countries it was 8%, which corresponds to about 350 million affected individuals; averaged across countries that are currently planning for malaria elimination, the prevalence was 5.3% (nearly 100 million affected individuals). Finally, the researchers used data on the geographical occurrence of G6PD variants classified according to their enzyme activity levels as mild or severe to derive an index of hemolytic risk from G6PDd for each malaria-endemic country. The greatest risk was in the Arabian Peninsula and west Asia where the predicted prevalence of G6PDd and the occurrence of severe G6PD variants were both high.
What Do These Findings Mean?
These findings suggest that G6PDd is widespread and spatially heterogeneous across most of the malaria-endemic countries where primaquine would be valuable for malaria control and elimination. The accuracy of these findings is limited, however, by the assumptions made in the geostatistical model, by the accuracy of the data fed into the model, and by the lack of data for some malaria-endemic countries. Moreover, there is considerable uncertainty associated with the proposed index of hemolysis risk because it is based on phenotypic G6PDd enzyme activity classifications, which is presumed, but not widely demonstrated, to be a surrogate marker for hemolysis. Nevertheless, these findings pave the way for further data collection and for the refinement of G6PDd maps that, in the absence of non-toxic alternatives to primaquine, will guide the design of safe primaquine regimens for the elimination of malaria.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001339.
Information is available from the World Health Organization on malaria; its 2011 World Malaria Report provides details of the current global malaria situation (some information is available in several languages)
The US Centers for Disease Control and Prevention provide information on malaria (in English and Spanish), including a selection of personal stories about malaria
Information is available from the Roll Back Malaria Partnership on the global control of malaria and on the Global Malaria Action Plan
Information on the global mapping of malaria is available at the Malaria Atlas Project website where G6PD deficiency prevalence maps, population estimates and the data used in this study can also be accessed
Information about G6PD deficiency for affected families can be found on KidsHealth from the Nemous Children's Health System and the G6PD Deficiency Association website
MedlinePlus provides links to additional information on malaria; the MedlinePlus Encyclopedia provides information about G6PD deficiency (in English and Spanish)
doi:10.1371/journal.pmed.1001339
PMCID: PMC3496665  PMID: 23152723
21.  Lymphatic Filariasis in Nigeria; Micro-stratification Overlap Mapping (MOM) as a Prerequisite for Cost-Effective Resource Utilization in Control and Surveillance 
Background
Nigeria has a significant burden of lymphatic filariasis (LF) caused by the parasite Wuchereria bancrofti. A major concern to the expansion of the LF elimination programme is the risk of serious adverse events (SAEs) associated with the use of ivermectin in areas co-endemic with Loa filariasis. To better understand this, as well as other factors that may impact on LF elimination, we used Micro-stratification Overlap Mapping (MOM) to highlight the distribution and potential impact of multiple disease interventions that geographically coincide in LF endemic areas and which will impact on LF and vice versa.
Methodology/Principal findings
LF data from the literature and Federal Ministry of Health (FMoH) were collated into a database. LF prevalence distributions; predicted prevalence of loiasis; ongoing onchocerciasis community-directed treatment with ivermectin (CDTi); and long-lasting insecticidal mosquito net (LLIN) distributions for malaria were incorporated into overlay maps using geographical information system (GIS) software. LF was prevalent across most regions of the country. The mean prevalence determined by circulating filarial antigen (CFA) was 14.0% (n = 134 locations), and by microfilaria (Mf) was 8.2% (n = 162 locations). Overall, LF endemic areas geographically coincided with CDTi priority areas, however, LLIN coverage was generally low (<50%) in areas where LF prevalence was high or co-endemic with L. loa.
Conclusions/Significance
The extensive database and series of maps produced in this study provide an important overview for the LF Programme and will assist to maximize existing interventions, ensuring cost effective use of resources as the programme scales up. Such information is a prerequisite for the LF programme, and will allow for other factors to be included into planning, as well as monitoring and evaluation activities given the broad spectrum impact of the drugs used.
Author Summary
Nigeria is estimated to have the highest burden of lymphatic filariasis (LF), a disease also known as elephantiasis, which is transmitted by mosquitoes and caused by the parasite Wuchereria bancrofti. The National LF Elimination Programme is planning to scale up the elimination programme through mass drug administration of ivermectin and albendazole. However, a major constraint to this expansion is the risk of serious adverse events (SAEs) associated with the use of ivermectin in areas co-endemic with Loa, the causative agent of tropical eye worm (loiasis). To better understand this and other factors that may impact on LF elimination, we collated and mapped all available LF data, and highlighted the overlaps with predicted loiasis prevalence distributions, onchocerciasis ivermectin treatment areas, and bed net distributions for malaria. This study provides a baseline overview for the LF Programme and will help to maximize existing disease interventions, ensuring cost effective use of resources as the programme scales up.
doi:10.1371/journal.pntd.0002416
PMCID: PMC3764235  PMID: 24040432
22.  Putting Beta-Diversity on the Map: Broad-Scale Congruence and Coincidence in the Extremes 
PLoS Biology  2007;5(10):e272.
Beta-diversity, the change in species composition between places, is a critical but poorly understood component of biological diversity. Patterns of beta-diversity provide information central to many ecological and evolutionary questions, as well as to conservation planning. Yet beta-diversity is rarely studied across large extents, and the degree of similarity of patterns among taxa at such scales remains untested. To our knowledge, this is the first broad-scale analysis of cross-taxon congruence in beta-diversity, and introduces a new method to map beta-diversity continuously across regions. Congruence between amphibian, bird, and mammal beta-diversity in the Western Hemisphere varies with both geographic location and spatial extent. We demonstrate that areas of high beta-diversity for the three taxa largely coincide, but areas of low beta-diversity exhibit little overlap. These findings suggest that similar processes lead to high levels of differentiation in amphibian, bird, and mammal assemblages, while the ecological and biogeographic factors influencing homogeneity in vertebrate assemblages vary. Knowledge of beta-diversity congruence can help formulate hypotheses about the mechanisms governing regional diversity patterns and should inform conservation, especially as threat from global climate change increases.
Author Summary
Beta-diversity—how species composition varies from place to place—is a fundamental attribute of biodiversity. However, despite its recognized importance, beta-diversity is rarely studied across large spatial scales. Here we use a new method to compare amphibian, bird, and mammal beta-diversity across large regions within the Western Hemisphere. We show that although the areas of low beta-diversity are different for the three groups, areas of high beta-diversity largely coincide. Moreover, we find that the degree to which the groups exhibit similar patterns of beta-diversity depends on the geographic location and extent at which it is measured. Beta-diversity is high where species are most susceptible to climate change, such as in areas with complex topography or high environmental variation. Identifying where areas of high beta-diversity coincide for different species groups is essential to the design of effective protected area networks.
A new method to compare amphibian, bird, and mammal beta-diversity within the Western Hemisphere reveals that areas of high beta-diversity coincide, with implications for understanding regional diversity patterns and for conservation.
doi:10.1371/journal.pbio.0050272
PMCID: PMC2001212  PMID: 17927449
23.  A World Malaria Map: Plasmodium falciparum Endemicity in 2007 
PLoS Medicine  2009;6(3):e1000048.
Background
Efficient allocation of resources to intervene against malaria requires a detailed understanding of the contemporary spatial distribution of malaria risk. It is exactly 40 y since the last global map of malaria endemicity was published. This paper describes the generation of a new world map of Plasmodium falciparum malaria endemicity for the year 2007.
Methods and Findings
A total of 8,938 P. falciparum parasite rate (PfPR) surveys were identified using a variety of exhaustive search strategies. Of these, 7,953 passed strict data fidelity tests for inclusion into a global database of PfPR data, age-standardized to 2–10 y for endemicity mapping. A model-based geostatistical procedure was used to create a continuous surface of malaria endemicity within previously defined stable spatial limits of P. falciparum transmission. These procedures were implemented within a Bayesian statistical framework so that the uncertainty of these predictions could be evaluated robustly. The uncertainty was expressed as the probability of predicting correctly one of three endemicity classes; previously stratified to be an informative guide for malaria control. Population at risk estimates, adjusted for the transmission modifying effects of urbanization in Africa, were then derived with reference to human population surfaces in 2007. Of the 1.38 billion people at risk of stable P. falciparum malaria, 0.69 billion were found in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africa+), and 0.04 billion in the Americas. All those exposed to stable risk in the Americas were in the lowest endemicity class (PfPR2−10 ≤ 5%). The vast majority (88%) of those living under stable risk in CSE Asia were also in this low endemicity class; a small remainder (11%) were in the intermediate endemicity class (PfPR2−10 > 5 to < 40%); and the remaining fraction (1%) in high endemicity (PfPR2−10 ≥ 40%) areas. High endemicity was widespread in the Africa+ region, where 0.35 billion people are at this level of risk. Most of the rest live at intermediate risk (0.20 billion), with a smaller number (0.11 billion) at low stable risk.
Conclusions
High levels of P. falciparum malaria endemicity are common in Africa. Uniformly low endemic levels are found in the Americas. Low endemicity is also widespread in CSE Asia, but pockets of intermediate and very rarely high transmission remain. There are therefore significant opportunities for malaria control in Africa and for malaria elimination elsewhere. This 2007 global P. falciparum malaria endemicity map is the first of a series with which it will be possible to monitor and evaluate the progress of this intervention process.
Incorporating data from nearly 8,000 surveys ofPlasmodium falciparum parasite rates, Simon Hay and colleagues employ a model-based geostatistical procedure to create a map of global malaria endemicity.
Editors' Summary
Background.
Malaria is one of the most common infectious diseases in the world and one of the greatest global public health problems. The Plasmodium falciparum parasite causes approximately 500 million cases each year and over one million deaths in sub-Saharan Africa. More than 40% of the world's population is at risk of malaria. The parasite is transmitted to people through the bites of infected mosquitoes. These insects inject a life stage of the parasite called sporozoites, which invade human liver cells where they reproduce briefly. The liver cells then release merozoites (another life stage of the parasite), which invade red blood cells. Here, they multiply again before bursting out and infecting more red blood cells, causing fever and damaging vital organs. The infected red blood cells also release gametocytes, which infect mosquitoes when they take a blood meal. In the mosquito, the gametocytes multiply and develop into sporozoites, thus completing the parasite's life cycle. Malaria can be prevented by controlling the mosquitoes that spread the parasite and by avoiding mosquito bites by sleeping under insecticide-treated bed nets. Effective treatment with antimalarial drugs also helps to decrease malaria transmission.
Why Was This Study Done?
In 1998, the World Health Organization and several other international agencies launched Roll Back Malaria, a global partnership that aims to reduce the human and socioeconomic costs of malaria. Targets have been continually raised since this time and have culminated in the Roll Back Malaria Global Malaria Action Plan of 2008, where universal coverage of locally appropriate interventions is called for by 2010 and the long-term goal of malaria eradication again tabled for the international community. For malaria control and elimination initiatives to be effective, financial resources must be concentrated in regions where they will have the most impact, so it is essential to have up-to-date and accurate maps to guide effort and expenditure. In 2008, researchers of the Malaria Atlas Project constructed a map that stratified the world into three levels of malaria risk: no risk, unstable transmission risk (occasional focal outbreaks), and stable transmission risk (endemic areas where the disease is always present). Now, researchers extend this work by describing a new evidence-based method for generating continuous maps of P. falciparum endemicity within the area of stable malaria risk over the entire world's surface. They then use this method to produce a P. falciparum endemicity map for 2007. Endemicity is important as it is a guide to the level of morbidity and mortality a population will suffer, as well as the intensity of the interventions that that will be required to bring the disease under control or additionally to interrupt transmission.
What Did the Researchers Do and Find?
The researchers identified nearly 8,000 surveys of P. falciparum parasite rates (PfPR; the percentage of a population with parasites detectable in their blood) completed since 1985 that met predefined criteria for inclusion into a global database of PfPR data. They then used “model-based geostatistics” to build a world map of P. falciparum endemicity for 2007 that took into account where and, importantly, when and all these surveys were done. Predictions were comprehensive (for every area of stable transmission globally) and continuous (predicted as a endemicity value between 0% and 100%). The population at risk of three levels of malaria endemicity were identified to help summarize these findings: low endemicity, where PfPR is below 5% and where it should be technically feasible to eliminate malaria; intermediate endemicity where PfPR is between 5% and 40% and it should be theoretically possible to interrupt transmission with the universal coverage of bed nets; high endemicity is where PfPR is above 40% and suites of locally appropriate intervention will be needed to bring malaria under control. The global level of malaria endemicity is much reduced when compared with historical maps. Nevertheless, the resulting map indicates that in 2007 almost 60% of the 2.4 billion people at malaria risk were living in areas with a stable risk of P. falciparum transmission—0.69 billion people in Central and South East Asia (CSE Asia), 0.66 billion in Africa, Yemen, and Saudi Arabia (Africa+), and 0.04 billion in the Americas. The people of the Americas were all in the low endemicity class. Although most people exposed to stable risk in CSE Asia were also in the low endemicity class (88%), 11% were in the intermediate class, and 1% were in the high endemicity class. By contrast, high endemicity was most common and widespread in the Africa+ region (53%), but with significant numbers in the intermediate (30%), and low (17%) endemicity classes.
What Do These Findings Mean?
The accuracy of this new world map of P. falciparum endemicity depends on the assumptions made in its construction and critically on the accuracy of the data fed into it, but because of the statistical methods used to construct this map, it is possible to quantify the uncertainty in the results for all users. Thus, this map (which, together with the data used in its construction, will be freely available) represents an important new resource that clearly indicates areas where malaria control can be improved (for example, Africa) and other areas where malaria elimination may be technically possible. In addition, planned annual updates of the global P. falciparum endemicity map and the PfPR database by the Malaria Atlas Project will help public-health experts to monitor the progress of the malaria control community towards international control and elimination targets.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1000048.
A PLoS Medicine Health in Action article (Hay SI, Snow RW (2006) The Malaria Atlas Project: Developing Global Maps of Malaria Risk. PLoS Med 3(12): e473) and a Research Article (Guerra CA, Gikandi PW, Tatem AJ, Noor AM, Smith DL, et al. (2008) The Limits and Intensity of Plasmodium falciparum Transmission: Implications for Malaria Control and Elimination Worldwide. PLoS Med 5(2): e38) also provide further details about the global mapping of malaria risk, and a further Research Article (Snow RW, Guerra CA, Mutheu JJ, Hay SI (2008) International Funding for Malaria Control in Relation to Populations at Risk of Stable Plasmodium falciparum Transmission. PLoS Med 5(7): e142) discusses the financing of malaria control in relation to this risk
Additional national and regional level maps and more information on the global mapping of malaria are available at the Malaria Atlas Project
The MedlinePlus encyclopedia contains a page on malaria (in English and Spanish)
Information is available from the World Health Organization on malaria (in several languages)
The US Centers for Disease Control and Prevention provide information on malaria (in English and Spanish)
Information is available from the Roll Back Malaria Partnership on its approach to the global control of malaria, and on malaria control efforts in specific parts of the world
doi:10.1371/journal.pmed.1000048
PMCID: PMC2659708  PMID: 19323591
24.  Conservation Priorities in a Biodiversity Hotspot: Analysis of Narrow Endemic Plant Species in New Caledonia 
PLoS ONE  2013;8(9):e73371.
New Caledonia is a global biodiversity hotspot facing extreme environmental degradation. Given the urgent need for conservation prioritisation, we have made a first-pass quantitative assessment of the distribution of Narrow Endemic Species (NES) in the flora to identify species and sites that are potentially important for conservation action. We assessed the distributional status of all angiosperm and gymnosperm species using data from taxonomic descriptions and herbarium samples. We characterised species as being NES if they occurred in 3 or fewer locations. In total, 635 of the 2930 assessed species were classed as NES, of which only 150 have been subjected to the IUCN conservation assessment. As the distributional patterns of un-assessed species from one or two locations correspond well with assessed species which have been classified as Critically Endangered or Endangered respectively, we suggest that our distributional data can be used to prioritise species for IUCN assessment. We also used the distributional data to produce a map of “Hotspots of Plant Narrow Endemism” (HPNE). Combined, we used these data to evaluate the coincidence of NES with mining activities (a major source of threat on New Caledonia) and also areas of conservation protection. This is to identify species and locations in most urgent need of further conservation assessment and subsequent action. Finally, we grouped the NES based on the environments they occurred in and modelled the habitat distribution of these groups with a Maximum Entropy Species Distribution Model (MaxEnt). The NES were separable into three different groups based primarily on geological differences. The distribution of the habitat types for each group coincide partially with the HPNE described above and also indicates some areas which have high habitat suitability but few recorded NES. Some of these areas may represent under-sampled hotspots of narrow endemism and are priorities for further field work.
doi:10.1371/journal.pone.0073371
PMCID: PMC3776834  PMID: 24058470
25.  Mapping Genetic Diversity of Cherimoya (Annona cherimola Mill.): Application of Spatial Analysis for Conservation and Use of Plant Genetic Resources 
PLoS ONE  2012;7(1):e29845.
There is a growing call for inventories that evaluate geographic patterns in diversity of plant genetic resources maintained on farm and in species' natural populations in order to enhance their use and conservation. Such evaluations are relevant for useful tropical and subtropical tree species, as many of these species are still undomesticated, or in incipient stages of domestication and local populations can offer yet-unknown traits of high value to further domestication. For many outcrossing species, such as most trees, inbreeding depression can be an issue, and genetic diversity is important to sustain local production. Diversity is also crucial for species to adapt to environmental changes. This paper explores the possibilities of incorporating molecular marker data into Geographic Information Systems (GIS) to allow visualization and better understanding of spatial patterns of genetic diversity as a key input to optimize conservation and use of plant genetic resources, based on a case study of cherimoya (Annona cherimola Mill.), a Neotropical fruit tree species. We present spatial analyses to (1) improve the understanding of spatial distribution of genetic diversity of cherimoya natural stands and cultivated trees in Ecuador, Bolivia and Peru based on microsatellite molecular markers (SSRs); and (2) formulate optimal conservation strategies by revealing priority areas for in situ conservation, and identifying existing diversity gaps in ex situ collections. We found high levels of allelic richness, locally common alleles and expected heterozygosity in cherimoya's putative centre of origin, southern Ecuador and northern Peru, whereas levels of diversity in southern Peru and especially in Bolivia were significantly lower. The application of GIS on a large microsatellite dataset allows a more detailed prioritization of areas for in situ conservation and targeted collection across the Andean distribution range of cherimoya than previous studies could do, i.e. at province and department level in Ecuador and Peru, respectively.
doi:10.1371/journal.pone.0029845
PMCID: PMC3253804  PMID: 22253801

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