Institut de Recherche pour le Développement

Freshwater biodiversity is the over-riding conservation priority during the International Decade for Action - 'Water for Life' - 2005 to 2015. Fresh water makes up only 0.01% of the World's water and approximately 0.8% of the Earth's surface, yet this tiny fraction of global water supports at least 100000 species out of approximately 1.8 million - almost 6% of all described species. Inland waters and freshwater biodiversity constitute a valuable natural resource, in economic, cultural, aesthetic, scientific and educational terms. Their conservation and management are critical to the interests of all humans, nations and governments. Yet this precious heritage is in crisis. Fresh waters are experiencing declines in biodiversity far greater than those in the most affected terrestrial ecosystems, and if trends in human demands for water remain unaltered and species losses continue at current rates, the opportunity to conserve much of the remaining biodiversity in fresh water will vanish before the 'Water for Life' decade ends in 2015. Why is this so, and what is being done about it? This article explores the special features of freshwater habitats and the biodiversity they support that makes them especially vulnerable to human activities. We document threats to global freshwater biodiversity under five headings: overexploitation; water pollution; flow modification; destruction or degradation of habitat; and invasion by exotic species. Their combined and interacting influences have resulted in population declines and range reduction of freshwater biodiversity worldwide. Conservation of biodiversity is complicated by the landscape position of rivers and wetlands as 'receivers' of land-use effluents, and the problems posed by endemism and thus non-substitutability. In addition, in many parts of the world, fresh water is subject to severe competition among multiple human stakeholders. Protection of freshwater biodiversity is perhaps the ultimate conservation challenge because it is influenced by the upstream drainage network, the surrounding land, the riparian zone, and - in the case of migrating aquatic fauna - downstream reaches. Such prerequisites are hardly ever met. Immediate action is needed where opportunities exist to set aside intact lake and river ecosystems within large protected areas. For most of the global land surface, trade-offs between conservation of freshwater biodiversity and human use of ecosystem goods and services are necessary. We advocate continuing attempts to check species loss but, in many situations, urge adoption of a compromise position of management for biodiversity conservation, ecosystem functioning and resilience, and human livelihoods in order to provide a viable long-term basis for freshwater conservation. Recognition of this need will require adoption of a new paradigm for biodiversity protection and freshwater ecosystem management - one that has been appropriately termed 'reconciliation ecology'.

Introduction Recent decades have seen a major international effort to inventory tree communities in the Amazon Basin and Guiana Shield (Amazonia), but the vast extent and record diversity of these forests have hampered an understanding of basinwide patterns. To overcome this obstacle, we compiled and standardized species-level data on more than half a million trees in 1170 plots sampling all major lowland forest types to explore patterns of commonness, rarity, and richness. Methods The ~6-million-km 2 Amazonian lowlands were divided into 1° cells, and mean tree density was estimated for each cell by using a loess regression model that included no environmental data but had its basis exclusively in the geographic location of tree plots. A similar model, allied with a bootstrapping exercise to quantify sampling error, was used to generate estimated Amazon-wide abundances of the 4962 valid species in the data set. We estimated the total number of tree species in the Amazon by fitting the mean rank-abundance data to Fisher’s log-series distribution. Results Our analyses suggest that lowland Amazonia harbors 3.9 × 10 11 trees and ~16,000 tree species. We found 227 “hyperdominant” species (1.4% of the total) to be so common that together they account for half of all trees in Amazonia, whereas the rarest 11,000 species account for just 0.12% of trees. Most hyperdominants are habitat specialists that have large geographic ranges but are only dominant in one or two regions of the basin, and a median of 41% of trees in individual plots belong to hyperdominants. A disproportionate number of hyperdominants are palms, Myristicaceae, and Lecythidaceae. Discussion The finding that Amazonia is dominated by just 227 tree species implies that most biogeochemical cycling in the world’s largest tropical forest is performed by a tiny sliver of its diversity. The causes underlying hyperdominance in these species remain unknown. Both competitive superiority and widespread pre-1492 cultivation by humans are compelling hypotheses that deserve testing. Although the data suggest that spatial models can effectively forecast tree community composition and structure of unstudied sites in Amazonia, incorporating environmental data may yield substantial improvements. An appreciation of how thoroughly common species dominate the basin has the potential to simplify research in Amazonian biogeochemistry, ecology, and vegetation mapping. Such advances are urgently needed in light of the >10,000 rare, poorly known, and potentially threatened tree species in the Amazon.

Abstract Soils are the main sources of the greenhouse gas nitrous oxide (N 2 O). The N 2 O emission at the soil surface is the result of production and consumption processes. So far, research has concentrated on net N 2 O production. However, in the literature, there are numerous reports of net negative fluxes of N 2 O, (i.e. fluxes from the atmosphere to the soil). Such fluxes are frequent and substantial and cannot simply be dismissed as experimental noise. Net N 2 O consumption has been measured under various conditions from the tropics to temperate areas, in natural and agricultural systems. Low mineral N and large moisture contents have sometimes been found to favour N 2 O consumption. This fits in with denitrification as the responsible process, reducing N 2 O to N 2 . However, it has also been reported that nitrifiers consume N 2 O in nitrifier denitrification. A contribution of various processes could explain the wide range of conditions found to allow N 2 O consumption, ranging from low to high temperatures, wet to dry soils, and fertilized to unfertilized plots. Generally, conditions interfering with N 2 O diffusion in the soil seem to enhance N 2 O consumption. However, the factors regulating N 2 O consumption are not yet well understood and merit further study. Frequent literature reports of net N 2 O consumption suggest that a soil sink could help account for the current imbalance in estimated global budgets of N 2 O. Therefore, a systematic investigation into N 2 O consumption is necessary. This should concentrate on the organisms, reactions, and environmental factors involved.

BACKGROUND: Nitrogen is an essential nutrient in plant growth. The ability of a plant to supply all or part of its requirements from biological nitrogen fixation (BNF) thanks to interactions with endosymbiotic, associative and endophytic symbionts, confers a great competitive advantage over non-nitrogen-fixing plants. SCOPE: Because BNF in legumes is well documented, this review focuses on BNF in non-legume plants. Despite the phylogenic and ecological diversity among diazotrophic bacteria and their hosts, tightly regulated communication is always necessary between the microorganisms and the host plant to achieve a successful interaction. Ongoing research efforts to improve knowledge of the molecular mechanisms underlying these original relationships and some common strategies leading to a successful relationship between the nitrogen-fixing microorganisms and their hosts are presented. CONCLUSIONS: Understanding the molecular mechanism of BNF outside the legume-rhizobium symbiosis could have important agronomic implications and enable the use of N-fertilizers to be reduced or even avoided. Indeed, in the short term, improved understanding could lead to more sustainable exploitation of the biodiversity of nitrogen-fixing organisms and, in the longer term, to the transfer of endosymbiotic nitrogen-fixation capacities to major non-legume crops.

Abstract Aim We surveyed the empirical literature to determine how well six diversity hypotheses account for spatial patterns in species richness across varying scales of grain and extent. Location Worldwide. Methods We identified 393 analyses (‘cases’) in 297 publications meeting our criteria. These criteria included the requirement that more than one diversity hypothesis was tested for its relationship with species richness. We grouped variables representing the hypotheses into the following ‘correlate types’: climate/productivity, environmental heterogeneity, edaphics/nutrients, area, biotic interactions and dispersal/history (colonization limitation or other historical or evolutionary effect). For each case we determined the ‘primary’ variable: the one most strongly correlated with taxon richness. We defined ‘primacy’ as the proportion of cases in which each correlate type was represented by the primary variable, relative to the number of times it was studied. We tested for differences in both primacy and mean coefficient of determination of the primary variable between the hypotheses and between categories of five grouping variables: grain, extent, taxon (animal vs. plant), habitat medium (land vs. water) and insularity (insular vs. connected). Results Climate/productivity had the highest overall primacy, and environmental heterogeneity and dispersal/history had the lowest. Primacy of climate/productivity was much higher in large‐grain and large‐extent studies than at smaller scales. It was also higher on land than in water, and much higher in connected systems than in insular ones. For other hypotheses, differences were less pronounced. Throughout, studies on plants and animals showed similar patterns. Coefficients of determination of the primary variables differed little between hypotheses and across the grouping variables, the strongest effects being low means in the smallest grain class and for edaphics/nutrients variables, and a higher mean for water than for land in connected systems but vice versa in insular systems. We highlight areas of data deficiency. Main conclusions Our results support the notion that climate and productivity play an important role in determining species richness at large scales, particularly for non‐insular, terrestrial habitats. At smaller extents and grain sizes, the primacy of the different types of correlates appears to differ little from null expectation. In our analysis, dispersal/history is rarely the best correlate of species richness, but this may reflect the difficulty of incorporating historical factors into regression models, and the collinearity between past and current climates. Our findings are consistent with the view that climate determines the capacity for species richness. However, its influence is less evident at smaller spatial scales, probably because (1) studies small in extent tend to sample little climatic range, and (2) at large grains some other influences on richness tend to vary mainly within the sampling unit.

Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations.

BACKGROUND: A Chikungunya (CHIK) outbreak hit La Réunion Island in 2005-2006. The implicated vector was Aedes albopictus. Here, we present the first study on the susceptibility of Ae. albopictus populations to sympatric CHIKV isolates from La Réunion Island and compare it to other virus/vector combinations. METHODOLOGY AND FINDINGS: We orally infected 8 Ae. albopictus collections from La Réunion and 3 from Mayotte collected in March 2006 with two Chikungunya virus (CHIKV) from La Réunion: (i) strain 05.115 collected in June 2005 with an Alanine at the position 226 of the glycoprotein E1 and (ii) strain 06.21 collected in November 2005 with a substitution A226V. Two other CHIKV isolates and four additional mosquito strains/species were also tested. The viral titer of the infectious blood-meal was 10(7) plaque forming units (pfu)/mL. Dissemination rates were assessed by immunofluorescent staining on head squashes of surviving females 14 days after infection. Rates were at least two times higher with CHIKV 06.21 compared to CHIKV 05.115. In addition, 10 individuals were analyzed every day by quantitative RT-PCR. Viral RNA was quantified on (i) whole females and (ii) midguts and salivary glands of infected females. When comparing profiles, CHIKV 06.21 produced nearly 2 log more viral RNA copies than CHIKV 05.115. Furthermore, females infected with CHIKV 05.115 could be divided in two categories: weakly susceptible or strongly susceptible, comparable to those infected by CHIKV 06.21. Histological analysis detected the presence of CHIKV in salivary glands two days after infection. In addition, Ae. albopictus from La Réunion was as efficient vector as Ae. aegypti and Ae. albopictus from Vietnam when infected with the CHIKV 06.21. CONCLUSIONS: Our findings support the hypothesis that the CHIK outbreak in La Réunion Island was due to a highly competent vector Ae. albopictus which allowed an efficient replication and dissemination of CHIKV 06.21.

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

Increased demand and advanced techniques could lead to more refined mapping and management of soils.

In plants, the developmental mechanisms that regulate the positioning of lateral organs along the primary root are currently unknown. We present evidence on how lateral root initiation is controlled in a spatiotemporal manner in the model plant Arabidopsis thaliana. First, lateral roots are spaced along the main axis in a regular left-right alternating pattern that correlates with gravity-induced waving and depends on AUX1, an auxin influx carrier essential for gravitropic response. Second, we found evidence that the priming of pericycle cells for lateral root initiation might take place in the basal meristem, correlating with elevated auxin sensitivity in this part of the root. This local auxin responsiveness oscillates with peaks of expression at regular intervals of 15 hours. Each peak in the auxin-reporter maximum correlates with the formation of a consecutive lateral root. Third, auxin signaling in the basal meristem triggers pericycle cells for lateral root initiation prior to the action of INDOLE-3-ACETIC ACID14 (SOLITARY ROOT).

Low-trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low-trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.

, 2017 WHO categorized snakebite envenomation into the Category A of the Neglected Tropical Diseases. This new situation will allow access to new funding, paving the way for wider and deeper researches. It should also expand the accessibility of antivenoms. Let us hope that it also leads to cooperation among stakeholders, aiming at improving the management of snakebites in developing countries.

The pyrethroid knockdown resistance gene (kdr) has become widespread in Anopheles gambiae in West Africa. A trial to test the continuing efficacy of insecticide-treated nets (ITN) and indoor residual spraying (IRS) was undertaken in experimental huts at 2 sites in Benin, the first where kdr is present at high frequency (Ladji), the second-where An. gambiae is susceptible (Malanville). Holes were made in the nets to mimic worn nets. At Malanville, 96% of susceptible An. gambiae were inhibited from blood-feeding, whereas at Ladji feeding was uninhibited by ITNs. The mortality rate of An. gambiae in ITN huts was 98% in Malanville but only 30% at Ladji. The efficacy of IRS was equally compromised. Mosquitoes at Ladji had higher oxidase and esterase activity than in a laboratory-susceptible strain, but this fact did not seem to contribute to resistance. Pyrethroid resistance in An. gambiae appears to threaten the future of ITN and IRS in Benin.

Twelve years after the Kikwit Ebola outbreak in 1995, Ebola virus reemerged in the Occidental Kasaï province of the Democratic Republic of Congo (DRC) between May and November 2007, affecting more than 260 humans and causing 186 deaths. During this latter outbreak we conducted several epidemiological investigations to identify the underlying ecological conditions and animal sources. Qualitative social and environmental data were collected through interviews with villagers and by direct observation. The local populations reported no unusual morbidity or mortality among wild or domestic animals, but they described a massive annual fruit bat migration toward the southeast, up the Lulua River. Migrating bats settled in the outbreak area for several weeks, between April and May, nestling in the numerous fruit trees in Ndongo and Koumelele islands as well as in palm trees of a largely abandoned plantation. They were massively hunted by villagers, for whom they represented a major source of protein. By tracing back the initial human-human transmission events, we were able to show that, in May, the putative first human victim bought freshly killed bats from hunters to eat. We were able to reconstruct the likely initial human-human transmission events that preceded the outbreak. This study provides the most likely sequence of events linking a human Ebola outbreak to exposure to fruit bats, a putative virus reservoir. These findings support the suspected role of bats in the natural cycle of Ebola virus and indicate that the massive seasonal fruit bat migrations should be taken into account in operational Ebola risk maps and seasonal alerts in the DRC.

Aedes albopictus is a mosquito originating from Asia, which has extended its range worldwide the last decades. It is a competent vector for several arboviruses. It was first described in La Réunion (an island of the South West part of the Indian Ocean) in 1913. Since then, it has become the dominant Aedes species and a serious threat to public health, especially during the two last arboviruses outbreaks of dengue (1977) and chikungunya (2005-2006). Despite its pest status, data on the biology of this vector are scarce, especially the population present in the Indian Ocean (IO), which has never been studied in detail. Therefore, the immature development, survival, longevity, fecundity, and gonotrophic cycles of Ae. albopictus were studied for an F2 population of the IO. These biological parameters were studied in controlled conditions at eight constant temperatures (5, 10, 15, 20, 25, 30, 35, and 40 degrees C). The minimal threshold of immature stages development was found at 10.4 degrees C and its optimum at 29.7 degrees C. The shortest periods for immature development were found at 30 degrees C, with in average of 8.8 d. The optimum intrinsic rate of growth (r) was observed between 25 and 30 degrees C. The gonotrophic cycles were also evaluated, and the shortest cycles were found at 30 degrees C (mean, 3.5 d). Those results are according to the field repartition of this species in La Réunion, allowing Ae. albopictus survival at a large range of temperatures.

Abstract Climate and litter quality are primary drivers of terrestrial decomposition and, based on evidence from multisite experiments at regional and global scales, are universally factored into global decomposition models. In contrast, soil animals are considered key regulators of decomposition at local scales but their role at larger scales is unresolved. Soil animals are consequently excluded from global models of organic mineralization processes. Incomplete assessment of the roles of soil animals stems from the difficulties of manipulating invertebrate animals experimentally across large geographic gradients. This is compounded by deficient or inconsistent taxonomy. We report a global decomposition experiment to assess the importance of soil animals in C mineralization, in which a common grass litter substrate was exposed to natural decomposition in either control or reduced animal treatments across 30 sites distributed from 43°S to 68°N on six continents. Animals in the mesofaunal size range were recovered from the litter by Tullgren extraction and identified to common specifications, mostly at the ordinal level. The design of the trials enabled faunal contribution to be evaluated against abiotic parameters between sites. Soil animals increase decomposition rates in temperate and wet tropical climates, but have neutral effects where temperature or moisture constrain biological activity. Our findings highlight that faunal influences on decomposition are dependent on prevailing climatic conditions. We conclude that (1) inclusion of soil animals will improve the predictive capabilities of region‐ or biome‐scale decomposition models, (2) soil animal influences on decomposition are important at the regional scale when attempting to predict global change scenarios, and (3) the statistical relationship between decomposition rates and climate, at the global scale, is robust against changes in soil faunal abundance and diversity.

BACKGROUND: The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. RESULTS: In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. CONCLUSIONS: The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits that cosegregate with these markers. Finally, the oil palm EST-SSRs derived from vegetative and reproductive development will be useful for studies on the evolution of the functional diversity within the palm family.

For the past two decades, network approaches have led to many conceptual and empirical developments in the studies of international migration as well as of technological innovation. However, surprisingly, such approaches have hardly been used for the study of what is at the intersection of both fields, namely the mobility of highly skilled persons or knowledge workers. This article draws on recent evidence brought by case studies on intellectual diaspora networks to bridge this gap and to explore the issue. These highly skilled expatriate networks, through a connectionist approach linking diaspora members with their countries of origin, turn the brain drain into a brain gain approach. These persons and groups also provide original information that questions conventional human capital based assumptions. The article argues that descriptions in terms of network open interesting perspectives for the understanding as well as management of the current global skills’ circulation. The network approach under consideration combines input from migration as well as from innovation studies. This suggests an expanded version of the network approach, referring to actors and intermediaries, of which traditional kinship ties are but a part of more systematic associative dynamics actually at work.

The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis.

BACKGROUND: Behavioral modification of malaria vectors in response to vector control methods is of great concern. We investigated whether full coverage of long-lasting insecticide-treated mosquito nets (LLINs) may induce a switch in biting behavior in Anopheles funestus, a major malaria vector in Africa. METHODS: Human-landing collections were conducted indoor and outdoor in 2 villages (Lokohouè and Tokoli) in Benin before and 1 year and 3 years after implementation of universal LLIN coverage. Proportion of outdoor biting (POB) and median catching times (MCT) were compared. The resistance of A. funestus to deltamethrin was monitored using bioassays. RESULTS: MCT of A. funestus switched from 2 AM in Lokohoué and 3 AM in Tokoli to 5 AM after 3 years (Mann-Whitney U test, P < .0001). In Tokoli, POB increased from 45% to 68.1% (odds ratio = 2.55; 95 confidence interval = 1.72-3.78; P < .0001) 1 year after the universal coverage, whereas POB was unchanged in Lokohoué. In Lokohoué, however, the proportion of A. funestus that bites after 6 am was 26%. Bioassays showed no resistance to deltamethrin. CONCLUSIONS: This study provides evidence for a switch in malaria vectors' biting behavior after the implementation of LLIN at universal coverage. These findings might have direct consequences for malaria control in Africa and highlighted the need for alternative strategies for better targeting malaria vectors.