Laboratoire écologie, évolution, interactions des systèmes amazoniens

Warmer and drier climates over Amazonia have been predicted for the next century with expected changes in regional water and carbon cycles. We examined the impact of interannual and seasonal variations in climate conditions on ecosystem-level evapotranspiration (ET) and water use efficiency (WUE) to determine key climatic drivers and anticipate the response of these ecosystems to climate change. We used daily climate and eddyflux data recorded at the Guyaflux site in French Guiana from 2004 to 2014. ET and WUE exhibited weak interannual variability. The main climatic driver of ET and WUE was global radiation (Rg), but relative extractable water (REW) and soil temperature (Ts) did also contribute. At the seasonal scale, ET and WUE showed a modal pattern driven by Rg, with maximum values for ET in July and August and for WUE at the beginning of the year. By removing radiation effects during water depleted periods, we showed that soil water stress strongly reduced ET. In contrast, drought conditions enhanced radiation-normalized WUE in almost all the years, suggesting that the lack of soil water had a more severe effect on ecosystem evapotranspiration than on photosynthesis. Our results are of major concern for tropical ecosystem modeling because they suggest that under future climate conditions, tropical forest ecosystems will be able to simultaneously adjust CO2 and H2O fluxes. Yet, for tropical forests under future conditions, the direction of change in WUE at the ecosystem scale is hard to predict, since the impact of radiation on WUE is counterbalanced by adjustments to soil water limitations. Developing mechanistic models that fully integrate the processes associated with CO2 and H2O flux control should help researchers understand and simulate future functional adjustments in these ecosystems.

Amphibian chytridiomycosis, an emerging infectious disease caused by the fungus Batrachochytrium dendrobatidis (Bd), has been a significant driver of amphibian declines. While globally widespread, Bd had not yet been reported from within Madagascar. We document surveys conducted across the country between 2005 and 2014, showing Bd's first record in 2010. Subsequently, Bd was detected in multiple areas, with prevalence reaching up to 100%. Detection of Bd appears to be associated with mid to high elevation sites and to have a seasonal pattern, with greater detectability during the dry season. Lineage-based PCR was performed on a subset of samples. While some did not amplify with any lineage probe, when a positive signal was observed, samples were most similar to the Global Panzootic Lineage (BdGPL). These results may suggest that Bd arrived recently, but do not exclude the existence of a previously undetected endemic Bd genotype. Representatives of all native anuran families have tested Bd-positive, and exposure trials confirm infection by Bd is possible. Bd's presence could pose significant threats to Madagascar's unique "megadiverse" amphibians.

Marine and coastal activities are closely interrelated, and conflicts among different sectors can undermine management and conservation objectives. Governance systems for fisheries, power generation, irrigation, aquaculture, marine biodiversity conservation, and other coastal and maritime activities are typically organized to manage conflicts within sectors, rather than across them. Based on the discussions around eight case studies presented at a workshop held in Brest in June 2019, this paper explores institutional approaches to move beyond managing conflicts within a sector. We primarily focus on cases where the groups and sectors involved are heterogeneous in terms of: the jurisdiction they fall under; their objectives; and the way they value ecosystem services. The paper first presents a synthesis of frameworks for understanding and managing cross-sectoral governance conflicts, drawing from social and natural sciences. We highlight commonalities but also conceptual differences across disciplines to address these issues. We then propose a novel analytical framework which we used to evaluate the eight case studies. Based on the main lessons learned from case studies, we then discuss the feasibility and key determinants of stakeholder collaboration as well as compensation and incentive schemes. The discussion concludes with future research needs to support policy development and inform integrated institutional regimes that consider the diversity of stakeholder interests and the potential benefits of cross-sectoral coordination.

Abstract: Among the hypotheses formulated to explain the origin of Amazonian biodiversity, two (the riverine-barrier and the river-refuge hypotheses) focus on the role that rivers play as biotic barriers promoting speciation. However, empirical results have both supported and refuted these hypotheses. This is likely due, at least in part, to river-specific hydrologic characteristics and the biology of the focal species. The rivers of the Guiana Shield represent a model system because they have had more stable courses over time than those of the western Amazon Basin, where most tests of riverine barrier effects have taken place. We tested whether life-history traits (body size, habitat and larval development), expected to be important in determining dispersal ability, of 28 frog species are associated with genetic structure and genetic distances of individuals sampled from both banks of the Oyapock River. Thirteen of these species displayed genetic structure consistent with the river acting as a barrier to dispersal. Surprisingly, body size was not correlated with trans-riverine population structure. However, leaf-litter dwellers and species lacking free-living tadpoles were found to exhibit higher river-associated structure than open habitat/arboreal species and those with exotrophic tadpoles. These results demonstrate that rivers play an important role in structuring the genetic diversity of many frog species though the permeability of such riverine barriers is highly dependent on species-specific traits.

Abstract. Measuring in situ soil fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) continuously at high frequency requires appropriate technology. We tested the combination of a commercial automated soil CO2 flux chamber system (LI-8100A) with a CH4 and N2O analyzer (Picarro G2308) in a tropical rainforest for 4 months. A chamber closure time of 2 min was sufficient for a reliable estimation of CO2 and CH4 fluxes (100 % and 98.5 % of fluxes were above minimum detectable flux – MDF, respectively). This closure time was generally not suitable for a reliable estimation of the low N2O fluxes in this ecosystem but was sufficient for detecting rare major peak events. A closure time of 25 min was more appropriate for reliable estimation of most N2O fluxes (85.6 % of measured fluxes are above MDF ± 0.002 nmol m−2 s−1). Our study highlights the importance of adjusted closure time for each gas.

Abstract Many species of Neotropical frogs have evolved to deposit their tadpoles in small water bodies inside plant structures called phytotelmata. These pools are small enough to exclude large predators but have limited nutrients and high desiccation risk. Here, we explore phytotelm use by three common Neotropical species: Osteocephalus oophagus , an arboreal frog that periodically feeds eggs to its tadpoles; Dendrobates tinctorius, a tadpole‐transporting poison frog with cannibalistic tadpoles; and Allobates femoralis, a terrestrial tadpole‐transporting poison frog with omnivorous tadpoles. We found that D . tinctorius occupies pools across the chemical and vertical gradient, whereas A. femoralis and O . oophagus appear to have narrower deposition options that are restricted primarily by pool height, water capacity, alkalinity, and salinity. Dendrobates tinctorius tadpoles are particularly flexible and can survive in a wide range of chemical, physical, and biological conditions, whereas O. oophagus seems to prefer small, clear pools and A. femoralis occupies medium‐sized pools with abundant leaf litter and low salinity. Together, these results show the possible niche partitioning of phytotelmata among frogs and provide insight into stressors and resilience of phytotelm breeders.

The 350-km long coast of Suriname, South America, is part of a unique system in the world characterized by large-scale mud supply from the Amazon and exposed to Atlantic waves. Large banks migrate alongshore from the Amazon to the Orinoco delta, separated by ‘inter-bank’ zones. Banks dissipate waves, and create new land, aided by mangroves, whereas waves in inter-bank areas cause shoreline erosion, mitigated where sandy/shelly cheniers develop. Cheniers are rare due to sand/shell burial by mud. They assure coastal protection, and recreational and ecological services, notably providing nesting sites for marine turtles. Cheniers close to urban centres are under pressure from sand mining. In order to gain a better understanding of how cheniers develop and evolve, a study was conducted on Braamspunt beach, a turtle-nesting chenier in Suriname constructed from sand supplied by the Maroni River. Satellite images between 1987 and 2018 show that Braamspunt beach has progressively shortened, mainly through isolation of the beach by a mud bank migrating alongshore. Downdrift of the mud bank, the beach has migrated landward by wave overwash. Active commercial sand mining has further affected the beach. Partial sand sequestering at a multi-decadal timescale by migrating mud banks results in temporally fragmented and alongshore-variable sand transport. Field surveys (high-resolution topometry, drone photogrammetry, and wave measurements) conducted in February, 2016, enabled differentiation between a reworked sector (immediately downdrift of the mud bank), and a ‘sink’ sector adjacent to the Suriname River estuary. Sand sequestering at the bank’s leading edge and landward chenier migration deprive the downdrift beach of sand, generating beach scarping and lowering downdrift to balance an under-saturated longshore transport. Over only 3-4 days, the beach lost over 4200 m3 as a result of mud blanketing and overwashing. The subsisting beach is currently preserved from mud in its downdrift sector by mud liquefaction at the mouth of the Suriname River. This preservation is a morphodynamic adjustment between beach and the river jet, and without which Braamspunt beach would cease to exist. This effect assures beach availability for turtle nesting. The continued existence of Braamspunt beach is, however, endangered by sand mining.

This study examined whether the antidermatophytic activity of essential oils (EOs) can be used as an indicator for the discovery of active natural products against Leishmania amazonensis. The aerial parts of seven plants were hydrodistilled. Using broth microdilution techniques, the obtained EOs were tested against three strains of dermatophytes (Trichophyton mentagrophytes, Microsporum gypseum and Microsporum canis). To compare the EOs antifungal and antiparasitic effects, the EOs activities against axenic amastigotes of L. amazonensis were concurrently evaluated. For the most promising EOs, their antileishmanial activities against parasites infecting peritoneal macrophages of BALB/c mice were measured. The most interesting antifungal candidates were the EOs from Cymbopogon citratus, Otacanthus azureus and Protium heptaphyllum, whereas O. azureus, Piper hispidum and P. heptaphyllum EOs exhibited the lowest 50% inhibitory concentration (IC50) values against axenic amastigotes, thus revealing a certain correspondence between both activities. The P. hispidum EO was identified as the most promising product in the results from the infected macrophages model (IC50: 4.7 µg/mL, safety index: 8). The most abundant compounds found in this EO were sesquiterpenes, notably curzerene and furanodiene. Eventually, the evaluation of the antidermatophytic activity of EOs appears to be an efficient method for identifying new potential drugs for the treatment of L. amazonensis.

BACKGROUND: French Guiana is characterized by a very multicultural population, made up of formerly settled groups (Amerindians, Maroons, Creoles) and more recent migrants (mostly from Latin America and the Caribbean). It is the ideal place to try to understand the influence of intercultural exchanges on the composition of medicinal floras and the evolution of phytotherapies under the effect of cross-culturalism. METHODS: A combination of qualitative and quantitative methods was used. Semi-directive interviews were conducted in 12 localities of French Guiana's coast between January 2016 and June 2017, and the responses to all closed questions collected during the survey were computerized in an Excel spreadsheet to facilitate quantitative processing. Herbarium vouchers were collected and deposited at the Cayenne Herbarium to determine Linnaean names of medicinal species mentioned by the interviewees. A list of indicator species for each cultural group considered was adapted from community ecology to this ethnobiological context, according to the Dufrêne-Legendre model, via the "labdsv" package and the "indval" function, after performing a redundancy analysis (RDA). RESULTS: A total of 205 people, belonging to 15 distinct cultural groups, were interviewed using semi-structured questionnaires. A total of 356 species (for 106 botanical families) were cited. We observed that pantropical and edible species hold a special place in these pharmacopeias. If compared to previous inventories, 31 recently introduced species can be counted. Furthermore, this study shows that the majority of the plants used are not specific to a particular group but shared by many communities. However, despite this obvious cross-culturalism of medicinal plants between the different cultural communities of French Guiana, divergent trends nevertheless appear through the importance of 29 indicator/cultural keystone species in 10 cultural groups. Finally, we have emphasized that the transmission of herbal medicine's knowledge in French Guiana is mainly feminine and intra-cultural. CONCLUSION: French Guianese medicinal flora is undoubtedly related to the multiple cultures that settled this territory through the last centuries. Cultural pharmacopeias are more hybrid than sometimes expected, but cultural keystone species nevertheless arise from a common background, allowing to understand, and define, the relationships between cultural groups.

Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene P that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly Heliconius numata. We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different H. numata morphs. Within the P interval, 30 and 17 of the 191 transcripts were expressed differentially in prepupae and day-1 pupae, respectively. Among these is the gene cortex, known to play a role in wing pattern formation in Heliconius and other Lepidoptera. Our in situ hybridization experiments confirmed the relationship between cortex expression and adult wing patterns. This study found the majority of genes in the P interval to be expressed in the developing wing discs during the critical stages of colour pattern formation, and detect drastic changes in expression patterns in multiple genes associated with structural variants. The patterns of expression of cortex only partially recapitulate the variation in adult phenotype, suggesting that the remaining phenotypic variation could be controlled by other genes within the P interval. Although functional studies on cortex are now needed to determine its exact developmental role, our results are in accordance with the classical supergene hypothesis, whereby several genes inherited together due to tight linkage control a major developmental switch.

Since antiquity, the sense of smell (olfaction) is considered as a distance sense, just like sight and hearing. Conversely, the sense of taste (gustation) is thought to operate by direct contact, similarly to touch. With the progress of natural sciences, information at molecular, anatomical, and neurobiological levels has also contributed to the taste-smell dichotomy, but much evidence inconsistent with a sharp differentiation of these two senses has emerged, especially when considering species other than humans. In spite of this, conflicting information has been interpreted so that it could conform to the traditional differentiation. As a result, a confirmation bias is currently affecting scientific research on chemosensory systems and is also hindering the development of a satisfactory narrative of the evolution of chemical communication across taxa. From this perspective, the chemosensory dichotomy loses its validity and usefulness. We thus propose the unification of all chemosensory modalities into a single sense, moving toward a synthetic, complex, and interconnected perspective on the gradual processes by which a vast variety of chemicals have become signals that are crucially important to communication among and within cells, organs, and organisms in a wide variety of environmental conditions.

ETHNOPHARMACOLOGICAL RELEVANCE: Quassia amara L. recently came into the spotlight in French Guiana, when it became the object of a biopiracy claim. Due to the numerous use records throughout the Guiana shield, at least since the 18th century, a thorough investigation of its origin seemed relevant and timely. In the light of the Convention on Biological Diversity (CBD) and the Nagoya protocol, questions about the origin of local knowledge are important to debate. AIM OF THE STUDY: Defining cultural biogeography as the dynamics through space and time of biocultural complexes, we used this theoretical framework to shed light on the complex biogeographical and cultural history of Q. amara. We explored in particular the possible transfer of medicinal knowledge on an Old World species to a botanically related New World one by enslaved Africans in Suriname. MATERIALS AND METHODS: Historical and contemporary literature research was performed by means of digitized manuscripts, archives and databases from the 17th to the 21st century. We retrieved data from digitized herbarium vouchers in herbaria of the Botanic Garden Meise (Belgium); Naturalis Biodiversity Center (the Netherlands); Missouri Botanical Garden, the Smithsonian National Museum of Natural History, the Field Museum (USA); Royal Botanic Gardens Kew (UK); the IRD Herbarium, French Guiana and the Museum National d'Histoire Naturelle (France). Vernacular names were retrieved from literature and herbarium specimens and compared to verify the origin of Quassia amara and its uses. RESULTS: Our exploration of digitized herbarium vouchers resulted in 1287 records, of which 661 were Q. amara and 636 were Q. africana. We observed that the destiny of this species, over at least 300 years, interweaves politics, economy, culture and medicine in a very complex way. Quassia amara's uses are difficult to attribute to specific cultural groups: the species is widely distributed in Central and South America, where it is popular among many ethnic groups. The species spread from Central to South America during the early 18th century due to political and economic reasons. This migration possibly resulted from simultaneous migration by religious orders (Jesuits) from Central America to northern South America and by Carib-speaking Amerindians (from northern South America to Suriname). Subsequently, through colonial trade networks, Q. amara spread to the rest of the world. The absence of African-derived local names in the Guiana shield suggests that Q. africana was not sufficiently familiar to enslaved Africans in the region that they preserved its names and transferred the associated medicinal knowledge to Q. amara. CONCLUSIONS: Cultural biogeography has proven an interesting concept to reconstruct the dynamics of biocultural interactions through space and time, while herbarium databases have shown to be useful to decipher evolution of local plant knowledge. Tracing the origin of a knowledge is nevertheless a complex adventure that deserves time and interdisciplinary studies.

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

This paper deals with fishery management in the face of the ecological and economic effects of global warming. To achieve this, a dynamic bioeconomic model and model-based scenarios are considered, in which the stock's growth function depends on the sea surface temperature. The model is empirically calibrated for the French Guiana shrimp fishery using time series collected over the period 1993-2009. Three fishing effort strategies are then compared under two contrasted IPCC climate scenarios (RCP 8.5 and RCP 2.6). A first harvesting strategy maintains the Status Quo in terms of fishing effort. A more ecologically-oriented strategy based on the closure of the fishery is also considered. A third strategy, which relates to Maximum Economic Yield (MEY), is based on the optimisation of the net present value derived from fishing. The results first show that 'Status Quo' fishing intensity combined with global warming leads to the collapse of the fishery in the long run. Secondly, it turns out that the Closure strategy preserves stock viability especially under the optimistic climate scenario. Thirdly, the MEY strategy makes it possible to satisfy bioeconomic performances requirements with positive stock and profit, once again, especially under the optimistic warming scenario. Consequently, MEY emerges as a relevant bioeconomic strategy in terms of adaptation to climate change but only in connection with climate change mitigation.

On the 1500 km-long mud-dominated Guianas coast of South America, between the mouths of the two mega-rivers, the Amazon and the Orinoco, debouch numerous small rivers draining the humid tropical/equatorial Guiana Shield. The geomorphic development of the mouths of these rivers reflects interactions among water discharge, fluvial sediment load, and the alongshore migration of Amazon-derived mud banks alternating with inter-bank areas. The mouth of the Maroni River, astride the French Guiana-Suriname border, shows advanced estuarine infill and geomorphic development characterized by a western (downdrift) side comprising numerous recent cheniers and an eastern (updrift) side bound by an old (> 2000 years B.P.) chenier. A multi-decadal analysis of the beach bounding this chenier shows little net overall mobility notwithstanding significant decadal to sub-decadal variation. The overall stability reflects the diversion of sand supply from the Maroni River towards the downdrift coast and limited sand supply by the smaller Mana River further east, and the south bank of which was contiguous with this beach. The variability in beach multi-decadal mobility reflects the influence, on waves, of alongshore-migrating banks (strong wave dissipation, limited beach mobility) and inter-bank areas (limited wave dissipation, larger beach mobility), highlighted by a comparison, in the current bank phase, of offshore and inshore waves. Erosion of the beach between 2011 and 2017 coincides with the sealing of the mouth of the Mana by muddy progradation in 2011 and mouth relocation several kilometers eastward. The morphodynamics of the beach and shorter-term fluctuations in budget are related to: (1) interaction with estuarine sand dunes mobilized by strong tidal currents on the adjacent shallow shoreface, (2) the influence of the Maroni channel, and (3) rapid encroachment of the leading edge of the shore-attached mud bank on the eastern part of the beach. The beach morphodynamics and evolution highlight, thus, embedded levels of influence: the Maroni at the local scale, and the net westward sediment-transport system and bank and inter-bank alternations that affect the Guianas coast at a regional scale. The recent erosion poses a threat to the local communities by reducing beach space available for recreation and turtle-nesting.

values after removing sun glint effects). Current limitations in the applicability of this SWIR-based empirical automated method are mainly associated with the presence of high cloud coverage, thin clouds in the OLI scene or highly spatially variable marine or atmospheric signal (around 47%, 42% and 11%, respectively, of the total of 12% of failure over French Guiana OLI archive). The potential large applicability of the procedure developed in this work was eventually demonstrated over contrasted coastal environments.

Hunting sustainability in Amazonian ecosystems is a key challenge for modern stakeholders. Predictive models have evolved from first mostly biological data-based to more recent modelling including human behavior. We analyze here the hunting data collected in French Guiana through a panel of indices aiming at drawing the puzzle of parameters influencing hunting activity and impact in various socio ecological conditions across the country. Data were collected from five different study sites differing in cultural origins and remoteness from market economy, and over a ten years period. Most indices show an impact on wildlife populations, and using a full set of indicators allowed us to better understand some underlying mechanisms that lead to a community’s hunting profile. The results showed that there are noticeable differences between the study sites in the practices and the ways hunters face the changes in environment and resources availability

Photogrammetry is an old remote sensing technique that has undergone significant new developments related to the emergence of new computer vision algorithms, notably the workflow technique called Structure-from-Motion (SfM photogrammetry). These innovations facilitate the utilization of this technique by non-specialists. SfM photogrammetry now enables the production of high-resolution morphometric 3D models and derived products such as digital surface models (DSMs) and orthophotographs. We conducted three SfM-photogrammetric experiments, in French Guiana on an embayed beach in Cayenne and on a small mudflat sector of a coastal mud bank near the Sinnamary estuary, and finally in the French southern Alps on a section of the braided Buëch River near Sisteron. We developed a simple field protocol based on subvertical aerial photography from a microlight aircraft at low altitude (1000 feet). We generated DSMs and the other products with user-friendly Agisoft Photoscan Professional © software. These SfM implementations were aimed at highlighting the subtle morphological variations characterising these features and some of the processes involved in morphological change. The DSMs were produced at a resolution of 5 to 10 cm per pixel and had a mean vertical accuracy less than 10 cm compared to the Real-Time Kinematic Differential Global Positioning System (RTK-DGPS) control points, with a maximum of 20 cm in marginal sectors near high vegetation such as trees and shrubs and on wet surfaces close to water-filled channels or in the lower intertidal zone. Low-cost, user-friendly SfM photogrammetry offers interesting new perspectives in the fields of coastal and fluvial geomorphology requiring high-resolution topographic data. The technique combines the advantages of the reproducibility of GPS topographic surveys and the high density and accuracy of airborne LIDAR, but at very advantageous cost compared to the latter.

The goal of this article is to understand the contemporary transformations of indigenous territories in relation to several factors, including urbanisation, population growth, economic development and conservation policies. Using socio‐economic, governance and land use data, we explain the current territorial reorganisations of the W ayãpi and T eko indigenous peoples. We demonstrate the existence of an emerging ‘multi‐sited’ land use system that allows these indigenous peoples to benefit from resources in both urban and forest areas and ensures sovereignty over the territory. We emphasise the role of the delimitation of protected areas in catalysing identity claims and the process of land use reformulation.

We undertook a 15-day survey of the amphibian fauna of the Mitaraka massif in southwestern French Guiana during the rainy season. We detected 56 species (12 species detected for the first time), including six only thanks to their calls. Thirteen additional species were previously detected from nearby sites. The total number of species occurring in the area is at least 69 but most of the species associated with temporary ponds remained undetected. Therefore, we assume the amphibian community of the Mitaraka massif could reach at least 75 species, which represents one of the richest amphibian faunas of the Guiana Shield. With at least six species not occurring further north in French Guiana, the amphibian fauna of the Mitaraka massif is notably distinct from the rest of the territory. Seven of the species discovered during the survey are highlighted here either because these new records represent range extensions or because they are putative new species.